101
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Yin Q, Zhang Z, Zhao YF. Studies of interaction between a new synthesized minor-groove targeting artificial nuclease and DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2007; 66:904-8. [PMID: 16876466 DOI: 10.1016/j.saa.2006.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2006] [Revised: 04/29/2006] [Accepted: 05/03/2006] [Indexed: 05/11/2023]
Abstract
Nuclease plays an important role in molecular biology, such as DNA sequencing. Synthetic polyamide conjugates can be considered as new tool in the selective inhibition of gene expression and as potential drugs in anticancer or antiviral chemotherapy. In this paper, a new synthesized minor-groove targeting artificial nuclease, oligopyrrol-containing peptide, was reported. It was found that this new compound can bind DNA in AT-riched minor groove with high affinity and site specificity. DNA binding behavior was determined by UV-vis and circular dichroism (CD) methods. It was indicated that compound 6 can enhance the Tm of oligomer DNA from 51.8 to 63.5 degrees C and possesses large binding constant (Kb=8.83x10(4)L/mol).
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Affiliation(s)
- Qiang Yin
- The Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, PR China.
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102
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David-Cordonnier MH, Hildebrand MP, Baldeyrou B, Lansiaux A, Keuser C, Benzschawel K, Lemster T, Pindur U. Design, synthesis and biological evaluation of new oligopyrrole carboxamides linked with tricyclic DNA-intercalators as potential DNA ligands or topoisomerase inhibitors. Eur J Med Chem 2007; 42:752-71. [PMID: 17433851 DOI: 10.1016/j.ejmech.2006.12.039] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2006] [Revised: 11/27/2006] [Accepted: 12/07/2006] [Indexed: 10/23/2022]
Abstract
In the context of the design and synthesis of minor groove binding and intercalating DNA ligands some new oligopyrrole carboxamides were synthesized. These hybrid molecules (combilexins) possess a variable and conformatively flexible spacer at the N-terminal end. As intercalating tricyclic systems acridone, acridine, anthraquinones and in a special case iminostilbene terminate the N-terminal end of the pyrrole chain. The cytotoxicity was examined by the NCI antitumor screening, furthermore, biophysical as well as biochemical studies were performed in order to get some information about the DNA binding properties and topoisomerase inhibition effect of this new series of molecules.
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Affiliation(s)
- Marie-Hélène David-Cordonnier
- INSERM U837-JPARC, Equipe N degrees 4, Institut de Recherches sur le Cancer de Lille, Place de Verdun, 59045 Lille Cedex, France
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103
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Chaudhuri P, Ganguly B, Bhattacharya S. An Experimental and Computational Analysis on the Differential Role of the Positional Isomers of Symmetric Bis-2-(pyridyl)-1H-benzimidazoles as DNA Binding Agents. J Org Chem 2007; 72:1912-23. [PMID: 17305396 DOI: 10.1021/jo0619433] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Three symmetrical positional isomers of bis-2-(n-pyridyl)-1H-benzimidazoles (n=2, 3, 4) were synthesized and DNA binding studies were performed with these isomeric derivatives. Like bisbenzimidazole compound Hoechst 33258, these molecules also demonstrate AT-specific DNA binding. The binding affinities of 3-pyridine (m-pyben) and 4-pyridine (p-pyben) derivatized bisbenzimidazoles to double-stranded DNA were significantly higher compared to 2-pyridine derivatized benzimidazole o-pyben. This has been established by combined experimental results of isothermal fluorescence titration, circular dichroism, and thermal denaturation of DNA. To rationalize the origin of their differential binding characteristics with double-stranded DNA, computational structural analyses of the uncomplexed ligands were performed using ab initio/Density Functional Theory. The molecular conformations of the symmetric head-to-head bisbenzimidazoles have been computed. The existence of intramolecular hydrogen bonding was established in o-pyben, which confers a conformational rigidity to the molecule about the bond connecting the pyridine and benzimidazole units. This might cause reduction in its binding affinity to double-stranded DNA compared to its para and meta counterparts. Additionally, the predicted stable conformations for p-, m-, and o-pyben at the B3LYP/6-31G* and RHF/6-31G* levels were further supported by experimental pKa determination. The results provide important information on the molecular recognition process of such symmetric head to head bisbenzimidazoles toward duplex DNA.
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Affiliation(s)
- Padmaparna Chaudhuri
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India
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104
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Myari A, Hadjiliadis N, Garoufis A, Malina J, Brabec V. NMR analysis of duplex d(CGCGATCGCG)2 modified by Λ- and Δ-[Ru(bpy)2(m-GHK)]Cl2 and DNA photocleavage study. J Biol Inorg Chem 2006; 12:279-92. [PMID: 17089162 DOI: 10.1007/s00775-006-0184-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Accepted: 10/05/2006] [Indexed: 11/25/2022]
Abstract
The interaction of the diastereomeric complexes Lambda-[Ru(bpy)2(m-GHK)]Cl2 and Delta-[Ru(bpy)2(m-GHK)]Cl2 (bpy is 2,2'-bipyridine, GHK is glycine-L-histidine-L-lysine) with the deoxynucleotide duplex d(5'-CGCGATCGCG)2 was studied by means of 1H NMR spectroscopy. At a Delta-isomer to DNA ratio of 1:1, significant shifts for the metal complex are observed, whereas there is negligible effect on the oligonucleotide protons and only one intermolecular nuclear Overhauser effect (NOE) is present at the 2D nuclear Overhauser enhancement spectroscopy spectrum. The 1Eta NMR spectrum at ratio 2:1 is characterized by a slight shift for the Delta-isomer's bpy aromatic protons as well as significant shifts for the decanucleotide G4 H1' and Eta2'', A5 H2, G10 H1', T6 NH and G2 NH protons. Furthermore, at ratio 2:1, 11 intermolecular NOEs are observed. The majority of the NOEs involve the sugar Eta2' and Eta2'' protons sited in the major groove of the decanucleotide. Increasing the Delta-isomer to d(CGCGATCGCG)2 ratio to 5:1 results in noteworthy spectral changes. The Delta-isomer's proton shifts are reduced, whereas significant shifts are observed for the decanucleotide protons, especially the sugar protons, as well as for the exchangeable protons. Interaction is characterized by the presence of only one intermolecular NOE. Furthermore, there is significant broadening of the imino proton signals as the ratio of the Delta-isomer to DNuAlpha increases, which is attributed to the opening of the two strands of the duplex. The Lambda-isomer, on the other hand, approaches the minor groove of the oligonucleotide and interacts only weakly, possibly by electrostatic interactions. Photocleavage studies were also conducted with the plasmid pUC19 and a 158-bp restriction fragment, showing that both diastereomers cleave DNA with similar efficiency, attacking mainly the guanines of the sequence probably by generating active oxygen species.
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Affiliation(s)
- Alexandra Myari
- Laboratory of Inorganic and General Chemistry, Department of Chemistry, University of Ioannina, Ioannina, 45110, Greece
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105
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Purnell B, Sato A, O'kelley A, Price C, Summerville K, Hudson S, O'hare C, Kiakos K, Asao T, Lee M, Hartley JA. DNA interstrand crosslinking agents: Synthesis, DNA interactions, and cytotoxicity of dimeric achiral seco-amino-CBI and conjugates of achiral seco-amino-CBI with pyrrolobenzodiazepine (PBD). Bioorg Med Chem Lett 2006; 16:5677-81. [PMID: 16919946 DOI: 10.1016/j.bmcl.2006.08.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2006] [Revised: 07/27/2006] [Accepted: 08/01/2006] [Indexed: 11/19/2022]
Abstract
The design and synthesis of three novel bisalkylating agents derived from the achiral seco-duocarmycin or CC-1065 analogs and pyrrolobenzodiazepines (PBDs) are described: achiral seco-CBI (cyclopropanebenz[e]indoline)-PBD 11, achiral seco-CI-PBD 12, and achiral seco-CBI dimer 13. Compounds 11 and 12 demonstrated enhanced cytotoxicity over the monomer counterparts against the growth of P815 murine mastocytoma cells in culture. Conjugate 11 was found to covalently react with adenine-N3 positions within the minor groove at AT-rich sequences and to produce DNA interstrand crosslinks. Both compounds were found to induce apoptosis in P815 cells. Due to its poor water solubility, dimer 13 did not give any appreciable DNA binding or cytotoxicity.
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Affiliation(s)
- Bethany Purnell
- Department of Chemistry, Furman University, 3300 Pointsett Highway, Greenville, SC 29613, USA
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106
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Kahane AL, Bruice TC. DNA sequence recognition in the minor groove by hairpin microgonotropens. Bioorg Med Chem Lett 2006; 16:6255-61. [PMID: 17035007 DOI: 10.1016/j.bmcl.2006.09.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2006] [Revised: 09/01/2006] [Accepted: 09/07/2006] [Indexed: 11/20/2022]
Abstract
Two novel microgonotropens (MGTs) comprised of hairpin N-propylaminepyrrole polyamides linked to a Hoechst 33258 (Ht) analogue (3 and 4) were synthesized on solid phase by adopting an Fmoc technique using a series of HOBt mediated coupling reactions. The dsDNA-binding properties of MGTs 3 and 4 were determined by thermal denaturation experiments. Both MGTs were found to be selective for their nine-bp match dsDNA sequence 9 and were less tolerant of G/C bp substitutions in the binding region than linear progenitor MGT 1. MGT 3 was intolerant of a G/C substitution located in the middle of the binding region and did not bind to sequences 13 and 14. MGT 4 also did not bind to sequence 13, and its linker-bound Ht moiety was found to be more sensitive to a G/C substitution in the Ht-binding target, as demonstrated by the lack of binding to sequence 16.
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Affiliation(s)
- Alexandra L Kahane
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, CA 93106, USA
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107
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108
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Dai J, Chen D, Jones RA, Hurley LH, Yang D. NMR solution structure of the major G-quadruplex structure formed in the human BCL2 promoter region. Nucleic Acids Res 2006; 34:5133-44. [PMID: 16998187 PMCID: PMC1636422 DOI: 10.1093/nar/gkl610] [Citation(s) in RCA: 293] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2006] [Revised: 08/03/2006] [Accepted: 08/03/2006] [Indexed: 01/22/2023] Open
Abstract
BCL2 protein functions as an inhibitor of cell apoptosis and has been found to be aberrantly expressed in a wide range of human diseases. A highly GC-rich region upstream of the P1 promoter plays an important role in the transcriptional regulation of BCL2. Here we report the NMR solution structure of the major intramolecular G-quadruplex formed on the G-rich strand of this region in K+ solution. This well-defined mixed parallel/antiparallel-stranded G-quadruplex structure contains three G-tetrads of mixed G-arrangements, which are connected with two lateral loops and one side loop, and four grooves of different widths. The three loops interact with the core G-tetrads in a specific way that defines and stabilizes the overall G-quadruplex structure. The loop conformations are in accord with the experimental mutation and footprinting data. The first 3-nt loop adopts a lateral loop conformation and appears to determine the overall folding of the BCL2 G-quadruplex. The third 1-nt double-chain-reversal loop defines another example of a stable parallel-stranded structural motif using the G3NG3 sequence. Significantly, the distinct major BCL2 promoter G-quadruplex structure suggests that it can be specifically involved in gene modulation and can be an attractive target for pathway-specific drug design.
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Affiliation(s)
- Jixun Dai
- College of Pharmacy, The University of Arizona1703 E. Mabel Street, Tucson, AZ 85721, USA
| | - Ding Chen
- College of Pharmacy, The University of Arizona1703 E. Mabel Street, Tucson, AZ 85721, USA
| | - Roger A. Jones
- Department of Chemistry and Chemical Biology, Rutgers University610 Taylor Road, Piscataway, NJ 08854, USA
| | - Laurence H. Hurley
- College of Pharmacy, The University of Arizona1703 E. Mabel Street, Tucson, AZ 85721, USA
- Arizona Cancer Center1515 N. Campbell Avenue, Tucson, AZ 85724, USA
- BIO5 Institute, The University of Arizona1140 E. South Campus Dr, Tucson, AZ 85721, USA
| | - Danzhou Yang
- College of Pharmacy, The University of Arizona1703 E. Mabel Street, Tucson, AZ 85721, USA
- Arizona Cancer Center1515 N. Campbell Avenue, Tucson, AZ 85724, USA
- BIO5 Institute, The University of Arizona1140 E. South Campus Dr, Tucson, AZ 85721, USA
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109
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Chaires JB. A thermodynamic signature for drug–DNA binding mode. Arch Biochem Biophys 2006; 453:26-31. [PMID: 16730635 DOI: 10.1016/j.abb.2006.03.027] [Citation(s) in RCA: 306] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2006] [Accepted: 03/25/2006] [Indexed: 11/15/2022]
Abstract
A number of small molecules bind directly and selectively to DNA, acting as chemotherapeutic agents by inhibiting replication, transcription or topoisomerase activity. Two common binding modes for these small molecules are intercalation or groove-binding. Intercalation results from insertion of a planar aromatic substituent between DNA base pairs, with concomitant unwinding and lengthening of the DNA helix. Groove binding, in contrast, does not perturb the duplex structure to any great extent. Groove-binders are typically crescent-shaped, and fit snugly into the minor groove with little distortion of the DNA structure. Recent calorimetric studies have determined the enthalpic and entropic contributions to the DNA binding of representative DNA binding compounds. Analysis of such thermodynamic data culled from the literature reveals distinctive thermodynamic signatures for groove-binding and intercalating compounds. Plots of the binding enthalpy (DeltaH) against binding entropy (-TDeltaS) for 26 drug-DNA interactions reveal that groove-binding interactions are clustered in a region of the graph with favorable entropy contributions to the free energy, while intercalators are clustered in a region with unfavorable entropy but favorable enthalpy contributions. Groove-binding is predominantly entropically driven, while intercalation in enthalpically driven. The molecular basis of the contrasting thermodynamic signatures for the two binding modes is by no means clear, but the pattern should be of use in categorizing new DNA binding agents.
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Affiliation(s)
- Jonathan B Chaires
- James Graham Brown Cancer Center, University of Louisville, 529 S. Jackson Street, Louisville, KY 40202, USA.
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110
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Correa BJ, Canzio D, Kahane AL, Reddy PM, Bruice TC. DNA sequence recognition by Hoechst 33258 conjugates of hairpin pyrrole/imidazole polyamides. Bioorg Med Chem Lett 2006; 16:3745-50. [PMID: 16682192 DOI: 10.1016/j.bmcl.2006.04.047] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2006] [Accepted: 04/19/2006] [Indexed: 11/20/2022]
Abstract
A series of hairpin pyrrole/imidazole polyamides linked to a Hoechst 33258 (Ht) analogue (5-7) were synthesized on solid-phase by adopting an Fmoc technique using a series of PyBOP/HOBt mediated coupling reactions. The dsDNA binding properties of Ht-polyamides 5-7 were determined by thermal denaturation experiments. Hairpin Ht-polyamides 5-7 bound to dsDNA sequences 16 and 18 show DeltaTm values that are 14-18 degrees higher than linear Ht-polyamides bound to the same sequences. All three Ht-polyamides were found to be selective for their 9-bp match dsDNA sequences, supporting a relative stronger interaction of an Im/Py anti-parallel dimer with an appropriately positioned G/Cbp rather than sequences containing only A/Tbps. In addition, Ht-polyamides 5 and 7 showed a 20-fold preference for a properly placed G/Cbp over a C/Gbp, while 6 showed a 10-fold preference.
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Affiliation(s)
- Bryan J Correa
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, CA 93106, USA
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111
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112
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Yang CH, Jeng KCG, Yang WH, Chen YL, Hung CC, Lin JW, Chen ST, Richardson S, Martin CRH, Waring MJ, Sheh L. Unusually Strong Positive Cooperativity in Binding of Peptides to Latent Membrane Protein-1 DNA Fragments of the Epstein-Barr Viral Gene. Chembiochem 2006; 7:1187-96. [PMID: 16810657 DOI: 10.1002/cbic.200600083] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The DNA-binding preferences of two oligopeptide amides, (His-Pro-Arg-Lys)(3)NH(2) (HR-12) and (Ser-Pro-Arg-Lys)(3)NH(2) (SP-12), have been examined by quantitative DNase I footprinting studies. Two different DNA fragments were investigated: a pair of 5'-(32)P-labeled duplexes from pBR322 with one or other of the complementary strands labeled and a corresponding pair of 5'-(32)P-labeled duplexes representing fragments of the latent membrane protein (LMP-1) gene from a pathogenic Epstein-Barr virus variant derived from nasopharyngeal carcinoma. The major objective was to examine molecular recognition and cooperative features associated with sequence-selective binding of synthetic peptides to the LMP-1 fragments. At various binding sites on the pBR322 fragments, Hill coefficients (n(H)) ranging from 1.9-2.2 were observed; these results indicate modest positive cooperativity between binding sites for both peptides. By contrast, unusually high values of n(H), ranging from 4.0-9.3, were observed at various binding sites on the LMP-1 fragments. Allosteric models can be constructed to interpret the observed cooperative interactions between different DNA recognition sites in the LMP-1 gene upon binding of the peptide ligands. It is noteworthy that these models feature a novel network of cooperativity interconnecting multiple DNA allosteric sites. The evidence of sequence selectivity and strong cooperativity discovered in this work may prove to be a general feature of peptide interactions with some nucleic acids.
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Affiliation(s)
- Chia-Hung Yang
- Department of Chemistry, Tunghai Christian University, Taichung, Taiwan 407, R.O.C
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113
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Borgions F, Ghyssels D, Van Aerschot A, Rozenski J, Herdewijn P. Synthetic dsDNA-Binding Peptides Using Natural Compounds as Model. Helv Chim Acta 2006. [DOI: 10.1002/hlca.200690118] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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114
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Athri P, Wenzler T, Ruiz P, Brun R, Boykin DW, Tidwell R, Wilson WD. 3D QSAR on a library of heterocyclic diamidine derivatives with antiparasitic activity. Bioorg Med Chem 2006; 14:3144-52. [PMID: 16442293 DOI: 10.1016/j.bmc.2005.12.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2005] [Revised: 11/24/2005] [Accepted: 12/16/2005] [Indexed: 11/26/2022]
Abstract
African trypanosomes, Trypanosoma brucei rhodesiense (TBR) and Trypanosoma brucei gambiense (TBG), affect hundreds of thousands of lives in tropical regions of the world. The toxicity of the diamidine pentamidine, an effective drug against TBG, necessitates the design of better drugs. An orally effective prodrug of the diamidine, furamidine (DB75), presently scheduled for phase III clinical trials, has excellent activity against TBG with toxicity lower than that of pentamidine. As part of an effort to develop additional and improved diamidines against African trypanosomes, CoMFA and CoMSIA 3D QSAR analyses have been conducted with furamidine and a set of 25 other structurally related compounds. Two different alignment strategies, based on a putative kinetoplast DNA minor groove target, were used. Due to conserved electrostatic properties across the compounds, models that used only steric and electronic properties did not perform well in predicting biological results. An extended CoMSIA model with additional descriptors for hydrophobic, donor, and acceptor properties had good predictive ability with a q2=0.699, r2=0.974, SEE, standard error of estimate=0.1, and F=120.04. The results have been used as a guide to design compounds that, potentially, have better activity against African trypanosomes.
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Affiliation(s)
- Prashanth Athri
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
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115
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Werner S, Iyer PS, Fodor MD, Coleman CM, Twining LA, Mitasev B, Brummond KM. Solution-phase synthesis of a tricyclic pyrrole-2-carboxamide discovery library applying a stetter-Paal-Knorr reaction sequence. JOURNAL OF COMBINATORIAL CHEMISTRY 2006; 8:368-80. [PMID: 16677007 PMCID: PMC3433767 DOI: 10.1021/cc050160c] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The solution-phase synthesis of a discovery library of 178 tricyclic pyrrole-2-carboxamides was accomplished in nine steps and seven purifications starting with three benzoyl-protected amino acid methyl esters. Further diversity was introduced by two glyoxaldehydes and 41 primary amines. The combination of Pauson-Khand, Stetter, and microwave-assisted Paal-Knorr reactions was applied as a key sequence. The discovery library was designed with the help of QikProp 2.1, and physicochemical data are presented for all pyrroles. Library members were synthesized and purified in parallel and analyzed by LC/MS. Selected compounds were fully characterized.
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Affiliation(s)
- Stefan Werner
- University of Pittsburgh Center for Chemical Methodologies and Library Development, Pennsylvania 15260, USA.
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116
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Di Micco S, Bassarello C, Bifulco G, Riccio R, Gomez-Paloma L. Differential-Frequency Saturation Transfer Difference NMR Spectroscopy Allows the Detection of Different Ligand-DNA Binding Modes. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200501344] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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117
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Turlington M, Mackay H, Rutledge C, Taherbhai Z, Nguyen B, Wilson D, Lee M. SYNTHESIS AND BIOPHYSICAL TESTING OF A NOVEL PYRROLE-CONTAINING POLYAMIDE-BENZAMIDINE HYBRID. HETEROCYCL COMMUN 2006. [DOI: 10.1515/hc.2006.12.2.89] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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118
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Qin Y, Pang JY, Chen WH, Cai Z, Jiang ZH. Synthesis, DNA-binding affinities, and binding mode of berberine dimers. Bioorg Med Chem 2006; 14:25-32. [PMID: 16169735 DOI: 10.1016/j.bmc.2005.07.069] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2005] [Revised: 07/26/2005] [Accepted: 07/27/2005] [Indexed: 10/25/2022]
Abstract
Six novel berberine dimers (3a-f) were synthesized in 37-84% yield from the reaction of berberrubine (2) with dihaloalkanes of varying lengths from two to seven carbons. Their interactions with calf thymus (CT) DNA and three double helical oligodeoxynucleotides, d(AAGAATTCTT)2, d(AAGCATGCTT)2, and d(TAAGAATTCTTA)2, were investigated by means of fluorometric titration and ethidium bromide (EB) displacement experiments. Compared with the monomeric parent berberine (1), these dimers' DNA-binding affinities increased up to approximately 100-fold, suggesting a cooperative interaction of the two berberine subunits in the molecules. Furthermore, these dimers linked by different spacers show a prominent structure-activity relationship when bound with oligodeoxynucleotides. The relative binding affinities are in the order of 3b>3a>3c>3d>3e>3f with d(AAGAATTCTT)2 and d(TAAGAATTCTTA)2, and 3b>3c>3a>3d>3e>3f with d(AAGCATGCTT)2. Dimer 3b, linked with a propyl chain, exhibits the highest binding affinity. This suggests that a propyl chain may be the most suitable spacer to bridge the two berberine units for DNA binding. Spectrophotometric titration and competitive EB displacement of berberine (1) and dimer 3b indicate that both berberine and its dimers form intercalating complexes with duplex DNA. A larger redshift, a stronger hypochromic effect, and a much higher EB displacement ratio, observed in 3b, indicate that the dimer is in more intimate contact with DNA than berberine. In addition, no obvious binding of canadine (4), a hydrogenated product of berberine, with CT DNA was observed, suggesting critical roles of the quaternary ammonium cation and planar structure in the DNA-binding of berberine.
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Affiliation(s)
- Yong Qin
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong
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119
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Di Micco S, Bassarello C, Bifulco G, Riccio R, Gomez-Paloma L. Differential-Frequency Saturation Transfer Difference NMR Spectroscopy Allows the Detection of Different Ligand-DNA Binding Modes. Angew Chem Int Ed Engl 2006; 45:224-8. [PMID: 16304663 DOI: 10.1002/anie.200501344] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Simone Di Micco
- Dipartimento di Scienze Farmaceutiche, Università di Salerno via Ponte don Melillo, 84084 Fisciano, Salerno, Italy
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120
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Huang HS, Chiu HF, Lu WC, Yuan CL. Synthesis and antitumor activity of 1,8-diaminoanthraquinone derivatives. Chem Pharm Bull (Tokyo) 2005; 53:1136-9. [PMID: 16141583 DOI: 10.1248/cpb.53.1136] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Continuing our ongoing studies on cytotoxic substances, a series of regioisomeric disubstituted aminoanthraquinone (DAAQ) derivatives have been synthesized as cytotoxic activity based on a proposed bioactive amino conformation. To assess the biological activity of amino-substitution in the side-chains of anthraquinone located at positions 1 and 8 of the anthraquinone ring system. The aim of the study was to determine if members of the anthraquinone family could be used as adjuncts to increase the growth inhibiting effect of anticancer agents in rat glioma C6 cells, human hepatoma G2 cells and 2.2.15 cells. In vitro cytotoxicity data is reported for the compounds and some indications of structure--activity relationships have been discerned. A number of compounds were found to have good cytotoxicity against proliferation in these three cell lines. This has led to the discovery some of the DAAQ as a conformationally constrained structure possessing anticancer properties that displays cytotoxicity for these above cell lines and is being investigated further.
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Affiliation(s)
- Hsu-Shan Huang
- School of Pharmacy, National Defense Medical Center, Neihu, Taipei 11490, Taiwan, R.O.C.
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121
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Pham VC, Ma J, Thomas SJ, Xu Z, Hecht SM. Alkaloids from Alangium javanicum and Alangium grisolleoides that mediate Cu2+-dependent DNA strand scission. JOURNAL OF NATURAL PRODUCTS 2005; 68:1147-52. [PMID: 16124751 DOI: 10.1021/np058013j] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Crude CH2Cl2-MeOH extracts prepared from Alangium javanicum and A. grisolleoides were found to induce DNA strand breakage in the presence of Cu2+ and were subjected to bioassay-guided fractionation to permit identification of the active principle(s). Javaniside (1), a novel alkaloid possessing an unusual monoterpenoid oxindole skeleton, was identified as an active principle contributing to the DNA cleavage activity observed for the crude extract of A. javanicum. Alangiside (2), a tetrahydroisoquinoline monoterpene glucoside widely distributed in the genus Alangium, was also isolated from A. grisolleoides as a new type of Cu2+-dependent DNA cleavage agent. The relative configuration of the asymmetric centers in javaniside was established by analysis of 1H-1H coupling constants and NOESY correlations. Semisynthesis of javaniside from secologanin (3) established the absolute stereochemistry of javaniside.
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Affiliation(s)
- Van Cuong Pham
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, USA
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122
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Tse WC, Boger DL. Sequence-selective DNA recognition: natural products and nature's lessons. ACTA ACUST UNITED AC 2005; 11:1607-17. [PMID: 15610844 DOI: 10.1016/j.chembiol.2003.08.012] [Citation(s) in RCA: 185] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2003] [Revised: 08/21/2003] [Accepted: 08/25/2003] [Indexed: 11/24/2022]
Abstract
Biologically active, therapeutically useful, DNA binding natural products continue to reveal new paradigms for sequence-selective recognition, to enlist beautiful mechanisms of in situ activation for DNA modification, to define new therapeutic targets, to exploit new mechanisms to achieve cellular selectivity, and to provide a rich source of new drugs. These attributes arise in compact structures of complex integrated function.
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Affiliation(s)
- Winston C Tse
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
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123
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Jin Y, Cowan JA. DNA Cleavage by Copper−ATCUN Complexes. Factors Influencing Cleavage Mechanism and Linearization of dsDNA. J Am Chem Soc 2005; 127:8408-15. [PMID: 15941274 DOI: 10.1021/ja0503985] [Citation(s) in RCA: 217] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reactivity of two [peptide-Cu] complexes ([GGH-Cu](-) and [KGHK-Cu](+)) toward DNA cleavage has been quantitatively investigated. Neither complex promoted hydrolytic cleavage, but efficient oxidative cleavage was observed in the presence of a mild reducing agent (ascorbate) and dioxygen. Studies with scavengers of ROS confirmed hydrogen peroxide to be an obligatory diffusible intermediate. While oxidative cleavage of DNA was observed for Cu(2+)(aq) under the conditions used, the kinetics of cleavage and reaction products/pathway were distinct from those displayed by [peptide-Cu] complexes. DNA cleavage chemistry is mediated by the H(2)O-dependent pathway following C-4'H abstraction from the minor groove. Such a cleavage path also provides a ready explanation for the linearization reaction promoted by [KGHK-Cu](+). Kinetic activities and reaction pathways are compared to published results on other chemical nucleases. Both [peptide-Cu] complexes were found to display second-order kinetics, with rate constants k(2) approximately 39 and 93 M(-1) s(-1) for [GGH-Cu](-) and [KGHK-Cu](+), respectively. Neither complex displayed enzyme-like saturation behavior, consistent with the relatively low binding affinity and residence time expected for association with dsDNA, and the absence of a prereaction complex. However, the intrinsic activity of each is superior to other catalyst systems, as determined from relative k(2) or k(cat)/K(m) values. Linearization of DNA was observed for [KGHK-Cu](+) relative to [GGH-Cu](-), consistent with the increased positive charge and longer residency time on dsDNA.
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Affiliation(s)
- Yan Jin
- Evans Laboratory of Chemistry, Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
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124
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Myari A, Hadjiliadis N, Garoufis A. Synthesis and characterization of the diastereomers Lambda- and Delta-[Ru(bpy)2(m-bpy-L-Arg-Gly-L-Asn-L-Ala-L-His-L-Glu-L-Arg)]Cl2 1H NMR studies on their interactions with the deoxynucleotide duplex d[(5'-GCGCTTAAGCGC-3')2] and d[(5'-CGCGATCGCG-3')2]. J Inorg Biochem 2005; 99:616-26. [PMID: 15621296 DOI: 10.1016/j.jinorgbio.2004.11.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2004] [Revised: 11/11/2004] [Accepted: 11/13/2004] [Indexed: 11/15/2022]
Abstract
The diastereomeric complexes Lambda- and Delta-[Ru(bpy)(2)(m-bpy-7p)]Cl(2), (bpy=2,2'-bipyridine, m-bpy-7p=4-methyl-4'-Arg-Gly-Asn-Ala-His-Glu-Arg-CONH(2)-2,2'-bipyridine) were synthesized and characterized and their binding properties to the deoxynucleotide duplexes d(5'-CGCGATCGCG-3')(2) and d(5'-GCGCTTAAGCGC-3')(2) were studied by means of (1)H NMR spectroscopy. 7p is part of the recognition loop of the restriction endonuclease MunI, a type II restriction enzyme from Mycoplasma unidentified which recognizes the palindromic hexanucleotide sequence C/AATTG and cleaves it as indicated by the slash. The Delta-isomer binds to the terminal CG/GC major groove of d(CGCGATCGCG)(2) decanucleotide, whereas the Lambda-isomer approaches the GCT/CGA sequence. On the other hand, weak binding of the Delta-isomer to the end of d(GCGCTTAAGCGC)(2) into two different orientations is observed. In the case of the Lambda-isomer, the bpy ligand(s) are located into the major groove of the central TT/AA sequence. The role of appended peptide sequences in sequence selectivity binding to DNA is being addressed.
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Affiliation(s)
- Alexandra Myari
- Laboratory of Inorganic and General Chemistry, Department of Chemistry, University of Ioannnina, Ioannina 45110, Greece
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125
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Buchmueller KL, Staples AM, Howard CM, Horick SM, Uthe PB, Le NM, Cox KK, Nguyen B, Pacheco KAO, Wilson WD, Lee M. Extending the language of DNA molecular recognition by polyamides: unexpected influence of imidazole and pyrrole arrangement on binding affinity and specificity. J Am Chem Soc 2005; 127:742-50. [PMID: 15643900 DOI: 10.1021/ja044359p] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pyrrole (Py) and imidazole (Im) polyamides can be designed to target specific DNA sequences. The effect that the pyrrole and imidazole arrangement, plus DNA sequence, have on sequence specificity and binding affinity has been investigated using DNA melting (DeltaT(M)), circular dichroism (CD), and surface plasmon resonance (SPR) studies. SPR results obtained from a complete set of triheterocyclic polyamides show a dramatic difference in the affinity of f-ImPyIm for its cognate DNA (K(eq) = 1.9 x 10(8) M(-1)) and f-PyPyIm for its cognate DNA (K(eq) = 5.9 x 10(5) M(-1)), which could not have been anticipated prior to characterization of these compounds. Moreover, f-ImPyIm has a 10-fold greater affinity for CGCG than distamycin A has for its cognate, AATT. To understand this difference, the triamide dimers are divided into two structural groupings: central and terminal pairings. The four possible central pairings show decreasing selectivity and affinity for their respective cognate sequences: -ImPy > -PyPy- >> -PyIm- approximately -ImIm-. These results extend the language of current design motifs for polyamide sequence recognition to include the use of "words" for recognizing two adjacent base pairs, rather than "letters" for binding to single base pairs. Thus, polyamides designed to target Watson-Crick base pairs should utilize the strength of -ImPy- and -PyPy- central pairings. The f/Im and f/Py terminal groups yielded no advantage for their respective C/G or T/A base pairs. The exception is with the -ImPy- central pairing, for which f/Im has a 10-fold greater affinity for C/G than f/Py has for T/A.
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Affiliation(s)
- Karen L Buchmueller
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, USA
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126
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Dolenc J, Borštnik U, Hodošček M, Koller J, Janežič D. An ab initio QM/MM study of the conformational stability of complexes formed by netropsin and DNA. The importance of van der Waals interactions and hydrogen bonding. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.theochem.2004.12.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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127
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Buchmueller KL, Staples AM, Uthe PB, Howard CM, Pacheco KAO, Cox KK, Henry JA, Bailey SL, Horick SM, Nguyen B, Wilson WD, Lee M. Molecular recognition of DNA base pairs by the formamido/pyrrole and formamido/imidazole pairings in stacked polyamides. Nucleic Acids Res 2005; 33:912-21. [PMID: 15703305 PMCID: PMC549405 DOI: 10.1093/nar/gki238] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Polyamides containing an N-terminal formamido (f) group bind to the minor groove of DNA as staggered, antiparallel dimers in a sequence-specific manner. The formamido group increases the affinity and binding site size, and it promotes the molecules to stack in a staggered fashion thereby pairing itself with either a pyrrole (Py) or an imidazole (Im). There has not been a systematic study on the DNA recognition properties of the f/Py and f/Im terminal pairings. These pairings were analyzed here in the context of f-ImPyPy, f-ImPyIm, f-PyPyPy and f-PyPyIm, which contain the central pairing modes, -ImPy- and -PyPy-. The specificity of these triamides towards symmetrical recognition sites allowed for the f/Py and f/Im terminal pairings to be directly compared by SPR, CD and DeltaT (M) experiments. The f/Py pairing, when placed next to the -ImPy- or -PyPy- central pairings, prefers A/T and T/A base pairs to G/C base pairs, suggesting that f/Py has similar DNA recognition specificity to Py/Py. With -ImPy- central pairings, f/Im prefers C/G base pairs (>10 times) to the other Watson-Crick base pairs; therefore, f/Im behaves like the Py/Im pair. However, the f/Im pairing is not selective for the C/G base pair when placed next to the -PyPy- central pairings.
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Affiliation(s)
| | | | - Peter B. Uthe
- Department of Chemistry, Furman UniversityGreenville, SC 29613, USA
| | - Cameron M. Howard
- Department of Chemistry, Furman UniversityGreenville, SC 29613, USA
- Department of Chemistry, Georgia State UniversityAtlanta, GA 30303, USA
| | - Kimberly A. O. Pacheco
- Department of Chemistry and Biochemistry, University of Northern ColoradoGreeley, CO 80639, USA
| | - Kari K. Cox
- Department of Chemistry, Furman UniversityGreenville, SC 29613, USA
| | - James A. Henry
- Department of Chemistry, Furman UniversityGreenville, SC 29613, USA
| | | | - Sarah M. Horick
- Department of Chemistry, Furman UniversityGreenville, SC 29613, USA
| | - Binh Nguyen
- Department of Chemistry, Georgia State UniversityAtlanta, GA 30303, USA
| | - W. David Wilson
- Department of Chemistry, Georgia State UniversityAtlanta, GA 30303, USA
| | - Moses Lee
- Department of Chemistry, Furman UniversityGreenville, SC 29613, USA
- To whom correspondence should be addressed. Tel: +1 864 294 3368; Fax: +1 864 294 3559;
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128
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Ryabinin VA, Boutorine AS, Hélène C, Pyshnyi DV, Sinyakov AN. Oligonucleotide-minor groove binder conjugates and their complexes with complementary DNA: effect of conjugate structural factors on the thermal stability of duplexes. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 23:789-803. [PMID: 15281367 DOI: 10.1081/ncn-120039358] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Synthetic polycarboxamide minor groove binders (MGB) consisting of N-methylpyrrole (Py), N-methylimidazole (Im), N-methyl-3-hydroxypyrrole (Hp) and beta-alanine (beta) show strong and sequence-specific interaction with the DNA minor groove in side-by-side antiparallel or parallel orientation. Two MGB moieties covalently linked to the same terminal phosphate of one DNA strand stabilize DNA duplexes formed by this strand with a complementary one in a sequence-specific manner, similarly to the corresponding mono-conjugated hairpin structures. The series of conjugates with the general formula Oligo-(L-MGB-R)m was synthesized, where m = 1 or 2, L = linker, R = terminal charged or neutral group, MGB = -(Py)n-, -(Im)n- or -[(Py/Im)n-(CH2)3CONH-(Py/Im)n-] and I < n < 5. Using thermal denaturation, we studied effects of structural factors such as m and n, linker L length, nature and orientation of the MGB monomers, the group R and the backbone (DNA or RNA), etc. on the stability of the duplexes. Structural factors are more important for linear and hairpin monophosphoroamidates than for parallel bis-phosphoroamidates. No more than two oligocarboxamide strands can be inserted into the duplex minor groove. Attachment of the second sequence-specific parallel ligand [-L(Py)4R] to monophosphoroamidate conjugate CGTTTATT-L(Py)4R leads to the increase of the duplex Tm, whereas attachment of [-L(Im)4R] leads to its decrease. The mode of interaction between oligonucleotide duplex and attached ligands could be different (stacking with the terminal A:T pair of the duplex or its insertion into the minor groove) depending on the length and structure of the MGB.
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Affiliation(s)
- Vladimir A Ryabinin
- State Research Center of Virology and Biotechnology Vector, Kol'tsovo, Institute of Molecular Biology, Novosibirsk Region, Russia
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129
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Ma J, Jones SH, Hecht SM. A dihydroflavonol glucoside from Commiphora africana that mediates DNA strand scission. JOURNAL OF NATURAL PRODUCTS 2005; 68:115-117. [PMID: 15679332 DOI: 10.1021/np0400510] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A crude CH(2)Cl(2)-MeOH extract prepared from Commiphora africana was found to mediate Cu(2+)-dependent relaxation of supercoiled plasmid DNA. Bioassay-guided fractionation of this extract was carried out and was monitored by the use of an in vitro DNA strand scission assay. The dihydroflavonol glucoside phellamurin (1) was identified as the active principle responsible for the DNA cleavage activity of the crude extract.
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Affiliation(s)
- Ji Ma
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, USA
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130
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Chaires JB, Ren J, Hamelberg D, Kumar A, Pandya V, Boykin DW, Wilson WD. Structural selectivity of aromatic diamidines. J Med Chem 2004; 47:5729-42. [PMID: 15509172 DOI: 10.1021/jm049491e] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Competition dialysis was used to study the interactions of 13 substituted aromatic diamidine compounds with 13 nucleic acid structures and sequences. The results show a striking selectivity of these compounds for the triplex structure poly dA:(poly dT)2, a novel aspect of their interaction with nucleic acids not previously described. The triplex selectivity of selected compounds was confirmed by thermal denaturation studies. Triplex selectivity was found to be modulated by the location of amidine substituents on the core phenyl-furan-phenyl ring scaffold. Molecular models were constructed to rationalize the triplex selectivity of DB359, the most selective compound in the series. Its triplex selectivity was found to arise from optimal ring stacking on base triplets, along with proper positioning of its amidine substituents to occupy the minor and the major-minor grooves of the triplex. New insights into the molecular recognition of nucleic acid structures emerged from these studies, adding to the list of available design principles for selectively targeting DNA and RNA.
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Affiliation(s)
- Jonathan B Chaires
- James Graham Brown Cancer Center, Department of Medicine, Health Sciences Center, University of Louisville, 529 S. Jackson St., Louisville, Kentucky 40202, USA.
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131
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Lah J, Vesnaver G. Energetic diversity of DNA minor-groove recognition by small molecules displayed through some model ligand-DNA systems. J Mol Biol 2004; 342:73-89. [PMID: 15313608 DOI: 10.1016/j.jmb.2004.07.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2004] [Revised: 07/05/2004] [Accepted: 07/06/2004] [Indexed: 11/22/2022]
Abstract
Energetics of interactions occurring in the model ligand-DNA systems constituted from distamycin A (DST), netropsin (NET) and the oligomeric duplexes d(GCAAGTTGCGATATACG)d(CGTATATCGCAACTTGC)=D#1 and d(GCAAGTTGCGAAAAACG)d(CGTTTTTCGCAACTTGC)=D#2 was studied by spectropolarimetry, UV-absorption spectroscopy and isothermal titration calorimetry. Model analysis of the measured signals was applied to describe individual and competitive binding in terms of populations of various species in the solution. Our results reveal several unprecedented ligand-DNA binding features. DST binds to the neighboring 5'-AAGTT-3' and 5'-ATATA-3' sites of D#1 statistically in a 2:1 binding mode. By contrast, its association to D#2 appears to be a 2:1 binding event only at the DST/D#2 molar ratios between 0 and 2 while its further binding to D#2 may be considered as a step-by-step binding to the unoccupied 5'-AAAAA-3' sites resulting first in DST3D#2 and finally in DST4D#2 complex formation. Competition between DST and NET binding shows that for the most part DST displaces NET from its complexes with D#1 and D#2. In contrast to the obligatory 1:1 binding of DST to the ligand-free 5'-AAAAA-3' sites observed at DST/5'-AAAAA-3' <1 the displacement of NET bound to the 5'-AAAAA-3' sites by added DST occurs even at the smallest additions of DST in a 2:1 manner. NET can also displace DST molecules but only those bound monomerically to the 5'-AAAAA-3' sites of DST3D#2. Actually, only half of these molecules can be displaced due to the simultaneous rebinding of the displaced DST to the unreacted 5'-AAAAA-3' sites in DST3D#2. Binding of DST and NET to D#1 and D#2 is an enthalpy driven process accompanied by large unfavorable (DST), small (NET) or large favorable (NET binding to 5'-AAAAA-3') entropy contributions and negative deltaCP degrees that are reasonably close to deltaCP degrees predicted from the calculated changes in solvent-accessible surface areas that accompany complex formation. Although various modes of DST and NET binding within D#1 and D#2 are characterized by significant energetic differences they seem to be governed by the same driving forces; the hydrophobic transfer of ligand from the solution into the duplex binding site and the accompanying specific non-covalent ligand-DNA and ligand-ligand interactions occurring within the DNA minor groove.
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Affiliation(s)
- Jurij Lah
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Askerceva 5, 1000, Slovenia
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132
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Lee J, Guelev V, Sorey S, Hoffman DW, Iverson BL. NMR Structural Analysis of a Modular Threading Tetraintercalator Bound to DNA. J Am Chem Soc 2004; 126:14036-42. [PMID: 15506767 DOI: 10.1021/ja046335o] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The synthesis and NMR structural studies are reported for a modular threading tetraintercalator bound to DNA. The tetraintercalator design is based on 1,4,5,8-tetracarboxylic naphthalene diimide units connected through flexible peptide linkers. Aided by an overall C(2) symmetry, NMR analysis verified a threading polyintercalation mode of binding, with linkers alternating in the order minor groove, major groove, minor groove, analogous to how a snake might climb a ladder. This study represents the first NMR analysis of a threading tetraintercalator and, as such, structurally characterizes a new topology for molecules that bind to relatively long DNA sequences with extensive access to both DNA grooves.
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Affiliation(s)
- Jeeyeon Lee
- Department of Chemistry and Biochemistry, The University of Texas, Austin, Texas 78712, USA
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133
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Mallena S, Lee MPH, Bailly C, Neidle S, Kumar A, Boykin DW, Wilson WD. Thiophene-Based Diamidine Forms a “Super” AT Binding Minor Groove Agent. J Am Chem Soc 2004; 126:13659-69. [PMID: 15493923 DOI: 10.1021/ja048175m] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The DNA minor groove is the interaction site for many enzymes and transcription control proteins and as a result, development of compounds that target the minor groove is an active research area. In an effort to develop biologically active minor groove agents, we are preparing and exploring the DNA interactions of a systematic set of diamidine derivatives with a powerful array of methods including DNase I footprinting, biosensor-SPR methods, and X-ray crystallography. Surprisingly, conversion of the parent phenyl-furan-phenyl diamidine to a phenyl-thiophene-benzimidazole derivative yields a compound with over 10-fold-increased affinity for the minor groove at AT sequences. Single conversion of the furan to a thiophene or a phenyl to benzimidazole does not cause a similar increase in affinity. X-ray results indicate a small bond angle difference between the C-S-C angle of thiophene and the C-O-C angle of furan that, when amplified out to the terminal amidines of the benzimidazole compounds, yields a very significant difference in the positions of the amidines and their DNA interaction strength.
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Affiliation(s)
- Sirish Mallena
- Department of Chemistry, Georgia State University, P.O. Box 4098, Atlanta, Georgia 30302-4098, USA
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134
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Dogan Z, Paulini R, Rojas Stütz JA, Narayanan S, Richert C. 5'-Tethered stilbene derivatives as fidelity- and affinity-enhancing modulators of DNA duplex stability. J Am Chem Soc 2004; 126:4762-3. [PMID: 15080664 DOI: 10.1021/ja0394434] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of 5'-linked stilbene-DNA conjugates with different substituents in the distal aromatic ring of the stilbene was prepared, and the effect of the modifications on duplex stability was determined via UV-melting curves. A trimethoxystilbene derivative as a 5'-substituent increases duplex melting points by up to 12.2 degrees C per modification. With this alkoxystilbene substituent, terminal mismatches in DNA duplexes lower the melting point by up to 23.4 degrees C over the perfectly matched control, whereas terminal mismatches in unmodified DNA cause melting point depressions of no more than 6.1 degrees C. An aminomethylstilbene substituent linked to an oligopyrrolamide minor groove binder increases the melting point of an all-A/T decamer by up to 32.7 degrees C, thus shifting the melting point into a range typical for duplexes with statistical G/C-content. An affinity- and selectivity-enhancing effect was also observed when the trimethoxystilbene cap was employed on a small DNA microarray. The phosphoramidite of the trimethoxystilbene can be readily employed in automatic DNA synthesis, facilitating the generation of DNA chips with improved fidelity.
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Affiliation(s)
- Zeynep Dogan
- Institute for Organic Chemistry, University of Karlsruhe (TH), D-76131 Karlsruhe, Germany
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135
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Reddy PM, Dexter R, Bruice TC. DNA sequence recognition in the minor groove by hairpin pyrrole polyamide–Hoechst 33258 analogue conjugate. Bioorg Med Chem Lett 2004; 14:3803-7. [PMID: 15203166 DOI: 10.1016/j.bmcl.2004.04.089] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2004] [Revised: 04/27/2004] [Accepted: 04/27/2004] [Indexed: 11/22/2022]
Abstract
A hairpin pyrrole polyamide conjugated to a Hoechst 33258 (Ht) analogue, PyPyPy-gamma-PyPyPy-gamma-Ht, was synthesized on solid-phase by adaptation of an Fmoc technique using a series of PyBOP/HOBt mediated coupling reactions. Sequence selectivity and complex stabilities were characterized by spectrofluorometric titrations and thermal melting studies. The polyamide of the conjugate was observed to bind in a hairpin motif forming 1:1 conjugate:dsDNA complexes. The conjugate is able to recognize nine contiguous A/T bps, discriminating from the sequences containing fewer than nine contiguous A/T bps.
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Affiliation(s)
- Putta Mallikarjuna Reddy
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, CA 93106, USA
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136
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Yang CH, Chen WF, Jong MC, Jong BJ, Chang JC, Waring MJ, Ma L, Sheh L. Semiquinone Footprinting. J Am Chem Soc 2004; 126:8104-5. [PMID: 15225037 DOI: 10.1021/ja040051m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A novel DNA footprinting method employing strong semiquinone radical species generated from a dipeptide-hydroquinone conjugate is described.
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Affiliation(s)
- Chia-Hung Yang
- Department of Chemistry, Tunghai Christian University, Taichung, Taiwan 407, ROC
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137
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Jacquemard U, Routier S, Tatibouët A, Kluza J, Laine W, Bal C, Bailly C, Mérour JY. Synthesis of diphenylcarbazoles as cytotoxic DNA binding agents. Org Biomol Chem 2004; 2:1476-83. [PMID: 15136803 DOI: 10.1039/b401445f] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the synthesis of a series of novel diphenylcarbazoles designed to interact with DNA. The compounds bearing two or three dimethylaminoalkyloxy side chains were found to bind much more tightly to DNA, preferentially at AT-rich sites, than the corresponding hydroxy compounds. The DNA binding compounds exhibit potent cytotoxic activity toward P388 leukemia cells. The 3,6-diphenylcarbazole thus represent an interesting scaffold to develop antitumor agents interacting with nucleic acids.
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Affiliation(s)
- Ulrich Jacquemard
- Institut de Chimie Organique et Analytique, UMR 6005, Universite d'Orleans, B.P. 6759, 45067 Orleans 2, France
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138
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Lacy ER, Nguyen B, Le M, Cox KK, OHare C, Hartley JA, Lee M, Wilson WD. Energetic basis for selective recognition of T*G mismatched base pairs in DNA by imidazole-rich polyamides. Nucleic Acids Res 2004; 32:2000-7. [PMID: 15064359 PMCID: PMC390366 DOI: 10.1093/nar/gkh515] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To complement available structure and binding results and to develop a detailed understanding of the basis for selective molecular recognition of T.G mismatches in DNA by imidazole containing polyamides, a full thermodynamic profile for formation of the T.G-polyamide complex has been determined. The amide-linked heterocycles f-ImImIm and f-PyImIm (where f is formamido group, Im is imidazole and Py is pyrrole) were studied by using biosensor-surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) with a T.G mismatch containing DNA hairpin duplex and a similar DNA with only Watson-Crick base pairs. Large negative binding enthalpies for all of the polyamide-DNA complexes indicate that the interactions are enthalpically driven. SPR results show slower complex formation and stronger binding of f-ImImIm to the T.G than to the match site. The thermodynamic analysis indicates that the enhanced binding to the T.G site is the result of better entropic contributions. Negative heat capacity changes for the complex are correlated with calculated solvent accessible surface area changes and indicate hydrophobic contributions to complex formation. DNase I footprinting analysis in a long DNA sequence provided supporting evidence that f-ImImIm binds selectively to T.G mismatch sites.
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Affiliation(s)
- Eilyn R Lacy
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
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139
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Abstract
The DNA binding characteristics of a series of homologous 2,6-disubstituted anthraquinone threading intercalators bearing one to four ethylene glycol units in their side chains have been studied. Binding constants were measured via surface plasmon resonance (SPR). These compounds bind to an AT-rich hairpin with slightly higher affinity than to a GC-rich hairpin. The binding constants decrease as the length of the side chain increases.
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Affiliation(s)
- Ruel E McKnight
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
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140
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141
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Chang JC, Yang CH, Chou PY, Yang WH, Chou IC, Lu CT, Lin PH, Hou RCW, Jeng KCG, Cheng CC, Sheh L. DNA sequence-specific recognition of peptides incorporating the HPRK and polyamide motifs. Bioorg Med Chem 2004; 12:53-61. [PMID: 14697770 DOI: 10.1016/j.bmc.2003.10.049] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Three peptide amides, HPRK(Py)(4)HPRK-NH(2) (PyH-12), HPRK(Py)(3)HPRK-NH(2) (PyH-11) and HPRK(Py)(2)HPRK-NH(2) (PyH-10), incorporating two HPRK motifs and various 4-amino-1-methylpyrrole-2-carboxylic acid residues (Py) were synthesized by solid-phase peptide methodology. The binding of these three peptides to a 5'-32P-labeled 158-mer DNA duplex (Watson fragment) and to a 5'-32P-labeled 135-mer DNA duplex (complementary Crick fragment) was investigated by quantitative DNase I footprinting. On the 158-mer Watson strand, the most distinctive DNase I blockages seen with all three peptides occur around positions 105-112 and 76-79, corresponding to the sequences 5'-GAGAAAAT-3' and 5'-CGGT-3', respectively. However, on the complementary Crick strand, only PyH-12 strongly discriminates the 5'-TTT-3' site around positions 108-110 whereas both PyH-11 and PyH-10 have moderate binding around positions 102-112 comprising the sequence 5'-ATTTTCTCCTT-3'. Possible bidentate and single interactions of the side-chain functions and alpha-amino protons of the peptides with DNA bases are discussed.
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Affiliation(s)
- Jung-Cheng Chang
- Department of Chemistry, Tunghai Christian University, 407, ROC, Taichung, Taiwan
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142
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Abstract
Double-helical DNA accelerates the rate of ligation of two six-ring hairpin polyamides which bind adjacent sites in the minor groove via a 1,3-dipolar cycloaddition to form a tandem dimer. The rate of the templated reaction is dependent on DNA sequence as well as on the distance between the hairpin-binding sites. The tandem dimer product of the DNA-templated reaction has improved binding properties with respect to the smaller hairpin fragments. Since cell and nuclear uptake of DNA-binding polyamides will likely be dependent on size, this is a minimum first step toward the design of self-assembling small gene-regulating fragments to produce molecules of increasing complexity with more specific genomic targeting capabilities.
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Affiliation(s)
- Adam T Poulin-Kerstien
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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143
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Tse WC, Ishii T, Boger DL. Comprehensive high-resolution analysis of hairpin polyamides utilizing a fluorescent intercalator displacement (FID) assay. Bioorg Med Chem 2003; 11:4479-86. [PMID: 13129584 DOI: 10.1016/s0968-0896(03)00455-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Four hairpin polyamides bearing subtle N- and C-terminal substitutions were examined in a fluorescent intercalator displacement (FID) assay enlisting a library of 512 DNA hairpins that contain all possible five base pair sequences in a challenging probe of its capabilities for establishing DNA binding sequence selectivity. Not only did the assay define the global sequence selectivity expected based on known structural interactions and Dervan's pairing rules establishing the utility of the method for characterizing such polyamides, but previously unappreciated subtle substituent effects on global sequence selectivity were also revealed. Thus, we report the discovery of a novel five base pair high affinity binding site of the form 5'-WWCWW (vs 5'-WGWWW) for the polyamide ImPyPy-gamma-PyPyPy-beta-Dp and its structural basis.
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Affiliation(s)
- Winston C Tse
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550N. Torrey Pines Road, La Jolla, CA 92037, USA
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144
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Affiliation(s)
| | - Burkhard König
- Institut für Organische Chemie, Universität Regensburg, 93040 Regensburg, Germany
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145
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Eckel R, Ros R, Ros A, Wilking SD, Sewald N, Anselmetti D. Identification of binding mechanisms in single molecule-DNA complexes. Biophys J 2003; 85:1968-73. [PMID: 12944309 PMCID: PMC1303368 DOI: 10.1016/s0006-3495(03)74624-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Changes in the elastic properties of single deoxyribonucleic acid (DNA) molecules in the presence of different DNA-binding agents are identified using atomic force microscope single molecule force spectroscopy. We investigated the binding of poly(dG-dC) dsDNA with the minor groove binder distamycin A, two supposed major groove binders, an alpha-helical and a 3(10)-helical peptide, the intercalants daunomycin, ethidium bromide and YO, and the bis-intercalant YOYO. Characteristic mechanical fingerprints in the overstretching behavior of the studied single DNA-ligand complexes were observed allowing the distinction between different binding modes. Docking of ligands to the minor or major groove of DNA has the effect that the intramolecular B-S transition remains visible as a distinct plateau in the force-extension trace. By contrast, intercalation of small molecules into the double helix is characterized by the vanishing of the B-S plateau. These findings lead to the conclusion that atomic force microscope force spectroscopy can be regarded as a single molecule biosensor and is a potent tool for the characterization of binding motives of small ligands to DNA.
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Affiliation(s)
- Rainer Eckel
- Experimental Biophysics and Applied Nanosciences, Faculty of Physics, Bielefeld University, 33615 Bielefeld, Germany
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146
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Reddy PM, Jindra PT, Satz AL, Bruice TC. Sequence selective recognition in the minor groove of dsDNA by pyrrole, imidazole-substituted bis-benzimidazole conjugates. J Am Chem Soc 2003; 125:7843-8. [PMID: 12823002 DOI: 10.1021/ja035116k] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of pyrrole, imidazole-substituted bis-benzimidazole conjugates, Py-Py-Im-gamma-biBenz, Py-Py-gamma-biBenz, Py-Im-gamma-biBenz, and Im-Py-gamma-biBenz (1-4), were prepared in an attempt to target dsDNA sequences possessing both A/T and G/C bps. The dsDNA interactions and sequence specificity of the conjugates have been characterized via spectrofluorometric titrations and thermal melting studies. All conjugates form 1:1 complexes with dsDNA at subnanomolar concentrations. The Im moiety selectively recognizes a G/C bp embedded in the A/T-rich binding site. This represents the first clear example of sequence selective recognition in a 1:1 motif.(1) The equilibrium association constant (K(1)) for complexation of a specific nine-bp dsDNA site, 5'-gcggTATGAAATTcgacg-3', by conjugate 1 is approximately 2.6 x 10(9) M(-1). Displacement of the G/C position or G/C-->A/T substitution within the nine-bp site decreases the K(1) by approximately 8-fold, whereas two continuous G/C bps decrease the K(1) by approximately 50-fold magnitude. The K(1) values for seven-bp dsDNA, 5'-gcggtaTGAAATTcgacg-3' and 5'-gcggtaCAAAATTcgacg-3', binding sites by conjugates Py-Im-gamma-biBenz (3) and Im-Py-gamma-biBenz (4) are approximately 2.3 x 10(9) and approximately 1.2 x 10(9) M(-1), respectively. However, the conjugates with no Im moiety, Py-Py-gamma-biBenz (2) and Py-Py-Py-gamma-biBenz (5 and 6), are specific for seven- to nine-bp A/T-rich sites and single A/T-->G/C bp substitution within the binding site decreases the K(1) values by 1-2 orders of magnitude.
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Affiliation(s)
- Putta Mallikarjuna Reddy
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, CA 93106, USA
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147
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Affiliation(s)
- A M Nikitin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow, 117984 Russia
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148
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Bailly C, Chessari G, Carrasco C, Joubert A, Mann J, Wilson WD, Neidle S. Sequence-specific minor groove binding by bis-benzimidazoles: water molecules in ligand recognition. Nucleic Acids Res 2003; 31:1514-24. [PMID: 12595560 PMCID: PMC149830 DOI: 10.1093/nar/gkg237] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The binding of two symmetric bis-benzimidazole compounds, 2,2-bis-[4'-(3"-dimethylamino-1"-propyloxy)phenyl]-5,5-bi-1H-benzimidazole and its piperidinpropylphenyl analog, to the minor groove of DNA, have been studied by DNA footprinting, surface plasmon resonance (SPR) methods and molecular dynamics simulations in explicit solvent. The footprinting and SPR methods find that the former compound has enhanced affinity and selectivity for AT sequences in DNA. The molecular modeling studies have suggested that, due to the presence of the oxygen atom in each side chain of the former compound, a water molecule is immobilized and effectively bridges between side chain and DNA base edges via hydrogen bonding interactions. This additional contribution to ligand-DNA interactions would be expected to result in enhanced DNA affinity, as is observed.
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Affiliation(s)
- Christian Bailly
- INSERM U-524 et Laboratoire de Pharmacologie Antitumorale du Centre Oscar Lambret, IRCL, Place de Verdun, 59045 Lille, France
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149
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Carrasco C, Helissey P, Haroun M, Baldeyrou B, Lansiaux A, Colson P, Houssier C, Giorgi-Renault S, Bailly C. Design of a composite ethidium-netropsin-anilinoacridine molecule for DNA recognition. Chembiochem 2003; 4:50-61. [PMID: 12512076 DOI: 10.1002/cbic.200390014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Control of gene expression is a cherished goal of cancer chemotherapy. Small ligand molecules able to bind tightly to DNA in a well-defined configuration are being actively searched for. With this goal in mind, we have designed and synthesized the trifunctional molecule R-132, which combines a bispyrrole skeleton for minor groove DNA recognition and two different chromophores, anilinoacridine and ethidium. The affinity and mode of binding of R-132 to DNA were studied by a combination of complementary biochemical and biophysical techniques, which included absorption and fluorescence spectroscopy and circular and linear dichroism. A surface plasmon resonance biosensor analysis was also performed to quantify the kinetic parameters of the drug-DNA interaction process. Altogether, the results demonstrate that the three moieties of the hybrid molecule are engaged in the interaction process, thus validating the rational design strategy. At the biological level, R-132 stabilizes topoisomerase-II-DNA covalent complexes and displays potent cytotoxic activities, which are attributable to its DNA-binding properties. R-132 easily enters and accumulates in cell nuclei, as evidenced by confocal microscopy. R-132 therefore provides a novel lead compound for the design of gene-targeted anticancer agents.
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Affiliation(s)
- Carolina Carrasco
- INSERM U-524 et Laboratoire de Pharmacologie Antitumorale du Centre Oscar Lambret, IRCL, Place de Verdun, 59045 Lille, France
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150
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Markowska A, Rózański A, Wołczyński S, Midura-Nowaczek K. Synthesis and biological activity of carbocyclic lexitropsins with a bioreductive fragment. FARMACO (SOCIETA CHIMICA ITALIANA : 1989) 2002; 57:1019-23. [PMID: 12564478 DOI: 10.1016/s0014-827x(02)01289-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Carbocyclic oligopeptides containing of two, three or four aromatic rings with N,N-dimethylpropyl-1,3-diamine group as C-terminus fragment of compounds and 5-[bis(2-chloroethyl)amino]-2,4-dinitrobenzamide as N-terminal were synthesized. These lexitropsins present antitumour activity on the neoplastic cells hepatoblastoma HEP G2. These experiments were evaluated in hypoxic and oxygen conditions. Significant differences of activity in oxygen and hypoxic conditions were shown only in compound, N-(3-dimethylaminopropyl)-N'-([3-[5-bis(2-chlorethyl)amino]-2,4-dinitrobenzamide])-phenyl]urea dihydrochloride 1 (IC50 = 8545 nM in oxygen vs. IC50 = 710 nM in hypoxia). The rest of compounds (2-6) do not indicate differences of activity in oxygen and hypoxia.
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Affiliation(s)
- Agnieszka Markowska
- Department of Organic Chemistry, Medical Academy of Białystok, Mickiewicza Str. 2A, 15-230 Białystok 8, Pologne, Poland.
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