1
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Liu B, Wang S, Aston K, Koeller KJ, Kermani SFH, Castañeda CH, Scuderi MJ, Luo R, Bashkin JK, Wilson WD. β-Alanine and N-terminal cationic substituents affect polyamide-DNA binding. Org Biomol Chem 2018; 15:9880-9888. [PMID: 29143012 DOI: 10.1039/c7ob02513k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Minor-groove binding hairpin polyamides (PAs) bind specific DNA sequences. Synthetic modifications can improve PA-DNA binding affinity and include flexible modules, such as β-alanine (β) motifs to replace pyrroles (Py), and increasing compound charge using N-terminal cationic substituents. To better understand the variations in kinetics and affinities caused by these modifications on PA-DNA interactions, a comprehensive set of PAs with different numbers and positions of β and different types of N-cationic groups was systematically designed and synthesized to bind their cognate sequence, the λB motif. The λB motif is also a strong binding promoter site of the major groove targeting transcription factor PU.1. The PA binding affinities and kinetics were evaluated using a spectrum of powerful biophysical methods: thermal melting, biosensor surface plasmon resonance and circular dichroism. The results show that β inserts affect PA-DNA interactions in a number and position dependent manner. Specifically, a β replacement between two imidazole heterocycles (ImβIm) generally strengthens binding. In addition, N-terminal cationic groups can accelerate the association between PA and DNA, but the bulky size of TMG can cause steric hindrance and unfavourable repulsive electrostatic interactions in some PAs. The future design of stronger binding PA requires careful combination of βs and cationic substituents.
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Affiliation(s)
- Beibei Liu
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA.
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2
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Kawamoto Y, Bando T, Sugiyama H. Sequence-specific DNA binding Pyrrole-imidazole polyamides and their applications. Bioorg Med Chem 2018; 26:1393-1411. [PMID: 29439914 DOI: 10.1016/j.bmc.2018.01.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/25/2018] [Accepted: 01/28/2018] [Indexed: 12/25/2022]
Abstract
Pyrrole-imidazole polyamides (Py-Im polyamides) are cell-permeable compounds that bind to the minor groove of double-stranded DNA in a sequence-specific manner without causing denaturation of the DNA. These compounds can be used to control gene expression and to stain specific sequences in cells. Here, we review the history, structural variations, and functional investigations of Py-Im polyamides.
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Affiliation(s)
- Yusuke Kawamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan.
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan; Institute for Integrated Cell-Material Science (iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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3
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Taylor RD, Chandran A, Kashiwazaki G, Hashiya K, Bando T, Nagase H, Sugiyama H. Selective Targeting of the KRAS Codon 12 Mutation Sequence by Pyrrole-Imidazole Polyamideseco-CBI Conjugates. Chemistry 2015; 21:14996-5003. [DOI: 10.1002/chem.201501870] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Indexed: 12/16/2022]
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4
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Wang S, Aston K, Koeller KJ, Harris GD, Rath NP, Bashkin JK, Wilson WD. Modulation of DNA-polyamide interaction by β-alanine substitutions: a study of positional effects on binding affinity, kinetics and thermodynamics. Org Biomol Chem 2015; 12:7523-36. [PMID: 25141096 DOI: 10.1039/c4ob01456a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Hairpin polyamides (PAs) are an important class of sequence-specific DNA minor groove binders, and frequently employ a flexible motif, β-alanine (β), to reduce the molecular rigidity to maintain the DNA recognition register. To better understand the diverse effects that β can have on DNA-PA binding affinity, selectivity, and especially kinetics, which have rarely been reported, we have initiated a detailed study for an eight-heterocyclic hairpin PA and its β derivatives with their cognate and mutant sequences. With these derivatives, all internal pyrroles of the parent PA are systematically substituted with single or double βs. A set of complementary experiments have been conducted to evaluate the molecular interactions in detail: UV-melting, biosensor-surface plasmon resonance, circular dichroism and isothermal titration calorimetry. The β substitutions generally weaken the binding affinities of these PAs with cognate DNA, and have large and diverse influences on PA binding kinetics in a position- and number-dependent manner. The DNA base mutations have also shown positional effects on the binding of a single PA. Besides the β substitutions, the monocationic Dp group [3-(dimethylamino)propylamine] in parent PA has been modified into a dicationic Ta group (3,3'-diamino-N-methyldipropylamine) to minimize the frequently observed PA aggregation with ITC experiments. The results clearly show that the Ta modification not only maintains the DNA binding mode and affinity of PA, but also significantly reduces PA aggregation and allows the complete thermodynamic signature of eight-ring hairpin PA to be determined for the first time. This combined set of results significantly extends our understanding of the energetic basis of specific DNA recognition by PAs.
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Affiliation(s)
- Shuo Wang
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
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5
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Taylor RD, Asamitsu S, Takenaka T, Yamamoto M, Hashiya K, Kawamoto Y, Bando T, Nagase H, Sugiyama H. Sequence-Specific DNA Alkylation Targeting for Kras Codon 13 Mutation by Pyrrole-Imidazole Polyamideseco-CBI Conjugates. Chemistry 2013; 20:1310-7. [DOI: 10.1002/chem.201303295] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 10/31/2013] [Indexed: 12/13/2022]
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6
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Wolfe AL, Duncan KK, Lajiness JP, Zhu K, Duerfeldt AS, Boger DL. A fundamental relationship between hydrophobic properties and biological activity for the duocarmycin class of DNA-alkylating antitumor drugs: hydrophobic-binding-driven bonding. J Med Chem 2013; 56:6845-57. [PMID: 23944748 DOI: 10.1021/jm400665c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Two systematic series of increasingly hydrophilic derivatives of duocarmycin SA that feature the incorporation of ethylene glycol units (n = 1-5) into the methoxy substituents of the trimethoxyindole subunit are described. These derivatives exhibit progressively increasing water solubility along with progressive decreases in cell growth inhibitory activity and DNA alkylation efficiency with the incremental ethylene glycol unit incorporations. Linear relationships of cLogP with -log IC50 for cell growth inhibition and -log AE (AE = cell-free DNA alkylation efficiency) were observed, with the cLogP values spanning the productive range of 2.5-0.49 and the -log IC50 values spanning the range of 11.2-6.4, representing IC50 values that vary by a factor of 10(5) (0.008 to 370 nM). The results quantify the fundamental role played by the hydrophobic character of the compound in the expression of the biological activity of members in this class (driving the intrinsically reversible DNA alkylation reaction) and define the stunning magnitude of its effect.
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Affiliation(s)
- Amanda L Wolfe
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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7
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Dupureur CM, Bashkin JK, Aston K, Koeller KJ, Gaston KR, He G. Fluorescence assay of polyamide-DNA interactions. Anal Biochem 2012; 423:178-83. [PMID: 22342620 DOI: 10.1016/j.ab.2012.01.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 01/12/2012] [Accepted: 01/18/2012] [Indexed: 01/11/2023]
Abstract
Polyamides (PAs) are distamycin-type ligands of DNA that bind the minor groove and are capable of sequence selective recognition. This capability provides a viable route to their development as therapeutics. Presented here is a simple and convenient fluorescence assay for PA-DNA binding. PAs are titrated into a sample of a hairpin DNA featuring a TAMRA dye attached to an internal dU near the PA binding site. In a study of 6 PAs, PA binding leads to a steady reproducible decrease in fluorescence intensity that can be used to generate binding isotherms. The assay works equally well with both short (6- to 8-ring) and long (14-ring) PAs, and K(d) values ranging from approximately 1 nM to at least 140 nM were readily obtained using a simple monochromator or filter configuration. Competition assays provide a means to assessing possible dye interference, which can be negligible. The assay can also be used to determine PA extinction coefficients and to measure binding kinetics; thus, it is an accessible and versatile tool for the study of PA properties and PA-DNA interactions.
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Affiliation(s)
- Cynthia M Dupureur
- Department of Chemistry and Biochemistry and Center for Nanoscience, University of Missouri-St. Louis, St. Louis, MO 63121, USA.
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8
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Ghosh S, Usharani D, De S, Jemmis ED, Bhattacharya S. Photophysical and duplex-DNA-binding properties of distamycin dimers based on 4,4'- and 2,2'-dialkoxyazobenzenes as the core. Chem Asian J 2009; 3:1949-61. [PMID: 18810740 DOI: 10.1002/asia.200800151] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Distamycin-based tetrapeptide (1) was covalently tethered to both ends of the central dihydroxyazobenzene moiety at either the 2,2' or 4,4' positions. This afforded two isomeric, distamycin-azobenzene-distamycin systems, 2 (para) and 3 (ortho), both of them being photoisomerizable. Illumination of these conjugates in solution at approximately 360 nm induced photoisomerization and the time course of the process was followed by UV/Vis and (1)H NMR spectroscopy. The kinetics of the thermal reversion at various temperatures of cis to trans isomers of the conjugates obtained after photoillumination were also examined. This afforded the respective thermal-activation parameters. Both the molecular architecture and the location of the substituent around the core azobenzene determined the rate and activation-energy barrier for the cis-to-trans back-isomerization of these conjugates in solution. Duplex-DNA binding of the conjugates and the changes in DNA-binding efficiency upon photoisomerization was also examined by CD spectroscopy, thermal denaturation studies, and a Hoechst displacement assay. The conjugate 2 showed higher DNA-binding affinity and a greater change in the DNA-binding efficiency upon photoisomerization compared with its 2,2'-disubstituted counterpart. The experimental findings were substantiated by using molecular-docking studies involving each conjugate with a model duplex d[(GC(AT)(10)CG)](2) DNA molecule.
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Affiliation(s)
- Sumana Ghosh
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India
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9
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Ghosh S, Usharani D, Paul A, De S, Jemmis ED, Bhattacharya S. Design, Synthesis, and DNA Binding Properties of Photoisomerizable Azobenzene−Distamycin Conjugates: An Experimental and Computational Study. Bioconjug Chem 2008; 19:2332-45. [DOI: 10.1021/bc800130u] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sumana Ghosh
- Department of Organic Chemistry and Department of Inorganic and Physical Chemistry, Indian Institute of Science, and Chemical Biology Unit, Jawaharlal Nehru Centre of Advanced Scientific Research, Bangalore 560 012, India
| | - Dandamudi Usharani
- Department of Organic Chemistry and Department of Inorganic and Physical Chemistry, Indian Institute of Science, and Chemical Biology Unit, Jawaharlal Nehru Centre of Advanced Scientific Research, Bangalore 560 012, India
| | - Ananya Paul
- Department of Organic Chemistry and Department of Inorganic and Physical Chemistry, Indian Institute of Science, and Chemical Biology Unit, Jawaharlal Nehru Centre of Advanced Scientific Research, Bangalore 560 012, India
| | - Susmita De
- Department of Organic Chemistry and Department of Inorganic and Physical Chemistry, Indian Institute of Science, and Chemical Biology Unit, Jawaharlal Nehru Centre of Advanced Scientific Research, Bangalore 560 012, India
| | - Eluvathingal D. Jemmis
- Department of Organic Chemistry and Department of Inorganic and Physical Chemistry, Indian Institute of Science, and Chemical Biology Unit, Jawaharlal Nehru Centre of Advanced Scientific Research, Bangalore 560 012, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry and Department of Inorganic and Physical Chemistry, Indian Institute of Science, and Chemical Biology Unit, Jawaharlal Nehru Centre of Advanced Scientific Research, Bangalore 560 012, India
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10
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Tse WC, Boger DL. A fluorescent intercalator displacement assay for establishing DNA binding selectivity and affinity. ACTA ACUST UNITED AC 2008; Chapter 8:Unit 8.5. [PMID: 18428943 DOI: 10.1002/0471142700.nc0805s20] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A protocol for a fluorescent intercalator displacement (FID) assay useful for establishing DNA binding selectivity, affinity, stoichiometry, and binding site size, and for distinguishing modes of DNA binding is presented.
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11
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Metwally NH. Efficient Synthesis of Highly Substituted Furan, Thiophene, Pyrrole and 2‐Aminothiazole Derivatives. SYNTHETIC COMMUN 2007. [DOI: 10.1080/00397910701575384] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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12
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Nelson SM, Ferguson LR, Denny WA. Non-covalent ligand/DNA interactions: minor groove binding agents. Mutat Res 2007; 623:24-40. [PMID: 17507044 DOI: 10.1016/j.mrfmmm.2007.03.012] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Accepted: 03/31/2007] [Indexed: 05/15/2023]
Abstract
An understanding of the mechanism by which minor groove binding agents interact with DNA has led to the design of agents that can reversibly bind with high selectivity to extended DNA target sequences. Simple compounds, such as the polypyrroles and the bis-benzimidazoles, have been used as carriers for alkylating agents effectively directing alkylation to specific DNA sequences. The spectrum of DNA alkylation and mutation by classical alkylators, such as nitrogen mustards, has been profoundly modified by such attachment. The observed "side-by-side" binding of small polypyrrole antibiotics has led to the design of synthetic hairpin polyamides with programmable DNA sequence selectivity. These compounds are able to compete with natural substrates, such as specific transcription factors, and alter gene expression. They are being developed as artificial transcription factors, able to deliver activating peptides to specific recognition sequences, and as potential protein-DNA dimerization agents. Hairpin polyamides are also being used as carriers for the delivery of alkylators to defined DNA sites. The degree of control of gene expression thus offered by the hairpin polyamides suggests enormous promise for their clinical utility. Recent developments with other minor groove binding small molecules and technological advances are also discussed.
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Affiliation(s)
- Stephanie M Nelson
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland 10000, New Zealand.
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13
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Farkas ME, Tsai SM, Dervan PB. Alpha-diaminobutyric acid-linked hairpin polyamides. Bioorg Med Chem 2007; 15:6927-36. [PMID: 17869122 PMCID: PMC2140246 DOI: 10.1016/j.bmc.2007.07.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Revised: 07/20/2007] [Accepted: 07/31/2007] [Indexed: 11/25/2022]
Abstract
A hairpin polyamide-chlorambucil conjugate linked by alpha-diaminobutyric acid (alpha-DABA) has been shown to have interesting biological properties in cellular and small animal models. Remarkably, this new class of hairpin polyamides has not been previously characterized with regard to energetics and sequence specificity. Herein we present a series of pyrrole-imidazole hairpin polyamides linked by alpha-DABA and compare them to polyamides containing the standard gamma-DABA turn unit. The alpha-DABA hairpins have overall decreased binding affinities. However, alpha-DABA polyamide-chlorambucil conjugates are sequence-specific DNA alkylators with increased specificities. Affinity cleavage studies of alpha-DABA polyamide-EDTA conjugates confirmed their preference for binding DNA in a forward hairpin conformation. In contrast, an unsubstituted glycine-linked polyamide prefers to bind in an extended binding mode. Thus, substitution on the turn unit locks the alpha-DABA polyamide into the forward hairpin binding motif.
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Affiliation(s)
| | | | - Peter B. Dervan
- *Corresponding author: Tel.: +1 626 395 6002; Fax: +1 626 683 8753; E-mail:
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14
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Minoshima M, Bando T, Sasaki S, Shinohara KI, Shimizu T, Fujimoto J, Sugiyama H. DNA Alkylation by Pyrrole−Imidazole seco-CBI Conjugates with an Indole Linker: Sequence-Specific DNA Alkylation with 10-Base-Pair Recognition through Heterodimer Formation. J Am Chem Soc 2007; 129:5384-90. [PMID: 17425308 DOI: 10.1021/ja065235a] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The sequence-specific DNA alkylation by conjugates 4 and 5, which consist of N-methylpyrrole (Py)-N-methylimidazole (Im) polyamides and 1-(chloromethyl)-5-hydroxy-1,2-dihydro-3H-benz[e]indole (seco-CBI) linked with an indole linker, was investigated in the absence or presence of partner Py-Im polyamide 6. High-resolution denaturing polyacrylamide gel electrophoresis revealed that conjugate 4 alkylates DNA at the sequences 5'-(A/T)GCCTA-3' through hairpin formation, and alkylates 5'-GGAAAGAAAA-3' through an extended binding mode. However, in the presence of partner Py-Im polyamide 6, conjugate 4 alkylates DNA at a completely different sequence, 5'-AGGTTGTCCA-3'. Alkylation of 4 in the presence of 6 was effectively inhibited by a competitor 7. Surface plasmon resonance (SPR) results indicated that conjugate 4 does not bind to 5'-AGGTTGTCCA-3', whereas 6 binds tightly to this sequence. The results suggest that alkylation proceeds through heterodimer formation, indicating that this is a general way to expand the recognition sequence for DNA alkylation by Py-Im seco-CBI conjugates.
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Affiliation(s)
- Masafumi Minoshima
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
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15
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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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16
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Shirude PS, Kumar VA, Ganesh KN. BisPNA Targeting to DNA: Effect of Neutral Loop on DNA Duplex Strand Invasion byaepPNA-N7G/aepPNA-C Substituted Peptide Nucleic Acids. European J Org Chem 2005. [DOI: 10.1002/ejoc.200500544] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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17
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Reddy PM, Toporowski JW, Kahane AL, Bruice TC. Recognition of a 10 base pair sequence of DNA and stereochemical control of the binding affinity of chiral hairpin polyamide–Hoechst 33258 conjugates. Bioorg Med Chem Lett 2005; 15:5531-6. [PMID: 16203135 DOI: 10.1016/j.bmcl.2005.08.076] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2005] [Revised: 08/24/2005] [Accepted: 08/25/2005] [Indexed: 11/23/2022]
Abstract
Chiral hairpin polyamides linked to a Hoechst 33258 analogue at the alpha-position of the hairpin turn amino acid (1,2) were synthesized on solid phase by adopting Fmoc and ivDde techniques. The DNA-binding properties of enantiomeric conjugates 1 and 2, and N-terminal linked conjugate 3 for 8-14bp sequences were determined by spectrofluorometric and thermal melting studies. Conjugates 1 and 2 recognize a 10bp sequence, while conjugate 3 recognizes a 9bp sequence. Interestingly, R-enantiomer 1 exhibited 10- to 30-fold higher binding affinities than S-enantiomer 2 for the DNA sequences studied. These binding differences were accounted for by molecular modeling studies, which revealed that the amide proton nearest to the chiral center in R-conjugate 1 is better positioned to form hydrogen bonds to the DNA bases, while S-conjugate 2 does not.
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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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18
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Yeung BKS, Tse WC, Boger DL. Determination of binding affinities of triplex forming oligonucleotides using a fluorescent intercalator displacement (FID) assay. Bioorg Med Chem Lett 2004; 13:3801-4. [PMID: 14552783 DOI: 10.1016/j.bmcl.2003.07.005] [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] [Indexed: 10/27/2022]
Abstract
The binding affinities of several triplex forming oligonucleotides were determined using a fluorescent intercalator displacement (FID) assay.
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Affiliation(s)
- Bryan K S Yeung
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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19
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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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Affiliation(s)
| | - Burkhard König
- Institut für Organische Chemie, Universität Regensburg, 93040 Regensburg, Germany
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21
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Abstract
Many diseases, such as cancer, are related to aberrant gene expression. Regulating transcription by chemical methods could be important in human medicine. Minor groove-binding polyamides offer one chemical approach to DNA recognition.
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Affiliation(s)
- Peter B Dervan
- Division of Chemistry and Chemical Engineering, and Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA.
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22
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Boger DL. Solution-phase synthesis of combinatorial libraries designed to modulate protein-protein or protein-DNA interactions. Bioorg Med Chem 2003; 11:1607-13. [PMID: 12659745 DOI: 10.1016/s0968-0896(03)00031-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A short personal perspective on the development of an approach to the solution-phase synthesis of combinatorial libraries for modulating cellular signaling by inhibiting, promoting, or mimicking protein-protein or protein-DNA interactions is provided.
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Affiliation(s)
- Dale L Boger
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550North Torrey Pines Road, La Jolla, CA 92037, USA.
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Abstract
[reaction: see text] A series of 4-amino-1H-pyrrole-2-carboxylic acid benzyl esters has been synthesized in 61-84% yields on treatment of N-PhF-4-oxoproline benzyl ester and its 3-alkyl-substituted derivatives with different primary and secondary amines and a catalytic amount of TsOH in THF. 4-Hydroxy-1H-pyrrole-2-carboxylic acid benzyl esters were prepared in 59 and 70% yields by treatment of N-PhF-4-oxoproline benzyl esters with ammonium hydroxide in THF.
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Affiliation(s)
- Félix-Antoine Marcotte
- Département de chimie, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, Québec, Canada H3C 3J7
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