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Pett L, Kiakos K, Satam V, Patil P, Laughlin-Toth S, Gregory M, Bowerman M, Olson K, Savagian M, Lee M, Lee M, Wilson WD, Hochhauser D, Hartley JA. Modulation of topoisomerase IIα expression and chemosensitivity through targeted inhibition of NF-Y:DNA binding by a diamino p-anisyl-benzimidazole (Hx) polyamide. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2017; 1860:617-629. [PMID: 27750031 PMCID: PMC5757371 DOI: 10.1016/j.bbagrm.2016.10.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/11/2016] [Accepted: 10/12/2016] [Indexed: 11/21/2022]
Abstract
BACKGROUND Sequence specific polyamide HxIP 1, targeted to the inverted CCAAT Box 2 (ICB2) on the topoisomerase IIα (topo IIα) promoter can inhibit NF-Y binding, re-induce gene expression and increase sensitivity to etoposide. To enhance biological activity, diamino-containing derivatives (HxI*P 2 and HxIP* 3) were synthesised incorporating an alkyl amino group at the N1-heterocyclic position of the imidazole/pyrrole. METHODS DNase I footprinting was used to evaluate DNA binding of the diamino Hx-polyamides, and their ability to disrupt the NF-Y:ICB2 interaction assessed using EMSAs. Topo IIα mRNA (RT-PCR) and protein (Immunoblotting) levels were measured following 18h polyamide treatment of confluent A549 cells. γH2AX was used as a marker for etoposide-induced DNA damage after pre-treatment with HxIP* 3 and cell viability was measured using Cell-Titer Glo®. RESULTS Introduction of the N1-alkyl amino group reduced selectivity for the target sequence 5'-TACGAT-3' on the topo IIα promoter, but increased DNA binding affinity. Confocal microscopy revealed both fluorescent diamino polyamides localised in the nucleus, yet HxI*P 2 was unable to disrupt the NF-Y:ICB2 interaction and showed no effect against the downregulation of topo IIα. In contrast, inhibition of NF-Y binding by HxIP* 3 stimulated dose-dependent (0.1-2μM) re-induction of topo IIα and potentiated cytotoxicity of topo II poisons by enhancing DNA damage. CONCLUSIONS Polyamide functionalisation at the N1-position offers a design strategy to improve drug-like properties. Dicationic HxIP* 3 increased topo IIα expression and chemosensitivity to topo II-targeting agents. GENERAL SIGNIFICANCE Pharmacological modulation of topo IIα expression has the potential to enhance cellular sensitivity to clinically-used anticancer therapeutics. This article is part of a Special Issue entitled: Nuclear Factor Y in Development and Disease, edited by Prof. Roberto Mantovani.
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Affiliation(s)
- Luke Pett
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, London, WC1E 6BT, UK
| | - Konstantinos Kiakos
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, London, WC1E 6BT, UK
| | - Vijay Satam
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Pravin Patil
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Sarah Laughlin-Toth
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Matthew Gregory
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Michael Bowerman
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Kevin Olson
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Mia Savagian
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Megan Lee
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Moses Lee
- Department of Chemistry, Hope College, Holland, MI 49423, United States; Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Daniel Hochhauser
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, London, WC1E 6BT, UK
| | - John A Hartley
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, London, WC1E 6BT, UK.
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del Mundo IMA, Siters KE, Fountain MA, Morrow JR. Structural basis for bifunctional zinc(II) macrocyclic complex recognition of thymine bulges in DNA. Inorg Chem 2012; 51:5444-57. [PMID: 22507054 DOI: 10.1021/ic3004245] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The zinc(II) complex of 1-(4-quinoylyl)methyl-1,4,7,10-tetraazacyclododecane (cy4q) binds selectively to thymine bulges in DNA and to a uracil bulge in RNA. Binding constants are in the low-micromolar range for thymine bulges in the stems of hairpins, for a thymine bulge in a DNA duplex, and for a uracil bulge in an RNA hairpin. Binding studies of Zn(cy4q) to a series of hairpins containing thymine bulges with different flanking bases showed that the complex had a moderate selectivity for thymine bulges with neighboring purines. The dissociation constants of the most strongly bound Zn(cy4q)-DNA thymine bulge adducts were 100-fold tighter than similar sequences with fully complementary stems or than bulges containing cytosine, guanine, or adenine. In order to probe the role of the pendent group, three additional zinc(II) complexes containing 1,4,7,10-tetraazacyclododecane (cyclen) with aromatic pendent groups were studied for binding to DNA including 1-(2-quinolyl)methyl-1,4,7,10-tetraazacyclododecane (cy2q), 1-(4-biphenyl)methyl-1,4,7,10-tetraazacyclododecane (cybp), and 5-(1,4,7,10-tetraazacyclododecan-1-ylsulfonyl)-N,N-dimethylnaphthalen-1-amine (dsc). The Zn(cybp) complex binds with moderate affinity but little selectivity to DNA hairpins with thymine bulges and to DNA lacking bulges. Similarly, Zn(dsc) binds weakly both to thymine bulges and hairpins with fully complementary stems. The zinc(II) complex of cy2q has the 2-quinolyl moiety bound to the Zn(II) center, as shown by (1)H NMR spectroscopy and pH-potentiometric titrations. As a consequence, only weak (500 μM) binding is observed to DNA with no appreciable selectivity. An NMR structure of a thymine-bulge-containing hairpin shows that the thymine is extrahelical but rotated toward the major groove. NMR data for Zn(cy4q) bound to DNA containing a thymine bulge is consistent with binding of the zinc(II) complex to the thymine N3(-) and stacking of the quinoline on top of the thymine. The thymine-bulge bound zinc(II) complex is pointed into the major groove, and there are interactions with the guanine positioned 5' to the thymine bulge.
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Affiliation(s)
- Imee Marie A del Mundo
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
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Asare-Okai PN, Chow CS. A modified fluorescent intercalator displacement assay for RNA ligand discovery. Anal Biochem 2011; 408:269-76. [PMID: 20863807 PMCID: PMC2980581 DOI: 10.1016/j.ab.2010.09.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 09/13/2010] [Indexed: 11/21/2022]
Abstract
Fluorescent intercalator displacement (FID) is a convenient and practical tool for identifying new nucleic acid-binding ligands. The success of FID is based on the fact that it can be fashioned into a versatile screening assay for assessing the relative binding affinities of compounds to nucleic acids. FID is a tagless approach; the target RNAs and the ligands or small molecules under investigation do not need to be modified in order to be examined. In this study, a modified FID assay for screening RNA-binding ligands was established using 3-methyl-2-((1-(3-(trimethylammonio)propyl)-4-quinolinylidene)methyl)benzothiazolium (TO-PRO) as the fluorescent indicator. Electrospray ionization mass spectrometry (ESI-MS) results provide direct evidence that correlates the reduction in fluorescence intensity observed in the FID assay with displacement of the dye molecule from RNA. The assay was successfully applied to screen a variety of RNA-binding ligands with a set of small hairpin RNAs. Ligands that bind with moderate affinity to the chosen RNA constructs (A-site, TAR [transactivation response element], h31 [helix 31], and H69 [helix 69] were identified.
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4
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Willis B, Arya DP. Triple recognition of B-DNA by a neomycin-Hoechst 33258-pyrene conjugate. Biochemistry 2010; 49:452-69. [PMID: 20000367 DOI: 10.1021/bi9016796] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Recent developments have indicated that aminoglycoside binding is not limited to RNA, but to nucleic acids that, like RNA, adopt conformations similar to its A-form. We further sought to expand the utility of aminoglycoside binding to B-DNA structures by conjugating neomycin, an aminoglycoside antibiotic, with the B-DNA minor groove binding ligand Hoechst 33258. Envisioning a dual groove binding mode, we have extended the potential recognition process to include a third, intercalative moiety. Similar conjugates, which vary in the number of binding moieties but maintain identical linkages to allow direct comparisons to be made, have also been prepared. We report herein novel neomycin- and Hoechst 33258-based conjugates developed in our laboratories for exploring the recognition potential with B-DNA. Spectroscopic studies such as UV melting, differential scanning calorimetry, isothermal fluorescence titrations, and circular dichroism together illustrate the triple recognition of the novel conjugate containing neomycin, Hoechst 33258, and pyrene. This study represents the first example of DNA molecular recognition capable of minor versus major groove recognition in conjunction with intercalation.
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Affiliation(s)
- Bert Willis
- Laboratories of Medicinal Chemistry, Clemson University, Clemson, South Carolina 29634, USA
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5
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Pushechnikov A, Lee MM, Childs-Disney JL, Sobczak K, French JM, Thornton CA, Disney MD. Rational design of ligands targeting triplet repeating transcripts that cause RNA dominant disease: application to myotonic muscular dystrophy type 1 and spinocerebellar ataxia type 3. J Am Chem Soc 2009; 131:9767-79. [PMID: 19552411 PMCID: PMC2731475 DOI: 10.1021/ja9020149] [Citation(s) in RCA: 148] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Herein, we describe the design of high affinity ligands that bind expanded rCUG and rCAG repeat RNAs expressed in myotonic dystrophy type 1 (DM1) and spinocerebellar ataxia type 3. These ligands also inhibit, with nanomolar IC(50) values, the formation of RNA-protein complexes that are implicated in both disorders. The expanded rCUG and rCAG repeats form stable RNA hairpins with regularly repeating internal loops in the stem and have deleterious effects on cell function. The ligands that bind the repeats display a derivative of the bisbenzimidazole Hoechst 33258, which was identified by searching known RNA-ligand interactions for ligands that bind the internal loop displayed in these hairpins. A series of 13 modularly assembled ligands with defined valencies and distances between ligand modules was synthesized to target multiple motifs in these RNAs simultaneously. The most avid binder, a pentamer, binds the rCUG repeat hairpin with a K(d) of 13 nM. When compared to a series of related RNAs, the pentamer binds to rCUG repeats with 4.4- to >200-fold specificity. Furthermore, the affinity of binding to rCUG repeats shows incremental gains with increasing valency, while the background binding to genomic DNA is correspondingly reduced. Then, it was determined whether the modularly assembled ligands inhibit the recognition of RNA repeats by Muscleblind-like 1 (MBNL1) protein, the expanded-rCUG binding protein whose sequestration leads to splicing defects in DM1. Among several compounds with nanomolar IC(50) values, the most potent inhibitor is the pentamer, which also inhibits the formation of rCAG repeat-MBNL1 complexes. Comparison of the binding data for the designed synthetic ligands and MBNL1 to repeating RNAs shows that the synthetic ligand is 23-fold higher affinity and more specific to DM1 RNAs than MBNL1. Further studies show that the designed ligands are cell permeable to mouse myoblasts. Thus, cell permeable ligands that bind repetitive RNAs have been designed that exhibit higher affinity and specificity for binding RNA than natural proteins. These studies suggest a general approach to targeting RNA, including those that cause RNA dominant disease.
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Affiliation(s)
- Alexei Pushechnikov
- Department of Chemistry and The Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, The State University of New York, 657 Natural Sciences Complex, Buffalo, NY 14260
| | - Melissa M. Lee
- Department of Chemistry and The Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, The State University of New York, 657 Natural Sciences Complex, Buffalo, NY 14260
| | | | - Krzysztof Sobczak
- Department of Neurology, University of Rochester, Rochester, NY, 14620
| | - Jonathan M. French
- Department of Chemistry and The Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, The State University of New York, 657 Natural Sciences Complex, Buffalo, NY 14260
| | | | - Matthew D. Disney
- Department of Chemistry and The Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, The State University of New York, 657 Natural Sciences Complex, Buffalo, NY 14260
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Wolter FE, Schneider K, Davies BP, Socher ER, Nicholson G, Seitz O, Süssmuth RD. Total Synthesis of Proximicin A−C and Synthesis of New Furan-Based DNA Binding Agents. Org Lett 2009; 11:2804-7. [DOI: 10.1021/ol901003p] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Falko E. Wolter
- Institut für Chemie, TU Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany, Institut für Chemie, HU Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany, and Institut für Chemie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | - Kathrin Schneider
- Institut für Chemie, TU Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany, Institut für Chemie, HU Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany, and Institut für Chemie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | - Brian P. Davies
- Institut für Chemie, TU Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany, Institut für Chemie, HU Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany, and Institut für Chemie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | - Elke R. Socher
- Institut für Chemie, TU Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany, Institut für Chemie, HU Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany, and Institut für Chemie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | - Graeme Nicholson
- Institut für Chemie, TU Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany, Institut für Chemie, HU Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany, and Institut für Chemie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | - Oliver Seitz
- Institut für Chemie, TU Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany, Institut für Chemie, HU Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany, and Institut für Chemie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | - Roderich D. Süssmuth
- Institut für Chemie, TU Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany, Institut für Chemie, HU Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany, and Institut für Chemie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
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7
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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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8
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Streltsov SA, Gromyko AV, Oleinikov VA, Zhuze AL. The Hoechst 33258 covalent dimer covers a total turn of the double-stranded DNA. J Biomol Struct Dyn 2007; 24:285-302. [PMID: 17054387 DOI: 10.1080/07391102.2006.10507121] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
With the goal to design ligands recognizing extended regions on dsDNA, a covalent dimer of the fluorescent dye Hoechst 33258 [bis-HT(NMe)] composed of two dye molecules linked via the phenol oxygen atoms with a (CH2)3-N+ H(CH3)-(CH2)3 fragment was constructed using computer modeling and then synthesized. Its interactions with the double-stranded DNA (dsDNA) were studied by fluorescent and UV-Vis spectroscopy and circular (CD) and linear dichroism (LD). Based on variations in the affinity to the dsDNA, it was shown that complexes of three types are formed. The first type complexes result from binding of a bis-HT(NMe) monomer in the open conformation; in this case the ligand covers the total dsDNA turn and is located in the minor groove according to the positive value of CD at 370 nm. In addition, the ability to form bis-HT(NMe)-bridges between two dsDNA molecules, i.e., each of the two bis-HT(NMe) ends binds to two different dsDNA molecules, was demonstrated for the first type complexes. Spectral characteristics (maximal absorption at 362 nm, positive sign, and maximal value of CD at 370 nm) of the first type complexes conform to those of the specific Hoechst 33258 complex with poly[d(A-T)] x poly[d(A-T]. The second type complexes correspond to the bis-HT(NMe) sandwich (as an inter- or intramolecular) binding to dsDNA with stoichiometry > or = 5 bp. Thereby, a negative LD at 360 nm and the location of bis-HT(NMe) sandwiches in the minor groove of B form dsDNA seems contradictory. Spectral characteristics (maximal positive CD at 345 nm, a dramatic decrease in fluorescence intensity and the shift of its maximum to 490 nm) of these complexes favor a suggestion that this binding correlates to the formation of nonspecific dimeric Hoechst 33258 complex with dsDNA. The third type complexes are characterized by stoichiometry of one bis-HT(NMe) molecule per approximately 2 bp and the tendency to zero of LD values at 270 and 360 nm. We assume that in these complexes bis-HT(NMe) sandwich dimers are formed on dsDNA. The complexes of this type conform to the aggregation type complex of Hoechst 33258 with dsDNA. The ability of bis-HT(NMe) to cover the whole dsDNA turn or form bridges with two dsDNA upon the formation of the first type complexes essentially distinguishes it from Hoechst 33258, which can only occupy 5 bp and does not form such bridges. This specific property of bis-HT(NMe) may support new biological activities.
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Affiliation(s)
- S A Streltsov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow 119991, Russia.
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9
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Xi Z, Zhang R, Yu Z, Ouyang D. The interaction between tylophorine B and TMV RNA. Bioorg Med Chem Lett 2006; 16:4300-4. [PMID: 16759858 DOI: 10.1016/j.bmcl.2006.05.059] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2006] [Revised: 04/30/2006] [Accepted: 05/18/2006] [Indexed: 10/24/2022]
Abstract
Tylophorine B exhibits 60% inhibition against tobacco mosaic virus (TMV) at a concentration of 1.0 x 10(-6) g/ml. In our study, high affinity for TMV RNA and assembly origin of TMV RNA (oriRNA) was revealed, accompanied by the conformational change of RNA. Considering that TMV assembly begins with the specific recognition by the coat protein aggregate of oriRNA, and that tylophorine B has favorable interaction with oriRNA, we speculate that tylophorine B likely exerts its virus inhibition by binding to oriRNA and interfering with virus assembly initiation. This work may shed light on the possible molecular inhibition mechanism against TMV by tylophorine B, and provide clues in rational design of sequence-specific RNA binding antivirus drugs.
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Affiliation(s)
- Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, Nankai University, Tianjin, China.
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10
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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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11
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Xi Z, Zhang R, Yu Z, Ouyang D, Huang R. Selective interaction between tylophorine B and bulged DNA. Bioorg Med Chem Lett 2005; 15:2673-7. [PMID: 15863340 DOI: 10.1016/j.bmcl.2005.02.022] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2005] [Revised: 02/07/2005] [Accepted: 02/08/2005] [Indexed: 10/25/2022]
Abstract
Tylophorine B exhibits pronounced cytotoxicity and antitumor activity. In order to survey the structure selectivity to DNA afforded by tylophorine B, we have synthesized a variety of duplex, bulge- and hairpin-containing oligodeoxyribonucleotides. Their binding to tylophorine B has been assayed by fluorescence spectroscopy and thermal melting experiments. The results indicate that oligonucleotides interact with tylophorine B at submicromolar concentration, and the affinity for DNA bulge is optimal (with Kd of 0.018 microM). In addition, the bulged hairpin oligonucleotides are stabilized by binding to tylophorine B. These findings may shed some light on tylophorine B's mode of action in biological systems and result in the rational design of sequence-specific DNA binding molecules.
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Affiliation(s)
- Zhen Xi
- State Key Laboratory of Elemento-Organic Chemistry and Department of Chemical Biology, Nankai University, Tianjin 300071, China.
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12
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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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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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14
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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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White CM, Satz AL, Gawron LS, Bruice TC, Beerman TA. Inhibiting transcription factor/DNA complexes using fluorescent microgonotropens (FMGTs). BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1574:100-8. [PMID: 11955618 DOI: 10.1016/s0167-4781(01)00351-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Fluorescent microgonotropens (FMGTs) are A/T selective, minor groove-binding bisbenzimidazole ligands. Basic side chains extending from these agents electrostatically contact the major groove side of the phosphodiester backbone of DNA, endowing them with high binding affinity. Here, we evaluate the potential of these agents as inhibitors of transcription factor (TF) binding to DNA and explore whether their ability to contact both grooves enhances their inhibitory activity. A series of FMGTs (L2-L5), with polyamine tails of varying lengths and degrees of branching, were compared to an analog lacking these basic side chains (L1), and the classical bisbenzimidazole Hoechst 33342 for effects on TF complex formation on the c-fos serum response element (SRE). Although L1 could not inhibit TF/SRE interactions, L2-L5 did so at submicromolar concentrations. Moreover, the FMGTs were up to 50 times more potent than Hoechst 33342 in inhibiting TF complex formation in electrophoretic mobility shift assays. The FMGTs also inhibited c-fos promoter-driven cell-free transcription and topoisomerase II activity in nuclei. These studies establish the potential of FMGTs as TF/DNA complex inhibitors in cell-free systems, provide insight into the relationship between their structure and biological activities, and demonstrate the benefits of functionalizing minor groove binding-agents with major groove-contacting groups.
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Affiliation(s)
- Christine M White
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
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Satz AL, Bruice TC. Recognition of nine base pair sequences in the minor groove of DNA at subpicomolar concentrations by a novel microgonotropen. Bioorg Med Chem 2002; 10:241-52. [PMID: 11741772 DOI: 10.1016/s0968-0896(01)00272-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The dsDNA interactions of the novel microgonotropen L1 have been characterized via spectrofluorometric titrations and thermal melting studies. A microgonotropen consists of a DNA minor groove binding moiety attached to a basic side chain capable of reaching out of the minor groove and grasping the acidic DNA phosphodiester backbone. L1 was synthesized employing solid-phase chemistry. L1 is shown to distinguish nine base pair A/T rich binding sites from sites possessing fewer than nine contiguous A/T base pairs. Further, L1 binds its preferred dsDNA sequences at subpicomolar concentrations. The equilibrium constant for complexation (K(1)) of a nine base pair A/T rich dsDNA binding site by L1 is roughly 10(13) M(-1). Single base pair A/T --> G/C substitutions within the nine base pair A/T rich binding site of L1 decreases the equilibrium constant for DNA binding by 1-2 orders of magnitude. The three proplyamine side chains of L1 enhance the agents free energy of binding by more than 5 kcal. Molecular modeling suggests that L1 adopts a 'spiral-like' conformation which fits almost a full turn of the DNA helix.
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Affiliation(s)
- Alexander L Satz
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA
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White CM, Satz AL, Bruice TC, Beerman TA. Inhibition of transcription factor-DNA complexes and gene expression by a microgonotropen. Proc Natl Acad Sci U S A 2001; 98:10590-5. [PMID: 11535831 PMCID: PMC58510 DOI: 10.1073/pnas.191374698] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Developing minor groove-binding drugs to selectively inhibit transcription factor (TF)/DNA interactions and accompanying gene expression is a current goal in drug development studies. Equipping minor groove-binding agents with positively charged, major groove-contacting side chains yields microgonotropens (MGTs). Previously, we demonstrated that MGTs were superior inhibitors of TF/DNA complexes in cell-free assays compared with "classical" groove binders, but MGTs showed limited ability to inhibit gene expression. To determine what chemical characteristics contribute to or improve activity, we evaluate five MGTs for their effectiveness in inhibiting TF complex formation and resultant transcription by using the c-fos serum response element (SRE) as a target. MGT L1 binds DNA via a bisbenzimidazole equipped with a tripyrrole moiety. It is compared with analog L2, which has been functionalized with propylamines on each of the three pyrroles. L2, which binds DNA at subpicomolar concentrations, was at least three orders of magnitude more potent than L1 at inhibiting TF binding to the c-fos SRE in cell-free assays. Unlike L1 and previous MGTs, L2 also inhibited endogenous c-fos expression in NIH 3T3 cells at micromolar levels. Structure/activity relationships suggest that, although the tripyrrole/polyamine functional group of L2 may be largely responsible for its inhibition of TF complexes in cell-free assays, its bisbenzimidazole moiety appears to impart improved cellular uptake and activity. These findings make L2 a promising lead candidate for future, rational MGT design.
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Affiliation(s)
- C M White
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
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