1
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Zou M, Mao T, Li M, Mu Y, Pan L, Zheng C. Kinetic model of microwave-induced quaternarization using dimensional analysis. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2022.118008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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2
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Single position substitution of hairpin pyrrole-imidazole polyamides imparts distinct DNA-binding profiles across the human genome. PLoS One 2020; 15:e0243905. [PMID: 33351840 PMCID: PMC7755219 DOI: 10.1371/journal.pone.0243905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/01/2020] [Indexed: 01/21/2023] Open
Abstract
Pyrrole–imidazole (Py–Im) polyamides are synthetic molecules that can be rationally designed to target specific DNA sequences to both disrupt and recruit transcriptional machinery. While in vitro binding has been extensively studied, in vivo effects are often difficult to predict using current models of DNA binding. Determining the impact of genomic architecture and the local chromatin landscape on polyamide-DNA sequence specificity remains an unresolved question that impedes their effective deployment in vivo. In this report we identified polyamide–DNA interaction sites across the entire genome, by covalently crosslinking and capturing these events in the nuclei of human LNCaP cells. This technique confirms the ability of two eight ring hairpin-polyamides, with similar architectures but differing at a single ring position (Py to Im), to retain in vitro specificities and display distinct genome-wide binding profiles.
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3
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Repression of the transcriptional activity of ERRα with sequence-specific DNA-binding polyamides. Med Chem Res 2020; 29:607-616. [PMID: 34552311 DOI: 10.1007/s00044-019-02493-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The orphan nuclear receptors estrogen-related receptors (ERRs) bind to the estrogen-related receptor response element (ERRE) to regulate transcriptional programs in cellular metabolism and cancer cell growth. In this study, we evaluated the potential for a pyrrole-imidazole polyamide to block ERRα binding to ERREs to inhibit gene expression. We demonstrated that the ERRE-targeted polyamide 1 blocked the binding of ERRα to the consensus ERRE and reduced the transcriptional activity of ERRα in cell culture. We further showed that inhibiting ERRα transcriptional activity with polyamide 1 led to reduced mitochondrial oxygen consumption, a primary biological effect regulated by ERRα. Finally, our data demonstrated that polyamide 1 is an inhibitor for cancer cell growth.
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4
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Heinrich B, Vázquez O. 4-Methyltrityl-Protected Pyrrole and Imidazole Building Blocks for Solid Phase Synthesis of DNA-Binding Polyamides. Org Lett 2020; 22:533-536. [PMID: 31904984 DOI: 10.1021/acs.orglett.9b04288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA-binding polyamides are synthetic oligomers of pyrrole/imidazole units with high specificity and affinity for double-stranded DNA. To increase their synthetic diversity, we report a mild methodology based on 4-methyltrityl (Mtt) solid phase peptide synthesis (SPPS), whose building blocks are more accessible than the standard Fmoc and Boc SPPS ones. We demonstrate the robustness of the approach by preparing and studying a hairpin with all precursors. Importantly, our strategy is orthogonal and compatible with sensitive molecules and could be readily automated.
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Affiliation(s)
- Benedikt Heinrich
- Fachbereich Chemie , Philipps-Universität Marburg , Hans-Meerwein-Straße 4 , 35043 Marburg , Germany
| | - Olalla Vázquez
- Fachbereich Chemie , Philipps-Universität Marburg , Hans-Meerwein-Straße 4 , 35043 Marburg , Germany
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5
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Wu C, Wang W, Fang L, Su W. Programmable pyrrole-imidazole polyamides: A potent tool for DNA targeting. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2018.05.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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6
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Synthesis of pyrrole-imidazole polyamide oligomers based on a copper-catalyzed cross-coupling strategy. Bioorg Med Chem Lett 2017; 27:2197-2200. [PMID: 28389153 DOI: 10.1016/j.bmcl.2017.03.052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 03/17/2017] [Accepted: 03/20/2017] [Indexed: 02/08/2023]
Abstract
Pyrrole-imidazole (Py-Im) polyamides are useful tools for chemical biology and medicinal chemistry studies due to their unique binding properties to the minor groove of DNA. We developed a novel method of synthesizing Py-Im polyamide oligomers based on a Cu-catalyzed cross-coupling strategy. All four patterns of dimer fragments could be synthesized using a Cu-catalyzed Ullmann-type cross-coupling with easily prepared monomer units. Moreover, we demonstrated that pyrrole dimer, trimer, and tetramer building blocks for Py-Im polyamide synthesis were accessible by combining site selective iodination of the pyrrole/pyrrole coupling adduct.
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7
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Abstract
Bio-inspired synthetic backbones leading to foldamers can provide effective biopolymer mimics with new and improved properties in a physiological environment, and in turn could serve as useful tools to study biology and lead to practical applications in the areas of diagnostics or therapeutics. Remarkable progress has been accomplished over the past 20 years with the discovery of many potent bioactive foldamers originating from diverse backbones and targeting a whole spectrum of bio(macro)molecules such as membranes, protein surfaces, and nucleic acids. These current achievements, future opportunities, and key challenges that remain are discussed in this article.
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8
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RNA polymerase II senses obstruction in the DNA minor groove via a conserved sensor motif. Proc Natl Acad Sci U S A 2016; 113:12426-12431. [PMID: 27791148 DOI: 10.1073/pnas.1612745113] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
RNA polymerase II (pol II) encounters numerous barriers during transcription elongation, including DNA strand breaks, DNA lesions, and nucleosomes. Pyrrole-imidazole (Py-Im) polyamides bind to the minor groove of DNA with programmable sequence specificity and high affinity. Previous studies suggest that Py-Im polyamides can prevent transcription factor binding, as well as interfere with pol II transcription elongation. However, the mechanism of pol II inhibition by Py-Im polyamides is unclear. Here we investigate the mechanism of how these minor-groove binders affect pol II transcription elongation. In the presence of site-specifically bound Py-Im polyamides, we find that the pol II elongation complex becomes arrested immediately upstream of the targeted DNA sequence, and is not rescued by transcription factor IIS, which is in contrast to pol II blockage by a nucleosome barrier. Further analysis reveals that two conserved pol II residues in the Switch 1 region contribute to pol II stalling. Our study suggests this motif in pol II can sense the structural changes of the DNA minor groove and can be considered a "minor groove sensor." Prolonged interference of transcription elongation by sequence-specific minor groove binders may present opportunities to target transcription addiction for cancer therapy.
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9
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Castaneda CH, Scuderi MJ, Edwards TG, Harris GD, Dupureur CM, Koeller KJ, Fisher C, Bashkin JK. Improved Antiviral Activity of a Polyamide Against High-Risk Human Papillomavirus Via N-Terminal Guanidinium Substitution. MEDCHEMCOMM 2016; 7:2076-2082. [PMID: 27840672 DOI: 10.1039/c6md00371k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report the synthesis of two novel pyrrole-imidazole polyamides with N-terminal guanidinium or tetramethylguanidinium groups and evaluate their antiviral activity against three cancer-causing human papillomavirus strains. Introduction of guanidinium improves antiviral activity when compared to an unsubstituted analog, especially in IC90 values. These substitutions change DNA-binding preferences, while binding affinity remains unchanged.
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Affiliation(s)
- C H Castaneda
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO 63121, USA
| | - M J Scuderi
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO 63121, USA
| | - T G Edwards
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO 63121, USA
| | - G D Harris
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO 63121, USA
| | - C M Dupureur
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO 63121, USA
| | - K J Koeller
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO 63121, USA
| | - C Fisher
- NanoVir, LLC, Kalamazoo, MI 49008 (USA)
| | - J K Bashkin
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO 63121, USA; NanoVir, LLC, Kalamazoo, MI 49008 (USA)
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10
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A sequence-specific DNA binding small molecule triggers the release of immunogenic signals and phagocytosis in a model of B-cell lymphoma. Q Rev Biophys 2016; 48:453-64. [PMID: 26537405 PMCID: PMC4743504 DOI: 10.1017/s0033583515000104] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Means to cause an immunogenic cell death could lead to significant insight into how cancer escapes immune control. In this study, we screened a library of five pyrrole–imidazole polyamides coding for different DNA sequences in a model of B-cell lymphoma for the upregulation of surface calreticulin, a pro-phagocytosis signal implicated in immunogenic cell death. We found that hairpin polyamide 1 triggers the release of the damage-associated molecular patterns calreticulin, ATP and HMGB1 in a slow necrotic-type cell death. Consistent with this signaling, we observed an increase in the rate of phagocytosis by macrophages after the cancer cells were exposed to polyamide 1. The DNA sequence preference of polyamide 1 is 5′-WGGGTW-3′ (where W = A/T), indicated by the pairing rules and confirmed by the Bind-n-Seq method. The close correspondence of this sequence with the telomere-repeat sequence suggests a potential mechanism of action through ligand binding at the telomere. This study reveals a chemical means to trigger an inflammatory necrotic cell death in cancer cells.
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11
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Abstract
Aromatic amide foldamers constitute a growing class of oligomers that adopt remarkably stable folded conformations. The folded structures possess largely predictable shapes and open the way toward the design of synthetic mimics of proteins. Important examples of aromatic amide foldamers include oligomers of 7- or 8-amino-2-quinoline carboxylic acid that have been shown to exist predominantly as well-defined helices, including when they are combined with α-amino acids to which they may impose their folding behavior. To rapidly iterate their synthesis, solid phase synthesis (SPS) protocols have been developed and optimized for overcoming synthetic difficulties inherent to these backbones such as low nucleophilicity of amine groups on electron poor aromatic rings and a strong propensity of even short sequences to fold on the solid phase during synthesis. For example, acid chloride activation and the use of microwaves are required to bring coupling at aromatic amines to completion. Here, we report detailed SPS protocols for the rapid production of: (1) oligomers of 8-amino-2-quinolinecarboxylic acid; (2) oligomers containing 7-amino-8-fluoro-2-quinolinecarboxylic acid; and (3) heteromeric oligomers of 8-amino-2-quinolinecarboxylic acid and α-amino acids. SPS brings the advantage to quickly produce sequences having varied main chain or side chain components without having to purify multiple intermediates as in solution phase synthesis. With these protocols, an octamer could easily be synthesized and purified within one to two weeks from Fmoc protected amino acid monomer precursors.
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12
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Tumor Repression of VCaP Xenografts by a Pyrrole-Imidazole Polyamide. PLoS One 2015; 10:e0143161. [PMID: 26571387 PMCID: PMC4646452 DOI: 10.1371/journal.pone.0143161] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 11/02/2015] [Indexed: 12/21/2022] Open
Abstract
Pyrrole-imidazole (Py-Im) polyamides are high affinity DNA-binding small molecules that can inhibit protein-DNA interactions. In VCaP cells, a human prostate cancer cell line overexpressing both AR and the TMPRSS2-ERG gene fusion, an androgen response element (ARE)-targeted Py-Im polyamide significantly downregulates AR driven gene expression. Polyamide exposure to VCaP cells reduced proliferation without causing DNA damage. Py-Im polyamide treatment also reduced tumor growth in a VCaP mouse xenograft model. In addition to the effects on AR regulated transcription, RNA-seq analysis revealed inhibition of topoisomerase-DNA binding as a potential mechanism that contributes to the antitumor effects of polyamides in cell culture and in xenografts. These studies support the therapeutic potential of Py-Im polyamides to target multiple aspects of transcriptional regulation in prostate cancers without genotoxic stress.
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13
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Fang L, Yao G, Pan Z, Wu C, Wang HS, Burley GA, Su W. Fully Automated Synthesis of DNA-Binding Py-Im Polyamides Using a Triphosgene Coupling Strategy. Org Lett 2014; 17:158-61. [DOI: 10.1021/ol503388a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Lijing Fang
- Guangdong
Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology,
Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, P. R. China
| | - Guiyang Yao
- Key Laboratory for the Chemistry and Molecular Engineer of Medicinal Resources, School of Chemistry & Pharmaceutical Sciences of Guangxi Normal University, Guilin 541004, P. R. China
| | - Zhengyin Pan
- Guangdong
Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology,
Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, P. R. China
| | - Chunlei Wu
- Guangdong
Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology,
Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, P. R. China
| | - Heng-Shan Wang
- Key Laboratory for the Chemistry and Molecular Engineer of Medicinal Resources, School of Chemistry & Pharmaceutical Sciences of Guangxi Normal University, Guilin 541004, P. R. China
| | - Glenn A Burley
- Department of Pure & Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K
| | - Wu Su
- Guangdong
Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology,
Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, P. R. China
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14
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Shang J, Gan Q, Dawson SJ, Rosu F, Jiang H, Ferrand Y, Huc I. Self-Association of Aromatic Oligoamide Foldamers into Double Helices in Water. Org Lett 2014; 16:4992-5. [DOI: 10.1021/ol502259y] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Jie Shang
- Université Bordeaux, CBMN, UMR 5248, Institut Européen de
Chimie Biologie, 2 rue Robert Escarpit 33607 Pessac, France
- CNRS, CBMN, UMR 5248, 33607 Pessac, France
- Beijing
National Laboratory for Molecular Sciences, CAS Key Laboratory of
Photochemistry, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190, China
| | - Quan Gan
- Université Bordeaux, CBMN, UMR 5248, Institut Européen de
Chimie Biologie, 2 rue Robert Escarpit 33607 Pessac, France
- CNRS, CBMN, UMR 5248, 33607 Pessac, France
| | - Simon J. Dawson
- Université Bordeaux, CBMN, UMR 5248, Institut Européen de
Chimie Biologie, 2 rue Robert Escarpit 33607 Pessac, France
- CNRS, CBMN, UMR 5248, 33607 Pessac, France
| | - Frédéric Rosu
- Université Bordeaux, UMS 3033/US 001, IECB, 2 rue Robert Escarpit 33607 Pessac, France
- CNRS, IECB, UMS 3033, 33607 Pessac, France
| | - Hua Jiang
- Beijing
National Laboratory for Molecular Sciences, CAS Key Laboratory of
Photochemistry, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190, China
| | - Yann Ferrand
- Université Bordeaux, CBMN, UMR 5248, Institut Européen de
Chimie Biologie, 2 rue Robert Escarpit 33607 Pessac, France
- CNRS, CBMN, UMR 5248, 33607 Pessac, France
| | - Ivan Huc
- Université Bordeaux, CBMN, UMR 5248, Institut Européen de
Chimie Biologie, 2 rue Robert Escarpit 33607 Pessac, France
- CNRS, CBMN, UMR 5248, 33607 Pessac, France
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15
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Fallows AJ, Singh I, Dondi R, Cullis PM, Burley GA. Highly efficient synthesis of DNA-binding polyamides using a convergent fragment-based approach. Org Lett 2014; 16:4654-7. [PMID: 25162625 DOI: 10.1021/ol502203y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Two advances in the synthesis of hairpin pyrrole-imidazole polyamides (PAs) are described. First, the application of a convergent synthetic strategy is shown, involving the Boc-based solid phase synthesis of a C-terminal fragment and the solution phase synthesis of the N-terminal fragment. Second a new hybrid resin is developed that allows for the preparation of hairpin PAs lacking a C-terminal β-alanine tail. Both methods are compatible with a range of coupling reagents and provide a facile, modular route to prepare PA libraries in high yield and crude purity.
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Affiliation(s)
- Andrew J Fallows
- Department of Chemistry, University of Leicester , University Road, Leicester, LE1 7RH, U.K
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16
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Hirata A, Nokihara K, Kawamoto Y, Bando T, Sasaki A, Ide S, Maeshima K, Kasama T, Sugiyama H. Structural Evaluation of Tandem Hairpin Pyrrole–Imidazole Polyamides Recognizing Human Telomeres. J Am Chem Soc 2014; 136:11546-54. [DOI: 10.1021/ja506058e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Akiyoshi Hirata
- HiPep Laboratories, Nakatsukasa-cho 486-46, Kamigyo-ku Kyoto, 602-8158, Japan
| | - Kiyoshi Nokihara
- HiPep Laboratories, Nakatsukasa-cho 486-46, Kamigyo-ku Kyoto, 602-8158, Japan
| | - 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
| | - Asuka Sasaki
- Biological
Macromolecules Laboratory, Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Satoru Ide
- Biological
Macromolecules Laboratory, Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Kazuhiro Maeshima
- Biological
Macromolecules Laboratory, Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Takeshi Kasama
- Research
Center for Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroshi Sugiyama
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Institute
for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
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17
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Raskatov JA, Puckett JW, Dervan PB. A C-14 labeled Py-Im polyamide localizes to a subcutaneous prostate cancer tumor. Bioorg Med Chem 2014; 22:4371-5. [PMID: 24780272 DOI: 10.1016/j.bmc.2014.04.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 04/06/2014] [Indexed: 02/08/2023]
Abstract
In an effort to quantitate Py-Im polyamide concentrations in vivo, we synthesized the C-14 radioactively labeled compounds 1-3, and investigated their tumor localization in a subcutaneous xenograft model of prostate cancer (LNCaP). Tumor concentrations were compared with representative host tissues, and exhibited a certain degree of preferential localization to the xenograft. Compound accumulation upon repeated administration was measured. Py-Im polyamide 1 was found to accumulate in LNCaP tumors at concentrations similar to the IC50 value for this compound in cell culture experiments.
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Affiliation(s)
- Jevgenij A Raskatov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, United States
| | - James W Puckett
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, United States
| | - Peter B Dervan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, United States.
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18
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Kang JS, Meier JL, Dervan PB. Design of sequence-specific DNA binding molecules for DNA methyltransferase inhibition. J Am Chem Soc 2014; 136:3687-94. [PMID: 24502234 PMCID: PMC3985849 DOI: 10.1021/ja500211z] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The CpG dyad, an important genomic feature in DNA methylation and transcriptional regulation, is an attractive target for small molecules. To assess the utility of minor groove binding oligomers for CpG recognition, we screened a small library of hairpin pyrrole-imidazole polyamides targeting the sequence 5'-CGCG-3' and assessed their sequence specificity using an unbiased next-generation sequencing assay. Our findings indicate that hairpin polyamide of sequence PyImβIm-γ-PyImβIm (1), previously identified as a high affinity 5'-CGCG-3' binder, favors 5'-GCGC-3' in an unanticipated reverse binding orientation. Replacement of one β alanine with Py to afford PyImPyIm-γ-PyImβIm (3) restores the preference for 5'-CGCG-3' binding in a forward orientation. The minor groove binding hairpin 3 inhibits DNA methyltransferase activity in the major groove at its target site more effectively than 1, providing a molecular basis for design of sequence-specific antagonists of CpG methylation.
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Affiliation(s)
- JeenJoo S Kang
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
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19
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Yang F, Nickols NG, Li BC, Szablowski JO, Hamilton SR, Meier JL, Wang CM, Dervan PB. Animal toxicity of hairpin pyrrole-imidazole polyamides varies with the turn unit. J Med Chem 2013; 56:7449-57. [PMID: 24015881 PMCID: PMC3788622 DOI: 10.1021/jm401100s] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
![]()
A hairpin
pyrrole-imidazole polyamide (1) targeted
to the androgen receptor consensus half-site was found to exert antitumor
effects against prostate cancer xenografts. A previous animal study
showed that 1, which has a chiral amine at the α-position
of the γ-aminobutyric acid turn (γ-turn), did not exhibit
toxicity at doses less than 10 mg/kg. In the same study, a polyamide
with an acetamide at the β-position of the γ-turn resulted
in animal morbidity at 2.3 mg/kg. To identify structural motifs that
cause animal toxicity, we synthesized polyamides 1–4 with variations at the α- and β-positions in
the γ-turn. Weight loss, histopathology, and serum chemistry
were analyzed in mice post-treatment. While serum concentration was
similar for all four polyamides after injection, dose-limiting liver
toxicity was only observed for three polyamides. Polyamide 3, with an α-acetamide, caused no significant evidence of rodent
toxicity and retains activity against LNCaP xenografts.
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Affiliation(s)
- Fei Yang
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
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20
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Blackledge MS, Melander C. Programmable DNA-binding small molecules. Bioorg Med Chem 2013; 21:6101-14. [PMID: 23665141 DOI: 10.1016/j.bmc.2013.04.023] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 03/29/2013] [Accepted: 04/05/2013] [Indexed: 10/26/2022]
Abstract
Aberrant gene expression is responsible for a myriad of human diseases from infectious diseases to cancer. Precise regulation of these genes via specific interactions with the DNA double helix could pave the way for novel therapeutics. Pyrrole-imidazole polyamides are small molecules capable of binding to pre-determined DNA sequences up to 16 base pairs with affinity and specificity comparable to natural transcription factors. In the three decades since their development, great strides have been made relating to synthetic accessibility and improved sequence specificity and binding affinity. This perspective presents a brief history of early seminal developments in the field and highlights recent reports of the utility of polyamides as both genetic modulators and molecular probes.
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Affiliation(s)
- Meghan S Blackledge
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8024, United States
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21
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Nickols NG, Szablowski JO, Hargrove AE, Li BC, Raskatov JA, Dervan PB. Activity of a Py-Im polyamide targeted to the estrogen response element. Mol Cancer Ther 2013; 12:675-84. [PMID: 23443804 DOI: 10.1158/1535-7163.mct-12-1040] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Pyrrole-imidazole (Py-Im) polyamides are a class of programmable DNA minor groove binders capable of modulating the activity of DNA-binding proteins and affecting changes in gene expression. Estrogen receptor alpha (ERα) is a ligand-activated hormone receptor that binds as a homodimer to estrogen response elements (ERE) and is a driving oncogene in a majority of breast cancers. We tested a selection of structurally similar Py-Im polyamides with differing DNA sequence specificity for activity against 17β-estadiol (E2)-induced transcription and cytotoxicity in ERα positive, E2-stimulated T47DKBluc cells, which express luciferase under ERα control. The most active polyamide targeted the sequence 5'-WGGWCW-3' (W = A or T), which is the canonical ERE half site. Whole transcriptome analysis using RNA-Seq revealed that treatment of E2-stimulated breast cancer cells with this polyamide reduced the effects of E2 on the majority of those most strongly affected by E2 but had much less effect on the majority of E2-induced transcripts. In vivo, this polyamide circulated at detectable levels following subcutaneous injection and reduced levels of ER-driven luciferase expression in xenografted tumors in mice after subcutaneous compound administration without significant host toxicity.
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Affiliation(s)
- Nicholas G Nickols
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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22
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Abstract
Many cancer therapeutics target DNA and exert cytotoxicity through the induction of DNA damage and inhibition of transcription. We report that a DNA minor groove binding hairpin pyrrole-imidazole (Py-Im) polyamide interferes with RNA polymerase II (RNAP2) activity in cell culture. Polyamide treatment activates p53 signaling in LNCaP prostate cancer cells without detectable DNA damage. Genome-wide mapping of RNAP2 binding shows reduction of occupancy, preferentially at transcription start sites, but occupancy at enhancer sites is unchanged. Polyamide treatment results in a time- and dose-dependent depletion of the RNAP2 large subunit RPB1 that is preventable with proteasome inhibition. This polyamide demonstrates antitumor activity in a prostate tumor xenograft model with limited host toxicity.
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Hussein WM, Liu TY, Toth I, Skwarczynski M. Microwave-assisted synthesis of difficult sequence-containing peptides using the isopeptide method. Org Biomol Chem 2013; 11:2370-6. [DOI: 10.1039/c3ob00030c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Abstract
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Cyclic Py-Im polyamides containing two GABA turn units
exhibit
enhanced DNA binding affinity, but extensive studies of their biological
properties have been hindered due to synthetic inaccessibility. A
facile modular approach toward cyclic polyamides has been developed
via microwave-assisted solid-phase synthesis of hairpin amino acid
oligomer intermediates followed by macrocyclization. A focused library
of cyclic polyamides 1–7 targeted
to the androgen response element (ARE) and the estrogen response element
(ERE) were synthesized in 12–17% overall yield. The Fmoc protection
strategy also allows for selective modifications on the GABA turn
units that have been shown to improve cellular uptake properties.
The DNA binding affinities of a library of cyclic polyamides were
measured by DNA thermal denaturation assays and compared to the corresponding
hairpin polyamides. Fluorescein-labeled cyclic polyamides have been
synthesized and imaged via confocal microscopy in A549 and T47D cell
lines. The IC50 values of compounds 1–7 and 9–11 were determined,
revealing remarkably varying levels of cytotoxicity.
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Affiliation(s)
- Benjamin C Li
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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Gene expression changes in a tumor xenograft by a pyrrole-imidazole polyamide. Proc Natl Acad Sci U S A 2012; 109:16041-5. [PMID: 22988074 DOI: 10.1073/pnas.1214267109] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Gene regulation by DNA binding small molecules could have important therapeutic applications. This study reports the investigation of a DNA-binding pyrrole-imidazole polyamide targeted to bind the DNA sequence 5'-WGGWWW-3' with reference to its potency in a subcutaneous xenograft tumor model. The molecule is capable of trafficking to the tumor site following subcutaneous injection and modulates transcription of select genes in vivo. An FITC-labeled analogue of this polyamide can be detected in tumor-derived cells by confocal microscopy. RNA deep sequencing (RNA-seq) of tumor tissue allowed the identification of further affected genes, a representative panel of which was interrogated by quantitative reverse transcription-PCR and correlated with cell culture expression levels.
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