1
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Yu Z, Pandian GN, Hidaka T, Sugiyama H. Therapeutic gene regulation using pyrrole-imidazole polyamides. Adv Drug Deliv Rev 2019; 147:66-85. [PMID: 30742856 DOI: 10.1016/j.addr.2019.02.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/22/2018] [Accepted: 02/04/2019] [Indexed: 12/13/2022]
Abstract
Recent innovations in cutting-edge sequencing platforms have allowed the rapid identification of genes associated with communicable, noncommunicable and rare diseases. Exploitation of this collected biological information has facilitated the development of nonviral gene therapy strategies and the design of several proteins capable of editing specific DNA sequences for disease control. Small molecule-based targeted therapeutic approaches have gained increasing attention because of their suggested clinical benefits, ease of control and lower costs. Pyrrole-imidazole polyamides (PIPs) are a major class of DNA minor groove-binding small molecules that can be predesigned to recognize specific DNA sequences. This programmability of PIPs allows the on-demand design of artificial genetic switches and fluorescent probes. In this review, we detail the progress in the development of PIP-based designer ligands and their prospects as advanced DNA-based small-molecule drugs for therapeutic gene modulation.
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2
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Direct Targeting of MYCN Gene Amplification by Site-Specific DNA Alkylation in Neuroblastoma. Cancer Res 2018; 79:830-840. [DOI: 10.1158/0008-5472.can-18-1198] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 10/23/2018] [Accepted: 12/17/2018] [Indexed: 11/16/2022]
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3
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Poynton FE, Bright SA, Blasco S, Williams DC, Kelly JM, Gunnlaugsson T. The development of ruthenium(ii) polypyridyl complexes and conjugates for in vitro cellular and in vivo applications. Chem Soc Rev 2018; 46:7706-7756. [PMID: 29177281 DOI: 10.1039/c7cs00680b] [Citation(s) in RCA: 284] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ruthenium(ii) [Ru(ii)] polypyridyl complexes have been the focus of intense investigations since work began exploring their supramolecular interactions with DNA. In recent years, there have been considerable efforts to translate this solution-based research into a biological environment with the intention of developing new classes of probes, luminescent imaging agents, therapeutics and theranostics. In only 10 years the field has expanded with diverse applications for these complexes as imaging agents and promising candidates for therapeutics. In light of these efforts this review exclusively focuses on the developments of these complexes in biological systems, both in cells and in vivo, and hopes to communicate to readers the diversity of applications within which these complexes have found use, as well as new insights gained along the way and challenges that researchers in this field still face.
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Affiliation(s)
- Fergus E Poynton
- School of Chemistry and Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, The University of Dublin, Dublin 2, Ireland.
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4
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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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Erwin GS, Grieshop MP, Bhimsaria D, Eguchi A, Rodríguez-Martínez JA, Ansari AZ. Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC (Crosslinking of Small Molecules to Isolate Chromatin). J Vis Exp 2016:e53510. [PMID: 26863565 DOI: 10.3791/53510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The genome is the target of some of the most effective chemotherapeutics, but most of these drugs lack DNA sequence specificity, which leads to dose-limiting toxicity and many adverse side effects. Targeting the genome with sequence-specific small molecules may enable molecules with increased therapeutic index and fewer off-target effects. N-methylpyrrole/N-methylimidazole polyamides are molecules that can be rationally designed to target specific DNA sequences with exquisite precision. And unlike most natural transcription factors, polyamides can bind to methylated and chromatinized DNA without a loss in affinity. The sequence specificity of polyamides has been extensively studied in vitro with cognate site identification (CSI) and with traditional biochemical and biophysical approaches, but the study of polyamide binding to genomic targets in cells remains elusive. Here we report a method, the crosslinking of small molecules to isolate chromatin (COSMIC), that identifies polyamide binding sites across the genome. COSMIC is similar to chromatin immunoprecipitation (ChIP), but differs in two important ways: (1) a photocrosslinker is employed to enable selective, temporally-controlled capture of polyamide binding events, and (2) the biotin affinity handle is used to purify polyamide-DNA conjugates under semi-denaturing conditions to decrease DNA that is non-covalently bound. COSMIC is a general strategy that can be used to reveal the genome-wide binding events of polyamides and other genome-targeting chemotherapeutic agents.
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Affiliation(s)
- Graham S Erwin
- Department of Biochemistry, University of Wisconsin-Madison
| | | | - Devesh Bhimsaria
- Department of Biochemistry, University of Wisconsin-Madison; Department of Electrical and Computer Engineering, University of Wisconsin-Madison
| | - Asuka Eguchi
- Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison
| | | | - Aseem Z Ansari
- Department of Biochemistry, University of Wisconsin-Madison; The Genome Center, University of Wisconsin-Madison;
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6
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Mishra R, Watanabe T, Kimura MT, Koshikawa N, Ikeda M, Uekusa S, Kawashima H, Wang X, Igarashi J, Choudhury D, Grandori C, Kemp CJ, Ohira M, Verma NK, Kobayashi Y, Takeuchi J, Koshinaga T, Nemoto N, Fukuda N, Soma M, Kusafuka T, Fujiwara K, Nagase H. Identification of a novel E-box binding pyrrole-imidazole polyamide inhibiting MYC-driven cell proliferation. Cancer Sci 2015; 106:421-9. [PMID: 25611295 PMCID: PMC4406810 DOI: 10.1111/cas.12610] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 01/09/2015] [Accepted: 01/11/2015] [Indexed: 12/23/2022] Open
Abstract
The MYC transcription factor plays a crucial role in the regulation of cell cycle progression, apoptosis, angiogenesis, and cellular transformation. Due to its oncogenic activities and overexpression in a majority of human cancers, it is an interesting target for novel drug therapies. MYC binding to the E-box (5'-CACGTGT-3') sequence at gene promoters contributes to more than 4000 MYC-dependent transcripts. Owing to its importance in MYC regulation, we designed a novel sequence-specific DNA-binding pyrrole-imidazole (PI) polyamide, Myc-5, that recognizes the E-box consensus sequence. Bioinformatics analysis revealed that the Myc-5 binding sequence appeared in 5'- MYC binding E-box sequences at the eIF4G1, CCND1, and CDK4 gene promoters. Furthermore, ChIP coupled with detection by quantitative PCR indicated that Myc-5 has the ability to inhibit MYC binding at the target gene promoters and thus cause downregulation at the mRNA level and protein expression of its target genes in human Burkitt's lymphoma model cell line, P493.6, carrying an inducible MYC repression system and the K562 (human chronic myelogenous leukemia) cell line. Single i.v. injection of Myc-5 at 7.5 mg/kg dose caused significant tumor growth inhibition in a MYC-dependent tumor xenograft model without evidence of toxicity. We report here a compelling rationale for the identification of a PI polyamide that inhibits a part of E-box-mediated MYC downstream gene expression and is a model for showing that phenotype-associated MYC downstream gene targets consequently inhibit MYC-dependent tumor growth.
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Affiliation(s)
- Rajeev Mishra
- Division of Cancer Genetics, Department of Advanced Medical Science, Nihon University Research Institute of Medical Science, Tokyo, Japan; Department of Medicine, Cedars-Sinai Medical Center, Samuel Oschin Comprehensive Cancer Institute, Los Angeles, California, USA
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7
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Jin L, Chen Y, Mu X, Lian Q, Deng H, Ge R. Phosphoproteomic analysis of gossypol-induced apoptosis in ovarian cancer cell line, HOC1a. BIOMED RESEARCH INTERNATIONAL 2014; 2014:123482. [PMID: 25180175 PMCID: PMC4144078 DOI: 10.1155/2014/123482] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 07/18/2014] [Accepted: 07/20/2014] [Indexed: 11/17/2022]
Abstract
Ovarian cancer is a major cause for death of gynecological cancer patients. The efficacy of traditional surgery and chemotherapy is rather compromised and platinum-resistant cancer recurs. Finding new therapeutic targets is urgently needed to increase the survival rate and to improve life quality of patients with ovarian cancer. In the present work, phosphoproteomic analysis was carried out on untreated and gossypol-treated ovarian cancer cell line, HOC1a. We identified approximately 9750 phosphopeptides from 3030 phosphoproteins, which are involved in diverse cellular processes including cytoskeletal organization, RNA and nucleotide binding, and cell cycle regulation. Upon gossypol treatment, changes in phosphorylation of twenty-nine proteins including YAP1 and AKAP12 were characterized. Western blotting and qPCR analysis were used to determine expression levels of proteins in YAP1-related Hippo pathway showing that gossypol induced upregulation of LATS1, which phosphorylates YAP1 at Ser 61. Furthermore, our data showed that gossypol targets the actin cytoskeletal organization through mediating phosphorylation states of actin-binding proteins. Taken together, our data provide valuable information to understand effects of gossypol on protein phosphorylation and apoptosis of ovarian cancer cells.
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Affiliation(s)
- Lixu Jin
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Yuling Chen
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xinlin Mu
- Peking University People's Hospital, Beijing 100044, China
| | - Qingquan Lian
- The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Institute of Reproductive Biomedicine, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Haiyun Deng
- The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Institute of Reproductive Biomedicine, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Renshan Ge
- The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Institute of Reproductive Biomedicine, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
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8
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Satam V, Patil P, Babu B, Rice T, Porte A, Alger S, Zeller M, Lee M. Orthogonally Positioned Diamino Pyrrole- and Imidazole-Containing Polyamides: Synthesis of 1-(3-Substituted-propyl)-4-nitropyrrole-2-carboxylic Acid and 1-(3-Chloropropyl)-4-nitroimidazole-2-carboxylic Acid. SYNTHETIC COMMUN 2014. [DOI: 10.1080/00397911.2013.839795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Vijay Satam
- a Department of Chemistry , Hope College , Holland , Michigan , USA
| | - Pravin Patil
- a Department of Chemistry , Hope College , Holland , Michigan , USA
| | - Balaji Babu
- b Department of Chemistry , Youngstown State University , Youngstown , Ohio , USA
| | - Toni Rice
- a Department of Chemistry , Hope College , Holland , Michigan , USA
| | - Alexander Porte
- a Department of Chemistry , Hope College , Holland , Michigan , USA
| | - Shannon Alger
- a Department of Chemistry , Hope College , Holland , Michigan , USA
| | - Matthias Zeller
- b Department of Chemistry , Youngstown State University , Youngstown , Ohio , USA
| | - Moses Lee
- a Department of Chemistry , Hope College , Holland , Michigan , USA
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9
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Ramos JP, Babu B, Chavda S, Liu Y, Plaunt A, Ferguson A, Savagian M, Lee M, Tzou S, Lin S, Kiakos K, Wang S, Lee M, Hartley JA, Wilson WD. Affinity and kinetic modulation of polyamide-DNA interactions by N-modification of the heterocycles. Biopolymers 2013; 99:497-507. [PMID: 23712486 PMCID: PMC3872963 DOI: 10.1002/bip.22205] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 12/31/2012] [Accepted: 01/02/2013] [Indexed: 12/27/2022]
Abstract
Synthetic N-methyl imidazole and N-pyrrole containing polyamides (PAs) that can form "stacked" dimers can be programmed to target and bind to specific DNA sequences and control gene expression. To accomplish this goal, the development of PAs with lower molecular mass which allows for the molecules to rapidly penetrate cells and localize in the nucleus, along with increased water solubility, while maintaining DNA binding sequence specificity and high binding affinity is key. To meet these challenges, six novel f-ImPy*Im PA derivatives that contain different orthogonally positioned moieties were designed to target 5'-ACGCGT-3'. The synthesis and biophysical characterization of six f-ImPy*Im were determined by CD, ΔTM, DNase I footprinting, SPR, and ITC studies, and were compared with those of their parent compound, f-ImPyIm. The results gave evidence for the minor groove binding and selectivity of PAs 1 and 6 for the cognate sequence 5'-ACGCGT-3', and with strong affinity, Keq = 2.8 × 10(8) M(-1) and Keq = 6.2 × 10(7) M(-1), respectively. The six novel PAs presented in this study demonstrated increased water solubility, while maintaining low molecular mass, sequence specificity, and binding affinity, addressing key issues in therapeutic development.
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Affiliation(s)
- Joseph P. Ramos
- Department of Chemistry, Georgia State University, Atlanta, GA 30303
| | - Balaji Babu
- Department of Chemistry and the Division of Natural and Applied Sciences, Hope College, MI 49423
| | - Sameer Chavda
- Department of Chemistry and the Division of Natural and Applied Sciences, Hope College, MI 49423
| | - Yang Liu
- Department of Chemistry, Georgia State University, Atlanta, GA 30303
| | - Adam Plaunt
- Department of Chemistry and the Division of Natural and Applied Sciences, Hope College, MI 49423
| | - Amanda Ferguson
- Department of Chemistry and the Division of Natural and Applied Sciences, Hope College, MI 49423
| | - Mia Savagian
- Department of Chemistry and the Division of Natural and Applied Sciences, Hope College, MI 49423
| | - Megan Lee
- Department of Chemistry and the Division of Natural and Applied Sciences, Hope College, MI 49423
| | - Samuel Tzou
- Department of Chemistry and the Division of Natural and Applied Sciences, Hope College, MI 49423
| | - Shicai Lin
- Cancer Research, UK Drug–DNA Interactions Research Group, UCL Cancer Institute, Paul O’ Gorman Building, 72 Huntley Street, London WCIE 6BT, UK
| | - Konstantinos Kiakos
- Cancer Research, UK Drug–DNA Interactions Research Group, UCL Cancer Institute, Paul O’ Gorman Building, 72 Huntley Street, London WCIE 6BT, UK
| | - Shuo Wang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303
| | - Moses Lee
- Department of Chemistry and the Division of Natural and Applied Sciences, Hope College, MI 49423
| | - John A. Hartley
- Cancer Research, UK Drug–DNA Interactions Research Group, UCL Cancer Institute, Paul O’ Gorman Building, 72 Huntley Street, London WCIE 6BT, UK
| | - W. David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303
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10
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Wang J, Jin L, Li X, Deng H, Chen Y, Lian Q, Ge R, Deng H. Gossypol induces apoptosis in ovarian cancer cells through oxidative stress. MOLECULAR BIOSYSTEMS 2013; 9:1489-97. [PMID: 23532321 DOI: 10.1039/c3mb25461e] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
In the present work, metabolomic and redox proteomic analyses were carried out on an untreated- and gossypol-treated ovarian cancer cell line, SKOV3. Gossypol treatment resulted in cell death through oxidative stress. Metabolite analysis showed that gossypol induces a decrease of the cellular levels of GSH, aspartic acid, and FAD. Using a combination of double labeling and LC-MS-MS, we identified changes in thiol-redox states of 545 cysteine-containing peptides from 356 proteins. The frequently occurring amino acid residue immediately before or after the cysteine in these peptides is the non-polar and neutral leucine, valine, or alanine. These redox sensitive proteins participate in a variety of cellular processes. We have characterized the redox-sensitive cysteine residues in PKM2, HSP60, malate dehydrogenase and other proteins that play important roles in metabolism homeostasis and stress responses. The three cysteine residues of HSP60 exhibit different responses to gossypol treatment: an increase of thiol/disulfide ratio for the Cys447 residue due to a decrease of the cellular GSH level, and a decrease of thiol/disulfide ratios for Cys442 and Cys237 residues due to oxidation and sulfation. This study suggests that thiol/disulfide ratios are dependent on the level of cellular GSH. Our data provide a valuable resource for deciphering the redox regulation of proteins and for understanding gossypol-induced apoptosis in ovarian cancer cells.
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Affiliation(s)
- Jia Wang
- The Second Affiliated Hospital of Wenzhou Medical College, Wenzhou, China
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11
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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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12
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Satam V, Patil P, Babu B, Gregory M, Bowerman M, Savagian M, Lee M, Tzou S, Olson K, Liu Y, Ramos J, Wilson WD, Bingham JP, Kiakos K, Hartley JA, Lee M. Hx-amides: DNA sequence recognition by the fluorescent Hx (p-anisylbenzimidazole)•pyrrole and Hx•imidazole pairings. Bioorg Med Chem Lett 2013; 23:1699-702. [PMID: 23395654 DOI: 10.1016/j.bmcl.2013.01.075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Revised: 01/06/2013] [Accepted: 01/16/2013] [Indexed: 01/01/2023]
Abstract
Hx-amides are fluorescent hybrids of imidazole (I)- and pyrrole (P)-containing polyamides and Hoechst 33258, and they bind in the minor groove of specific DNA sequences. Synthesis and DNA binding studies of HxII (5) complete our studies on the first set of Hx-amides: Hx-I/P-I/P. HxPP (2), HxIP (3) and HxPI (4) were reported earlier. Results from DNase I footprinting, biosensor-SPR, CD and ΔTM studies showed that Hx-amides interacted with DNA via the anti-parallel and stacked, side-by-side motif. Hx was found to mimic the DNA recognition properties of two consecutive pyrrole units (PP) in polyamides. Accordingly, the stacked Hx/PP pairing binds preferentially to two consecutive AT base pairs, A/T-A/T; Hx/IP prefers C-A/T; Hx/PI prefers A/T-C; and Hx/II prefers C-C. The results also showed that Hx-amides bound their cognate sequence at a higher affinity than their formamido-triamide counterparts.
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Affiliation(s)
- Vijay Satam
- Division of Natural & Applied Sciences and Department of Chemistry, Hope College, Holland, MI 49423, USA
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13
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Synthesis and DNA binding properties of 1-(3-aminopropyl)-imidazole-containing triamide f-Im∗PyIm: A novel diamino polyamide designed to target 5′-ACGCGT-3′. Bioorg Med Chem Lett 2012; 22:5898-902. [DOI: 10.1016/j.bmcl.2012.07.071] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 07/20/2012] [Indexed: 12/27/2022]
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14
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Chromatin structure determines accessibility of a hairpin polyamide-chlorambucil conjugate at histone H4 genes in pancreatic cancer cells. Bioorg Med Chem Lett 2012; 22:4068-71. [PMID: 22607671 DOI: 10.1016/j.bmcl.2012.04.090] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 04/16/2012] [Indexed: 01/25/2023]
Abstract
We have shown that a specific pyrrole-imidazole polyamide-DNA alkylator (chlorambucil) conjugate, 1R-Chl, alters the growth characteristics of various cancer cell lines in culture, and causes these cells to arrest in the G2/M stage of the cell cycle, without apparent cytotoxicity. This molecule has also shown efficacy in several mouse xenograft models, preventing tumor growth. Previous microarray studies have suggested that members of the histone H4 gene family, H4c and H4j/k, are the primary targets of this molecule, leading to reduced histone mRNA synthesis and growth arrest in cancer cells. In the present study, we examine the effects of 1R-Chl on transcription of other members of the H4 gene family, with the result that mRNA transcription of most genomic copies of H4 are down-regulated by 1R-Chl in a human pancreatic cancer cell line (MIA PaCa-2), but not in a cell line of non-cancerous origin (HEK293 cells). The basis for this differential effect is likely an open chromatin conformation within the H4 genes in cancer cells. Chromatin immunoprecipitation experiments show increased histone acetylation on the histone H4 genes in cancer cells, compared to HEK293 cells, explaining the differential activity of this molecule in cancer versus non-cancer cells.
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15
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Kashiwazaki G, Bando T, Yoshidome T, Masui S, Takagaki T, Hashiya K, Pandian GN, Yasuoka J, Akiyoshi K, Sugiyama H. Synthesis and Biological Properties of Highly Sequence-Specific-Alkylating N-Methylpyrrole–N-Methylimidazole Polyamide Conjugates. J Med Chem 2012; 55:2057-66. [DOI: 10.1021/jm201225z] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Gengo Kashiwazaki
- Department of Chemistry, Graduate
School of Science, Kyoto University, Kitashirakawa-oiwakecho,
Sakyo-ku, Kyoto 606-8502
| | - Toshikazu Bando
- Department of Chemistry, Graduate
School of Science, Kyoto University, Kitashirakawa-oiwakecho,
Sakyo-ku, Kyoto 606-8502
| | - Tomofumi Yoshidome
- Department of Chemistry, Graduate
School of Science, Kyoto University, Kitashirakawa-oiwakecho,
Sakyo-ku, Kyoto 606-8502
| | - Seiji Masui
- Department of Chemistry, Graduate
School of Science, Kyoto University, Kitashirakawa-oiwakecho,
Sakyo-ku, Kyoto 606-8502
| | - Toshiki Takagaki
- Department of Chemistry, Graduate
School of Science, Kyoto University, Kitashirakawa-oiwakecho,
Sakyo-ku, Kyoto 606-8502
| | - Kaori Hashiya
- Department of Chemistry, Graduate
School of Science, Kyoto University, Kitashirakawa-oiwakecho,
Sakyo-ku, Kyoto 606-8502
| | - Ganesh N. Pandian
- Institute for Integrated Cell-Material
Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho,
Sakyo-ku, Kyoto 606-8501
| | - Junichi Yasuoka
- Institute of Biomaterials and
Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062
| | - Kazunari Akiyoshi
- Institute of Biomaterials and
Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062
- Graduate School of Engineering, Kyoto University, Kyoto daigaku-Katsura, Nishikyo-ku,
Kyoto 615-8530
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate
School of Science, Kyoto University, Kitashirakawa-oiwakecho,
Sakyo-ku, Kyoto 606-8502
- Institute for Integrated Cell-Material
Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho,
Sakyo-ku, Kyoto 606-8501
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16
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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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Satam V, Babu B, Chavda S, Savagian M, Sjoholm R, Tzou S, Ramos J, Liu Y, Kiakos K, Lin S, David Wilson W, Hartley JA, Lee M. Novel diamino imidazole and pyrrole-containing polyamides: Synthesis and DNA binding studies of mono- and diamino-phenyl-ImPy*Im polyamides designed to target 5'-ACGCGT-3'. Bioorg Med Chem 2011; 20:693-701. [PMID: 22222156 DOI: 10.1016/j.bmc.2011.12.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 12/04/2011] [Accepted: 12/06/2011] [Indexed: 12/28/2022]
Abstract
Pyrrole- and imidazole-containing polyamides are widely investigated as DNA sequence selective binding agents that have potential use as gene control agents. The key challenges that must be overcome to realize this goal is the development of polyamides with low molar mass so the molecules can readily diffuse into cells and concentrate in the nucleus. In addition, the molecules must have appreciable water solubility, bind DNA sequence specifically, and with high affinity. It is on this basis that the orthogonally positioned diamino/dicationic polyamide Ph-ImPy*Im 5 was designed to target the sequence 5'-ACGCGT-3'. Py* denotes the pyrrole unit that contains a N-substituted aminopropyl pendant group. The DNA binding properties of diamino polyamide 5 were determined using a number of techniques including CD, ΔT(M), DNase I footprinting, SPR and ITC studies. The effects of the second amino moiety in Py* on DNA binding affinity over its monoamino counterpart Ph-ImPyIm 3 were assessed by conducting DNA binding studies of 3 in parallel with 5. The results confirmed the minor groove binding and selectivity of both polyamides for the cognate sequence 5'-ACGCGT-3'. The diamino/dicationic polyamide 5 showed enhanced binding affinity and higher solubility in aqueous media over its monoamino/monocationic counterpart Ph-ImPyIm 3. The binding constant of 5, determined from SPR studies, was found to be 1.5 × 10(7)M(-1), which is ∼3 times higher than that for its monoamino analog 3 (4.8 × 10(6)M(-1)). The affinity of 5 is now approaching that of the parent compound f-ImPyIm 1 and its diamino equivalent 4. The advantages of the design of diamino polyamide 5 over 1 and 4 are its sequence specificity and the ease of synthesis compared to the N-terminus pyrrole analog 2.
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Affiliation(s)
- Vijay Satam
- Division of Natural and Applied Sciences, Department of Chemistry, Hope College, 35 East, 12th Street, Holland, MI 49423, USA
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Lewis EA, Munde M, Wang S, Rettig M, Le V, Machha V, Wilson WD. Complexity in the binding of minor groove agents: netropsin has two thermodynamically different DNA binding modes at a single site. Nucleic Acids Res 2011; 39:9649-58. [PMID: 21890907 PMCID: PMC3239193 DOI: 10.1093/nar/gkr699] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Structural results with minor groove binding agents, such as netropsin, have provided detailed, atomic level views of DNA molecular recognition. Solution studies, however, indicate that there is complexity in the binding of minor groove agents to a single site. Netropsin, for example, has two DNA binding enthalpies in isothermal titration calorimetry (ITC) experiments that indicate the compound simultaneously forms two thermodynamically different complexes at a single AATT site. Two proposals for the origin of this unusual observation have been developed: (i) two different bound species of netropsin at single binding sites and (ii) a netropsin induced DNA hairpin to duplex transition. To develop a better understanding of DNA recognition complexity, the two proposals have been tested with several DNAs and the methods of mass spectrometry (MS), polyacrylamide gel electrophoresis (PAGE) and nuclear magnetic resonance spectroscopy in addition to ITC. All of the methods with all of the DNAs investigated clearly shows that netropsin forms two different complexes at AATT sites, and that the proposal for an induced hairpin to duplex transition in this system is incorrect.
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Affiliation(s)
- Edwin A Lewis
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA
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Abstract
The term epigenetic landscape was coined by CH Waddington to describe how cell fates were established in development, visualized as valleys and ridges directing the irreversibility of cell type differentiation. It is now clear that normal differentiation control breaks down during tumor development and that all tumor types show aberrant regulation of the epigenetic code, including changes in DNA methylation, histone modification and microRNAs. This has led to much interest in the development of epigenetic cancer therapies to target this aberrant epigenetic regulation. Histone deacetylase and DNA methyltransferase inhibitors are now used in the treatment of certain hematological malignancies. However, their more general applicability to solid tumors may be limited by lack of specificity and delivery challenges. Approaches to overcome these limitations and how to develop more specific drugs are discussed. The use of RNAi in the context of genome regulation as well as the possibility to use polyamides and engineered zinc fingers to target master regulators in the future is examined. Ultimately, improved specificity of epigenetic therapies will require increased mapping of the aberrant epigenetic landscape in cancer and cancer-specific target validation using chemical epigenetic approaches.
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Babu B, Liu Y, Plaunt A, Riddering C, Ogilvie R, Westrate L, Davis R, Ferguson A, Mackay H, Rice T, Chavda S, Wilson D, Lin S, Kiakos K, Hartley JA, Lee M. Design, synthesis and DNA binding properties of orthogonally positioned diamino containing polyamide f-IPI. Biochem Biophys Res Commun 2011; 404:848-52. [DOI: 10.1016/j.bbrc.2010.12.073] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 12/15/2010] [Indexed: 11/15/2022]
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Collar CJ, Lee M, Wilson WD. Setting Anchor in the Minor Groove: in Silico Investigation into Formamido N-Methylpyrrole and N-Methylimidazole Polyamides Bound by Cognate DNA Sequences. J Chem Inf Model 2010; 50:1611-22. [DOI: 10.1021/ci100191a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Catharine J. Collar
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303 and Department of Chemistry, Division of Natural and Applied Sciences, Hope College, Holland, Michigan 49423
| | - Moses Lee
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303 and Department of Chemistry, Division of Natural and Applied Sciences, Hope College, Holland, Michigan 49423
| | - W. David Wilson
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303 and Department of Chemistry, Division of Natural and Applied Sciences, Hope College, Holland, Michigan 49423
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Comparative analysis of DNA alkylation by conjugates between pyrrole–imidazole hairpin polyamides and chlorambucil or seco-CBI. Bioorg Med Chem 2010; 18:1236-43. [DOI: 10.1016/j.bmc.2009.12.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Revised: 12/09/2009] [Accepted: 12/10/2009] [Indexed: 11/20/2022]
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23
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Minoshima M, Chou JC, Lefebvre S, Bando T, Shinohara KI, Gottesfeld JM, Sugiyama H. Potent activity against K562 cells by polyamide–seco-CBI conjugates targeting histone H4 genes. Bioorg Med Chem 2010; 18:168-74. [DOI: 10.1016/j.bmc.2009.11.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Revised: 11/02/2009] [Accepted: 11/03/2009] [Indexed: 10/20/2022]
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Fukasawa A, Aoyama T, Nagashima T, Fukuda N, Ueno T, Sugiyama H, Nagase H, Matsumoto Y. Pharmacokinetics of pyrrole-imidazole polyamides after intravenous administration in rat. Biopharm Drug Dispos 2009; 30:81-9. [DOI: 10.1002/bdd.648] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Growth arrest of BCR-ABL positive cells with a sequence-specific polyamide-chlorambucil conjugate. PLoS One 2008; 3:e3593. [PMID: 18974832 PMCID: PMC2571993 DOI: 10.1371/journal.pone.0003593] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Accepted: 10/14/2008] [Indexed: 11/19/2022] Open
Abstract
Chronic myeloid leukemia (CML) is characterized by the presence of a constitutively active Abl kinase, which is the product of a chimeric BCR-ABL gene, caused by the genetic translocation known as the Philadelphia chromosome. Imatinib, a selective inhibitor of the Bcr-Abl tyrosine kinase, has significantly improved the clinical outcome of patients with CML. However, subsets of patients lose their response to treatment through the emergence of imatinib-resistant cells, and imatinib treatment is less durable for patients with late stage CML. Although alternative Bcr-Abl tyrosine kinase inhibitors have been developed to overcome drug resistance, a cocktail therapy of different kinase inhibitors and additional chemotherapeutics may be needed for complete remission of CML in some cases. Chlorambucil has been used for treatment of B cell chronic lymphocytic leukemia, non-Hodgkin's and Hodgkin's disease. Here we report that a DNA sequence-specific pyrrole-imidazole polyamide-chlorambucil conjugate, 1R-Chl, causes growth arrest of cells harboring both unmutated BCR-ABL and three imatinib resistant strains. 1R-Chl also displays selective toxicities against activated lymphocytes and a high dose tolerance in a murine model.
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In vivo imaging of pyrrole-imidazole polyamides with positron emission tomography. Proc Natl Acad Sci U S A 2008; 105:13039-44. [PMID: 18753620 DOI: 10.1073/pnas.0806308105] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The biodistribution profiles in mice of two pyrrole-imidazole polyamides were determined by PET. Pyrrole-imidazole polyamides are a class of small molecules that can be programmed to bind a broad repertoire of DNA sequences, disrupt transcription factor-DNA interfaces, and modulate gene expression pathways in cell culture experiments. The (18)F-radiolabeled polyamides were prepared by oxime ligation between 4-[(18)F]-fluorobenzaldehyde and a hydroxylamine moiety at the polyamide C terminus. Small animal PET imaging of radiolabeled polyamides administered to mice revealed distinct differences in the biodistribution of a 5-ring beta-linked polyamide versus an 8-ring hairpin, which exhibited better overall bioavailability. In vivo imaging of pyrrole-imidazole polyamides by PET is a minimum first step toward the translation of polyamide-based gene regulation from cell culture to small animal studies.
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