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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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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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Controlling gene networks and cell fate with precision-targeted DNA-binding proteins and small-molecule-based genome readers. Biochem J 2014; 462:397-413. [PMID: 25145439 DOI: 10.1042/bj20140400] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Transcription factors control the fate of a cell by regulating the expression of genes and regulatory networks. Recent successes in inducing pluripotency in terminally differentiated cells as well as directing differentiation with natural transcription factors has lent credence to the efforts that aim to direct cell fate with rationally designed transcription factors. Because DNA-binding factors are modular in design, they can be engineered to target specific genomic sequences and perform pre-programmed regulatory functions upon binding. Such precision-tailored factors can serve as molecular tools to reprogramme or differentiate cells in a targeted manner. Using different types of engineered DNA binders, both regulatory transcriptional controls of gene networks, as well as permanent alteration of genomic content, can be implemented to study cell fate decisions. In the present review, we describe the current state of the art in artificial transcription factor design and the exciting prospect of employing artificial DNA-binding factors to manipulate the transcriptional networks as well as epigenetic landscapes that govern cell fate.
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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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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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Zhou CY, Wu YB, Yang P. Synthesis, characterization, and studies on DNA binding of the complex Fe(Sal2dienNO3·H2O). BIOCHEMISTRY (MOSCOW) 2010; 75:505-493. [DOI: 10.1134/s0006297910040152] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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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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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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