1
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Nagase H, Watanabe T, Koshikawa N, Yamamoto S, Takenaga K, Lin J. Mitochondria: Endosymbiont bacteria DNA sequence as a target against cancer. Cancer Sci 2021; 112:4834-4843. [PMID: 34533888 PMCID: PMC8645765 DOI: 10.1111/cas.15143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/10/2021] [Accepted: 09/12/2021] [Indexed: 12/21/2022] Open
Abstract
As the energy factory for the cell, the mitochondrion, through its role of adenosine triphosphate production by oxidative phosphorylation, can be regarded as the guardian of well regulated cellular metabolism; the integrity of mitochondrial functions, however, is particularly vulnerable in cancer due to the lack of superstructures such as histone and lamina folds to protect the mitochondrial genome from unintended exposure, which consequently elevates risks of mutation. In cancer, mechanisms responsible for enforcing quality control surveillance for identifying and eliminating defective mitochondria are often poorly regulated, and certain uneliminated mitochondrial DNA (mtDNA) mutations and polymorphisms can be advantageous for the proliferation, progression, and metastasis of tumor cells. Such pathogenic mtDNA aberrations are likely to increase and occasionally be homoplasmic in cancer cells and, intriguingly, in normal cells in the proximity of tumor microenvironments as well. Distinct characteristics of these abnormalities in mtDNA may provide a new path for cancer therapy. Here we discuss a promising novel therapeutic strategy, using the sequence‐specific properties of pyrrole‐imidazole polyamide‐triphenylphosphonium conjugates, against cancer for clearing abnormal mtDNA by reactivating mitochondrial quality control surveillance.
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Affiliation(s)
- Hiroki Nagase
- Division of Cancer Genetics, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Takayoshi Watanabe
- Division of Innovative Cancer Therapeutics, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Nobuko Koshikawa
- Division of Cancer Genetics, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Seigi Yamamoto
- Division of Cancer Genetics, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Keizo Takenaga
- Division of Cancer Genetics, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Jason Lin
- Division of Cancer Genetics, Chiba Cancer Center Research Institute, Chiba, Japan
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2
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Bando T, Sugiyama H. Epigenetic Drug Discovery by Artificial Genetic Switches. J SYN ORG CHEM JPN 2020. [DOI: 10.5059/yukigoseikyokaishi.78.476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science Kyoto University
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3
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Bando T, Sugiyama H. Sequence-Specific PI Polyamides Make It Possible to Regulate DNA Structure and Function. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20190311] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomaecho, Sakyo-ku, Kyoto 606-8501, Japan
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4
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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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5
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Vaijayanthi T, Pandian GN, Sugiyama H. Chemical Control System of Epigenetics. CHEM REC 2018; 18:1833-1853. [DOI: 10.1002/tcr.201800067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/07/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Thangavel Vaijayanthi
- Department of ChemistryGraduate School of ScienceKyoto University Kitashirakawa-Oiwakecho, Sakyo-ku Kyoto 606-8502, Japan
| | - Ganesh N. Pandian
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS)Kyoto University Yoshida-Ushinomaecho, Sakyo-ku Kyoto 606-8501 Japan
| | - Hiroshi Sugiyama
- Department of ChemistryGraduate School of ScienceKyoto University Kitashirakawa-Oiwakecho, Sakyo-ku Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS)Kyoto University Yoshida-Ushinomaecho, Sakyo-ku Kyoto 606-8501 Japan
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6
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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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7
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Alagarswamy K, Shinohara KI, Takayanagi S, Fukuyo M, Okabe A, Rahmutulla B, Yoda N, Qin R, Shiga N, Sugiura M, Sato H, Kita K, Suzuki T, Nemoto T, Kaneda A. Region-specific alteration of histone modification by LSD1 inhibitor conjugated with pyrrole-imidazole polyamide. Oncotarget 2018; 9:29316-29335. [PMID: 30034620 PMCID: PMC6047668 DOI: 10.18632/oncotarget.25451] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 05/07/2018] [Indexed: 12/26/2022] Open
Abstract
Epigenome regulates gene expression to determine cell fate, and accumulation of epigenomic aberrations leads to diseases, including cancer. NCD38 inhibits lysine-specific demethylase-1 (LSD1), a histone demethylase targeting H3K4me1 and H3K4me2, but not H3K4me3. In this study, we conjugated NCD38 with a potent small molecule called pyrrole (Py) imidazole (Im) polyamide, to analyze whether targets of the inhibitor could be regulated in a sequence-specific manner. We synthesized two conjugates using β-Ala (β) as a linker, i.e., NCD38-β-β-Py-Py-Py-Py (NCD38-β2P4) recognizing WWWWWW sequence, and NCD38-β-β-Py-Im-Py-Py (NCD38-β2PIPP) recognizing WWCGWW sequence. When RKO cells were treated with NCD38, H3K4me2 levels increased in 103 regions with significant activation of nearby genes (P = 0.03), whereas H3K4me3 levels were not obviously increased. H3K27ac levels were also increased in 458 regions with significant activation of nearby genes (P = 3 × 10-10), and these activated regions frequently included GC-rich sequences, but less frequently included AT-rich sequences (P < 1 × 10-15) or WWCGWW sequences (P = 2 × 10-13). When treated with NCD38-β2P4, 234 regions showed increased H3K27ac levels with significant activation of nearby genes (P = 2 × 10-11), including significantly fewer GC-rich sequences (P < 1 × 10-15) and significantly more AT-rich sequences (P < 1 × 10-15) compared with NCD38 treatment. When treated with NCD38-β2PIPP, 82 regions showed increased H3K27ac levels, including significantly fewer GC-rich sequences (P = 1 × 10-11) and fewer AT-rich sequences (P = 0.005), but significantly more WWCGWW sequences (P = 0.0001) compared with NCD38 treatment. These indicated that target regions of epigenomic inhibitors could be modified in a sequence-specific manner and that conjugation of Py-Im polyamides may be useful for this purpose.
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Affiliation(s)
| | - Ken-Ichi Shinohara
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
| | - Shihori Takayanagi
- Department of Pharmaceutical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Okabe
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
| | - Natsumi Yoda
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
| | - Rui Qin
- Department of Pharmaceutical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Naoki Shiga
- Department of Pharmaceutical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Masahiro Sugiura
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
| | - Hiroaki Sato
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
| | - Kazuko Kita
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
| | - Takayoshi Suzuki
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tetsuhiro Nemoto
- Department of Pharmaceutical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, School of Medicine, Chiba University, Chiba, Japan
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8
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Taniguchi J, Feng Y, Pandian GN, Hashiya F, Hidaka T, Hashiya K, Park S, Bando T, Ito S, Sugiyama H. Biomimetic Artificial Epigenetic Code for Targeted Acetylation of Histones. J Am Chem Soc 2018; 140:7108-7115. [DOI: 10.1021/jacs.8b01518] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Junichi Taniguchi
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Yihong Feng
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Ganesh N. Pandian
- Institute for Integrated Cell-Material Sciences, Institute for Advanced Study, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Fumitaka Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Takuya Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Soyoung Park
- 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
| | - Shinji Ito
- Medical Research Support Center, Graduate School of Medicine, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Sciences, Institute for Advanced Study, Kyoto University, Sakyo, Kyoto 606-8501, Japan
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9
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Zou T, Kizaki S, Sugiyama H. Investigating Nucleosome Accessibility for MNase, FeII
Peplomycin, and Duocarmycin B2
by Using Capillary Electrophoresis. Chembiochem 2018; 19:664-668. [DOI: 10.1002/cbic.201700643] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Tingting Zou
- Department of Science; Graduate School of Science; Kyoto University; Sakyo Kyoto 606-8502 Japan
| | - Seiichiro Kizaki
- Department of Science; Graduate School of Science; Kyoto University; Sakyo Kyoto 606-8502 Japan
| | - Hiroshi Sugiyama
- Department of Science; Graduate School of Science; Kyoto University; Sakyo Kyoto 606-8502 Japan
- Institute for Integrated Cell-Material Sciences (iCeMS); Kyoto University; Yoshida Ushinomiya-cho Sakyo Kyoto 606-8501 Japan
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10
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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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11
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Taniguchi J, Pandian GN, Hidaka T, Hashiya K, Bando T, Kim KK, Sugiyama H. A synthetic DNA-binding inhibitor of SOX2 guides human induced pluripotent stem cells to differentiate into mesoderm. Nucleic Acids Res 2017; 45:9219-9228. [PMID: 28934500 PMCID: PMC5766170 DOI: 10.1093/nar/gkx693] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 07/21/2017] [Accepted: 07/25/2017] [Indexed: 12/20/2022] Open
Abstract
Targeted differentiation of human induced pluripotent stem cells (hiPSCs) using only chemicals would have value-added clinical potential in the regeneration of complex cell types including cardiomyocytes. Despite the availability of several chemical inhibitors targeting proteins involved in signaling pathways, no bioactive synthetic DNA-binding inhibitors, targeting key cell fate-controlling genes such as SOX2, are yet available. Here, we demonstrate a novel DNA-based chemical approach to guide the differentiation of hiPSCs using pyrrole-imidazole polyamides (PIPs), which are sequence-selective DNA-binding synthetic molecules. Harnessing knowledge about key transcriptional changes during the induction of cardiomyocyte, we developed a DNA-binding inhibitor termed PIP-S2, targeting the 5'-CTTTGTT-3' and demonstrated that inhibition of SOX2-DNA interaction by PIP-S2 triggers the mesoderm induction in hiPSCs. Genome-wide gene expression analyses revealed that PIP-S2 induced mesoderm by targeted alterations in SOX2-associated gene regulatory networks. Also, employment of PIP-S2 along with a Wnt/β-catenin inhibitor successfully generated spontaneously contracting cardiomyocytes, validating our concept that DNA-binding inhibitors could drive the directed differentiation of hiPSCs. Because PIPs can be fine-tuned to target specific DNA sequences, our DNA-based approach could be expanded to target and regulate key transcription factors specifically associated with desired cell types.
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Affiliation(s)
- Junichi Taniguchi
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Ganesh N. Pandian
- Institute for Integrated Cell-Materials Science (WPI-iCeMS) Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Takuya Hidaka
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Materials Science (WPI-iCeMS) Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
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12
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Yu Z, Taniguchi J, Wei Y, Pandian GN, Hashiya K, Bando T, Sugiyama H. Antiproliferative and apoptotic activities of sequence-specific histone acetyltransferase inhibitors. Eur J Med Chem 2017; 138:320-327. [DOI: 10.1016/j.ejmech.2017.06.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/30/2017] [Accepted: 06/22/2017] [Indexed: 11/29/2022]
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13
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Wei Y, Pandian GN, Zou T, Taniguchi J, Sato S, Kashiwazaki G, Vaijayanthi T, Hidaka T, Bando T, Sugiyama H. A Multi-target Small Molecule for Targeted Transcriptional Activation of Therapeutically Significant Nervous System Genes. ChemistryOpen 2016; 5:517-521. [PMID: 28032018 PMCID: PMC5167308 DOI: 10.1002/open.201600125] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Indexed: 12/17/2022] Open
Abstract
An integrated multi‐target small molecule capable of altering dynamic epigenetic and transcription programs associated with the brain and nervous system has versatile applications in the regulation of therapeutic and cell‐fate genes. Recently, we have been constructing targeted epigenetic ON switches by integrating sequence‐specific DNA binding pyrrole‐imidazole polyamides with a potent histone deacetylase inhibitor SAHA. Here, we identified a DNA‐based epigenetic ON switch termed SAHA‐L as the first‐ever multi‐target small molecule capable of inducing transcription programs associated with the human neural system and brain synapses networks in BJ human foreskin fibroblasts and 201B7‐iPS cells. Ingenuity pathway analysis showed that SAHA‐L activates the signaling of synaptic receptors like glutamate and γ‐aminobutyric acid, which are key components of autism spectrum disorders. The long‐term incubation of SAHA‐L in 201B7‐iPS cells induced morphology changes and promoted a neural progenitor state. Our finding suggests that the tunable SAHA‐L could be advanced as a cell‐type‐independent multi‐target small molecule for therapeutic and/or cell‐fate gene modulation.
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Affiliation(s)
- Yulei Wei
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Ganesh N Pandian
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS) Kyoto University Yoshida-ushinomiyacho, Sakyo-ku Kyoto 606-8501 Japan
| | - Tingting Zou
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Junichi Taniguchi
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Shinsuke Sato
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS) Kyoto University Yoshida-ushinomiyacho, Sakyo-ku Kyoto 606-8501 Japan
| | - Gengo Kashiwazaki
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Thangavel Vaijayanthi
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Takuya Hidaka
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Toshikazu Bando
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Hiroshi Sugiyama
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto606-8502 Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS) Kyoto University Yoshida-ushinomiyacho, Sakyo-ku Kyoto 606-8501 Japan
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14
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Kawamoto Y, Sasaki A, Chandran A, Hashiya K, Ide S, Bando T, Maeshima K, Sugiyama H. Targeting 24 bp within Telomere Repeat Sequences with Tandem Tetramer Pyrrole–Imidazole Polyamide Probes. J Am Chem Soc 2016; 138:14100-14107. [DOI: 10.1021/jacs.6b09023] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Yusuke Kawamoto
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Asuka Sasaki
- 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
| | - Anandhakumar Chandran
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kaori Hashiya
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Satoru Ide
- 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
| | - Toshikazu Bando
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kazuhiro Maeshima
- 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
| | - 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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15
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Chandran A, Syed J, Li Y, Sato S, Bando T, Sugiyama H. Genome-Wide Assessment of the Binding Effects of Artificial Transcriptional Activators by High-Throughput Sequencing. Chembiochem 2016; 17:1905-1910. [DOI: 10.1002/cbic.201600274] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Anandhakumar Chandran
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-oiwakecho Sakyo-ku Kyoto 606-8502 Japan
| | - Junetha Syed
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-oiwakecho Sakyo-ku Kyoto 606-8502 Japan
| | - Yue Li
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-oiwakecho Sakyo-ku Kyoto 606-8502 Japan
| | - Shinsuke Sato
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS); Kyoto University; Yoshida-ushinomiyacho Sakyo-ku Kyoto 606-8501 Japan
| | - Toshikazu Bando
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-oiwakecho Sakyo-ku Kyoto 606-8502 Japan
| | - Hiroshi Sugiyama
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa-oiwakecho Sakyo-ku Kyoto 606-8502 Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS); Kyoto University; Yoshida-ushinomiyacho Sakyo-ku Kyoto 606-8501 Japan
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16
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Pandian GN, Sugiyama H. Nature-Inspired Design of Smart Biomaterials Using the Chemical Biology of Nucleic Acids. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2016. [DOI: 10.1246/bcsj.20160062] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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17
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Han L, Pandian GN, Chandran A, Sato S, Taniguchi J, Kashiwazaki G, Sawatani Y, Hashiya K, Bando T, Xu Y, Qian X, Sugiyama H. A Synthetic DNA-Binding Domain Guides Distinct Chromatin-Modifying Small Molecules to Activate an Identical Gene Network. Angew Chem Int Ed Engl 2015; 54:8700-3. [PMID: 26094767 DOI: 10.1002/anie.201503607] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Indexed: 12/20/2022]
Abstract
Synthetic dual-function ligands targeting specific DNA sequences and histone-modifying enzymes were applied to achieve regulatory control over multi-gene networks in living cells. Unlike the broad array of targeting small molecules for histone deacetylases (HDACs), few modulators are known for histone acetyltransferases (HATs), which play a central role in transcriptional control. As a novel chemical approach to induce selective HAT-regulated genes, we conjugated a DNA-binding domain (DBD) "I" to N-(4-chloro-3-trifluoromethyl-phenyl)-2-ethoxy-benzamide (CTB), an artificial HAT activator. In vitro enzyme activity assays and microarray studies were used to demonstrate that distinct functional small molecules could be transformed to have identical bioactivity when conjugated with a targeting DBD. This proof-of-concept synthetic strategy validates the switchable functions of HDACs and HATs in gene regulation and provides a molecular basis for developing versatile bioactive ligands.
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Affiliation(s)
- Le Han
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan).,Shanghai Key Laboratory of Chemical Biology, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237 (China)
| | - Ganesh N Pandian
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University Yoshida-Ushinomiyacho, Sakyo-ku, Kyoto 606-8501 (Japan)
| | - Anandhakumar Chandran
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)
| | - Shinsuke Sato
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University Yoshida-Ushinomiyacho, Sakyo-ku, Kyoto 606-8501 (Japan)
| | - Junichi Taniguchi
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)
| | - Gengo Kashiwazaki
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)
| | - Yoshito Sawatani
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)
| | - Yufang Xu
- Shanghai Key Laboratory of Chemical Biology, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237 (China)
| | - Xuhong Qian
- Shanghai Key Laboratory of Chemical Biology, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237 (China)
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan). .,Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University Yoshida-Ushinomiyacho, Sakyo-ku, Kyoto 606-8501 (Japan).
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18
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Han L, Pandian GN, Chandran A, Sato S, Taniguchi J, Kashiwazaki G, Sawatani Y, Hashiya K, Bando T, Xu Y, Qian X, Sugiyama H. A Synthetic DNA-Binding Domain Guides Distinct Chromatin-Modifying Small Molecules to Activate an Identical Gene Network. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503607] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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19
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Syed J, Chandran A, Pandian GN, Taniguchi J, Sato S, Hashiya K, Kashiwazaki G, Bando T, Sugiyama H. A Synthetic Transcriptional Activator of Genes Associated with the Retina in Human Dermal Fibroblasts. Chembiochem 2015; 16:1497-501. [DOI: 10.1002/cbic.201500140] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Indexed: 01/30/2023]
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20
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AbstractsICBS 3rd Annual Conference Driving Biology with ChemistryNovember 17–19, 2014San Francisco, California. Assay Drug Dev Technol 2015. [DOI: 10.1089/adt.2014.1507.abstracts] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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21
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Pandian GN, Sato S, Anandhakumar C, Taniguchi J, Takashima K, Syed J, Han L, Saha A, Bando T, Nagase H, Sugiyama H. Identification of a small molecule that turns ON the pluripotency gene circuitry in human fibroblasts. ACS Chem Biol 2014; 9:2729-36. [PMID: 25366962 DOI: 10.1021/cb500724t] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A nontransgenic approach to reprogram mouse somatic cells into induced pluripotent stem cells using only small molecules got achieved to propose a potential clinical-friendly cellular reprogramming strategy. Consequently, the screening and identification of small molecules capable of inducing pluripotency genes in human cells are increasingly a focus of research. Because cellular reprogramming is multifactorial in nature, there is a need for versatile small molecules capable of modulating the complicated gene networks associated with pluripotency. We have developed a targeting small molecule called SAHA-PIP comprising the histone deacetylase inhibitor SAHA and the sequence-specific DNA binding pyrrole-imidazole polyamides for modulating distinct gene networks. Here, we report the identification of a SAHA-PIP termed Ì that could trigger genome-wide epigenetic reprogramming and turn ON the typically conserved core pluripotency gene network. Through independent lines of evidence, we report for the first time a synthetic small molecule inducer that target and activate the OCT-3/4 regulated pluripotency genes in human dermal fibroblasts.
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Affiliation(s)
- Ganesh N. Pandian
- Institute
for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Shinsuke Sato
- Institute
for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Chandran Anandhakumar
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Junichi Taniguchi
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Kazuhiro Takashima
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Junetha Syed
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Le Han
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
- Shanghai
Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor
Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | | | | | - Hiroki Nagase
- Division
of Cancer Genetics, Department of Advanced Medical Science, Nihon University School of Medicine, Tokyo 173-8610, Japan
- Division
of Cancer Genetics, Chiba Cancer Center, Research Institute, 666-2
Nitona-cho, Chuo-ku, Chiba-shi, Chiba 260-8717, Japan
| | - Hiroshi Sugiyama
- Institute
for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
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22
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Anandhakumar C, Kizaki S, Bando T, Pandian GN, Sugiyama H. Advancing Small-Molecule-Based Chemical Biology with Next-Generation Sequencing Technologies. Chembiochem 2014; 16:20-38. [DOI: 10.1002/cbic.201402556] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Indexed: 12/24/2022]
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23
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Anandhakumar C, Li Y, Kizaki S, Pandian GN, Hashiya K, Bando T, Sugiyama H. Next-Generation Sequencing Studies Guide the Design of Pyrrole-Imidazole Polyamides with Improved Binding Specificity by the Addition of β-Alanine. Chembiochem 2014; 15:2647-51. [DOI: 10.1002/cbic.201402497] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Indexed: 01/01/2023]
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24
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Hiroshi Sugiyama. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/anie.201403997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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25
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Saha A, Pandian GN, Sato S, Taniguchi J, Kawamoto Y, Hashiya K, Bando T, Sugiyama H. Chemical Modification of a Synthetic Small Molecule Boosts Its Biological Efficacy against Pluripotency Genes in Mouse Fibroblasts. ChemMedChem 2014; 9:2374-80. [DOI: 10.1002/cmdc.201402117] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Indexed: 12/25/2022]
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26
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Ali M, Gual A, Ebeling G, Dupont J. Ruthenium-Catalyzed Hydroformylation of Alkenes by using Carbon Dioxide as the Carbon Monoxide Source in the Presence of Ionic Liquids. ChemCatChem 2014. [DOI: 10.1002/cctc.201402226] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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27
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Hiroshi Sugiyama. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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28
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Taylor RD, Kawamoto Y, Hashiya K, Bando T, Sugiyama H. Sequence-Specific DNA Alkylation by Tandem Py-Im Polyamide Conjugates. Chem Asian J 2014; 9:2527-33. [DOI: 10.1002/asia.201402331] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Indexed: 12/13/2022]
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29
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Pandian GN, Taniguchi J, Sugiyama H. Cellular reprogramming for pancreatic β-cell regeneration: clinical potential of small molecule control. Clin Transl Med 2014; 3:6. [PMID: 24679123 PMCID: PMC3984496 DOI: 10.1186/2001-1326-3-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 03/17/2014] [Indexed: 12/14/2022] Open
Abstract
Recent scientific breakthroughs in stem cell biology suggest that a sustainable treatment approach to cure diabetes mellitus (DM) can be achieved in the near future. However, the transplantation complexities and the difficulty in obtaining the stem cells from adult cells of pancreas, liver, bone morrow and other cells is a major concern. The epoch-making strategy of transcription-factor based cellular reprogramming suggest that these barriers could be overcome, and it is possible to reprogram any cells into functional β cells. Contemporary biological and analytical techniques help us to predict the key transcription factors needed for β-cell regeneration. These β cell-specific transcription factors could be modulated with diverse reprogramming protocols. Among cellular reprogramming strategies, small molecule approach gets proclaimed to have better clinical prospects because it does not involve genetic manipulation. Several small molecules targeting certain epigenetic enzymes and/or signaling pathways have been successful in helping to induce pancreatic β-cell specification. Recently, a synthetic DNA-based small molecule triggered targeted transcriptional activation of pancreas-related genes to suggest the possibility of achieving desired cellular phenotype in a precise mode. Here, we give a brief overview of treating DM by regenerating pancreatic β-cells from various cell sources. Through a comprehensive overview of the available transcription factors, small molecules and reprogramming strategies available for pancreatic β-cell regeneration, this review compiles the current progress made towards the generation of clinically relevant insulin-producing β-cells.
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Affiliation(s)
| | | | - Hiroshi Sugiyama
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Sakyo, Kyoto 606-8502, Japan.
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30
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Distinct DNA-based epigenetic switches trigger transcriptional activation of silent genes in human dermal fibroblasts. Sci Rep 2014; 4:3843. [PMID: 24457603 PMCID: PMC3900999 DOI: 10.1038/srep03843] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 12/18/2013] [Indexed: 12/22/2022] Open
Abstract
The influential role of the epigenome in orchestrating genome-wide transcriptional activation instigates the demand for the artificial genetic switches with distinct DNA sequence recognition. Recently, we developed a novel class of epigenetically active small molecules called SAHA-PIPs by conjugating selective DNA binding pyrrole-imidazole polyamides (PIPs) with the histone deacetylase inhibitor SAHA. Screening studies revealed that certain SAHA-PIPs trigger targeted transcriptional activation of pluripotency and germ cell genes in mouse and human fibroblasts, respectively. Through microarray studies and functional analysis, here we demonstrate for the first time the remarkable ability of thirty-two different SAHA-PIPs to trigger the transcriptional activation of exclusive clusters of genes and noncoding RNAs. QRT-PCR validated the microarray data, and some SAHA-PIPs activated therapeutically significant genes like KSR2. Based on the aforementioned results, we propose the potential use of SAHA-PIPs as reagents capable of targeted transcriptional activation.
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Pandian GN, Taylor RD, Junetha S, Saha A, Anandhakumar C, Vaijayanthi T, Sugiyama H. Alteration of epigenetic program to recover memory and alleviate neurodegeneration: prospects of multi-target molecules. Biomater Sci 2014; 2:1043-1056. [DOI: 10.1039/c4bm00068d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Next-generation sequence-specific small molecules modulating the epigenetic enzymes (DNMT/HDAC) and signalling factors can precisely turn ‘ON’ the multi-gene network in a neural cell.
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Affiliation(s)
- Ganesh N. Pandian
- Institute for Integrated Cell-Material Sciences (iCeMS)
- Kyoto University
- Kyoto 606-8502, Japan
| | - Rhys D. Taylor
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8501, Japan
| | - Syed Junetha
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8501, Japan
| | - Abhijit Saha
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8501, Japan
| | - Chandran Anandhakumar
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8501, Japan
| | - Thangavel Vaijayanthi
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8501, Japan
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Material Sciences (iCeMS)
- Kyoto University
- Kyoto 606-8502, Japan
- Department of Chemistry
- Graduate School of Science
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32
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Wu YL, Pandian G, Ding YP, Zhang W, Tanaka Y, Sugiyama H. Clinical Grade iPS Cells: Need for Versatile Small Molecules and Optimal Cell Sources. ACTA ACUST UNITED AC 2013; 20:1311-22. [DOI: 10.1016/j.chembiol.2013.09.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 08/28/2013] [Accepted: 09/16/2013] [Indexed: 12/12/2022]
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