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Hirose Y, Hashiya K, Bando T, Sugiyama H. Evaluation of the DNA Alkylation Properties of a Chlorambucil-Conjugated Cyclic Pyrrole-Imidazole Polyamide. Chemistry 2021; 27:2782-2788. [PMID: 33145851 DOI: 10.1002/chem.202004421] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/30/2020] [Indexed: 01/31/2023]
Abstract
Hairpin pyrrole-imidazole polyamides (hPIPs) and their chlorambucil (Chb) conjugates (hPIP-Chbs) can alkylate DNA in a sequence-specific manner, and have been studied as anticancer drugs. Here, we conjugated Chb to a cyclic PIP (cPIP), which is known to have a higher binding affinity than the corresponding hPIP, and investigated the DNA alkylation properties of the resulting cPIP-Chb using the optimized capillary electrophoresis method and conventional HPLC product analysis. cPIP-Chb conjugate 3 showed higher alkylation activity at its binding sites than did hPIP-Chb conjugates 1 and 2. Subsequent HPLC analysis revealed that the alkylation site of conjugate 3, which was identified by capillary electrophoresis, was reliable and that conjugate 3 alkylates the N3 position of adenine as do hPIP-Chbs. Moreover, conjugate 3 showed higher cytotoxicity against LNCaP prostate cancer cells than did conjugate 1 and cytotoxicity comparable to that of conjugate 2. These results suggest that cPIP-Chbs could be novel DNA alkylating anticancer drugs.
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Affiliation(s)
- Yuki Hirose
- 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
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Science (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
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2
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Maeda R, Bando T, Sugiyama H. Application of DNA-Alkylating Pyrrole-Imidazole Polyamides for Cancer Treatment. Chembiochem 2021; 22:1538-1545. [PMID: 33453075 DOI: 10.1002/cbic.202000752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/28/2020] [Indexed: 12/13/2022]
Abstract
Pyrrole-imidazole (PI) polyamides, which target specific DNA sequences, have been studied as a class of DNA minor-groove-binding molecules. To investigate the potential of compounds for cancer treatment, PI polyamides were conjugated with DNA-alkylating agents, such as seco-CBI and chlorambucil. DNA-alkylating PI polyamides have attracted attention because of their sequence-specific alkylating activities, which contribute to reducing the severe side effects of current DNA-damaging drugs. Many of these types of conjugates have been developed as new candidates for anticancer drugs. Herein, we review recent progress into research on DNA-alkylating PI polyamides and their sequence-specific action on targets associated with cancer development.
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Affiliation(s)
- Rina Maeda
- Graduate School of Advanced Integrated Studies in Human Survivability, Kyoto University, Sakyo-ku, Kyoto, 606-8306, 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 Science (iCeMS), Kyoto University, Yoshida-Ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
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3
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Maeda R, Ito S, Hashiya K, Bando T, Sugiyama H. DNA Alkylation of the RUNX‐Binding Sequence by CBI–PI Polyamide Conjugates**. Chemistry 2020; 26:14639-14644. [DOI: 10.1002/chem.202002166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/14/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Rina Maeda
- Graduate School of Advanced Integrated Studies in Human Survivability Kyoto University Sakyo-ku Kyoto 6068306 Japan
| | - Shinji Ito
- Medical Research Support Center Graduate School of Medicine Kyoto University Sakyo-ku Kyoto 6068501 Japan
| | - Kaori Hashiya
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku Kyoto 6068502 Japan
| | - Toshikazu Bando
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku Kyoto 6068502 Japan
| | - Hiroshi Sugiyama
- Department of Chemistry Graduate School of Science Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku Kyoto 6068502 Japan
- Institute for Integrated Cell-Material Science (iCeMS) Kyoto University Yoshida-ushinomiyacho Sakyo-ku Kyoto 6068501 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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Maeda R, Sato S, Obata S, Ohno T, Hashiya K, Bando T, Sugiyama H. Molecular Characteristics of DNA-Alkylating PI Polyamides Targeting RUNX Transcription Factors. J Am Chem Soc 2019; 141:4257-4263. [DOI: 10.1021/jacs.8b08813] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Rina Maeda
- Graduate School of Advanced Integrated Studies in Human Survivability, Kyoto University, Sakyo, Kyoto 606-8306, Japan
| | - Shinsuke Sato
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Shunsuke Obata
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Tomo Ohno
- 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
| | - 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 (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
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6
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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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7
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Kashiwazaki G, Maeda R, Kawase T, Hashiya K, Bando T, Sugiyama H. Evaluation of alkylating pyrrole-imidazole polyamide conjugates by a novel method for high-throughput sequencer. Bioorg Med Chem 2018; 26:1-7. [DOI: 10.1016/j.bmc.2017.08.057] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 08/02/2017] [Accepted: 08/03/2017] [Indexed: 12/13/2022]
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8
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Economopoulou P, Psyrri A. Organ-specific gene modulation: Principles and applications in cancer research. Cancer Lett 2017; 387:18-24. [PMID: 27224891 DOI: 10.1016/j.canlet.2016.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 04/22/2016] [Accepted: 05/15/2016] [Indexed: 11/19/2022]
Abstract
Microarray and next generation sequencing has led to the exploration of correlated gene patterns and their shared functions. Gene modulators are proteins that alter the activity of transcription factors and influence the expression of their target genes. It is assumed that modulators are dependent on transcription factors. Several algorithms have been developed for the detection of gene modulators. On the other hand, it is becoming increasingly evident that modulators play a crucial role in carcinogenesis by interfering with fundamental biologic processes. Therapeutic gene modulation that is based on artificial modification of endogenous gene functions by designer molecules is an exciting new field of investigation.
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Affiliation(s)
- Panagiota Economopoulou
- Department of Internal Medicine, Section of Medical Oncology, Attikon University Hospital, National Kapodistrian University of Athens, School of Medicine, Athens, Greece.
| | - Amanda Psyrri
- Department of Internal Medicine, Section of Medical Oncology, Attikon University Hospital, National Kapodistrian University of Athens, School of Medicine, Athens, Greece
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9
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Thiazole-based nitrogen mustards: Design, synthesis, spectroscopic studies, DFT calculation, molecular docking, and antiproliferative activity against selected human cancer cell lines. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.04.058] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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10
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Kashiwazaki G, Chandran A, Asamitsu S, Kawase T, Kawamoto Y, Sawatani Y, Hashiya K, Bando T, Sugiyama H. Comparative Analysis of DNA-Binding Selectivity of Hairpin and Cyclic Pyrrole-Imidazole Polyamides Based on Next-Generation Sequencing. Chembiochem 2016; 17:1752-8. [DOI: 10.1002/cbic.201600282] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Indexed: 12/23/2022]
Affiliation(s)
- Gengo Kashiwazaki
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawaoiwakecho Sakyo Kyoto 606-8502 Japan
| | - Anandhakumar Chandran
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawaoiwakecho Sakyo Kyoto 606-8502 Japan
| | - Sefan Asamitsu
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawaoiwakecho Sakyo Kyoto 606-8502 Japan
| | - Takashi Kawase
- Department of Systems Science; Graduate School of Informatics; Kyoto University; Yoshida-Honmachi 36-1 Sakyo Kyoto 606-8501 Japan
| | - Yusuke Kawamoto
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawaoiwakecho Sakyo Kyoto 606-8502 Japan
| | - Yoshito Sawatani
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawaoiwakecho Sakyo Kyoto 606-8502 Japan
| | - Kaori Hashiya
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawaoiwakecho Sakyo Kyoto 606-8502 Japan
| | - Toshikazu Bando
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawaoiwakecho Sakyo Kyoto 606-8502 Japan
| | - Hiroshi Sugiyama
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawaoiwakecho Sakyo Kyoto 606-8502 Japan
- Institute for Integrated Cell-Material Sciences (iCeMS); Kyoto University; Yoshida-Ushinomiyacho Sakyo Kyoto 606-8501 Japan
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11
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12
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Yang WY, Wilson HD, Velagapudi SP, Disney MD. Inhibition of Non-ATG Translational Events in Cells via Covalent Small Molecules Targeting RNA. J Am Chem Soc 2015; 137:5336-45. [PMID: 25825793 PMCID: PMC4856029 DOI: 10.1021/ja507448y] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One major class of disease-causing RNAs is expanded repeating transcripts. These RNAs cause diseases via multiple mechanisms, including: (i) gain-of-function, in which repeating RNAs bind and sequester proteins involved in RNA biogenesis and (ii) repeat associated non-ATG (RAN) translation, in which repeating transcripts are translated into toxic proteins without use of a canonical, AUG, start codon. Herein, we develop and study chemical probes that bind and react with an expanded r(CGG) repeat (r(CGG)(exp)) present in a 5' untranslated region that causes fragile X-associated tremor/ataxia syndrome (FXTAS). Reactive compounds bind to r(CGG)(exp) in cellulo as shown with Chem-CLIP-Map, an approach to map small molecule binding sites within RNAs in cells. Compounds also potently improve FXTAS-associated pre-mRNA splicing and RAN translational defects, while not affecting translation of the downstream open reading frame. In contrast, oligonucleotides affect both RAN and canonical translation when they bind to r(CGG)(exp), which is mechanistically traced to a decrease in polysome loading. Thus, designer small molecules that react with RNA targets can be used to profile the RNAs to which they bind in cells, including identification of binding sites, and can modulate several aspects of RNA-mediated disease pathology in a manner that may be more beneficial than oligonucleotides.
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Affiliation(s)
- Wang-Yong Yang
- Department of Chemistry, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Henry D. Wilson
- Department of Chemistry, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Sai Pradeep Velagapudi
- Department of Chemistry, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, United States
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13
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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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14
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Zhu W, Fang S, Zhang Y, Li X. Functional vesicles formed by anticancer drug assembly. Bioorg Med Chem Lett 2014; 25:188-91. [PMID: 25515557 DOI: 10.1016/j.bmcl.2014.11.085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Revised: 11/21/2014] [Accepted: 11/28/2014] [Indexed: 12/25/2022]
Abstract
In this Letter, a new type of nitrogen mustard conjugate vesicles is developed to improve the stability and efficiency of anticancer drug. Benzoic acid nitrogen mustard-peptide (AAAK) conjugate was designed and synthesized, which was found to self-assemble into vesicles in water. The formation of the vesicles was confirmed by dynamic light scattering (DLS), transmission electron microscopy (TEM) and circular dichroism (CD). The degradation data revealed that the benzoic acid nitrogen mustard peptide (AAAK) conjugate vesicles are more stable than the parent drug in aqueous solution. Furthermore, MTT assay revealed that the free drug conjugate has similar antitumor activity against MCF-7, Hela, HepG-2 cell lines compared with the parent drug. The benzoic acid nitrogen mustard-peptide conjugate vesicles may have potential in the treatment of cancers.
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Affiliation(s)
- Wenjun Zhu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210096, China
| | - Shuo Fang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210096, China
| | - Yemin Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210096, China
| | - Xinsong Li
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 210096, China.
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15
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Wang X, Li J, Xu C, Li Y, Gong T, Sun X, Fu Y, He Q, Zhang Z. Scopine as a novel brain-targeting moiety enhances the brain uptake of chlorambucil. Bioconjug Chem 2014; 25:2046-54. [PMID: 25350514 DOI: 10.1021/bc5004108] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The blood brain barrier (BBB) represents the biggest challenge for therapeutic drugs to enter the brain. In our study, we selected chlorambucil (CHL), an alkylating agent, as the model therapeutic agent, and used scopine as a novel brain-targeting moiety. Here, we synthesized Chlorambucil-Scopine (CHLS) prodrug and evaluated its brain-targeting efficacy. The tissue distribution study after i.v. injection revealed that the AUC0-t and Cmax of CHLS in the brain were 14.25- and 12.20-fold of CHL, respectively. Specifically, CHLS accumulated in bEnd.3 and C6 cells in an energy-dependent manner. In C6 cells, superior anti-glioma activity with a significantly decreased IC50 of 65.42 nM/mL was observed for CHLS compared to CHL (IC50 > 400 nM/mL). The safety evaluation, including acute toxicity, pathology, and hematology study, showed minimal toxicity toward nontargeting tissues, and also reached a lower systemic toxicity at 5 mg/kg (i.v.). Our results suggested that scopine is a potential brain-targeting moiety for enhancing the brain uptake efficiency of CHL.
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Affiliation(s)
- Xinyi Wang
- Key Laboratory of Drug Targeting and Drug Delivery Systems, Ministry of Education, State Key Laboratory of Biotherapy, Sichuan University , Chengdu, 610041 Sichuan, China
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16
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Asamitsu S, Kawamoto Y, Hashiya F, Hashiya K, Yamamoto M, Kizaki S, Bando T, Sugiyama H. Sequence-specific DNA alkylation and transcriptional inhibition by long-chain hairpin pyrrole–imidazole polyamide–chlorambucil conjugates targeting CAG/CTG trinucleotide repeats. Bioorg Med Chem 2014; 22:4646-57. [DOI: 10.1016/j.bmc.2014.07.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/13/2014] [Accepted: 07/14/2014] [Indexed: 01/06/2023]
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17
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Di Antonio M, McLuckie KIE, Balasubramanian S. Reprogramming the mechanism of action of chlorambucil by coupling to a G-quadruplex ligand. J Am Chem Soc 2014; 136:5860-3. [PMID: 24697838 PMCID: PMC4132976 DOI: 10.1021/ja5014344] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The nitrogen mustard Chlorambucil (Chl) generates covalent adducts with double-helical DNA and inhibits cell proliferation. Among these adducts, interstrand cross-links (ICLs) are the most toxic, as they stall replication by generating DNA double strand breaks (DSBs). Conversely, intrastrand cross-links generated by Chl are efficiently repaired by a dedicated Nucleotide Excision Repair (NER) enzyme. We synthesized a novel cross-linking agent that combines Chl with the G-quadruplex (G4) ligand PDS (PDS-Chl). We demonstrated that PDS-Chl alkylates G4 structures at low μM concentrations, without reactivity toward double- or single-stranded DNA. Since intramolecular G4s arise from a single DNA strand, we reasoned that preferential alkylation of such structures might prevent the generation of ICLs, while favoring intrastrand cross-links. We observed that PDS-Chl selectively impairs growth in cells genetically deficient in NER, but did not show any sensitivity to the repair gene BRCA2, involved in double-stranded break repair. Our findings suggest that G4 targeting of this clinically important alkylating agent alters the overall mechanism of action. These insights may inspire new opportunities for intervention in diseases specifically characterized by genetic impairment of NER, such as skin and testicular cancers.
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Affiliation(s)
- Marco Di Antonio
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, U.K
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18
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Charak S, Shandilya M, Tyagi G, Mehrotra R. Spectroscopic and molecular docking studies on chlorambucil interaction with DNA. Int J Biol Macromol 2012; 51:406-11. [DOI: 10.1016/j.ijbiomac.2012.06.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Revised: 06/07/2012] [Accepted: 06/10/2012] [Indexed: 11/26/2022]
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19
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Pandian GN, Sugiyama H. Programmable genetic switches to control transcriptional machinery of pluripotency. Biotechnol J 2012; 7:798-809. [DOI: 10.1002/biot.201100361] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 01/30/2012] [Accepted: 03/26/2012] [Indexed: 12/30/2022]
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20
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Efimov VA, Fediunin SV, Chakhmakhcheva OG. [Cross-linked nucleic acids: formation, structure, and biological function]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010; 36:56-80. [PMID: 20386579 DOI: 10.1134/s1068162010010061] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Published data on the main types of reagents capable of introducing covalent interstrand cross links into nucleic acids (NA) are summarized in the present review. The reactivity of cross-linking agents, their preferred binding sites, and methods of determining the cross-link localization in a duplex are discussed. Cell response to DNA cross linking, namely, the blocking of replication and transcription, the initiation of reparation processes, and apoptotic death of the cell, are analyzed, as well as the use of cross-linking reagents in therapy and molecular biology.
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21
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Gates KS. An overview of chemical processes that damage cellular DNA: spontaneous hydrolysis, alkylation, and reactions with radicals. Chem Res Toxicol 2010; 22:1747-60. [PMID: 19757819 DOI: 10.1021/tx900242k] [Citation(s) in RCA: 348] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The sequence of heterocyclic bases on the interior of the DNA double helix constitutes the genetic code that drives the operation of all living organisms. With this said, it is not surprising that chemical modification of cellular DNA can have profound biological consequences. Therefore, the organic chemistry of DNA damage is fundamentally important to diverse fields including medicinal chemistry, toxicology, and biotechnology. This review is designed to provide a brief overview of the common types of chemical reactions that lead to DNA damage under physiological conditions.
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Affiliation(s)
- Kent S Gates
- Departments of Chemistry and Biochemistry, University of Missouri-Columbia, 125 Chemistry Building, Columbia, Missouri 65211.
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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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Ledesma A, Zinczuk J, López González J, Ben Altabef A, Brandán S. Structural and vibrational study of 4-(2′-furyl)-1-methylimidazole. J Mol Struct 2009. [DOI: 10.1016/j.molstruc.2009.01.058] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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24
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Bathaie SZ, Sedghgoo F, Jafarnejad A, Farzami B, Khayatian M. Spectroscopic studies of STZ-induced methylated-DNA in both in vivo and in vitro conditions. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2008; 71:803-808. [PMID: 18353708 DOI: 10.1016/j.saa.2008.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2007] [Revised: 01/28/2008] [Accepted: 02/01/2008] [Indexed: 05/26/2023]
Abstract
Alkylating agents after formation of DNA adduct not only possess their harmful role on living cells but also can transfer this information to the next generation. Different techniques have been introduced to study the alkylated DNA, most of which are specific and designed for investigation of specific target DNA. But the exact differences between spectroscopic and functional properties of alkylated DNA are not seen in the literature. In the present study DNA was methylated using streptozotocin (STZ) by both in vitro and in vivo protocols, then methylated-DNA was investigated by various techniques. Our results show that (1) the binding of ethidium bromide as an intercalating dye decreases to methylated-DNA in comparison with normal DNA, (2) CD spectra of methylated-DNA show changes including a decrease in the positive band at 275 nm and a shift from 258 nm crossover to a longer wavelength, which is caused by reduction of water around it, due to the presence of additional hydrophobic methyl groups, (3) the stability of methylated-DNA against DTAB as a denaturant is decreased and (4) the enzyme-like activity of methylated-DNA in an electron transfer reaction is reduced. In conclusion, additional methyl groups not only protrude water around DNA, but also cause the loss of hydrogen bonding, loosening of conformation, preventing desired interactions and thus normal function of DNA.
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Affiliation(s)
- S Z Bathaie
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, P.O. Box 14115-111, Tehran, Iran.
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25
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Simon P, Cannata F, Perrouault L, Halby L, Concordet JP, Boutorine A, Ryabinin V, Sinyakov A, Giovannangeli C. Sequence-specific DNA cleavage mediated by bipyridine polyamide conjugates. Nucleic Acids Res 2008; 36:3531-8. [PMID: 18450816 PMCID: PMC2441794 DOI: 10.1093/nar/gkn231] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The design of molecules that damage a selected DNA sequence provides a formidable opportunity for basic and applied biology. For example, such molecules offer new prospects for controlled manipulation of the genome. The conjugation of DNA-code reading molecules such as polyamides to reagents that induce DNA damages provides an approach to reach this goal. In this work, we showed that a bipyridine conjugate of polyamides was able to induce sequence-specific DNA breaks in cells. We synthesized compounds based on two polyamide parts linked to bipyridine at different positions. Bipyridine conjugates of polyamides were found to have a high affinity for the DNA target and one of them produced a specific and high-yield cleavage in vitro and in cultured cells. The bipyridine conjugate studied here, also presents cell penetrating properties since it is active when directly added to cell culture medium. Harnessing DNA damaging molecules such as bipyridine to predetermined genomic sites, as achieved here, provides an attractive strategy for targeted genome modification and DNA repair studies.
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26
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Nelson SM, Ferguson LR, Denny WA. Non-covalent ligand/DNA interactions: minor groove binding agents. Mutat Res 2007; 623:24-40. [PMID: 17507044 DOI: 10.1016/j.mrfmmm.2007.03.012] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Accepted: 03/31/2007] [Indexed: 05/15/2023]
Abstract
An understanding of the mechanism by which minor groove binding agents interact with DNA has led to the design of agents that can reversibly bind with high selectivity to extended DNA target sequences. Simple compounds, such as the polypyrroles and the bis-benzimidazoles, have been used as carriers for alkylating agents effectively directing alkylation to specific DNA sequences. The spectrum of DNA alkylation and mutation by classical alkylators, such as nitrogen mustards, has been profoundly modified by such attachment. The observed "side-by-side" binding of small polypyrrole antibiotics has led to the design of synthetic hairpin polyamides with programmable DNA sequence selectivity. These compounds are able to compete with natural substrates, such as specific transcription factors, and alter gene expression. They are being developed as artificial transcription factors, able to deliver activating peptides to specific recognition sequences, and as potential protein-DNA dimerization agents. Hairpin polyamides are also being used as carriers for the delivery of alkylators to defined DNA sites. The degree of control of gene expression thus offered by the hairpin polyamides suggests enormous promise for their clinical utility. Recent developments with other minor groove binding small molecules and technological advances are also discussed.
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Affiliation(s)
- Stephanie M Nelson
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland 10000, New Zealand.
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27
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Farkas ME, Tsai SM, Dervan PB. Alpha-diaminobutyric acid-linked hairpin polyamides. Bioorg Med Chem 2007; 15:6927-36. [PMID: 17869122 PMCID: PMC2140246 DOI: 10.1016/j.bmc.2007.07.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Revised: 07/20/2007] [Accepted: 07/31/2007] [Indexed: 11/25/2022]
Abstract
A hairpin polyamide-chlorambucil conjugate linked by alpha-diaminobutyric acid (alpha-DABA) has been shown to have interesting biological properties in cellular and small animal models. Remarkably, this new class of hairpin polyamides has not been previously characterized with regard to energetics and sequence specificity. Herein we present a series of pyrrole-imidazole hairpin polyamides linked by alpha-DABA and compare them to polyamides containing the standard gamma-DABA turn unit. The alpha-DABA hairpins have overall decreased binding affinities. However, alpha-DABA polyamide-chlorambucil conjugates are sequence-specific DNA alkylators with increased specificities. Affinity cleavage studies of alpha-DABA polyamide-EDTA conjugates confirmed their preference for binding DNA in a forward hairpin conformation. In contrast, an unsubstituted glycine-linked polyamide prefers to bind in an extended binding mode. Thus, substitution on the turn unit locks the alpha-DABA polyamide into the forward hairpin binding motif.
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Affiliation(s)
| | | | - Peter B. Dervan
- *Corresponding author: Tel.: +1 626 395 6002; Fax: +1 626 683 8753; E-mail:
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28
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Baraldi PG, Preti D, Fruttarolo F, Tabrizi MA, Romagnoli R. Hybrid molecules between distamycin A and active moieties of antitumor agents. Bioorg Med Chem 2007; 15:17-35. [PMID: 17081759 DOI: 10.1016/j.bmc.2006.07.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2006] [Revised: 06/29/2006] [Accepted: 07/01/2006] [Indexed: 10/24/2022]
Abstract
The DNA minor groove is an attractive target for the design and development of molecules able to specifically recognize predetermined DNA sequences. The pyrrole-amide skeleton of distamycin A has been also used as DNA sequence selective vehicle for the delivery of alkylating functions to DNA targets. Selectivity for specific sequences may be of particular importance in affecting the activity of regulatory genes (oncogenes and tumor suppressor genes). Recent work on a number of hybrid compounds, in which known antitumor compounds or simple active moieties of known antitumor agents have been tethered to distamycin frame or hairpin polyamides derived from distamycin, is reviewed. The DNA alkylating and growth inhibition activities against several tumor cell lines are reported and discussed in terms of their structural differences in relation to both the number of N-methyl pyrrolic rings and the type of the alkylating unit tethered to the oligopyrrolic frame.
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Affiliation(s)
- Pier Giovanni Baraldi
- University of Ferrara, Dipartimento di Scienze Farmaceutiche, Via Fossato di Mortara 17/19, 44100 Ferrara, Italy.
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29
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Tsai SM, Farkas ME, Chou CJ, Gottesfeld JM, Dervan PB. Unanticipated differences between alpha- and gamma-diaminobutyric acid-linked hairpin polyamide-alkylator conjugates. Nucleic Acids Res 2006; 35:307-16. [PMID: 17170006 PMCID: PMC1802559 DOI: 10.1093/nar/gkl1025] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2006] [Revised: 11/08/2006] [Accepted: 11/14/2006] [Indexed: 11/14/2022] Open
Abstract
Hairpin polyamide-chlorambucil conjugates containing an alpha-diaminobutyric acid (alpha-DABA) turn moiety are compared to their constitutional isomers containing the well-characterized gamma-DABA turn. Although the DNA-binding properties of unconjugated polyamides are similar, the alpha-DABA conjugates display increased alkylation specificity and decreased rate of reaction. Treatment of a human colon carcinoma cell line with alpha-DABA versus gamma-DABA hairpin conjugates shows only slight differences in toxicities while producing similar effects on cell morphology and G2/M stage cell cycle arrest. However, striking differences in animal toxicity between the two classes are observed. Although mice treated with an alpha-DABA hairpin polyamide do not differ significantly from control mice, the analogous gamma-DABA hairpin is lethal. This dramatic difference from a subtle structural change would not have been predicted.
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Affiliation(s)
- Sherry M. Tsai
- Division of Chemistry and Chemical Engineering, California Institute of Technology PasadenaCA 91125, USA
- Department of Molecular Biology, The Scripps Research Institute La JollaCA 92037, USA
| | - Michelle E. Farkas
- Division of Chemistry and Chemical Engineering, California Institute of Technology PasadenaCA 91125, USA
- Department of Molecular Biology, The Scripps Research Institute La JollaCA 92037, USA
| | - C. James Chou
- Department of Molecular Biology, The Scripps Research Institute La JollaCA 92037, USA
| | - Joel M. Gottesfeld
- Department of Molecular Biology, The Scripps Research Institute La JollaCA 92037, USA
| | - Peter B. Dervan
- To whom correspondence should be addressed. Tel: +1 626 395 6002; Fax: +1 626 683 8753;
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30
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Le Sann C, Baron A, Mann J, van den Berg H, Gunaratnam M, Neidle S. New mustard-linked 2-aryl-bis-benzimidazoles with anti-proliferative activity. Org Biomol Chem 2006; 4:1305-12. [PMID: 16557319 DOI: 10.1039/b600567e] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe new methodology for the synthesis of symmetric bis-benzimidazoles carrying 2-aryl moieties, including 2-[4-(3'-aminopropoxy)phenyl] and 2-[4-(3'-aminopropanamido)phenyl] substituents, together with the synthesis of novel hybrid molecules comprising bis-benzimidazoles in ester and amide combination with the N-mustard chlorambucil. The in vitro activities of these compounds against five cancer cell lines are also provided.
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Affiliation(s)
- Christine Le Sann
- School of Chemistry, Queen's University Belfast, Stranmillis Road, Belfast, UK BT9 5AG
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31
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Shinohara KI, Sasaki S, Minoshima M, Bando T, Sugiyama H. Alkylation of template strand of coding region causes effective gene silencing. Nucleic Acids Res 2006; 34:1189-95. [PMID: 16500890 PMCID: PMC1383623 DOI: 10.1093/nar/gkl005] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Revised: 02/10/2006] [Accepted: 02/10/2006] [Indexed: 11/12/2022] Open
Abstract
We recently developed a new type of pyrrole (Py)-imidazole (Im) polyamide-tetrahydrocyclopropabenzindolone (CBI) conjugate with an indole linker as a stable sequence-specific alkylating agent. In this study, we investigated the gene silencing activities of polyamides A, B and C, which selectively alkylate specific sequences in the promoter region, non-coding strand and coding strand, respectively, of the green fluorescent protein (GFP) gene. GFP vectors were transfected into human colon carcinoma cells (HCT116), and the cells were treated with 100 nM of the polyamides for 24 h. Fluorescence microscopy indicated that a significant reduction of GFP fluorescence was only observed in the cells that were treated with polyamide C. In clear contrast, polyamides A and B did not show such activity. Moreover, real-time PCR demonstrated selective reduction of the expression of GFP mRNA following treatment with polyamide C. These results suggest that alkylating Py-Im polyamides that target the coding strand represent a novel approach for sequence-specific gene silencing.
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Affiliation(s)
- Ken-ichi Shinohara
- Department of Chemistry, Graduate School of Science, Kyoto UniversityKitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan
| | - Shunta Sasaki
- Department of Chemistry, Graduate School of Science, Kyoto UniversityKitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan
| | - Masafumi Minoshima
- Department of Chemistry, Graduate School of Science, Kyoto UniversityKitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto UniversityKitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto UniversityKitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan
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32
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33
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Gniazdowski M, Denny WA, Nelson SM, Czyz M. Effects of anticancer drugs on transcription factor–DNA interactions. Expert Opin Ther Targets 2005; 9:471-89. [PMID: 15948668 DOI: 10.1517/14728222.9.3.471] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
DNA-interacting anticancer drugs are able to affect the propensity of DNA to interact with proteins through either reversible binding or covalent bond formation. The effect of the drugs on transcription factor interactions with DNA is reviewed. These effects can be classified as (i) competition between a drug and regulatory protein for target sequences; (ii) weakening of this interaction; (iii) enhancement of this interaction by chemical modification of the DNA and the creation of non-natural binding sites; and (iv) a 'suicide' mechanism, which is observed when a transcription factor induces changes in DNA structure, allowing a drug to bind to a target sequence. Several new strategies -- the antigene approach with oligonucleotides, peptide nucleic acids or locked nucleic acids, and sequence-specific polyamides -- are also reviewed.
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Affiliation(s)
- Marek Gniazdowski
- Department of Medicinal Chemistry, Institute of Physiology and Biochemistry, Medical University of Lódz, Mazowiecka 6/8, 92-215 Lódz, Poland.
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34
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Abstract
The chemical sciences are essential for the process of anticancer-drug discovery, and a range of chemical research techniques is needed to develop clinically effective drugs. Improved understanding of the cellular, molecular and genetic basis of cancer has increased the number of drug targets available. What chemical approaches are used to develop agents that target specific features of cancer cells and make these therapeutics more effective? We outline the roles that chemical synthesis and understanding of drug uptake have had in drug discovery over the past 100 years, as well as the chemical insights derived from knowledge of the three-dimensional structure of targets.
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Affiliation(s)
- Stephen Neidle
- Cancer Research UK, Biomolecular Structure Group, The School of Pharmacy, University of London, 29-39 Brunswick Square, London WC1N 1AX, UK.
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35
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Dickinson LA, Burnett R, Melander C, Edelson BS, Arora PS, Dervan PB, Gottesfeld JM. Arresting Cancer Proliferation by Small-Molecule Gene Regulation. ACTA ACUST UNITED AC 2004; 11:1583-94. [PMID: 15556009 DOI: 10.1016/j.chembiol.2004.09.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2004] [Revised: 09/03/2004] [Accepted: 09/09/2004] [Indexed: 12/31/2022]
Abstract
A small library of pyrrole-imidazole polyamide-DNA alkylator (chlorambucil) conjugates was screened for effects on morphology and growth characteristics of a human colon carcinoma cell line, and a compound was identified that causes cells to arrest in the G2/M stage of the cell cycle. Microarray analysis indicates that the histone H4c gene is significantly downregulated by this polyamide. RT-PCR and Western blotting experiments confirm this result, and siRNA to H4c mRNA yields the same cellular response. Strikingly, reduction of H4 protein by >50% does not lead to widespread changes in global gene expression. Sequence-specific alkylation within the coding region of the H4c gene in cell culture was confirmed by LM-PCR. The compound is active in a wide range of cancer cell lines, and treated cells do not form tumors in nude mice. The compound is also active in vivo, blocking tumor growth in mice, without obvious animal toxicity.
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Affiliation(s)
- Liliane A Dickinson
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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36
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Melander C, Burnett R, Gottesfeld JM. Regulation of gene expression with pyrrole–imidazole polyamides. J Biotechnol 2004; 112:195-220. [PMID: 15288953 DOI: 10.1016/j.jbiotec.2004.03.018] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2003] [Revised: 02/23/2004] [Accepted: 03/19/2004] [Indexed: 10/26/2022]
Abstract
The pyrrole-imidazole (Py-Im) polyamides represent the only available class of small molecules that can be designed to recognize virtually any predetermined DNA sequence. These molecules have affinities and specificities that equal or exceed natural eukaryotic transcriptional regulatory proteins. Studies with model gene systems, and a variety of eukaryotic and viral transcription factors, have shown that these molecules are potent inhibitors of protein-DNA interactions. Polyamides have been shown to regulate gene expression in simple in vitro systems using defined DNA templates and nuclear extracts as a source of the transcriptional machinery. Activation of gene expression has also been achieved in vitro with polyamide-activator peptide conjugates. Most importantly, polyamides are cell permeable and localize in the nucleus in various cultured cell lines and are capable of down regulating target genes in these cells. Polyamides have been shown to bind to their target sites in chromosomal DNA and both gain- and loss-of-function have been observed by targeting repeated DNA sequences in developing Drosophila embryos.
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Affiliation(s)
- Christian Melander
- Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
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37
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Seio K, Mizuta M, Terada T, Sekine M. Synthesis and properties of a pyrrole–imidazole polyamide having a ferrocene dicarboxylic amide linker. Tetrahedron Lett 2004. [DOI: 10.1016/j.tetlet.2004.07.060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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38
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Dudouet B, Burnett R, Dickinson LA, Wood MR, Melander C, Belitsky JM, Edelson B, Wurtz N, Briehn C, Dervan PB, Gottesfeld JM. Accessibility of nuclear chromatin by DNA binding polyamides. ACTA ACUST UNITED AC 2004; 10:859-67. [PMID: 14522056 DOI: 10.1016/j.chembiol.2003.09.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Pyrrole-imidazole polyamides bind DNA with affinities comparable to those of transcriptional regulatory proteins and inhibit the DNA binding activities of components of the transcription apparatus. If polyamides are to be useful for the regulation of gene expression in cell culture experiments, one pivotal issue is accessibility of specific sites in nuclear chromatin. We first determined the kinetics of uptake and subcellular distribution of polyamides in lymphoid and myeloid cells using fluorescent polyamide-bodipy conjugates and deconvolution microscopy. Then cells were incubated with a polyamide-chlorambucil conjugate, and the sites of specific DNA cleavage in the nuclear chromatin were assayed by ligation-mediated PCR. In addition, DNA microarray analysis revealed that two different polyamides generated distinct transcription profiles. Remarkably, the polyamides affected only a limited number of genes.
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Affiliation(s)
- Brigitte Dudouet
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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39
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Nelson SM, Ferguson LR, Denny WA. DNA and the chromosome - varied targets for chemotherapy. CELL & CHROMOSOME 2004; 3:2. [PMID: 15157277 PMCID: PMC421739 DOI: 10.1186/1475-9268-3-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2004] [Accepted: 05/24/2004] [Indexed: 12/29/2022]
Abstract
The nucleus of the cell serves to maintain, regulate, and replicate the critical genetic information encoded by the genome. Genomic DNA is highly associated with proteins that enable simple nuclear structures such as nucleosomes to form higher-order organisation such as chromatin fibres. The temporal association of regulatory proteins with DNA creates a dynamic environment capable of quickly responding to cellular requirements and distress. The response is often mediated through alterations in the chromatin structure, resulting in changed accessibility of specific DNA sequences that are then recognized by specific proteins. Anti-cancer drugs that target cellular DNA have been used clinically for over four decades, but it is only recently that nuclease specific drugs have been developed to not only target the DNA but also other components of the nuclear structure and its regulation. In this review, we discuss some of the new drugs aimed at primary DNA sequences, DNA secondary structures, and associated proteins, keeping in mind that these agents are not only important from a clinical perspective but also as tools for understanding the nuclear environment in normal and cancer cells.
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Affiliation(s)
- Stephanie M Nelson
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Auckland 10000, New Zealand
| | - Lynnette R Ferguson
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Auckland 10000, New Zealand
| | - William A Denny
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Auckland 10000, New Zealand
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40
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Edelson BS, Best TP, Olenyuk B, Nickols NG, Doss RM, Foister S, Heckel A, Dervan PB. Influence of structural variation on nuclear localization of DNA-binding polyamide-fluorophore conjugates. Nucleic Acids Res 2004; 32:2802-18. [PMID: 15155849 PMCID: PMC419610 DOI: 10.1093/nar/gkh609] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2004] [Revised: 04/22/2004] [Accepted: 04/22/2004] [Indexed: 11/14/2022] Open
Abstract
A pivotal step forward in chemical approaches to controlling gene expression is the development of sequence-specific DNA-binding molecules that can enter live cells and traffic to nuclei unaided. DNA-binding polyamides are a class of programmable, sequence-specific small molecules that have been shown to influence a wide variety of protein-DNA interactions. We have synthesized over 100 polyamide-fluorophore conjugates and assayed their nuclear uptake profiles in 13 mammalian cell lines. The compiled dataset, comprising 1300 entries, establishes a benchmark for the nuclear localization of polyamide-dye conjugates. Compounds in this series were chosen to provide systematic variation in several structural variables, including dye composition and placement, molecular weight, charge, ordering of the aromatic and aliphatic amino-acid building blocks and overall shape. Nuclear uptake does not appear to be correlated with polyamide molecular weight or with the number of imidazole residues, although the positions of imidazole residues affect nuclear access properties significantly. Generally negative determinants for nuclear access include the presence of a beta-Ala-tail residue and the lack of a cationic alkyl amine moiety, whereas the presence of an acetylated 2,4-diaminobutyric acid-turn is a positive factor for nuclear localization. We discuss implications of these data on the design of polyamide-dye conjugates for use in biological systems.
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Affiliation(s)
- Benjamin S Edelson
- Division of Chemistry and Chemical Engineering and The Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
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41
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Shinohara KI, Narita A, Oyoshi T, Bando T, Teraoka H, Sugiyama H. Sequence-Specific Gene Silencing in Mammalian Cells by Alkylating Pyrrole−Imidazole Polyamides. J Am Chem Soc 2004; 126:5113-8. [PMID: 15099094 DOI: 10.1021/ja031673v] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Gene silencing was examined by sequence-specific alkylation of DNA by N-methylpyrrole (Py)-N-methylimidazole (Im) hairpin polyamides. Polyamides ImImPyPygammaImImPyLDu86 (A) and ImImPyPygammaImPyPyLDu86 (B) selectively alkylated the coding regions of the renilla and firefly luciferases, respectively, according to the base pair recognition rule of Py-Im polyamides. Two different plasmids, encoding renilla luciferase and firefly luciferase, were used as vectors to examine the effect of alkylation on gene silencing. Transfection of the alkylated luciferase vectors-by polyamide A or B-into HeLa, 293, and NIH3T3 cells demonstrated that these sequence-specific DNA alkylations lead to selective silencing of gene expression. Next, the vectors were cotransfected into HeLa cells and the cells were treated with polyamide A or B. Selective reduction of luciferase activities was caused by both polyamides. On the basis of this sequence-specific alkylation and gene silencing activity, these alkylating Py-Im polyamides thus have potential as antitumor drugs to target specific gene expression in human cells.
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Affiliation(s)
- Ken-Ichi Shinohara
- Department of Pathological Biochemistry, Medical Research Institute, Tokyo Medical and Dental University, Chiyoda-ku, Tokyo 101-0062, Japan
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42
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Abstract
Chemical substances that can recognize and bind DNA in a sequence-specific manner have enormous importance in modern biology and medicine. When covalently linked, hairpin polyamides made up of N-methylpyrrole (Py) and N-methylimidazole (Im) can bind to DNA in a sequence-specific manner. An Im opposite a Py recognizes and binds G:C from C:G, whereas a Py opposite an Im recognizes and binds to C:G. A Py-Py pair degenerately binds to T:A or A:T, whereas a hydroxypyrrole opposite a Py recognizes and binds to T:A from A:T, and vice versa. A variant in this recognition is the beta-alanine (beta-ala-beta-ala) pair, which also degenerately binds to A:T or T:A. The hairpin polyamides are cell permeable and bind to DNA at nanomolar concentrations, with binding coefficients similar to those of transcription factors. This review comprehensively discusses the current literature on using the sequence-specific recognition ability of the polyamides to study various DNA-protein interactions.
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Affiliation(s)
- Musti Sree Rama Chandra Murty
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Surugadai, Kanda, Chiyoda-ku, Tokyo 101-0062, Japan
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Uil TG, Haisma HJ, Rots MG. Therapeutic modulation of endogenous gene function by agents with designed DNA-sequence specificities. Nucleic Acids Res 2003; 31:6064-78. [PMID: 14576293 PMCID: PMC275457 DOI: 10.1093/nar/gkg815] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Designer molecules that can specifically target pre-determined DNA sequences provide a means to modulate endogenous gene function. Different classes of sequence-specific DNA-binding agents have been developed, including triplex-forming molecules, synthetic polyamides and designer zinc finger proteins. These different types of designer molecules with their different principles of engineered sequence specificity are reviewed in this paper. Furthermore, we explore and discuss the potential of these molecules as therapeutic modulators of endogenous gene function, focusing on modulation by stable gene modification and by regulation of gene transcription.
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Affiliation(s)
- Taco G Uil
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
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