1
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Kuroda T, Huang Y, Nishio S, Goto Y, Suga H. Post-translational backbone-acyl shift yields natural product-like peptides bearing hydroxyhydrocarbon units. Nat Chem 2022; 14:1413-1420. [PMID: 36329180 DOI: 10.1038/s41557-022-01065-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 08/09/2022] [Indexed: 11/06/2022]
Abstract
Hydroxyhydrocarbon (Hhc) moieties in the backbone of peptidic natural products can exert a substantial influence on the bioactivities of the products, making Hhc units an attractive class of building blocks for de novo peptides. However, despite advances in in vitro genetic code reprogramming, the ribosomal incorporation of Hhc units remains challenging. Here we report a method for in vitro ribosomal synthesis of natural-product-like peptides bearing Hhc units. A series of azide/hydroxy acids were designed as chemical precursors of Hhc units and incorporated into the nascent peptide chain by means of genetic code reprogramming. Post-translational reduction of the azide induced an O-to-N acyl shift to rearrange the peptide backbone. This method allows for one-pot ribosomal synthesis of designer macrocycles bearing various β-, γ- and δ-type Hhc units. We also report the synthesis of a statine-containing peptidomimetic inhibitor of β-secretase 1 as a showcase example.
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Affiliation(s)
- Tomohiro Kuroda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Yichao Huang
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Soichiro Nishio
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan.
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan.
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2
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Wamhoff EC, Romanov A, Huang H, Read BJ, Ginsburg E, Knappe GA, Kim HM, Farrell NP, Irvine DJ, Bathe M. Controlling Nuclease Degradation of Wireframe DNA Origami with Minor Groove Binders. ACS NANO 2022; 16:8954-8966. [PMID: 35640255 PMCID: PMC9649841 DOI: 10.1021/acsnano.1c11575] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Viruslike particles (VLPs) fabricated using wireframe DNA origami are emerging as promising vaccine and gene therapeutic delivery platforms due to their programmable nature that offers independent control over their size and shape, as well as their site-specific functionalization. As materials that biodegrade in the presence of endonucleases, specifically DNase I and II, their utility for the targeting of cells, tissues, and organs depends on their stability in vivo. Here, we explore minor groove binders (MGBs) as specific endonuclease inhibitors to control the degradation half-life of wireframe DNA origami. Bare, unprotected DNA-VLPs composed of two-helix edges were found to be stable in fetal bovine serum under typical cell culture conditions and in human serum for 24 h but degraded within 3 h in mouse serum, suggesting species-specific endonuclease activity. Inhibiting endonucleases by incubating DNA-VLPs with diamidine-class MGBs increased their half-lives in mouse serum by more than 12 h, corroborated by protection against isolated DNase I and II. Our stabilization strategy was compatible with the functionalization of DNA-VLPs with HIV antigens, did not interfere with B-cell signaling activity of DNA-VLPs in vitro, and was nontoxic to B-cell lines. It was further found to be compatible with multiple wireframe DNA origami geometries and edge architectures. MGB protection is complementary to existing methods such as PEGylation and chemical cross-linking, offering a facile protocol to control DNase-mediated degradation rates for in vitro and possibly in vivo therapeutic and vaccine applications.
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Affiliation(s)
- Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Anna Romanov
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Hellen Huang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Benjamin J Read
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Eric Ginsburg
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| | - Grant A Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Hyun Min Kim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nicholas P Farrell
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| | - Darrell J Irvine
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02139, United States
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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3
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Wang M, Ma X, Zhou K, Mao H, Liu J, Xiong X, Zhao X, Narva S, Tanaka Y, Wu Y, Guo C, Sugiyama H, Zhang W. Discovery of Pyrrole-imidazole Polyamides as PD-L1 Expression Inhibitors and Their Anticancer Activity via Immune and Nonimmune Pathways. J Med Chem 2021; 64:6021-6036. [PMID: 33949196 DOI: 10.1021/acs.jmedchem.1c00120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In recent years, PD-1 immune checkpoint inhibitors based on monoclonal antibodies have revolutionized cancer therapy, but there still exist unresolved issues, such as the high cost, the relatively low response rates, and so on, compared with small-molecule drugs. Herein a type of pyrrole-imidazole (Py-Im) polyamide as a small-molecule DNA binder was designed and synthesized, which could competitively bind to the same double-stranded DNA stretch in the PD-L1 promoter region as the STAT3 binding site and thus downregulate PD-L1 expression. It was demonstrated that the Py-Im polyamides directly caused apoptosis in tumor cells and retarded cell migration in the absence of T cells through inhibiting the Akt/caspase-3 pathway. Also, in a coculture system, they enhanced the T-cell-mediated killing of tumor cells by the reversal of immune escape. Because such polyamides induced antitumor effects via both immune and nonimmune pathways, they could be further developed as promising PD-L1 gene-targeting antitumor drugs.
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Affiliation(s)
- Ming Wang
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China.,Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xudong Ma
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China.,Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Kang Zhou
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China.,Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Huijuan Mao
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China.,Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jiachun Liu
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China.,Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xuqiong Xiong
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China.,Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xiaoyin Zhao
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China.,Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Suresh Narva
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China.,Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yoshimasa Tanaka
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Yanling Wu
- Lab of Molecular Immunology, Virus Inspection Department, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Chuanxin Guo
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Wen Zhang
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China.,Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
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4
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Zhang M, Liang J, Jiang SK, Xu L, Wu YL, Awadasseid A, Zhao XY, Xiong XQ, Sugiyama H, Zhang W. Design, synthesis and anti-cancer activity of pyrrole-imidazole polyamides through target-downregulation of c-kit gene expression. Eur J Med Chem 2020; 207:112704. [DOI: 10.1016/j.ejmech.2020.112704] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/12/2020] [Accepted: 07/28/2020] [Indexed: 12/18/2022]
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5
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Zhou K, Liu J, Xiong X, Cheng M, Hu X, Narva S, Zhao X, Wu Y, Zhang W. Design, synthesis of 4,5-diazafluorene derivatives and their anticancer activity via targeting telomeric DNA G-quadruplex. Eur J Med Chem 2019; 178:484-499. [PMID: 31202994 DOI: 10.1016/j.ejmech.2019.06.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 06/02/2019] [Accepted: 06/03/2019] [Indexed: 01/19/2023]
Abstract
In our work, 19 novel 4,5-diazafluorene derivatives (11a-d, 12a-d, 13a-d, 14a-c, 15c, 16a-c) bearing a 1,3-disubstituted pyrazol/thioxothiazolidinone or thioxothiazolidinone-oxadiazole moieties were designed, synthesized, preliminarily explored for their antitumor activities and in vitro mechanism. All compounds showed different values of antiproliferative activity against A549, AGS, HepG2 and MCF-7 cell lines through CCK-8. Especially, the compound 14c exhibited the strongest activity and best selectivity against A549 cells with an IC50 1.13 μM and an SI value of 7.01 relative to MRC-5 cells, which was better than cisplatin (SI = 1.80) as a positive control. Experimental results at extracellular level demonstrated that compounds 14a-c could strongly interact with the G-quadruplex(es) formed in a 26 nt telomeric G-rich DNA, in particular, the 14c exhibits quite strong binding affinity with an association equilibrium constant (KA) of 7.04(±0.16) × 107 M-1 and more than 1000-fold specificity to G4-DNA over ds-DNA and Mut-DNA at the compound/G4-DNA ratio of 1:1. Further trap assay ascertained that compounds 14a-c owned strong inhibitory ability of telomerase activity in A549 cells, suggesting that these compounds have great possibility to target telomeric G-quadruplexes and consequently indirectly inhibit the telomerase activity. In addition, it is worthy of note that the remarkable inhibitory effects of 14a-c on the mobility of tested cancer cells were observed by wound healing assays. Furthermore, molecular docking and UV-Vis spectral results unclose the rationale for the interaction of compounds with such G-quadruplex(es). These results indicate that the growth and metastasis inhibition of cancer cells mediated by these 4,5-diazafluorene derivatives possibly result from their interaction with telomeric G-quadruplexes, suggesting that 4,5-diazafluorene derivatives, especially 14c, possess potential as anticancer drugs.
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Affiliation(s)
- Kang Zhou
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Lab of Chemical Biology and Molecular Drug Design, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Jiachun Liu
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Lab of Chemical Biology and Molecular Drug Design, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xuqiong Xiong
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Lab of Chemical Biology and Molecular Drug Design, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Mei Cheng
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Lab of Chemical Biology and Molecular Drug Design, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xiaolin Hu
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Lab of Chemical Biology and Molecular Drug Design, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Suresh Narva
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Lab of Chemical Biology and Molecular Drug Design, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xiaoyin Zhao
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Lab of Chemical Biology and Molecular Drug Design, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yanling Wu
- Lab of Molecular Immunology, Virus Inspection Department, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China.
| | - Wen Zhang
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Lab of Chemical Biology and Molecular Drug Design, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China.
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6
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Mukherjee A, Ghosh S, Sarkar R, Samanta S, Ghosh S, Pal M, Majee A, Sen SK, Singh B. Synthesis, characterization and unravelling the molecular interaction of new bioactive 4-hydroxycoumarin derivative with biopolymer: Insights from spectroscopic and theoretical aspect. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2018; 189:124-137. [DOI: 10.1016/j.jphotobiol.2018.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/31/2018] [Accepted: 10/04/2018] [Indexed: 01/18/2023]
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7
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Liu B, Wang S, Aston K, Koeller KJ, Kermani SFH, Castañeda CH, Scuderi MJ, Luo R, Bashkin JK, Wilson WD. β-Alanine and N-terminal cationic substituents affect polyamide-DNA binding. Org Biomol Chem 2018; 15:9880-9888. [PMID: 29143012 DOI: 10.1039/c7ob02513k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Minor-groove binding hairpin polyamides (PAs) bind specific DNA sequences. Synthetic modifications can improve PA-DNA binding affinity and include flexible modules, such as β-alanine (β) motifs to replace pyrroles (Py), and increasing compound charge using N-terminal cationic substituents. To better understand the variations in kinetics and affinities caused by these modifications on PA-DNA interactions, a comprehensive set of PAs with different numbers and positions of β and different types of N-cationic groups was systematically designed and synthesized to bind their cognate sequence, the λB motif. The λB motif is also a strong binding promoter site of the major groove targeting transcription factor PU.1. The PA binding affinities and kinetics were evaluated using a spectrum of powerful biophysical methods: thermal melting, biosensor surface plasmon resonance and circular dichroism. The results show that β inserts affect PA-DNA interactions in a number and position dependent manner. Specifically, a β replacement between two imidazole heterocycles (ImβIm) generally strengthens binding. In addition, N-terminal cationic groups can accelerate the association between PA and DNA, but the bulky size of TMG can cause steric hindrance and unfavourable repulsive electrostatic interactions in some PAs. The future design of stronger binding PA requires careful combination of βs and cationic substituents.
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Affiliation(s)
- Beibei Liu
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA.
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8
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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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9
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Obinata D, Takayama K, Takahashi S, Inoue S. Crosstalk of the Androgen Receptor with Transcriptional Collaborators: Potential Therapeutic Targets for Castration-Resistant Prostate Cancer. Cancers (Basel) 2017; 9:E22. [PMID: 28264478 PMCID: PMC5366817 DOI: 10.3390/cancers9030022] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 02/21/2017] [Accepted: 02/21/2017] [Indexed: 02/06/2023] Open
Abstract
Prostate cancer is the second leading cause of death from cancer among males in Western countries. It is also the most commonly diagnosed male cancer in Japan. The progression of prostate cancer is mainly influenced by androgens and the androgen receptor (AR). Androgen deprivation therapy is an established therapy for advanced prostate cancer; however, prostate cancers frequently develop resistance to low testosterone levels and progress to the fatal stage called castration-resistant prostate cancer (CRPC). Surprisingly, AR and the AR signaling pathway are still activated in most CRPC cases. To overcome this problem, abiraterone acetate and enzalutamide were introduced for the treatment of CRPC. Despite the impact of these drugs on prolonged survival, CRPC acquires further resistance to keep the AR pathway activated. Functional molecular studies have shown that some of the AR collaborative transcription factors (TFs), including octamer transcription factor (OCT1), GATA binding protein 2 (GATA2) and forkhead box A1 (FOXA1), still stimulate AR activity in the castration-resistant state. Therefore, elucidating the crosstalk between the AR and collaborative TFs on the AR pathway is critical for developing new strategies for the treatment of CRPC. Recently, many compounds targeting this pathway have been developed for treating CRPC. In this review, we summarize the AR signaling pathway in terms of AR collaborators and focus on pyrrole-imidazole (PI) polyamide as a candidate compound for the treatment of prostate cancer.
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Affiliation(s)
- Daisuke Obinata
- Department of Urology, Nihon University School of Medicine, Tokyo 173-8610, Japan.
- Department of Functional Biogerontology, Tokyo Metropolitan Institute of Gerontology, Tokyo 173-0015, Japan.
| | - Kenichi Takayama
- Department of Functional Biogerontology, Tokyo Metropolitan Institute of Gerontology, Tokyo 173-0015, Japan.
| | - Satoru Takahashi
- Department of Urology, Nihon University School of Medicine, Tokyo 173-8610, Japan.
| | - Satoshi Inoue
- Department of Functional Biogerontology, Tokyo Metropolitan Institute of Gerontology, Tokyo 173-0015, Japan.
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Saitama 350-1241, Japan.
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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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Wang S, Aston K, Koeller KJ, Harris GD, Rath NP, Bashkin JK, Wilson WD. Modulation of DNA-polyamide interaction by β-alanine substitutions: a study of positional effects on binding affinity, kinetics and thermodynamics. Org Biomol Chem 2015; 12:7523-36. [PMID: 25141096 DOI: 10.1039/c4ob01456a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Hairpin polyamides (PAs) are an important class of sequence-specific DNA minor groove binders, and frequently employ a flexible motif, β-alanine (β), to reduce the molecular rigidity to maintain the DNA recognition register. To better understand the diverse effects that β can have on DNA-PA binding affinity, selectivity, and especially kinetics, which have rarely been reported, we have initiated a detailed study for an eight-heterocyclic hairpin PA and its β derivatives with their cognate and mutant sequences. With these derivatives, all internal pyrroles of the parent PA are systematically substituted with single or double βs. A set of complementary experiments have been conducted to evaluate the molecular interactions in detail: UV-melting, biosensor-surface plasmon resonance, circular dichroism and isothermal titration calorimetry. The β substitutions generally weaken the binding affinities of these PAs with cognate DNA, and have large and diverse influences on PA binding kinetics in a position- and number-dependent manner. The DNA base mutations have also shown positional effects on the binding of a single PA. Besides the β substitutions, the monocationic Dp group [3-(dimethylamino)propylamine] in parent PA has been modified into a dicationic Ta group (3,3'-diamino-N-methyldipropylamine) to minimize the frequently observed PA aggregation with ITC experiments. The results clearly show that the Ta modification not only maintains the DNA binding mode and affinity of PA, but also significantly reduces PA aggregation and allows the complete thermodynamic signature of eight-ring hairpin PA to be determined for the first time. This combined set of results significantly extends our understanding of the energetic basis of specific DNA recognition by PAs.
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Affiliation(s)
- Shuo Wang
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
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12
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Hirata A, Nokihara K, Kawamoto Y, Bando T, Sasaki A, Ide S, Maeshima K, Kasama T, Sugiyama H. Structural Evaluation of Tandem Hairpin Pyrrole–Imidazole Polyamides Recognizing Human Telomeres. J Am Chem Soc 2014; 136:11546-54. [DOI: 10.1021/ja506058e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Akiyoshi Hirata
- HiPep Laboratories, Nakatsukasa-cho 486-46, Kamigyo-ku Kyoto, 602-8158, Japan
| | - Kiyoshi Nokihara
- HiPep Laboratories, Nakatsukasa-cho 486-46, Kamigyo-ku Kyoto, 602-8158, Japan
| | - Yusuke Kawamoto
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Asuka Sasaki
- Biological
Macromolecules Laboratory, Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Satoru Ide
- Biological
Macromolecules Laboratory, Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Kazuhiro Maeshima
- Biological
Macromolecules Laboratory, Structural Biology Center, National Institute
of Genetics, and Department of Genetics, School of Life Science, Graduate University for Advanced Studies (Sokendai), Mishima, Shizuoka 411-8540, Japan
| | - Takeshi Kasama
- Research
Center for Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroshi Sugiyama
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Institute
for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
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13
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Koeller KJ, Harris GD, Aston K, He G, Castaneda CH, Thornton MA, Edwards TG, Wang S, Nanjunda R, Wilson WD, Fisher C, Bashkin JK. DNA Binding Polyamides and the Importance of DNA Recognition in their use as Gene-Specific and Antiviral Agents. Med Chem 2014; 4:338-344. [PMID: 24839583 DOI: 10.4172/2161-0444.1000162] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
There is a long history for the bioorganic and biomedical use of N-methyl-pyrrole-derived polyamides (PAs) that are higher homologs of natural products such as distamycin A and netropsin. This work has been pursued by many groups, with the Dervan and Sugiyama groups responsible for many breakthroughs. We have studied PAs since about 1999, partly in industry and partly in academia. Early in this program, we reported methods to control cellular uptake of polyamides in cancer cell lines and other cells likely to have multidrug resistance efflux pumps induced. We went on to discover antiviral polyamides active against HPV31, where SAR showed that a minimum binding size of about 10 bp of DNA was necessary for activity. Subsequently we discovered polyamides active against two additional high-risk HPVs, HPV16 and 18, a subset of which showed broad spectrum activity against HPV16, 18 and 31. Aspects of our results presented here are incompatible with reported DNA recognition rules. For example, molecules with the same cognate DNA recognition properties varied from active to inactive against HPVs. We have since pursued the mechanism of action of antiviral polyamides, and polyamides in general, with collaborators at NanoVir, the University of Missouri-St. Louis, and Georgia State University. We describe dramatic consequences of β-alanine positioning even in relatively small, 8-ring polyamides; these results contrast sharply with prior reports. This paper was originally presented by JKB as a Keynote Lecture in the 2nd International Conference on Medicinal Chemistry and Computer Aided Drug Design Conference in Las Vegas, NV, October 2013.
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Affiliation(s)
- Kevin J Koeller
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St.Louis, MO 63121, USA
| | - G Davis Harris
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St.Louis, MO 63121, USA
| | - Karl Aston
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St.Louis, MO 63121, USA
| | - Gaofei He
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St.Louis, MO 63121, USA
| | - Carlos H Castaneda
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St.Louis, MO 63121, USA
| | - Melissa A Thornton
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St.Louis, MO 63121, USA
| | | | - Shuo Wang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Rupesh Nanjunda
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | | | - James K Bashkin
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St.Louis, MO 63121, USA ; NanoVir, LLC, Kalamazoo, MI 49008, USA
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14
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Han YW, Tsunaka Y, Yokota H, Matsumoto T, Kashiwazaki G, Morinaga H, Hashiya K, Bando T, Sugiyama H, Harada Y. Construction and characterization of Cy3- or Cy5-conjugated hairpin pyrrole–imidazole polyamides binding to DNA in the nucleosome. Biomater Sci 2014; 2:297-307. [DOI: 10.1039/c3bm60202h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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15
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Taylor RD, Asamitsu S, Takenaka T, Yamamoto M, Hashiya K, Kawamoto Y, Bando T, Nagase H, Sugiyama H. Sequence-Specific DNA Alkylation Targeting for Kras Codon 13 Mutation by Pyrrole-Imidazole Polyamideseco-CBI Conjugates. Chemistry 2013; 20:1310-7. [DOI: 10.1002/chem.201303295] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 10/31/2013] [Indexed: 12/13/2022]
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16
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Yamamoto M, Bando T, Morinaga H, Kawamoto Y, Hashiya K, Sugiyama H. Sequence-Specific DNA Recognition by Cyclic Pyrrole-Imidazole Cysteine-Derived Polyamide Dimers. Chemistry 2013; 20:752-9. [DOI: 10.1002/chem.201302482] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 10/21/2013] [Indexed: 11/12/2022]
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17
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Kameshima W, Ishizuka T, Minoshima M, Yamamoto M, Sugiyama H, Xu Y, Komiyama M. Conjugation of peptide nucleic acid with a pyrrole/imidazole polyamide to specifically recognize and cleave DNA. Angew Chem Int Ed Engl 2013; 52:13681-4. [PMID: 24155125 DOI: 10.1002/anie.201305489] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 09/03/2013] [Indexed: 11/06/2022]
Abstract
Cut loose: A pseudocomplementary peptide nucleic acid was tethered to a pyrrole/imidazole hairpin polyamide, and was used to selectively target a specific DNA sequence. Binding even occurs under high salt conditions. Furthermore, the conjugate facilitated sequence-specific scission of long dsDNA. This simple approach promises to resolve the technical difficulties in targeting DNA sequences with PNA.
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Affiliation(s)
- Wataru Kameshima
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904 (Japan)
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18
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Kameshima W, Ishizuka T, Minoshima M, Yamamoto M, Sugiyama H, Xu Y, Komiyama M. Conjugation of Peptide Nucleic Acid with a Pyrrole/Imidazole Polyamide to Specifically Recognize and Cleave DNA. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305489] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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19
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Taladriz-Sender A, Vicent C. Synthesis of cationic glyco-oligoamide for DNA–carbohydrate interaction studies. Supramol Chem 2013. [DOI: 10.1080/10610278.2013.814776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Andrea Taladriz-Sender
- Departamento de Síntesis, Estructura y Propiedades de los Compuestos Orgánicos (SEPCO), Instituto de Química Orgánica General, CSIC, C/Juan de la Cierva 3, 28006 Madrid, Spain
| | - Cristina Vicent
- Departamento de Síntesis, Estructura y Propiedades de los Compuestos Orgánicos (SEPCO), Instituto de Química Orgánica General, CSIC, C/Juan de la Cierva 3, 28006 Madrid, Spain
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20
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Effect of single pyrrole replacement with β-alanine on DNA binding affinity and sequence specificity of hairpin pyrrole/imidazole polyamides targeting 5′-GCGC-3′. Bioorg Med Chem 2013; 21:5436-41. [DOI: 10.1016/j.bmc.2013.06.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 06/03/2013] [Accepted: 06/04/2013] [Indexed: 12/27/2022]
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21
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Han YW, Matsumoto T, Yokota H, Kashiwazaki G, Morinaga H, Hashiya K, Bando T, Harada Y, Sugiyama H. Binding of hairpin pyrrole and imidazole polyamides to DNA: relationship between torsion angle and association rate constants. Nucleic Acids Res 2012; 40:11510-7. [PMID: 23042247 PMCID: PMC3526260 DOI: 10.1093/nar/gks897] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
N-methylpyrrole (Py)-N-methylimidazole (Im) polyamides are small organic molecules that bind to DNA with sequence specificity and can be used as synthetic DNA-binding ligands. In this study, five hairpin eight-ring Py-Im polyamides 1-5 with different number of Im rings were synthesized, and their binding behaviour was investigated with surface plasmon resonance assay. It was found that association rate (k(a)) of the Py-Im polyamides with their target DNA decreased with the number of Im in the Py-Im polyamides. The structures of four-ring Py-Im polyamides derived from density functional theory revealed that the dihedral angle of the Py amide carbonyl is 14∼18°, whereas that of the Im is significantly smaller. As the minor groove of DNA has a helical structure, planar Py-Im polyamides need to change their conformation to fit it upon binding to the minor groove. The data explain that an increase in planarity of Py-Im polyamide induced by the incorporation of Im reduces the association rate of Py-Im polyamides. This fundamental knowledge of the binding of Py-Im polyamides to DNA will facilitate the design of hairpin Py-Im polyamides as synthetic DNA-binding modules.
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Affiliation(s)
- Yong-Woon Han
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida Honmachi, Sakyo, Kyoto 606-8501, Japan.
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22
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Zhang HF, Wu YL, Jiang SK, Wang P, Sugiyama H, Chen XL, Zhang W, Ji YJ, Guo CX. Recognition by Nonaromatic and Stereochemical Subunit-Containing Polyamides of the Four Watson-Crick Base Pairs in the DNA Minor Groove. Chembiochem 2012; 13:1366-74. [DOI: 10.1002/cbic.201200137] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Indexed: 11/06/2022]
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23
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Zhang W, Jiang SK, Wu YL, Guo CX, Zhang HF, Sugiyama H, Chen XL. Discrimination between T/A and A/T Base Pairs of Pyrrole-Imidazole Polyamides Substituted with Chiral β-Hydroxy-γ-Aminobutyric Acid/β-Alanine Pairs. Chembiochem 2011; 13:47-50. [DOI: 10.1002/cbic.201100675] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Indexed: 11/08/2022]
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24
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Morinaga H, Bando T, Takagaki T, Yamamoto M, Hashiya K, Sugiyama H. Cysteine Cyclic Pyrrole–Imidazole Polyamide for Sequence-Specific Recognition in the DNA Minor Groove. J Am Chem Soc 2011; 133:18924-30. [DOI: 10.1021/ja207440p] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | | | - Hiroshi Sugiyama
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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25
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Yasuda A, Noguchi K, Minoshima M, Kashiwazaki G, Kanda T, Katayama K, Mitsuhashi J, Bando T, Sugiyama H, Sugimoto Y. DNA ligand designed to antagonize EBNA1 represses Epstein-Barr virus-induced immortalization. Cancer Sci 2011; 102:2221-30. [PMID: 21910783 DOI: 10.1111/j.1349-7006.2011.02098.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Epstein-Barr virus (EBV) transforms human B lymphocytes into immortalized cells in vitro and is associated with various malignancies in vivo. EBNA1, which is expressed in the majority of EBV-infected cells, recognizes specific DNA sequences at the cis-acting latent origin of plasmid replication (oriP) element of the EBV genome. EBNA1 plays a critical role in the viral episome maintenance and transactivates viral transforming genes in latently infected cells. Therefore, DNA-targeting agents that can disrupt the EBNA1-oriP interaction will offer novel functional inhibitors of EBNA1. Pyrrole-imidazole polyamides, sequence-specific DNA ligands, can be designed to interfere with the binding of various transcriptional factors. Here, we synthesized pyrrole-imidazole polyamides targeting EBNA1-bound DNA sequences and developed an inhibitor for the EBNA1-oriP interaction. A pyrrole-imidazole polyamide, designated as DSE-3, bound adjacent to the EBNA1 recognition sequences located in the dyad symmetry element of oriP, and selectively inhibited EBNA1-oriP binding both in vitro and in vivo. DSE-3 also inhibited the proliferation of established lymphoblastoid cell lines by eradicating EBV episomes from the cells. In addition, DSE-3 repressed the expression of viral transforming genes after infecting human peripheral blood mononuclear cells with EBV and, as a consequence, inhibited EBV-mediated B-cell immortalization. These results suggest that EBNA1 functions will be an attractive pharmacological target for EBV-associated diseases.
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Affiliation(s)
- Ai Yasuda
- Division of Chemotherapy, Keio University, Tokyo, Japan
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26
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Ohtsuki A, Kimura MT, Minoshima M, Suzuki T, Ikeda M, Bando T, Nagase H, Shinohara KI, Sugiyama H. Synthesis and properties of PI polyamide–SAHA conjugate. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.10.034] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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27
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Development of a molecule-recognized promoter DNA sequence for inhibition of HER2 expression. J Antibiot (Tokyo) 2009; 62:339-41. [DOI: 10.1038/ja.2009.35] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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28
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Takahashi T, Asami Y, Kitamura E, Suzuki T, Wang X, Igarashi J, Morohashi A, Shinojima Y, Kanou H, Saito K, Takasu T, Nagase H, Harada Y, Kuroda K, Watanabe T, Kumamoto S, Aoyama T, Matsumoto Y, Bando T, Sugiyama H, Yoshida-Noro C, Fukuda N, Hayashi N. Development of Pyrrole-Imidazole Polyamide for Specific Regulation of Human Aurora Kinase-A and -B Gene Expression. ACTA ACUST UNITED AC 2008; 15:829-41. [DOI: 10.1016/j.chembiol.2008.06.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2007] [Revised: 05/26/2008] [Accepted: 06/06/2008] [Indexed: 11/25/2022]
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29
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Minoshima M, Bando T, Sasaki S, Fujimoto J, Sugiyama H. Pyrrole-imidazole hairpin polyamides with high affinity at 5'-CGCG-3' DNA sequence; influence of cytosine methylation on binding. Nucleic Acids Res 2008; 36:2889-94. [PMID: 18385159 PMCID: PMC2396430 DOI: 10.1093/nar/gkn116] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
To investigate the binding of 5′–CpG–3′ sequences by small molecules, two pyrrole (Py)–imidazole (Im) hairpin polyamides, PyImPyIm–γ–PyImPyIm–β–Dp (1) and PyIm–β–Im–γ–PyIm–β–Im–β–Dp (2), which recognize the sequence 5′–CGCG–3′, were synthesized. The binding affinities of the 5′–CGCG–3′ sequence to the Py–Im hairpin polyamides were measured by surface plasmon resonance (SPR) analysis. SPR data revealed that dissociation equilibrium constants (Kd) of polyamides 1 and 2 were 1.1 (± 0.3) × 10–6 M and 1.7 (± 0.4) × 10–8 M, respectively. Polyamide 2 possesses great binding affinity for this sequence, 65-fold higher than polyamide 1. Moreover, when all cytosines in 5′–CpGpCpG–3′ were replaced with 5-methylcytosines (mCs), the Kd value of polyamide 2 increased to 5.8 (± 0.7) × 10–9 (M), which indicated about 3-fold higher binding than the unmethylated 5′–CGCG–3′ sequence. These results suggest that polyamide 2 would be suitable to target CpG-rich sequences in the genome.
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Affiliation(s)
- Masafumi Minoshima
- Department of Chemistry, Faculty of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
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30
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Bando T, Fujimoto J, Minoshima M, Shinohara KI, Sasaki S, Kashiwazaki G, Mizumura M, Sugiyama H. Detection of CAG repeat DNA sequences by pyrene-functionalized pyrrole-imidazole polyamides. Bioorg Med Chem 2007; 15:6937-42. [PMID: 17826098 DOI: 10.1016/j.bmc.2007.07.055] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2007] [Accepted: 07/30/2007] [Indexed: 11/16/2022]
Abstract
Five N-methylpyrrole-N-methylimidazole (Py-Im) polyamides possessing a fluorescent pyrene were synthesized by Fmoc solid-phase synthesis using Py/Im monomers and pyrenylbutyl-pyrrole monomer compound 9. The steady state fluorescence of conjugates 1-5 was examined in the presence and absence of (CAG)(12)-containing oligodeoxynucleotides (ODNs) 1 and 2. Of the conjugates, conjugate 1 showed no background emission around 470 nm in the absence of ODNs, and a clear increase of emission at 475 nm was observed upon addition of ODNs 1 and 2. The emission of conjugate 1 at 475 nm increased linearly with the concentration of ODN and the number of CAG repeats. The results indicate that conjugate 1 efficiently forms a pyrene excimer upon binding in the minor groove of DNA.
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Affiliation(s)
- Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
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31
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Minoshima M, Bando T, Sasaki S, Shinohara KI, Shimizu T, Fujimoto J, Sugiyama H. DNA Alkylation by Pyrrole−Imidazole seco-CBI Conjugates with an Indole Linker: Sequence-Specific DNA Alkylation with 10-Base-Pair Recognition through Heterodimer Formation. J Am Chem Soc 2007; 129:5384-90. [PMID: 17425308 DOI: 10.1021/ja065235a] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The sequence-specific DNA alkylation by conjugates 4 and 5, which consist of N-methylpyrrole (Py)-N-methylimidazole (Im) polyamides and 1-(chloromethyl)-5-hydroxy-1,2-dihydro-3H-benz[e]indole (seco-CBI) linked with an indole linker, was investigated in the absence or presence of partner Py-Im polyamide 6. High-resolution denaturing polyacrylamide gel electrophoresis revealed that conjugate 4 alkylates DNA at the sequences 5'-(A/T)GCCTA-3' through hairpin formation, and alkylates 5'-GGAAAGAAAA-3' through an extended binding mode. However, in the presence of partner Py-Im polyamide 6, conjugate 4 alkylates DNA at a completely different sequence, 5'-AGGTTGTCCA-3'. Alkylation of 4 in the presence of 6 was effectively inhibited by a competitor 7. Surface plasmon resonance (SPR) results indicated that conjugate 4 does not bind to 5'-AGGTTGTCCA-3', whereas 6 binds tightly to this sequence. The results suggest that alkylation proceeds through heterodimer formation, indicating that this is a general way to expand the recognition sequence for DNA alkylation by Py-Im seco-CBI conjugates.
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Affiliation(s)
- Masafumi Minoshima
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
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32
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Rich RL, Myszka DG. Survey of the year 2006 commercial optical biosensor literature. J Mol Recognit 2007; 20:300-66. [DOI: 10.1002/jmr.862] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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