1
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Hirose Y, Sato S, Hashiya K, Ooga M, Bando T, Sugiyama H. Chb-M', an Inhibitor of the RUNX Family Binding to DNA, Induces Apoptosis in p53-Mutated Non-Small Cell Lung Cancer and Inhibits Tumor Growth and Repopulation In Vivo. J Med Chem 2024; 67:9165-9172. [PMID: 38803164 DOI: 10.1021/acs.jmedchem.4c00315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Runt-related transcription factor (RUNX) proteins are considered to play various roles in cancer. Here, we evaluated the anticancer activity of Chb-M', a compound that specifically and covalently binds to the consensus sequence for RUNX family proteins, in p53-mutated non-small cell lung cancer cells. Chb-M' killed the cancer cells by inducing apoptosis. The compound showed an anticancer effect comparable to that of the clinically used drugs alectinib and ceritinib in vivo. Notably, Chb-M' extended the cancer-free survival of mice after ending treatment more effectively than did the other two drugs. The results presented here suggest that Chb-M' is an attractive candidate as an anticancer drug applicable to the treatment of non-small cell lung cancer and various other types of cancers.
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Affiliation(s)
- Yuki Hirose
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Shinsuke Sato
- 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
| | - Mitsuharu Ooga
- 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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2
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Abe K, Hirose Y, Kumagai T, Hashiya K, Hidaka K, Emura T, Bando T, Takeda K, Sugiyama H. Structural Studies of a Complex of a CAG/CTG Repeat Sequence-Specific Binding Molecule and A-A-Mismatch-Containing DNA. JACS AU 2024; 4:1801-1810. [PMID: 38818057 PMCID: PMC11134352 DOI: 10.1021/jacsau.3c00830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/04/2024] [Accepted: 03/06/2024] [Indexed: 06/01/2024]
Abstract
Triplet repeat diseases are caused by the abnormal elongation of repeated sequences comprising three bases. In particular, the elongation of CAG/CTG repeat sequences is thought to result in conditions such as Huntington's disease and myotonic dystrophy type 1. Although the causes of these diseases are known, fundamental treatments have not been established, and specific drugs are expected to be developed. Pyrrole imidazole polyamide (PIP) is a class of molecules that binds to the minor groove of the DNA duplex in a sequence-specific manner; because of this property, it shows promise in drug discovery applications. Earlier, it was reported that PIP designed to bind CAG/CTG repeat sequences suppresses the genes that cause triplet repeat diseases. In this study, we performed an X-ray crystal structure analysis of a complex of double-stranded DNA containing A-A mismatched base pairs and a cyclic-PIP that binds specifically to CAG/CTG sequences. Furthermore, the validity and characteristics of this structure were analyzed using in silico molecular modeling, ab initio energy calculations, gel electrophoresis, and surface plasmon resonance. With our direct observation using atomic force microscopy and DNA origami, we revealed that the PIP caused structural changes in the DNA strands carrying the expanded CAG/CTG repeat. Overall, our study provides new insight into PIP from a structural perspective.
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Affiliation(s)
- Katsuhiko Abe
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Yuki Hirose
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Tomotaka Kumagai
- 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
| | - Kumi Hidaka
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Tomoko Emura
- 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
| | - Kazuki Takeda
- Department
of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Institute
for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
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3
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Bai D, Ziadlou R, Vaijayanthi T, Karthikeyan S, Chinnathambi S, Parthasarathy A, Cai L, Brüggen MC, Sugiyama H, Pandian GN. Nucleic acid-based small molecules as targeted transcription therapeutics for immunoregulation. Allergy 2024; 79:843-860. [PMID: 38055191 DOI: 10.1111/all.15959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 11/02/2023] [Accepted: 11/09/2023] [Indexed: 12/07/2023]
Abstract
Transcription therapy is an emerging approach that centers on identifying the factors associated with the malfunctioning gene transcription machinery that causes diseases and controlling them with designer agents. Until now, the primary research focus in therapeutic gene modulation has been on small-molecule drugs that target epigenetic enzymes and critical signaling pathways. However, nucleic acid-based small molecules have gained popularity in recent years for their amenability to be pre-designed and realize operative control over the dynamic transcription machinery that governs how the immune system responds to diseases. Pyrrole-imidazole polyamides (PIPs) are well-established DNA-based small-molecule gene regulators that overcome the limitations of their conventional counterparts owing to their sequence-targeted specificity, versatile regulatory efficiency, and biocompatibility. Here, we emphasize the rational design of PIPs, their functional mechanisms, and their potential as targeted transcription therapeutics for disease treatment by regulating the immune response. Furthermore, we also discuss the challenges and foresight of this approach in personalized immunotherapy in precision medicine.
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Affiliation(s)
- Dan Bai
- Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto, Japan
- Research & Development Institute of Northwestern Polytechnical University in Shenzhen, Xi'an Key Laboratory of Special Medicine and Health Engineering, Xi'an, China
| | - Reihane Ziadlou
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Thangavel Vaijayanthi
- Chief Executive Officer, Regugene Co. Ltd., Kyoto, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, Japan
| | - Subramani Karthikeyan
- Centre for Healthcare Advancement, Innovation and Research, Vellore Institute of Technology, Chennai, Tamil Nadu, India
| | | | | | - Li Cai
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA
| | - Marie-Charlotte Brüggen
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Hiroshi Sugiyama
- Chief Executive Officer, Regugene Co. Ltd., Kyoto, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, Japan
| | - Ganesh N Pandian
- Chief Executive Officer, Regugene Co. Ltd., Kyoto, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, Japan
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4
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Ikenoshita S, Matsuo K, Yabuki Y, Kawakubo K, Asamitsu S, Hori K, Usuki S, Hirose Y, Bando T, Araki K, Ueda M, Sugiyama H, Shioda N. A cyclic pyrrole-imidazole polyamide reduces pathogenic RNA in CAG/CTG triplet repeat neurological disease models. J Clin Invest 2023; 133:e164792. [PMID: 37707954 PMCID: PMC10645379 DOI: 10.1172/jci164792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/12/2023] [Indexed: 09/16/2023] Open
Abstract
Expansion of CAG and CTG (CWG) triplet repeats causes several inherited neurological diseases. The CWG repeat diseases are thought to involve complex pathogenic mechanisms through expanded CWG repeat-derived RNAs in a noncoding region and polypeptides in a coding region, respectively. However, an effective therapeutic approach has not been established for the CWG repeat diseases. Here, we show that a CWG repeat DNA-targeting compound, cyclic pyrrole-imidazole polyamide (CWG-cPIP), suppressed the pathogenesis of coding and noncoding CWG repeat diseases. CWG-cPIP bound to the hairpin form of mismatched CWG DNA, interfering with transcription elongation by RNA polymerase through a preferential activity toward repeat-expanded DNA. We found that CWG-cPIP selectively inhibited pathogenic mRNA transcripts from expanded CWG repeats, reducing CUG RNA foci and polyglutamine accumulation in cells from patients with myotonic dystrophy type 1 (DM1) and Huntington's disease (HD). Treatment with CWG-cPIP ameliorated behavioral deficits in adeno-associated virus-mediated CWG repeat-expressing mice and in a genetic mouse model of HD, without cytotoxicity or off-target effects. Together, we present a candidate compound that targets expanded CWG repeat DNA independently of its genomic location and reduces both pathogenic RNA and protein levels. CWG-cPIP may be used for the treatment of CWG repeat diseases and improvement of clinical outcomes.
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Affiliation(s)
- Susumu Ikenoshita
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG)
- Department of Neurology, Graduate School of Medical Sciences
| | - Kazuya Matsuo
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG)
| | - Yasushi Yabuki
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG)
- Graduate School of Pharmaceutical Sciences, and
| | - Kosuke Kawakubo
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG)
- Graduate School of Pharmaceutical Sciences, and
| | - Sefan Asamitsu
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG)
| | - Karin Hori
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG)
| | - Shingo Usuki
- Liaison Laboratory Research Promotion Center, IMEG, Kumamoto University, Kumamoto, Japan
| | - Yuki Hirose
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Kimi Araki
- Institute of Resource Development and Analysis and
- Center for Metabolic Regulation of Healthy Aging, Kumamoto University, Kumamoto, Japan
| | - Mitsuharu Ueda
- Department of Neurology, Graduate School of Medical Sciences
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
- Institute for Integrated Cell-Material Science (iCeMS), Kyoto University, Kyoto, Japan
| | - Norifumi Shioda
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics (IMEG)
- Graduate School of Pharmaceutical Sciences, and
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5
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Hirose Y, Sato S, Hashiya K, Bando T, Sugiyama H. Anticancer Activities of DNA-Alkylating Pyrrole-Imidazole Polyamide Analogs Targeting RUNX Transcription Factors against p53-Mutated Pancreatic Cancer PANC-1 Cells. J Med Chem 2023; 66:12059-12068. [PMID: 37606185 DOI: 10.1021/acs.jmedchem.3c00613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
The runt-related transcription factor (RUNX) family is known to play important roles in the progression of cancer. Conjugate 1, which covalently binds to the RUNX-binding sequences, was reported to inhibit the binding of RUNX proteins to their target sites and suppress cancer growth. Here, we evaluated the anticancer effects of 1 and its analogs 2-4 against p53-mutated PANC-1 pancreatic cancer cells. We found that they possessed different DNA-alkylating properties in vitro. And conjugates 1-3 were shown to have anticancer effects by inducing apoptosis in PANC-1 cells. Furthermore, conjugates 2 and 3 suppressed cancer growth in PANC-1 xenograft mice, with activity equivalent to a 50-fold dose of gemcitabine. Especially, 3 showed the highest alkylation efficiency, specificity, and better anticancer effects against pancreatic cancer than 1 in vivo without significant body weight loss. Our results revealed the potential of our compounds as new candidates for cancer therapy.
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Affiliation(s)
- Yuki Hirose
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Shinsuke Sato
- 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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Hatanaka J, Hashiya K, Bando T, Sugiyama H. Substitution to hydrophobic linker and formation of host-guest complex enhanced the effect of synthetic transcription factor made of pyrrole-imidazole polyamide. Bioorg Med Chem 2023; 81:117208. [PMID: 36780807 DOI: 10.1016/j.bmc.2023.117208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/31/2023] [Accepted: 02/04/2023] [Indexed: 02/11/2023]
Abstract
GAA repeat expansion in the first intron of the frataxin (FXN) gene represses the transcription of FXN, and that induces Friedreich's ataxia (FRDA). Pyrrole-imidazole polyamides (PIPs) are the class of oligopeptide that targets double-stranded DNA with sequence selectivity. Previously, bromodomain inhibitors such as JQ1 conjugated with PIPs were reported to selectively increase transcription. Here, we report the synthesis of a compound that increases the transcription of FXN in cells derived from an FRDA patient. The compound was effective in lower (one tenth) concentration than the compound that previously reported. High concentration of the compound is toxic, but toxicity was reduced with a host-guest complex.
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Affiliation(s)
- Junnosuke Hatanaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto, Japan
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto, Japan.
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Yoshida-Ushinomiyacho, Sakyo, Kyoto, Japan.
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7
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Shibata T, Nakatani K. A small molecule binding to TGGAA pentanucleotide repeats that cause spinocerebellar ataxia type 31. Bioorg Med Chem Lett 2023; 79:129082. [PMID: 36414174 DOI: 10.1016/j.bmcl.2022.129082] [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: 10/02/2022] [Revised: 11/07/2022] [Accepted: 11/16/2022] [Indexed: 11/21/2022]
Abstract
Spinocerebellar ataxia type 31 is an autosomal dominant neurodegenerative disease caused by aberrant insertion of d(TGGAA)n into the intron shared by brain expressed, associated with Nedd4 and thymidine kinase 2 genes in chromosome 16. We reported that a naphthyridine dimer derivative with amidated linker structure (ND-amide) bound to GGA/GGA motifs in hairpin structures of d(TGGAA)n. The binding of naphthyridine dimer derivatives to the GGA/GGA motif was sensitive to the linker structures. The amidation of the linker in naphthyridine dimer improved the binding property to the GGA/GGA motif as compared with non-amidated naphthyridine dimer.
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Affiliation(s)
- Tomonori Shibata
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan.
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan.
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8
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Hatanaka J, Hirose Y, Hashiya K, Bando T, Sugiyama H. N‐terminal cationic modification of linear pyrrole−imidazole polyamide improves its binding to DNA. Chembiochem 2022; 23:e202200124. [DOI: 10.1002/cbic.202200124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/18/2022] [Indexed: 11/08/2022]
Affiliation(s)
| | - Yuki Hirose
- Kyoto University - Yoshida Campus: Kyoto Daigaku Chemistry JAPAN
| | - Kaori Hashiya
- Kyoto University - Yoshida Campus: Kyoto Daigaku Chemistry JAPAN
| | - Toshikazu Bando
- Kyoto University - Yoshida Campus: Kyoto Daigaku Chemistry JAPAN
| | - Hiroshi Sugiyama
- Kyoto University Department of Chemistry Kitashirakawa-Oiwakecho 606-8502 Kyoto JAPAN
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9
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Lee J, Li K, Zimmerman SC. A Selective Alkylating Agent for CTG Repeats in Myotonic Dystrophy Type 1. ACS Chem Biol 2022; 17:1103-1110. [PMID: 35483041 DOI: 10.1021/acschembio.1c00949] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Disease intervention at the DNA level generally has been avoided because of off-target effects. Recent advances in genome editing technologies using CRISPR-Cas9 have opened a new era in DNA-targeted therapeutic approaches. However, delivery of such systems remains a major challenge. Here, we report a selective DNA-modifying small molecule that targets a disease-specific structure and mismatches involved in myotonic dystrophy type 1 (DM1). This ligand alkylates T-T mismatch-containing hairpins formed in the expanded CTG repeats (d(CTG)exp) in DM1. Ligand alkylation of d(CTG)exp inhibits the transcription of d(CAG·CTG)exp, thereby reducing the level of the toxic r(CUG)exp transcript. The bioactivity of the ligand also included a reduction in DM1 pathological features such as disease foci formation and misregulation of pre-mRNA splicing in DM1 model cells. Furthermore, the CTG-alkylating ligand may change the d(CAG·CTG)exp repeat length dynamics in DM1 patient cells. Our strategy of linking an alkylating moiety to a DNA mismatch-selective small molecule may be generally applicable to other repeat expansion diseases such as Huntington's disease and amyotrophic lateral sclerosis.
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Affiliation(s)
- JuYeon Lee
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Ke Li
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Steven C. Zimmerman
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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10
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Hirose Y, Ohno T, Asamitsu S, Hashiya K, Bando T, Sugiyama H. Strong and Specific Recognition of CAG/CTG Repeat DNA (5'-dWGCWGCW-3') by a Cyclic Pyrrole-Imidazole Polyamide. Chembiochem 2021; 23:e202100533. [PMID: 34796607 PMCID: PMC9298716 DOI: 10.1002/cbic.202100533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/26/2021] [Indexed: 11/30/2022]
Abstract
Abnormally expanded CAG/CTG repeat DNA sequences lead to a variety of neurological diseases, such as Huntington's disease. Here, we synthesized a cyclic pyrrole‐imidazole polyamide (cPIP), which can bind to the minor groove of the CAG/CTG DNA sequence. The double‐stranded DNA melting temperature (Tm) and surface plasmon resonance assays revealed the high binding affinity of the cPIP. In addition, next‐generation sequencing showed that the cPIP had high specificity for its target DNA sequence.
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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
| | - Tomo Ohno
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Sefan Asamitsu
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.,Present address: Department of Genomic Neurology, Institute of Molecular Embryology and Genetics, Kumamoto University, Honjo, Chuo-ku, Kumamoto, 860-0811, 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, countryPart/>Kyoto, 606-8501, Japan
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11
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Li M, Lu D, Cheng Y, Wu C, Zhang J, Shi W, Ding Z, Li Y, Cheng B, Lin X, Shao X, Li H, Fang L, Liu K, Su W. A novel pyrrole-imidazole polyamide targets Aurora kinase A and suppresses tumor growth in vivo. Biochem Biophys Res Commun 2021; 571:167-173. [PMID: 34330060 DOI: 10.1016/j.bbrc.2021.07.077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 07/21/2021] [Indexed: 11/26/2022]
Abstract
Aurora kinase A (Aurora A) plays a critical role in regulating cell mitotic progression and has been considered as a promising drug target for cancer therapy. To develop a novel molecule targeting Aurora A with high selectivity and efficacy, we designed and synthesized a pyrrole-imidazole polyamide (PIP) Hoechst conjugate, PIP-Ht, targeting to a cell-cycle regulated DNA sequence locating at the promoter of human Aurora A gene (AURKA). PIP-Ht potently suppressed AURKA promoter activities, mRNA expression and protein level, induced tumor cell cycle delay and inhibited tumor cell proliferation in vitro. Furthermore, subcutaneous injection of PIP-Ht into mice bearing human cancer xenografts induced significant tumor growth suppression and cell apoptosis. Collectively, PIP-Ht exhibits the potential as an effective therapeutic candidate for the tumor treatment.
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Affiliation(s)
- Meiqing Li
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Danyi Lu
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Institute of Molecular Rhythm and Metabolism, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Yulian Cheng
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Nano Science and Technology Institute, University of Science and Technology of China, Suzhou, 215123, Jiangsu, China
| | - Chunlei Wu
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Jianchao Zhang
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Wenli Shi
- School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, China; Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Zhihao Ding
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yanyan Li
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Binghua Cheng
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xian Lin
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Ximing Shao
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Hongchang Li
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Lijing Fang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Ke Liu
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Wu Su
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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12
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Corvaglia V, Ait Mohamed Amar I, Garambois V, Letast S, Garcin A, Gongora C, Del Rio M, Denevault-Sabourin C, Joubert N, Huc I, Pourquier P. Internalization of Foldamer-Based DNA Mimics through a Site-Specific Antibody Conjugate to Target HER2-Positive Cancer Cells. Pharmaceuticals (Basel) 2021; 14:ph14070624. [PMID: 34203395 PMCID: PMC8308903 DOI: 10.3390/ph14070624] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 11/16/2022] Open
Abstract
Inhibition of protein-DNA interactions represents an attractive strategy to modulate essential cellular functions. We reported the synthesis of unique oligoamide-based foldamers that adopt single helical conformations and mimic the negatively charged phosphate moieties of B-DNA. These mimics alter the activity of DNA interacting enzymes used as targets for cancer treatment, such as DNA topoisomerase I, and they are cytotoxic only in the presence of a transfection agent. The aim of our study was to improve internalization and selective delivery of these highly charged molecules to cancer cells. For this purpose, we synthesized an antibody-drug conjugate (ADC) using a DNA mimic as a payload to specifically target cancer cells overexpressing HER2. We report the bioconjugation of a 16-mer DNA mimic with trastuzumab and its functional validation in breast and ovarian cancer cells expressing various levels of HER2. Binding of the ADC to HER2 increased with the expression of the receptor. The ADC was internalized into cells and was more efficient than trastuzumab at inhibiting their growth in vitro. These results provide proof of concept that it is possible to site-specifically graft high molecular weight payloads such as DNA mimics onto monoclonal antibodies to improve their selective internalization and delivery in cancer cells.
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Affiliation(s)
- Valentina Corvaglia
- Center for Integrated Protein Science, Department of Pharmacy, Ludwig-Maximilians-Universität, 81377 Munich, Germany; (V.C.); (I.H.)
| | - Imène Ait Mohamed Amar
- GICC EA7501, Equipe IMT, Université de Tours, 10 Boulevard Tonnellé, F-37032 Tours, France; (I.A.M.A.); (S.L.); (C.D.-S.); (N.J.)
| | - Véronique Garambois
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, F-34298 Montpellier, France; (V.G.); (A.G.); (C.G.); (M.D.R.)
| | - Stéphanie Letast
- GICC EA7501, Equipe IMT, Université de Tours, 10 Boulevard Tonnellé, F-37032 Tours, France; (I.A.M.A.); (S.L.); (C.D.-S.); (N.J.)
| | - Aurélie Garcin
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, F-34298 Montpellier, France; (V.G.); (A.G.); (C.G.); (M.D.R.)
| | - Céline Gongora
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, F-34298 Montpellier, France; (V.G.); (A.G.); (C.G.); (M.D.R.)
| | - Maguy Del Rio
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, F-34298 Montpellier, France; (V.G.); (A.G.); (C.G.); (M.D.R.)
| | - Caroline Denevault-Sabourin
- GICC EA7501, Equipe IMT, Université de Tours, 10 Boulevard Tonnellé, F-37032 Tours, France; (I.A.M.A.); (S.L.); (C.D.-S.); (N.J.)
| | - Nicolas Joubert
- GICC EA7501, Equipe IMT, Université de Tours, 10 Boulevard Tonnellé, F-37032 Tours, France; (I.A.M.A.); (S.L.); (C.D.-S.); (N.J.)
| | - Ivan Huc
- Center for Integrated Protein Science, Department of Pharmacy, Ludwig-Maximilians-Universität, 81377 Munich, Germany; (V.C.); (I.H.)
| | - Philippe Pourquier
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, F-34298 Montpellier, France; (V.G.); (A.G.); (C.G.); (M.D.R.)
- Correspondence: ; Tel.: +33-467-613-765; Fax: +33-467-613-787
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13
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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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14
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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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15
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Lu Y, Dohno C, Nakatani K. Recognition of expanded GGGGCC hexanucleotide repeat by synthetic ligand through interhelical binding. Biochem Biophys Res Commun 2020; 531:56-61. [DOI: 10.1016/j.bbrc.2020.03.107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 02/26/2020] [Accepted: 03/19/2020] [Indexed: 12/14/2022]
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16
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Corvaglia V, Carbajo D, Prabhakaran P, Ziach K, Mandal PK, Santos VD, Legeay C, Vogel R, Parissi V, Pourquier P, Huc I. Carboxylate-functionalized foldamer inhibitors of HIV-1 integrase and Topoisomerase 1: artificial analogues of DNA mimic proteins. Nucleic Acids Res 2019; 47:5511-5521. [PMID: 31073604 PMCID: PMC6582331 DOI: 10.1093/nar/gkz352] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/21/2019] [Accepted: 04/26/2019] [Indexed: 12/15/2022] Open
Abstract
Inspired by DNA mimic proteins, we have introduced aromatic foldamers bearing phosphonate groups as synthetic mimics of the charge surface of B-DNA and competitive inhibitors of some therapeutically relevant DNA-binding enzymes: the human DNA Topoisomerase 1 (Top1) and the human HIV-1 integrase (HIV-1 IN). We now report on variants of these anionic foldamers bearing carboxylates instead of phosphonates. Several new monomers have been synthesized with protecting groups suitable for solid phase synthesis (SPS). Six hexadecaamides have been prepared using SPS. Proof of their resemblance to B-DNA was brought by the first crystal structure of one of these DNA-mimic foldamers in its polyanionic form. While some of the foldamers were found to be as active as, or even more active than, the original phosphonate oligomers, others had no activity at all or could even stimulate enzyme activity in vitro. Some foldamers were found to have differential inhibitory effects on the two enzymes. These results demonstrate a strong dependence of inhibitory activity on foldamer structure and charge distribution. They open broad avenues for the development of new classes of derivatives that could inhibit the interaction of specific proteins with their DNA target thereby influencing the cellular pathways in which they are involved.
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Affiliation(s)
- Valentina Corvaglia
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, München 81377, Germany.,Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Institut Européen de Chimie et Biologie, Pessac 33600, France
| | - Daniel Carbajo
- Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Institut Européen de Chimie et Biologie, Pessac 33600, France
| | - Panchami Prabhakaran
- Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Institut Européen de Chimie et Biologie, Pessac 33600, France
| | - Krzysztof Ziach
- Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Institut Européen de Chimie et Biologie, Pessac 33600, France
| | - Pradeep Kumar Mandal
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, München 81377, Germany.,Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Institut Européen de Chimie et Biologie, Pessac 33600, France
| | | | - Carole Legeay
- Sanofi recherche & développement, Montpellier 34184, France
| | - Rachel Vogel
- Sanofi recherche & développement, Montpellier 34184, France
| | - Vincent Parissi
- Université de Bordeaux, CNRS, Laboratoire de Microbiologie Fondamentale et Pathogénicité (UMR 5234), Bordeaux 33146, France
| | - Philippe Pourquier
- INSERM U1194, Institut de Recherche en Cancérologie de Montpellier & Université de Montpellier, Montpellier 34298, France
| | - Ivan Huc
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, München 81377, Germany.,Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), Institut Européen de Chimie et Biologie, Pessac 33600, France
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17
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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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18
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Sato S, Asamitsu S, Bando T, Sugiyama H. Orientation preferences of hairpin pyrrole-imidazole polyamides toward mCGG site. Bioorg Med Chem 2019; 27:2167-2171. [PMID: 31000407 DOI: 10.1016/j.bmc.2019.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/02/2019] [Accepted: 04/04/2019] [Indexed: 11/16/2022]
Abstract
Hairpin pyrrole-imidazole (Py-Im) polyamides are promising medium-sized molecules that bind sequence-specifically to the minor groove of B-form DNA. Here, we synthesized a series of hairpin Py-Im polyamides and explored their binding affinities and orientation preferences to methylated DNA with the mCGG target sequence. Thermal denaturation assays revealed that the five hairpin Py-Im polyamides, which were anticipated to recognize mCGG in a forward orientation, bind to nontarget DNA, GGmC, in a reverse orientation. Therefore, we designed five Py-Im polyamides that could recognize mCGG in a reverse orientation. We found that the two Py-Im polyamides containing Im/β pairs preferentially bound to mCGG in a reverse orientation. The reverse binding Py-Im polyamide successfully inhibited TET1 binding on the methylated DNA. Taken together, this study illustrated the importance of designing reverse binding Py-Im polyamides for the target sequence, mCGG, which paved the way for Py-Im polyamides that can be used with otherwise difficult to access DNA with CG sequences.
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Affiliation(s)
- Shinsuke Sato
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Sefan Asamitsu
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan.
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan; Institute for Integrated Cell-Materials Science (WPI-iCeMS), Kyoto University, Sakyo-Ku, Kyoto 606-8501, Japan.
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19
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Development of novel macrocyclic small molecules that target CTG trinucleotide repeats. Bioorg Med Chem 2019; 27:2978-2984. [PMID: 31113691 DOI: 10.1016/j.bmc.2019.05.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 05/07/2019] [Accepted: 05/13/2019] [Indexed: 11/23/2022]
Abstract
We describe the molecular design, synthesis, and investigation of a series of acridine-triaminotriazine macrocycles that selectively bind to CTG trinucleotide repeats in DNA with minimal nonspecific binding. The limited conformational flexibility enforces the stacking of the triaminotriazine and acridine units. Isothermal titration calorimetry studies and Job plot analyses revealed that the ligands bound to d(CTG) mismatched sites. The acridine and triaminotriazine units were shown to intramolecularly π-stack in aqueous solutions. Compared to a noncyclic analog, the macrocycles showed an almost 10-fold lower cytotoxicity in HeLa cells and up to 4-fold higher transcription inhibition of d(CTG·CAG)74.
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20
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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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21
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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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22
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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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23
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Obata S, Asamitsu S, Hashiya K, Bando T, Sugiyama H. G-Quadruplex Induction by the Hairpin Pyrrole-Imidazole Polyamide Dimer. Biochemistry 2017; 57:498-502. [PMID: 29236465 DOI: 10.1021/acs.biochem.7b01059] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The G-quadruplex (G4) is one type of higher-order structure of nucleic acids and is thought to play important roles in various biological events such as regulation of transcription and inhibition of DNA replication. Pyrrole-imidazole polyamides (PIPs) are programmable small molecules that can sequence-specifically bind with high affinity to the minor groove of double-stranded DNA (dsDNA). Herein, we designed head-to-head hairpin PIP dimers and their target dsDNA in a model G4-forming sequence. Using an electrophoresis mobility shift assay and transcription arrest assay, we found that PIP dimers could induce the structural change to G4 DNA from dsDNA through the recognition by one PIP dimer molecule of two duplex-binding sites flanking both ends of the G4-forming sequence. This induction ability was dependent on linker length. This is the first study to induce G4 formation using PIPs, which are known to be dsDNA binders. The results reported here suggest that selective G4 induction in native sequences may be achieved with PIP dimers by applying the same design strategy.
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Affiliation(s)
- Shunsuke Obata
- Department of Chemistry, Graduate School of Science, Kyoto University , Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Sefan Asamitsu
- 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 Sciences (WPI-iCeMS), Kyoto University , Yoshida-Ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
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24
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Guo P, Paul A, Kumar A, Farahat AA, Kumar D, Wang S, Boykin DW, Wilson WD. The Thiophene "Sigma-Hole" as a Concept for Preorganized, Specific Recognition of G⋅C Base Pairs in the DNA Minor Groove. Chemistry 2016; 22:15404-15412. [PMID: 27624927 PMCID: PMC5214980 DOI: 10.1002/chem.201603422] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Indexed: 11/10/2022]
Abstract
In spite of its importance in cell function, targeting DNA is under-represented in the design of small molecules. A barrier to progress in this area is the lack of a variety of modules that recognize G⋅C base pairs (bp) in DNA sequences. To overcome this barrier, an entirely new design concept for modules that can bind to mixed G⋅C and A⋅T sequences of DNA is reported herein. Because of their successes in biological applications, minor-groove-binding heterocyclic cations were selected as the platform for design. Binding to A⋅T sequences requires hydrogen-bond donors whereas recognition of the G-NH2 requires an acceptor. The concept that we report herein uses pre-organized N-methylbenzimidazole (N-MeBI) thiophene modules for selective binding with mixed bp DNA sequences. The interaction between the thiophene sigma hole (positive electrostatic potential) and the electron-donor nitrogen of N-MeBI preorganizes the conformation for accepting an hydrogen bond from G-NH2 . The compound-DNA interactions were evaluated with a powerful array of biophysical methods and the results show that N-MeBI-thiophene monomer compounds can strongly and selectively recognize single G⋅C bp sequences. Replacing the thiophene with other moieties significantly reduces binding affinity and specificity, as predicted by the design concept. These results show that the use of molecular features, such as sigma-holes, can lead to new approaches for small molecules in biomolecular interactions.
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Affiliation(s)
- Pu Guo
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - Arvind Kumar
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - Abdelbasset A Farahat
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Dhiraj Kumar
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - Siming Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - W David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA.
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25
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Pandian GN, Sugiyama H. Nature-Inspired Design of Smart Biomaterials Using the Chemical Biology of Nucleic Acids. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2016. [DOI: 10.1246/bcsj.20160062] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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26
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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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27
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Asamitsu S, Li Y, Bando T, Sugiyama H. Ligand-Mediated G-Quadruplex Induction in a Double-Stranded DNA Context by Cyclic Imidazole/Lysine Polyamide. Chembiochem 2016; 17:1317-22. [DOI: 10.1002/cbic.201600198] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Indexed: 01/19/2023]
Affiliation(s)
- Sefan Asamitsu
- Department of Chemistry; Graduate School of Science; Kyoto University Kitashirakawa-Oiwakecho; Sakyo-ku Kyoto 606-8502 Japan
| | - Yue Li
- Department of Chemistry; Graduate School of Science; Kyoto University Kitashirakawa-Oiwakecho; Sakyo-ku Kyoto 606-8502 Japan
| | - Toshikazu Bando
- Department of Chemistry; Graduate School of Science; Kyoto University Kitashirakawa-Oiwakecho; Sakyo-ku Kyoto 606-8502 Japan
| | - Hiroshi Sugiyama
- Department of Chemistry; Graduate School of Science; Kyoto University Kitashirakawa-Oiwakecho; Sakyo-ku Kyoto 606-8502 Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS); Kyoto University Yoshida-Ushinomiyacho; Sakyo-ku Kyoto 606-8501 Japan
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Sawatani Y, Kashiwazaki G, Chandran A, Asamitsu S, Guo C, Sato S, Hashiya K, Bando T, Sugiyama H. Sequence-specific DNA binding by long hairpin pyrrole-imidazole polyamides containing an 8-amino-3,6-dioxaoctanoic acid unit. Bioorg Med Chem 2016; 24:3603-11. [PMID: 27301681 DOI: 10.1016/j.bmc.2016.05.070] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 05/28/2016] [Accepted: 05/30/2016] [Indexed: 12/13/2022]
Abstract
With the aim of improving aqueous solubility, we designed and synthesized five N-methylpyrrole (Py)-N-methylimidazole (Im) polyamides capable of recognizing 9-bp sequences. Their DNA-binding affinities and sequence specificities were evaluated by SPR and Bind-n-Seq analyses. The design of polyamide 1 was based on a conventional model, with three consecutive Py or Im rings separated by a β-alanine to match the curvature and twist of long DNA helices. Polyamides 2 and 3 contained an 8-amino-3,6-dioxaoctanoic acid (AO) unit, which has previously only been used as a linker within linear Py-Im polyamides or between Py-Im hairpin motifs for tandem hairpin. It is demonstrated herein that AO also functions as a linker element that can extend to 2-bp in hairpin motifs. Notably, although the AO-containing unit can fail to bind the expected sequence, polyamide 4, which has two AO units facing each other in a hairpin form, successfully showed the expected motif and a KD value of 16nM was recorded. Polyamide 5, containing a β-alanine-β-alanine unit instead of the AO of polyamide 2, was synthesized for comparison. The aqueous solubilities and nuclear localization of three of the polyamides were also examined. The results suggest the possibility of applying the AO unit in the core of Py-Im polyamide compounds.
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Affiliation(s)
- Yoshito Sawatani
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawaoiwakecho, Sakyo, Kyoto 606-8502, Japan
| | - 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
| | - Chuanxin Guo
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawaoiwakecho, Sakyo, Kyoto 606-8502, Japan
| | - Shinsuke Sato
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-Ushinomiyacho, Sakyo, Kyoto 606-8501, 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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Barros SA, Chenoweth DM. Triptycene-based small molecules modulate (CAG)·(CTG) repeat junctions. Chem Sci 2015; 6:4752-4755. [PMID: 26366282 PMCID: PMC4538686 DOI: 10.1039/c5sc01595b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 05/27/2015] [Indexed: 01/19/2023] Open
Abstract
A triptycene-based scaffold is used to develop a new class of ligands for modulating the structure of junction forming trinucleotide repeat expansion sequences.
Nucleic acid three-way junctions (3WJs) play key roles in biological processes such as nucleic acid replication in addition to being implicated as dynamic transient intermediates in trinucleotide repeat sequences. Structural modulation of specific nucleic acid junctions could allow for control of biological processes and disease states at the nucleic acid level. Trinucleotide repeat expansions are associated with several neurodegenerative diseases where dynamic slippage is thought to occur during replication, forming transient 3WJ intermediates with the complementary strand. Here, we report triptycene-based molecules that bind to a d(CAG)·(CTG) repeat using a gel shift assay, fluorescence-quenching and circular dichroism.
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Affiliation(s)
- Stephanie A Barros
- Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , PA 19104-6323 , USA .
| | - David M Chenoweth
- Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , PA 19104-6323 , USA .
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