1
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A Catalyst‐ and Solvent‐ Free Synthesis of Tetra‐Substituted Pyrroles by Multicomponent Reaction. ChemistrySelect 2023. [DOI: 10.1002/slct.202204564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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2
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Oh J, Jia T, Xu J, Chong J, Dervan PB, Wang D. RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder. Proc Natl Acad Sci U S A 2022; 119:e2114065119. [PMID: 35022237 PMCID: PMC8784135 DOI: 10.1073/pnas.2114065119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 12/07/2021] [Indexed: 02/06/2023] Open
Abstract
Elongating RNA polymerase II (Pol II) can be paused or arrested by a variety of obstacles. These obstacles include DNA lesions, DNA-binding proteins, and small molecules. Hairpin pyrrole-imidazole (Py-Im) polyamides bind to the minor groove of DNA in a sequence-specific manner and induce strong transcriptional arrest. Remarkably, this Py-Im-induced Pol II transcriptional arrest is persistent and cannot be rescued by transcription factor TFIIS. In contrast, TFIIS can effectively rescue the transcriptional arrest induced by a nucleosome barrier. The structural basis of Py-Im-induced transcriptional arrest and why TFIIS cannot rescue this arrest remain elusive. Here we determined the X-ray crystal structures of four distinct Pol II elongation complexes (Pol II ECs) in complex with hairpin Py-Im polyamides as well as of the hairpin Py-Im polyamides-dsDNA complex. We observed that the Py-Im oligomer directly interacts with RNA Pol II residues, introduces compression of the downstream DNA duplex, prevents Pol II forward translocation, and induces Pol II backtracking. These results, together with biochemical studies, provide structural insight into the molecular mechanism by which Py-Im blocks transcription. Our structural study reveals why TFIIS fails to promote Pol II bypass of Py-Im-induced transcriptional arrest.
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Affiliation(s)
- Juntaek Oh
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - Tiezheng Jia
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Jun Xu
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - Jenny Chong
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - Peter B Dervan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125;
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093;
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
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3
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Seedorf T, Kirschning A, Solga D. Natural and Synthetic Oligoarylamides: Privileged Structures for Medical Applications. Chemistry 2021; 27:7321-7339. [PMID: 33481284 PMCID: PMC8251530 DOI: 10.1002/chem.202005086] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Indexed: 12/13/2022]
Abstract
The term "privileged structure" refers to a single molecular substructure or scaffold that can serve as a starting point for high-affinity ligands for more than one receptor type. In this report, a hitherto overlooked group of privileged substructures is addressed, namely aromatic oligoamides, for which there are natural models in the form of cystobactamids, albicidin, distamycin A, netropsin, and others. The aromatic and heteroaromatic core, together with a flexible selection of substituents, form conformationally well-defined scaffolds capable of specifically binding to conformationally well-defined regions of biomacromolecules such as helices in proteins or DNA often by acting as helices mimics themselves. As such, these aromatic oligoamides have already been employed to inhibit protein-protein and nucleic acid-protein interactions. This article is the first to bring together the scattered knowledge about aromatic oligoamides in connection with biomedical applications.
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Affiliation(s)
- Tim Seedorf
- Institut für Organische Chemie und Biomolekulares Wirkstoffzentrum, (BMWZ)Leibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
| | - Andreas Kirschning
- Institut für Organische Chemie und Biomolekulares Wirkstoffzentrum, (BMWZ)Leibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
| | - Danny Solga
- Institut für Organische Chemie und Biomolekulares Wirkstoffzentrum, (BMWZ)Leibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
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4
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Koronatov AN, Afanaseva KK, Sakharov PA, Rostovskii NV, Khlebnikov AF, Novikov MS. Rh(ii)-Catalyzed denitrogenative 1-sulfonyl-1,2,3-triazole-1-alkyl-1,2,3-triazole cross-coupling as a route to 3-sulfonamido-1H-pyrroles and 1,2,3-triazol-3-ium ylides. Org Chem Front 2021. [DOI: 10.1039/d0qo01571g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The reaction of 1-alkyl-1H-1,2,3-triazoles with rhodium(ii) azavinyl carbenes, generated from 1-sulfonyl-1H-1,2,3-triazoles, was utilized to prepare 3-sulfonamido-1H-pyrroles and 1,2,3-triazol-3-ium ylides in good yields.
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Affiliation(s)
| | | | - Pavel A. Sakharov
- St Petersburg State University
- Institute of Chemistry
- St Petersburg
- Russia
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5
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Kurmis AA, Dervan PB. Sequence specific suppression of androgen receptor-DNA binding in vivo by a Py-Im polyamide. Nucleic Acids Res 2019; 47:3828-3835. [PMID: 30838415 PMCID: PMC6486638 DOI: 10.1093/nar/gkz153] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/20/2019] [Accepted: 02/22/2019] [Indexed: 12/11/2022] Open
Abstract
The crucial role of androgen receptor (AR) in prostate cancer development is well documented, and its inhibition is a mainstay of prostate cancer treatment. Here, we analyze the perturbations to the AR cistrome caused by a minor groove binding molecule that is designed to target a sequence found in a subset of androgen response elements (ARE). We find treatment with this pyrrole-imidazole (Py-Im) polyamide exhibits sequence selectivity in its repression of AR binding in vivo. Differentially changed loci are enriched for sequences resembling ARE half-sites that match the Py-Im polyamide binding preferences determined in vitro. Comparatively, permutations of the ARE half-site bearing single or double mismatches to the Py-Im polyamide binding sequence are not enriched. This study confirms that the in vivo perturbation pattern caused by a sequence specific polyamide correlates with its in vitro binding preference genome-wide in an unbiased manner.
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Affiliation(s)
- Alexis A Kurmis
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Peter B Dervan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
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6
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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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7
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Padroni G, Withers JM, Taladriz-Sender A, Reichenbach LF, Parkinson JA, Burley GA. Sequence-Selective Minor Groove Recognition of a DNA Duplex Containing Synthetic Genetic Components. J Am Chem Soc 2019; 141:9555-9563. [DOI: 10.1021/jacs.8b12444] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Giacomo Padroni
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Jamie M. Withers
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Andrea Taladriz-Sender
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Linus F. Reichenbach
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - John A. Parkinson
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Glenn A. Burley
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
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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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Peng J, Gao Y, Zhu C, Liu B, Gao Y, Hu M, Wu W, Jiang H. Synthesis of Polysubstituted 3-Amino Pyrroles via Palladium-Catalyzed Multicomponent Reaction. J Org Chem 2017; 82:3581-3588. [DOI: 10.1021/acs.joc.7b00098] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Jianwen Peng
- Key Laboratory of Functional
Molecular Engineering of Guangdong Province, School of Chemistry and
Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| | - Yang Gao
- Key Laboratory of Functional
Molecular Engineering of Guangdong Province, School of Chemistry and
Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| | - Chuanle Zhu
- Key Laboratory of Functional
Molecular Engineering of Guangdong Province, School of Chemistry and
Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| | - Bifu Liu
- Key Laboratory of Functional
Molecular Engineering of Guangdong Province, School of Chemistry and
Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| | - Yinglan Gao
- Key Laboratory of Functional
Molecular Engineering of Guangdong Province, School of Chemistry and
Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| | - Miao Hu
- Key Laboratory of Functional
Molecular Engineering of Guangdong Province, School of Chemistry and
Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| | - Wanqing Wu
- Key Laboratory of Functional
Molecular Engineering of Guangdong Province, School of Chemistry and
Chemical Engineering, South China University of Technology, Guangzhou 510640, China
| | - Huanfeng Jiang
- Key Laboratory of Functional
Molecular Engineering of Guangdong Province, School of Chemistry and
Chemical Engineering, South China University of Technology, Guangzhou 510640, China
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10
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RNA polymerase II senses obstruction in the DNA minor groove via a conserved sensor motif. Proc Natl Acad Sci U S A 2016; 113:12426-12431. [PMID: 27791148 DOI: 10.1073/pnas.1612745113] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
RNA polymerase II (pol II) encounters numerous barriers during transcription elongation, including DNA strand breaks, DNA lesions, and nucleosomes. Pyrrole-imidazole (Py-Im) polyamides bind to the minor groove of DNA with programmable sequence specificity and high affinity. Previous studies suggest that Py-Im polyamides can prevent transcription factor binding, as well as interfere with pol II transcription elongation. However, the mechanism of pol II inhibition by Py-Im polyamides is unclear. Here we investigate the mechanism of how these minor-groove binders affect pol II transcription elongation. In the presence of site-specifically bound Py-Im polyamides, we find that the pol II elongation complex becomes arrested immediately upstream of the targeted DNA sequence, and is not rescued by transcription factor IIS, which is in contrast to pol II blockage by a nucleosome barrier. Further analysis reveals that two conserved pol II residues in the Switch 1 region contribute to pol II stalling. Our study suggests this motif in pol II can sense the structural changes of the DNA minor groove and can be considered a "minor groove sensor." Prolonged interference of transcription elongation by sequence-specific minor groove binders may present opportunities to target transcription addiction for cancer therapy.
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11
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Tumor Repression of VCaP Xenografts by a Pyrrole-Imidazole Polyamide. PLoS One 2015; 10:e0143161. [PMID: 26571387 PMCID: PMC4646452 DOI: 10.1371/journal.pone.0143161] [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: 07/21/2015] [Accepted: 11/02/2015] [Indexed: 12/21/2022] Open
Abstract
Pyrrole-imidazole (Py-Im) polyamides are high affinity DNA-binding small molecules that can inhibit protein-DNA interactions. In VCaP cells, a human prostate cancer cell line overexpressing both AR and the TMPRSS2-ERG gene fusion, an androgen response element (ARE)-targeted Py-Im polyamide significantly downregulates AR driven gene expression. Polyamide exposure to VCaP cells reduced proliferation without causing DNA damage. Py-Im polyamide treatment also reduced tumor growth in a VCaP mouse xenograft model. In addition to the effects on AR regulated transcription, RNA-seq analysis revealed inhibition of topoisomerase-DNA binding as a potential mechanism that contributes to the antitumor effects of polyamides in cell culture and in xenografts. These studies support the therapeutic potential of Py-Im polyamides to target multiple aspects of transcriptional regulation in prostate cancers without genotoxic stress.
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12
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Lei X, Li L, He YP, Tang Y. Rhodium(II)-Catalyzed Formal [3 + 2] Cycloaddition of N-Sulfonyl-1,2,3-triazoles with Isoxazoles: Entry to Polysubstituted 3-Aminopyrroles. Org Lett 2015; 17:5224-7. [PMID: 26467532 DOI: 10.1021/acs.orglett.5b02570] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Xiaoqiang Lei
- College
of Chemistry, Chemical Engineering and Environmental Engineering, Liaoning Shihua University, Dandong Lu West 1, Fushun 113001, China
- Comprehensive AIDS Research Center, Department of Pharmacology & Pharmaceutical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Longbo Li
- Comprehensive AIDS Research Center, Department of Pharmacology & Pharmaceutical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yu-Peng He
- College
of Chemistry, Chemical Engineering and Environmental Engineering, Liaoning Shihua University, Dandong Lu West 1, Fushun 113001, China
| | - Yefeng Tang
- Comprehensive AIDS Research Center, Department of Pharmacology & Pharmaceutical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- Collaborative
Innovation Center for Biotherapy, State Key Laboratory of Biotherapy
and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
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13
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Wang Y, Lei X, Tang Y. Rh(ii)-catalyzed cycloadditions of 1-tosyl 1,2,3-triazoles with 2H-azirines: switchable reactivity of Rh-azavinylcarbene as [2C]- or aza-[3C]-synthon. Chem Commun (Camb) 2015; 51:4507-10. [DOI: 10.1039/c5cc00268k] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The Rh(ii)-catalyzed formal [3+2] and [3+3] cycloadditions of 1-tosyl 1,2,3-triazoles with 2H-azirines have been developed, which enable the efficient synthesis of polysubstituted 3-amino-pyrroles and 1,2-dihydropyrazines, respectively.
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Affiliation(s)
- Yuanhao Wang
- The Comprehensive AIDS Research Center and The Department of Pharmacology & Pharmaceutical Sciences
- School of Medicine
- Tsinghua University
- Beijing 100084
- P. R. China
| | - Xiaoqiang Lei
- The Comprehensive AIDS Research Center and The Department of Pharmacology & Pharmaceutical Sciences
- School of Medicine
- Tsinghua University
- Beijing 100084
- P. R. China
| | - Yefeng Tang
- The Comprehensive AIDS Research Center and The Department of Pharmacology & Pharmaceutical Sciences
- School of Medicine
- Tsinghua University
- Beijing 100084
- P. R. China
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14
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Kawamoto Y, Bando T, Kamada F, Li Y, Hashiya K, Maeshima K, Sugiyama H. Development of a new method for synthesis of tandem hairpin pyrrole-imidazole polyamide probes targeting human telomeres. J Am Chem Soc 2014; 135:16468-77. [PMID: 24083880 DOI: 10.1021/ja406737n] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Pyrrole–imidazole (PI) polyamides bind to the minor groove of DNA in a sequence-specific manner without causing denaturation of DNA. To visualize telomeres specifically, tandem hairpin PI polyamides conjugated with a fluorescent dye have been synthesized, but the study of telomeres using these PI polyamides has not been reported because of difficulties synthesizing these tandem hairpin PI polyamides. To synthesize tandem hairpin PI polyamides more easily, we have developed new PI polyamide fragments and have used them as units in Fmoc solid-phase peptide synthesis. Using this new method, we synthesized four fluorescent polyamide probes for the human telomeric repeat TTAGGG, and we examined the binding affinities and specificities of the tandem hairpin PI polyamides, the UV–vis absorption and fluorescence spectra of the fluorescent polyamide probes, and telomere staining in mouse MC12 and human HeLa cells. The polyamides synthesized using the new method successfully targeted to human and mouse telomeres under mild conditions and allow easier labeling of telomeres in the cells while maintaining the telomere structure. Using the fluorescent polyamides, we demonstrated that the telomere length at a single telomere level is related to the abundance of TRF1 protein, a shelterin complex component in the telomere.
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15
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He G, Vasilieva E, Harris GD, Koeller KJ, Bashkin JK, Dupureur CM. Binding studies of a large antiviral polyamide to a natural HPV sequence. Biochimie 2014; 102:83-91. [PMID: 24582833 DOI: 10.1016/j.biochi.2014.02.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 02/19/2014] [Indexed: 11/16/2022]
Abstract
PA1 is a large hairpin polyamide (dImPyPy-β-PyPyPy-γ-PyPy-β-PyPyPyPy-β-Ta; Py = pyrrole, Im = imidazole, β = beta alanine) that targets the sequence 5'-WWGWWWWWWW-3' (W = A or T) and is effective in eliminating HPV16 in cell culture (Edwards, T. G., Koeller, K. J., Slomczynska, U., Fok, K., Helmus, M., Bashkin, J. K., Fisher, C., Antiviral Res. 91 (2011) 177-186). Described here are its DNA binding properties toward a natural DNA, a 523 bp portion of HPV16 (2150-2672) containing three predicted perfect match sites. Strategies for obtaining binding data on large fragments using capillary electrophoresis are also described. Using an Fe EDTA conjugate of PA1, 19 affinity cleavage (AC) patterns were detected for this fragment. In many cases, there are multiple possible binding sequences (perfect, single and double mismatch sites) consistent with the AC data. Quantitative DNase I footprinting analysis indicates that perfect and most single mismatch sites bind PA1 with Kds between 0.7 and 4 nM, indicating excellent tolerance for the latter. Double mismatch sites exhibit Kds between 12 and 62 nM. A large fraction of the accessible sequence is susceptible to PA1 binding, much larger than predicted based on the literature of polyamide-DNA recognition rules.
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Affiliation(s)
- Gaofei He
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, United States
| | - Elena Vasilieva
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, United States
| | - George Davis Harris
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, United States
| | - Kevin J Koeller
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, United States
| | - James K Bashkin
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, United States.
| | - Cynthia M Dupureur
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, United States.
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16
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Addressable and unidirectional energy transfer along a DNA three-way junction programmed by pyrrole-imidazole polyamides. Sci Rep 2013; 3:1883. [PMID: 23703234 PMCID: PMC3662969 DOI: 10.1038/srep01883] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 05/10/2013] [Indexed: 11/23/2022] Open
Abstract
We describe a photonic waveguide where FRET is routed uni-directionally along a double-stranded DNA track. The efficiency of FRET is modulated by the supramolecular control of fluorophores along double-stranded DNA using fluorophore-tethered Pyrrole-Imidazole polyamides (PAs). We show that uni-directional FRET is enhanced by the complete assembly of each of the constituent parts, resulting in the selective routing of light along simple DNA duplexes as well as a three-way junction (3WJ).
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17
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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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18
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Yang F, Nickols NG, Li BC, Szablowski JO, Hamilton SR, Meier JL, Wang CM, Dervan PB. Animal toxicity of hairpin pyrrole-imidazole polyamides varies with the turn unit. J Med Chem 2013; 56:7449-57. [PMID: 24015881 PMCID: PMC3788622 DOI: 10.1021/jm401100s] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
![]()
A hairpin
pyrrole-imidazole polyamide (1) targeted
to the androgen receptor consensus half-site was found to exert antitumor
effects against prostate cancer xenografts. A previous animal study
showed that 1, which has a chiral amine at the α-position
of the γ-aminobutyric acid turn (γ-turn), did not exhibit
toxicity at doses less than 10 mg/kg. In the same study, a polyamide
with an acetamide at the β-position of the γ-turn resulted
in animal morbidity at 2.3 mg/kg. To identify structural motifs that
cause animal toxicity, we synthesized polyamides 1–4 with variations at the α- and β-positions in
the γ-turn. Weight loss, histopathology, and serum chemistry
were analyzed in mice post-treatment. While serum concentration was
similar for all four polyamides after injection, dose-limiting liver
toxicity was only observed for three polyamides. Polyamide 3, with an α-acetamide, caused no significant evidence of rodent
toxicity and retains activity against LNCaP xenografts.
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Affiliation(s)
- Fei Yang
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
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19
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Sheng J, Gan J, Huang Z. Structure-based DNA-targeting strategies with small molecule ligands for drug discovery. Med Res Rev 2013; 33:1119-73. [PMID: 23633219 DOI: 10.1002/med.21278] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nucleic acids are the molecular targets of many clinical anticancer drugs. However, compared with proteins, nucleic acids have traditionally attracted much less attention as drug targets in structure-based drug design, partially because limited structural information of nucleic acids complexed with potential drugs is available. Over the past several years, enormous progresses in nucleic acid crystallization, heavy-atom derivatization, phasing, and structural biology have been made. Many complicated nucleic acid structures have been determined, providing new insights into the molecular functions and interactions of nucleic acids, especially DNAs complexed with small molecule ligands. Thus, opportunities have been created to further discover nucleic acid-targeting drugs for disease treatments. This review focuses on the structure studies of DNAs complexed with small molecule ligands for discovering lead compounds, drug candidates, and/or therapeutics.
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Affiliation(s)
- Jia Sheng
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
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20
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Abstract
Many cancer therapeutics target DNA and exert cytotoxicity through the induction of DNA damage and inhibition of transcription. We report that a DNA minor groove binding hairpin pyrrole-imidazole (Py-Im) polyamide interferes with RNA polymerase II (RNAP2) activity in cell culture. Polyamide treatment activates p53 signaling in LNCaP prostate cancer cells without detectable DNA damage. Genome-wide mapping of RNAP2 binding shows reduction of occupancy, preferentially at transcription start sites, but occupancy at enhancer sites is unchanged. Polyamide treatment results in a time- and dose-dependent depletion of the RNAP2 large subunit RPB1 that is preventable with proteasome inhibition. This polyamide demonstrates antitumor activity in a prostate tumor xenograft model with limited host toxicity.
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21
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Abstract
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Cyclic Py-Im polyamides containing two GABA turn units
exhibit
enhanced DNA binding affinity, but extensive studies of their biological
properties have been hindered due to synthetic inaccessibility. A
facile modular approach toward cyclic polyamides has been developed
via microwave-assisted solid-phase synthesis of hairpin amino acid
oligomer intermediates followed by macrocyclization. A focused library
of cyclic polyamides 1–7 targeted
to the androgen response element (ARE) and the estrogen response element
(ERE) were synthesized in 12–17% overall yield. The Fmoc protection
strategy also allows for selective modifications on the GABA turn
units that have been shown to improve cellular uptake properties.
The DNA binding affinities of a library of cyclic polyamides were
measured by DNA thermal denaturation assays and compared to the corresponding
hairpin polyamides. Fluorescein-labeled cyclic polyamides have been
synthesized and imaged via confocal microscopy in A549 and T47D cell
lines. The IC50 values of compounds 1–7 and 9–11 were determined,
revealing remarkably varying levels of cytotoxicity.
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Affiliation(s)
- Benjamin C Li
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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22
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Meier JL, Yu AS, Korf I, Segal DJ, Dervan PB. Guiding the design of synthetic DNA-binding molecules with massively parallel sequencing. J Am Chem Soc 2012; 134:17814-22. [PMID: 23013524 PMCID: PMC3483022 DOI: 10.1021/ja308888c] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Genomic applications of DNA-binding molecules require
an unbiased
knowledge of their high affinity sites. We report the high-throughput
analysis of pyrrole-imidazole polyamide DNA-binding specificity in
a 1012-member DNA sequence library using affinity purification
coupled with massively parallel sequencing. We find that even within
this broad context, the canonical pairing rules are remarkably predictive
of polyamide DNA-binding specificity. However, this approach also
allows identification of unanticipated high affinity DNA-binding sites
in the reverse orientation for polyamides containing β/Im pairs.
These insights allow the redesign of hairpin polyamides with different
turn units capable of distinguishing 5′-WCGCGW-3′ from
5′-WGCGCW-3′. Overall, this study displays the power
of high-throughput methods to aid the optimal targeting of sequence-specific
minor groove binding molecules, an essential underpinning for biological
and nanotechnological applications.
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Affiliation(s)
- Jordan L Meier
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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23
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Bashkin JK, Aston K, Ramos JP, Koeller KJ, Nanjunda R, He G, Dupureur CM, David Wilson W. Promoter scanning of the human COX-2 gene with 8-ring polyamides: unexpected weakening of polyamide-DNA binding and selectivity by replacing an internal N-Me-pyrrole with β-alanine. Biochimie 2012; 95:271-9. [PMID: 23023196 DOI: 10.1016/j.biochi.2012.09.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 09/18/2012] [Indexed: 12/16/2022]
Abstract
Rules for polyamide-DNA recognition have proved invaluable for the design of sequence-selective DNA binding agents in cell-free systems. However, these rules are not fully transferrable to predicting activity in cells, tissues or animals, and additional refinements to our understanding of DNA recognition would help biomedical studies. Similar complexities are encountered when using internal β-alanines as polyamide building blocks in place of N-methylpyrrole; β-alanines were introduced in polyamide designs to maintain good hydrogen bonding registry with the target DNA, especially for long polyamides or those with several GC bp (P.B. Dervan, A.R. Urbach, Essays Contemp. Chem. (2001) 327-339). Thus, to clarify important subtleties of molecular recognition, we studied the effects of replacing a single pyrrole with β-alanine in 8-ring polyamides designed against the Ets-1 transcription factor. Replacement of a single internal N-methylpyrrole with β-alanine to generate a β/Im pairing in two 8-ring polyamides causes a decrease in DNA binding affinity by two orders of magnitude and decreases DNA binding selectivity, contrary to expectations based on the literature. Measurements were made by fluorescence spectroscopy, quantitative DNA footprinting and surface plasmon resonance, with these vastly different techniques showing excellent agreement. Furthermore, results were validated for a range of DNA substrates from small hairpins to long dsDNA sequences. Docking studies helped show that β-alanine does not make efficient hydrophobic contacts with the rest of the polyamide or nearby DNA, in contrast to pyrrole. These results help refine design principles and expectations for polyamide-DNA recognition.
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Affiliation(s)
- James K Bashkin
- Department of Chemistry & Biochemistry, Center for Nanoscience, University of Missouri-St. Louis, One University Blvd., St. Louis, MO 63121, USA.
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24
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Single-dose pharmacokinetic and toxicity analysis of pyrrole-imidazole polyamides in mice. Cancer Chemother Pharmacol 2012; 70:617-25. [PMID: 22907527 PMCID: PMC3456924 DOI: 10.1007/s00280-012-1954-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 08/03/2012] [Indexed: 12/22/2022]
Abstract
PURPOSE Pyrrole-imidazole (Py-Im) polyamides are programmable, sequence-specific DNA minor groove-binding ligands. Previous work in cell culture has shown that various polyamides can be used to modulate the transcriptional programs of oncogenic transcription factors. In this study, two hairpin polyamides with demonstrated activity against androgen receptor signaling in cell culture were administered to mice to characterize their pharmacokinetic properties. METHODS Py-Im polyamides were administered intravenously by tail vein injection. Plasma, urine, and fecal samples were collected over a 24-h period. Liver, kidney, and lung samples were collected postmortem. Concentrations of the administered polyamide in the plasma, excretion, and tissue samples were measured using LC/MS/MS. The biodistribution data were analyzed by both non-compartmental and compartmental pharmacokinetic models. Animal toxicity experiments were also performed by monitoring weight loss after a single subcutaneous (SC) injection of either polyamide. RESULTS The biodistribution profiles of both compounds exhibited rapid localization to the liver, kidneys, and lungs upon injection. Plasma distribution of the two compounds showed distinct differences in the rate of clearance, the volume of distribution, and the AUCs. These two compounds also have markedly different toxicities after SC injection in mice. CONCLUSIONS The variations in pharmacokinetics and toxicity in vivo stem from a minor chemical modification that is also correlated with differing potency in cell culture. The results obtained in this study could provide a structural basis for further improvement of polyamide activity both in cell culture and in animal models.
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25
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Zhou CQ, Lin YL, Chen JX, Chen WH. Synergetic DNA-Cleaving Activities of the Metal Complexes of a Polyether-Tethered Pyrrole-polyamide Dimer. Chem Biodivers 2012; 9:1125-32. [DOI: 10.1002/cbdv.201100183] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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26
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Hargrove AE, Raskatov JA, Meier JL, Montgomery DC, Dervan PB. Characterization and solubilization of pyrrole-imidazole polyamide aggregates. J Med Chem 2012; 55:5425-32. [PMID: 22607187 PMCID: PMC3375050 DOI: 10.1021/jm300380a] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
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To optimize the biological activity of pyrrole–imidazole
polyamide DNA-binding molecules, we characterized the aggregation
propensity of these compounds through dynamic light scattering and
fractional solubility analysis. Nearly all studied polyamides were
found to form measurable particles 50–500 nm in size under
biologically relevant conditions, while HPLC-based analyses revealed
solubility trends in both core sequences and peripheral substituents
that did not correlate with overall ionic charge. The solubility of
both hairpin and cyclic polyamides was increased upon addition of
carbohydrate solubilizing agents, in particular, 2-hydroxypropyl-β-cyclodextrin
(HpβCD). In mice, the use of HpβCD allowed for improved
injection conditions and subsequent investigations of the availability
of polyamides in mouse plasma to human cells. The results of these
studies will influence the further design of Py-Im polyamides and
facilitate their study in animal models.
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Affiliation(s)
- Amanda E Hargrove
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, California 91125, United States
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27
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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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28
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Krpetić Ž, Singh I, Su W, Guerrini L, Faulds K, Burley GA, Graham D. Directed Assembly of DNA-Functionalized Gold Nanoparticles Using Pyrrole–Imidazole Polyamides. J Am Chem Soc 2012; 134:8356-9. [DOI: 10.1021/ja3014924] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Željka Krpetić
- Centre for Molecular Nanometrology,
WestCHEM, Department of Pure and Applied Chemistry, The University of Strathclyde, 295 Cathedral Street, Glasgow
G1 1XL, United Kingdom
| | - Ishwar Singh
- Department of Pure and Applied
Chemistry, WestCHEM, The University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Wu Su
- Department of Chemistry, The University of Leicester, University Road, Leicester
LE1 7RH, United Kingdom
| | - Luca Guerrini
- Centre for Molecular Nanometrology,
WestCHEM, Department of Pure and Applied Chemistry, The University of Strathclyde, 295 Cathedral Street, Glasgow
G1 1XL, United Kingdom
| | - Karen Faulds
- Centre for Molecular Nanometrology,
WestCHEM, Department of Pure and Applied Chemistry, The University of Strathclyde, 295 Cathedral Street, Glasgow
G1 1XL, United Kingdom
| | - Glenn A. Burley
- Department of Pure and Applied
Chemistry, WestCHEM, The University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Duncan Graham
- Centre for Molecular Nanometrology,
WestCHEM, Department of Pure and Applied Chemistry, The University of Strathclyde, 295 Cathedral Street, Glasgow
G1 1XL, United Kingdom
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29
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Abstract
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Microwave synthesis was utilized to rapidly build Py-Im polyamides in high yields and purity using Boc-protection chemistry on Kaiser oxime resin. A representative polyamide targeting the 5′-WGWWCW-3′ (W = A or T) subset of the consensus Androgen and Glucocorticoid Response Elements was synthesized in 56% yield after 20 linear steps and HPLC purification. It was confirmed by Mosher amide derivatization of the polyamide that a chiral α-amino acid does not racemize after several additional coupling steps.
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Affiliation(s)
- James W Puckett
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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30
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Raskatov JA, Hargrove AE, So AY, Dervan PB. Pharmacokinetics of Py-Im polyamides depend on architecture: cyclic versus linear. J Am Chem Soc 2012; 134:7995-9. [PMID: 22509786 DOI: 10.1021/ja302588v] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The pharmacokinetic properties of three pyrrole-imidazole (Py-Im) polyamides of similar size and Py-Im content but different shape were studied in the mouse. Remarkably, hairpin and cyclic oligomers programmed for the same DNA sequence 5'-WGGWWW-3' displayed distinct pharmacokinetic properties. Furthermore, the hairpin 1 and cycle 2 exhibited vastly different animal toxicities. These data provide a foundation for design of DNA binding Py-Im polyamides to be tested in vivo.
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Affiliation(s)
- Jevgenij A Raskatov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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31
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Zhang Y, Sicot G, Cui X, Vogel M, Wuertzer CA, Lezon-Geyda K, Wheeler J, Harki DA, Muzikar KA, Stolper DA, Dervan PB, Perkins AS. Targeting a DNA binding motif of the EVI1 protein by a pyrrole-imidazole polyamide. Biochemistry 2011; 50:10431-41. [PMID: 22039883 PMCID: PMC3619939 DOI: 10.1021/bi200962u] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The zinc finger protein EVI1 is causally associated with acute myeloid leukemogenesis, and inhibition of its function with a small molecule therapeutic may provide effective therapy for EVI1-expressing leukemias. In this paper we describe the development of a pyrrole-imidazole polyamide to specifically block EVI1 binding to DNA. We first identify essential domains for leukemogenesis through structure-function studies on both EVI1 and the t(3;21)(q26;q22)-derived RUNX1-MDS1-EVI1 (RME) protein, which revealed that DNA binding to the cognate motif GACAAGATA via the first of two zinc finger domains (ZF1, encompassing fingers 1-7) is essential transforming activity. To inhibit DNA binding via ZF1, we synthesized a pyrrole-imidazole polyamide 1, designed to bind to a subsite within the GACAAGATA motif and thereby block EVI1 binding. DNase I footprinting and electromobility shift assays revealed a specific and high affinity interaction between polyamide 1 and the GACAAGATA motif. In an in vivo CAT reporter assay using NIH-3T3-derived cell line with a chromosome-embedded tet-inducible EVI1-VP16 as well as an EVI1-responsive reporter, polyamide 1 completely blocked EVI1-responsive reporter activity. Growth of a leukemic cell line bearing overexpressed EVI1 was also inhibited by treatment with polyamide 1, while a control cell line lacking EVI1 was not. Finally, colony formation by RME was attenuated by polyamide 1 in a serial replating assay. These studies provide evidence that a cell permeable small molecule may effectively block the activity of a leukemogenic transcription factor and provide a valuable tool to dissect critical functions of EVI1 in leukemogenesis.
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Affiliation(s)
- Yi Zhang
- Department of Pathology and Lab Medicine, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Géraldine Sicot
- Department of Pathology and Lab Medicine, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Xiaohui Cui
- Department of Pathology and Lab Medicine, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Marion Vogel
- Department of Pathology and Lab Medicine, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Charles A. Wuertzer
- Department of Pathology and Lab Medicine, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Kimberly Lezon-Geyda
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut 06510, United States
| | - John Wheeler
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut 06510, United States
| | - Daniel A. Harki
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Katy A. Muzikar
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | | | - Peter B. Dervan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Archibald S. Perkins
- Department of Pathology and Lab Medicine, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United States
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32
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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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33
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Meier JL, Montgomery DC, Dervan PB. Enhancing the cellular uptake of Py-Im polyamides through next-generation aryl turns. Nucleic Acids Res 2011; 40:2345-56. [PMID: 22080545 PMCID: PMC3300022 DOI: 10.1093/nar/gkr970] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Pyrrole–imidazole (Py–Im) hairpin polyamides are a class of programmable, sequence-specific DNA binding oligomers capable of disrupting protein–DNA interactions and modulating gene expression in living cells. Methods to control the cellular uptake and nuclear localization of these compounds are essential to their application as molecular probes or therapeutic agents. Here, we explore modifications of the hairpin γ-aminobutyric acid turn unit as a means to enhance cellular uptake and biological activity. Remarkably, introduction of a simple aryl group at the turn potentiates the biological effects of a polyamide targeting the sequence 5′-WGWWCW-3′ (W = A/T) by up to two orders of magnitude. Confocal microscopy and quantitative flow cytometry analysis suggest this enhanced potency is due to increased nuclear uptake. Finally, we explore the generality of this approach and find that aryl-turn modifications enhance the uptake of all polyamides tested, while having a variable effect on the upper limit of polyamide nuclear accumulation. Overall this provides a step forward for controlling the intracellular concentration of Py–Im polyamides that will prove valuable for future applications in which biological potency is essential.
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Affiliation(s)
- Jordan L Meier
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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34
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Wang J, Ji X, Shi J, Sun H, Jiang H, Liu H. Diastereoselective Michael reaction of chiral nickel(II) glycinate with nitroalkenes for asymmetric synthesis of β-substituted α,γ-diaminobutyric acid derivatives in water. Amino Acids 2011; 42:1685-94. [PMID: 21384130 DOI: 10.1007/s00726-011-0870-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Accepted: 02/22/2011] [Indexed: 10/18/2022]
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35
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Chenoweth DM, Dervan PB. Structural basis for cyclic Py-Im polyamide allosteric inhibition of nuclear receptor binding. J Am Chem Soc 2011; 132:14521-9. [PMID: 20812704 PMCID: PMC2954530 DOI: 10.1021/ja105068b] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
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Pyrrole-imidazole polyamides are a class of small molecules that can be programmed to bind a broad repertoire of DNA sequences, disrupt transcription factor−DNA interfaces, and modulate gene expression pathways in cell culture experiments. In this paper we describe a high-resolution X-ray crystal structure of a β-amino turn-linked eight-ring cyclic Py-Im polyamide bound to the central six base pairs of the sequence d(5′-CCAGTACTGG-3′)2, revealing significant modulation of DNA shape. We compare the DNA structural perturbations induced by DNA-binding transcripton factors, androgen receptor and glucocorticoid receptor, in the major groove to those induced by cyclic polyamide binding in the minor groove. The cyclic polyamide is an allosteric modulator that perturbs the DNA structure in such a way that nuclear receptor protein binding is no longer compatible. This allosteric perturbation of the DNA helix provides a molecular basis for disruption of transcription factor−DNA interfaces by small molecules, a minimum step in chemical control of gene networks.
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Affiliation(s)
- David M Chenoweth
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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36
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Sasada T, Sawada T, Ikeda R, Sakai N, Konakahara T. Approach to Trisubstituted 3-Aminopyrrole Derivatives by Yb(OTf)3-Catalyzed [4+1] Annulation of 2-Azadiene with Me3SiCN. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000241] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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37
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Jacobs CS, Dervan PB. Modifications at the C-terminus to improve pyrrole-imidazole polyamide activity in cell culture. J Med Chem 2009; 52:7380-8. [PMID: 19572551 DOI: 10.1021/jm900256f] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Pyrrole-imidazole (Py-Im) hairpin polyamides are a class of small molecule DNA minor groove binding compounds that have been shown to modulate endogenous gene expression in cell culture. Gene regulation by polyamides requires efficient cellular uptake and nuclear localization properties for candidate compounds. To further optimize Py-Im polyamides for enhanced potency in cell culture, a focused library of polyamides possessing various modifications at the C-terminus was synthesized and tested. Comparison of polyamide biological activity in two cell lines revealed tolerance for structural modifications and agreement in activity trends between cell lines. The use of an oxime linkage between the polyamide and an aromatic functionality on the C-terminus resulted in a approximately 20-fold increase in the potency of polyamides targeted to the androgen response element (ARE) in LNCaP cells by measuring AR-activated PSA expression.
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Affiliation(s)
- Claire S Jacobs
- Division of Chemistry and Chemical Engineering, The California Institute of Technology, 1200 E California Boulevard, Mail Code 164-30, Pasadena, California 91125, USA
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38
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Li T, Zhang D, Luo W, Lu M, Wang Z, Song Y, Wang H. Metal Cation Mediated-Capillary Electrophoresis of Nucleic Acids. Anal Chem 2009; 82:487-90. [DOI: 10.1021/ac9025708] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Tao Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center For Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road 18, Beijing 100085, China
| | - Dapeng Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center For Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road 18, Beijing 100085, China
| | - Wenru Luo
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center For Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road 18, Beijing 100085, China
| | - Meiling Lu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center For Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road 18, Beijing 100085, China
| | - Zhixin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center For Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road 18, Beijing 100085, China
| | - Yuling Song
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center For Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road 18, Beijing 100085, China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center For Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqing Road 18, Beijing 100085, China
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39
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Chenoweth DM, Harki DA, Dervan PB. Oligomerization route to Py-Im polyamide macrocycles. Org Lett 2009; 11:3590-3. [PMID: 19627138 DOI: 10.1021/ol901311m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyclic eight-ring pyrrole-imidazole polyamides are sequence-specific DNA-binding small molecules that are cell permeable and can regulate endogenous gene expression. Syntheses of cyclic polyamides have been achieved by solid-phase and solution-phase methods. A rapid solution-phase oligomerization approach to eight-ring symmetrical cyclic polyamides yields 12- and 16-membered macrocycles as well. A preference for DNA binding by the 8- and 16-membered oligomers was observed over the 12-ring macrocycle, which we attributed to a conformational constraint not present in the smaller and larger systems.
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Affiliation(s)
- David M Chenoweth
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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40
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Farkas ME, Li BC, Dose C, Dervan PB. DNA sequence selectivity of hairpin polyamide turn units. Bioorg Med Chem Lett 2009; 19:3919-23. [PMID: 19349175 PMCID: PMC3062503 DOI: 10.1016/j.bmcl.2009.03.072] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Revised: 03/13/2009] [Accepted: 03/18/2009] [Indexed: 10/21/2022]
Abstract
A class of hairpin polyamides linked by 3,4-diaminobutyric acid, resulting in a beta-amine residue at the turn unit, showed improved binding affinities relative to their alpha-amino-gamma-turn analogs for particular sequences. We incorporated beta-amino-gamma-turns in six-ring polyamides and determined whether there are any sequence preferences under the turn unit by quantitative footprinting titrations. Although there was an energetic penalty for G.C and C.G base pairs, we found little preference for T.A over A.T at the beta-amino-gamma-turn position. Fluorine and hydroxyl substituted alpha-amino-gamma-turns were synthesized for comparison. Their binding affinities and specificities in the context of six-ring polyamides demonstrated overall diminished affinity and no additional specificity at the turn position. We anticipate that this study will be a baseline for further investigation of the turn subunit as a recognition element for the DNA minor groove.
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Affiliation(s)
- Michelle E. Farkas
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 E California Blvd, Pasadena, CA 91125, United States
| | - Benjamin C. Li
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 E California Blvd, Pasadena, CA 91125, United States
| | - Christian Dose
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 E California Blvd, Pasadena, CA 91125, United States
| | - Peter B. Dervan
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 E California Blvd, Pasadena, CA 91125, United States
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Chenoweth DM, Harki DA, Phillips JW, Dose C, Dervan PB. Cyclic pyrrole-imidazole polyamides targeted to the androgen response element. J Am Chem Soc 2009; 131:7182-8. [PMID: 19413319 DOI: 10.1021/ja901309z] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hairpin pyrrole-imidazole (Py-Im) polyamides are a class of cell-permeable DNA-binding small molecules that can disrupt transcription factor-DNA binding and regulate endogenous gene expression. The covalent linkage of antiparallel Py-Im ring pairs with an gamma-amino acid turn unit affords the classical hairpin Py-Im polyamide structure. Closing the hairpin with a second turn unit yields a cyclic polyamide, a lesser-studied architecture mainly attributable to synthetic inaccessibility. We have applied our methodology for solution-phase polyamide synthesis to cyclic polyamides with an improved high-yield cyclization step. Cyclic 8-ring Py-Im polyamides 1-3 target the DNA sequence 5'-WGWWCW-3', which corresponds to the androgen response element (ARE) bound by the androgen receptor transcription factor to modulate gene expression. We find that cyclic Py-Im polyamides 1-3 bind DNA with exceptionally high affinities and regulate the expression of AR target genes in cell culture studies, from which we infer that the cycle is cell permeable.
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Affiliation(s)
- David M Chenoweth
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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42
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Chenoweth DM, Harki DA, Dervan PB. Solution-phase synthesis of pyrrole-imidazole polyamides. J Am Chem Soc 2009; 131:7175-81. [PMID: 19413320 DOI: 10.1021/ja901307m] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pyrrole-imidazole polyamides are DNA-binding molecules that are programmable for a large repertoire of DNA sequences. Typical syntheses of this class of heterocyclic oligomers rely on solid-phase methods. Solid-phase methodologies offer rapid assembly on a micromole scale sufficient for biophysical characterizations and cell culture studies. In order to produce gram-scale quantities necessary for efficacy studies in animals, polyamides must be readily synthesized in solution. An 8-ring hairpin polyamide 1, which targets the DNA sequence 5'-WGWWCW-3', was chosen for our synthesis studies as this oligomer exhibits androgen receptor antagonism in cell culture models of prostate cancer. A convergent solution-phase synthesis of 1 from a small set of commercially available building blocks is presented which highlights principles for preparing gram quantities of pyrrole-imidazole oligomers with minimal chromatography.
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Affiliation(s)
- David M Chenoweth
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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Spitzer GM, Wellenzohn B, Markt P, Kirchmair J, Langer T, Liedl KR. Hydrogen-bonding patterns of minor groove-binder-DNA complexes reveal criteria for discovery of new scaffolds. J Chem Inf Model 2009; 49:1063-9. [PMID: 19275189 DOI: 10.1021/ci800455f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Minor groove-binding ligands are able to control gene expression and are of great interest for therapeutic applications. We extracted hydrogen-bonding geometries from all available structures of minor groove-binder-DNA complexes of two noncovalent binding modes, namely 1:1 (including hairpin and cyclic ligands) and 2:1 ligand/DNA binding. Positions of the ligand atoms involved in hydrogen bonding deviate from idealized hydrogen bond geometries and do not exploit the possibilities indicated by water molecules. Therefore, we suggest the inclusion of shape-based descriptors rather than hydrogen-bond patterns in virtual screening protocols for the identification of innovative minor groove-binding scaffolds.
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Affiliation(s)
- Gudrun M Spitzer
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria.
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Balasubramanian S, Neidle S. G-quadruplex nucleic acids as therapeutic targets. Curr Opin Chem Biol 2009; 13:345-53. [PMID: 19515602 DOI: 10.1016/j.cbpa.2009.04.637] [Citation(s) in RCA: 465] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Revised: 04/28/2009] [Accepted: 04/30/2009] [Indexed: 11/30/2022]
Abstract
Nucleic acid sequences containing several short runs of guanine nucleotides can form complex higher order structures, termed quadruplexes. Their occurrence has been most extensively characterised at the telomeric ends of eukaryotic chromosomes, whose DNA comprises such sequences, and where the extreme 3' ends are single-stranded. This enables relatively facile formation of quadruplex arrangements under the influence of a quadruplex-selective small molecule to compete effectively with telomeric protein-DNA interactions. Occurrences of quadruplexes within the human and other genomes have been mapped by bioinformatics surveys, which have revealed over-representations in promoter regions, especially of genes involved in replication, such as oncogenes, as well as in 5'UTR regions. The highly distinctive nature of quadruplex topologies suggests that they can act as novel therapeutic targets, for example in the selective inhibition of transcription of a given oncogene, using designed small molecules to stabilise a particular quadruplex. This offers the prospect of an alternative to, for example, direct kinase targeting with small molecules, without the attendant issues of active-site resistance. We survey here the basis of these approaches, together with current progress, and discuss the mechanistic issues posed by quadruplex targeting.
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Spitzer GM, Fuchs JE, Markt P, Kirchmair J, Wellenzohn B, Langer T, Liedl KR. Sequence-Specific Positions of Water Molecules at the Interface between DNA and Minor Groove Binders. Chemphyschem 2008; 9:2766-71. [DOI: 10.1002/cphc.200800647] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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