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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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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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Zhou H, Gao J, Chen Z, Duan S, Li C, Qiao R. Double-strand cleavage of DNA by a polyamide-phenazine-di-N-oxide conjugate. Bioorg Med Chem Lett 2017; 28:284-288. [PMID: 29292228 DOI: 10.1016/j.bmcl.2017.12.058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/09/2017] [Accepted: 12/23/2017] [Indexed: 11/15/2022]
Abstract
Phenazine and its derivatives have been widely applied as nucleic acid cleavage agents due to active oxygen activating the C-H bond of the substrate. However, diffusion of oxygen radicals limits their potential applications in the DNA-targeted metal-free drug. Introduction of groove binder moiety such as polyamide enhanced the regional stability of radical molecules and reduced cytotoxicity of the drugs. In this work, we described the design and synthesis of a polyamide-modified phenazine-di-N-oxide as a DNA double-strand cleavage agent. The gel assays showed the hybrid conjugates can effectively break DNA double strands in a non-random manner under physiological conditions. The probable binding mode to DNA was investigated by sufficient spectral experiments, revealing weak interaction between hybrid ligand and nucleic acid molecules. The results of our study have implications on the design of groove-binding hybrid molecules as new artificial nucleases and may provide a strategy for developing efficient and safe DNA cleavage reagents.
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Affiliation(s)
- Hang Zhou
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Juanhong Gao
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Zhaohang Chen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Shan Duan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Chao Li
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China.
| | - Renzhong Qiao
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China; State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences, Peking University Health Sciences Center, Beijing 100083, PR China.
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Fallows AJ, Singh I, Dondi R, Cullis PM, Burley GA. Highly efficient synthesis of DNA-binding polyamides using a convergent fragment-based approach. Org Lett 2014; 16:4654-7. [PMID: 25162625 DOI: 10.1021/ol502203y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Two advances in the synthesis of hairpin pyrrole-imidazole polyamides (PAs) are described. First, the application of a convergent synthetic strategy is shown, involving the Boc-based solid phase synthesis of a C-terminal fragment and the solution phase synthesis of the N-terminal fragment. Second a new hybrid resin is developed that allows for the preparation of hairpin PAs lacking a C-terminal β-alanine tail. Both methods are compatible with a range of coupling reagents and provide a facile, modular route to prepare PA libraries in high yield and crude purity.
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Affiliation(s)
- Andrew J Fallows
- Department of Chemistry, University of Leicester , University Road, Leicester, LE1 7RH, U.K
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Boutorine AS, Novopashina DS, Krasheninina OA, Nozeret K, Venyaminova AG. Fluorescent probes for nucleic Acid visualization in fixed and live cells. Molecules 2013; 18:15357-97. [PMID: 24335616 PMCID: PMC6270009 DOI: 10.3390/molecules181215357] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/20/2013] [Accepted: 12/05/2013] [Indexed: 12/13/2022] Open
Abstract
This review analyses the literature concerning non-fluorescent and fluorescent probes for nucleic acid imaging in fixed and living cells from the point of view of their suitability for imaging intracellular native RNA and DNA. Attention is mainly paid to fluorescent probes for fluorescence microscopy imaging. Requirements for the target-binding part and the fluorophore making up the probe are formulated. In the case of native double-stranded DNA, structure-specific and sequence-specific probes are discussed. Among the latest, three classes of dsDNA-targeting molecules are described: (i) sequence-specific peptides and proteins; (ii) triplex-forming oligonucleotides and (iii) polyamide oligo(N-methylpyrrole/N-methylimidazole) minor groove binders. Polyamides seem to be the most promising targeting agents for fluorescent probe design, however, some technical problems remain to be solved, such as the relatively low sequence specificity and the high background fluorescence inside the cells. Several examples of fluorescent probe applications for DNA imaging in fixed and living cells are cited. In the case of intracellular RNA, only modified oligonucleotides can provide such sequence-specific imaging. Several approaches for designing fluorescent probes are considered: linear fluorescent probes based on modified oligonucleotide analogs, molecular beacons, binary fluorescent probes and template-directed reactions with fluorescence probe formation, FRET donor-acceptor pairs, pyrene excimers, aptamers and others. The suitability of all these methods for living cell applications is discussed.
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Affiliation(s)
- Alexandre S. Boutorine
- Muséum National d’Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France; E-Mail:
| | - Darya S. Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
| | - Olga A. Krasheninina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova Str., 2, Novosibirsk 630090, Russia
| | - Karine Nozeret
- Muséum National d’Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France; E-Mail:
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
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Ram RN, Soni VK, Gupta DK. Organocatalytic selective benzoylation of alcohols with trichloromethyl phenyl ketone: inverse selectivity in benzoylation of alcohols containing phenol or aromatic amine functionality. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.08.051] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Ghosh S, Usharani D, Paul A, De S, Jemmis ED, Bhattacharya S. Design, Synthesis, and DNA Binding Properties of Photoisomerizable Azobenzene−Distamycin Conjugates: An Experimental and Computational Study. Bioconjug Chem 2008; 19:2332-45. [DOI: 10.1021/bc800130u] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sumana Ghosh
- Department of Organic Chemistry and Department of Inorganic and Physical Chemistry, Indian Institute of Science, and Chemical Biology Unit, Jawaharlal Nehru Centre of Advanced Scientific Research, Bangalore 560 012, India
| | - Dandamudi Usharani
- Department of Organic Chemistry and Department of Inorganic and Physical Chemistry, Indian Institute of Science, and Chemical Biology Unit, Jawaharlal Nehru Centre of Advanced Scientific Research, Bangalore 560 012, India
| | - Ananya Paul
- Department of Organic Chemistry and Department of Inorganic and Physical Chemistry, Indian Institute of Science, and Chemical Biology Unit, Jawaharlal Nehru Centre of Advanced Scientific Research, Bangalore 560 012, India
| | - Susmita De
- Department of Organic Chemistry and Department of Inorganic and Physical Chemistry, Indian Institute of Science, and Chemical Biology Unit, Jawaharlal Nehru Centre of Advanced Scientific Research, Bangalore 560 012, India
| | - Eluvathingal D. Jemmis
- Department of Organic Chemistry and Department of Inorganic and Physical Chemistry, Indian Institute of Science, and Chemical Biology Unit, Jawaharlal Nehru Centre of Advanced Scientific Research, Bangalore 560 012, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry and Department of Inorganic and Physical Chemistry, Indian Institute of Science, and Chemical Biology Unit, Jawaharlal Nehru Centre of Advanced Scientific Research, Bangalore 560 012, India
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Brown T, Mackay H, Turlington M, Sutterfield A, Smith T, Sielaff A, Westrate L, Bruce C, Kluza J, O'Hare C, Nguyen B, Wilson WD, Hartley JA, Lee M. Modifying the N-terminus of polyamides: PyImPyIm has improved sequence specificity over f-ImPyIm. Bioorg Med Chem 2008; 16:5266-76. [PMID: 18353654 DOI: 10.1016/j.bmc.2008.03.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2008] [Accepted: 03/03/2008] [Indexed: 11/29/2022]
Abstract
Seven N-terminus modified derivatives of a previously published minor-groove binding polyamide (f-ImPyIm, 1) were synthesized and the biochemical and biophysical chemistry evaluated. These compounds were synthesized with the aim of attaining a higher level of sequence selectivity over f-ImPyIm (1), a previously published strong minor-groove binder. Two compounds possessing a furan or a benzofuran moiety at the N-terminus showed a footprint of 0.5microM at the cognate ACGCGT site (determined by DNase I footprinting); however, the specificity of these compounds was not improved. In contrast, PyImPyIm (4) produced a footprint of 0.5microM but showed a superior specificity using the same technique. When evaluated by thermal melting experiments and circular dichroism using ACGCGT and the non-cognate AAATTT sequence, all compounds were shown to bind in the minor-groove of DNA and stabilize the cognate sequence much better than the non-cognate (except for the non-amido-compound that did not bind either sequence, as expected). PyImPyIm (4) was interesting as the DeltaT(m) for this compound was only 4 degrees C but the footprint was very selective. No binding was observed for this compound with a third DNA (non-cognate, ACCGGT). ITC studies on compound 4 showed exothermic binding with ACGCGT and no heat change was observed for titrating the compound to the other two DNA sequences. The heat capacity (DeltaC(p)) of the PIPI/ACGCGT complex calculated from the hydrophobic interactions and SASA calculations was comparable to the experimental value obtained from ITC (-146calmol(-1)K(-1)). SPR results provided confirmation of the sequence specificity of PyImPyIm (4), with a K(eq) value determined to be 7.1x10(6) M(-1) for the cognate sequence and no observable binding to AAATTT and ACCGGT. Molecular dynamic simulations affirmed that PyImPyIm (4) binds as a dimer in an overlapped conformation, and it fits snugly in the minor-groove of the ACGCGT oligonucleotide. PyImPyIm (4) is an especially interesting molecule, because although the binding affinity is slightly reduced, the specificity with respect to f-ImPyIm (1) is significantly improved.
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Affiliation(s)
- Toni Brown
- Department of Chemistry, Furman University, Greenville, SC 29613, USA
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Hsu CF, Phillips JW, Trauger JW, Farkas ME, Belitsky JM, Heckel A, Olenyuk BZ, Puckett JW, Wang CCC, Dervan PB. Completion of a Programmable DNA-Binding Small Molecule Library. Tetrahedron 2007; 63:6146-6151. [PMID: 18596841 DOI: 10.1016/j.tet.2007.03.041] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Hairpin pyrrole-imidazole (Py-Im) polyamides are programmable oligomers that bind the DNA minor groove in a sequence-specific manner with affinities comparable to those of natural DNA-binding proteins. These cell-permeable small molecules have been shown to enter the nuclei of live cells and downregulate endogenous gene expression. We complete here a library of 27 hairpin Py-Im polyamides which bind 7-base-pair sequences of the general form 5'-WWGNNNW-3' (where W = A or T, N = W, G, or C). Their equilibrium association constants (K(a)) range from K(a) = 1×10(8) M(-1) to 4×10(10) M(-1) with good sequence specificity. A table of binding affinities and sequence contexts for this completed 27-member library has been assembled for the benefit of the chemical biology community interested in molecular control of transcription.
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Affiliation(s)
- Carey F Hsu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
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Edelson BS, Best TP, Olenyuk B, Nickols NG, Doss RM, Foister S, Heckel A, Dervan PB. Influence of structural variation on nuclear localization of DNA-binding polyamide-fluorophore conjugates. Nucleic Acids Res 2004; 32:2802-18. [PMID: 15155849 PMCID: PMC419610 DOI: 10.1093/nar/gkh609] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2004] [Revised: 04/22/2004] [Accepted: 04/22/2004] [Indexed: 11/14/2022] Open
Abstract
A pivotal step forward in chemical approaches to controlling gene expression is the development of sequence-specific DNA-binding molecules that can enter live cells and traffic to nuclei unaided. DNA-binding polyamides are a class of programmable, sequence-specific small molecules that have been shown to influence a wide variety of protein-DNA interactions. We have synthesized over 100 polyamide-fluorophore conjugates and assayed their nuclear uptake profiles in 13 mammalian cell lines. The compiled dataset, comprising 1300 entries, establishes a benchmark for the nuclear localization of polyamide-dye conjugates. Compounds in this series were chosen to provide systematic variation in several structural variables, including dye composition and placement, molecular weight, charge, ordering of the aromatic and aliphatic amino-acid building blocks and overall shape. Nuclear uptake does not appear to be correlated with polyamide molecular weight or with the number of imidazole residues, although the positions of imidazole residues affect nuclear access properties significantly. Generally negative determinants for nuclear access include the presence of a beta-Ala-tail residue and the lack of a cationic alkyl amine moiety, whereas the presence of an acetylated 2,4-diaminobutyric acid-turn is a positive factor for nuclear localization. We discuss implications of these data on the design of polyamide-dye conjugates for use in biological systems.
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Affiliation(s)
- Benjamin S Edelson
- Division of Chemistry and Chemical Engineering and The Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
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Best TP, Edelson BS, Nickols NG, Dervan PB. Nuclear localization of pyrrole-imidazole polyamide-fluorescein conjugates in cell culture. Proc Natl Acad Sci U S A 2003; 100:12063-8. [PMID: 14519850 PMCID: PMC218713 DOI: 10.1073/pnas.2035074100] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A series of hairpin pyrrole-imidazole polyamide-fluorescein conjugates were synthesized and assayed for cellular localization. Thirteen cell lines, representing 11 human cancers, one human transformed kidney cell line, and one murine leukemia cell line, were treated with 5 microM polyamide-fluorescein conjugates for 10-14 h, then imaged by confocal laser scanning microscopy. A conjugate containing a beta-alanine residue at the C terminus of the polyamide moiety showed no nuclear localization, whereas an analogous compound lacking the beta-alanine residue was strongly localized in the nuclei of all cell lines tested. The localization profiles of several other conjugates suggest that pyrrole-imidazole sequence and content, dye choice and position, linker composition, and molecular weight are determinants of nuclear localization. The attachment of fluorescein to the C terminus of a hairpin polyamide results in an approximately 10-fold reduction in DNA-binding affinity, with no loss of binding specificity with reference to mismatch binding sites.
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Affiliation(s)
- Timothy P Best
- Division of Chemistry and Chemical Engineering and The Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
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Abstract
Many diseases, such as cancer, are related to aberrant gene expression. Regulating transcription by chemical methods could be important in human medicine. Minor groove-binding polyamides offer one chemical approach to DNA recognition.
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Affiliation(s)
- Peter B Dervan
- Division of Chemistry and Chemical Engineering, and Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA.
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