1
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Chen Y, Onizuka K, Nagatsugi F. Michael addition-activated alkylation of G-quadruplex DNA with methylamine-protected vinyl-quinazolinone derivatives. Bioorg Med Chem Lett 2024; 109:129855. [PMID: 38908766 DOI: 10.1016/j.bmcl.2024.129855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/11/2024] [Accepted: 06/19/2024] [Indexed: 06/24/2024]
Abstract
The role of G-quadruplex (G4) in cellular processes can be investigated by the covalent modification of G4-DNA using alkylating reagents. Controllable alkylating reagents activated by external stimuli can react elegantly and selectively. Herein, we report a chemical activation system that can significantly boost the reaction rate of methylamine-protected vinyl-quinazolinone (VQ) derivative for the alkylation of G4-DNA. The two screened activators can transform low-reactive VQ-NHR' to highly reactive intermediates following the Michael addition mechanism. This approach expands the toolbox of activable G4 alkylating reagents.
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Affiliation(s)
- Yutong Chen
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan; Division for the Establishment of Frontier Sciences of Organization for Advanced Studies, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan.
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2
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Ooga M, Sahayasheela VJ, Hirose Y, Sasaki D, Hashiya K, Bando T, Sugiyama H. A dual DNA-binding conjugate that selectively recognizes G-quadruplex structures. Chem Commun (Camb) 2024. [PMID: 39072583 DOI: 10.1039/d4cc01572j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
G-quadruplex (G4) structures play roles in various biological processes, but the challenge lies in specific targeting. To address this, we synthesized a conjugate capable of recognizing the G4 structure and its proximal duplex. Our conjugate can enable recognition of specific G4s in the human genome to understand and target those structures.
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Affiliation(s)
- Mitsuharu Ooga
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Vinodh J Sahayasheela
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Yuki Hirose
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Daisuke Sasaki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan.
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3
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Iachettini S, Biroccio A, Zizza P. Therapeutic Use of G4-Ligands in Cancer: State-of-the-Art and Future Perspectives. Pharmaceuticals (Basel) 2024; 17:771. [PMID: 38931438 PMCID: PMC11206494 DOI: 10.3390/ph17060771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/31/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
G-quadruplexes (G4s) are guanine-rich non-canonical secondary structures of nucleic acids that were identified in vitro almost half a century ago. Starting from the early 1980s, these structures were also observed in eukaryotic cells, first at the telomeric level and later in regulatory regions of cancer-related genes, in regulatory RNAs and within specific cell compartments such as lysosomes, mitochondria, and ribosomes. Because of the involvement of these structures in a large number of biological processes and in the pathogenesis of several diseases, including cancer, the interest in G4 targeting has exponentially increased in the last few years, and a great number of novel G4 ligands have been developed. Notably, G4 ligands represent a large family of heterogeneous molecules that can exert their functions by recognizing, binding, and stabilizing G4 structures in multiple ways. Regarding anti-cancer activity, the efficacy of G4 ligands was originally attributed to the capability of these molecules to inhibit the activity of telomerase, an enzyme that elongates telomeres and promotes endless replication in cancer cells. Thereafter, novel mechanisms through which G4 ligands exert their antitumoral activities have been defined, including the induction of DNA damage, control of gene expression, and regulation of metabolic pathways, among others. Here, we provided a perspective on the structure and function of G4 ligands with particular emphasis on their potential role as antitumoral agents. In particular, we critically examined the problems associated with the clinical translation of these molecules, trying to highlight the main aspects that should be taken into account during the phases of drug design and development. Indeed, taking advantage of the successes and failures, and the more recent technological progresses in the field, it would be possible to hypothesize the development of these molecules in the future that would represent a valid option for those cancers still missing effective therapies.
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Affiliation(s)
| | | | - Pasquale Zizza
- Translational Oncology Research Unit, IRCCS—Regina Elena National Cancer Institute, Via Elio Chianesi, 53, 00144 Roma, Italy; (S.I.); (A.B.)
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4
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Aderinto SO, John T, Onawole A, Galleh RP, Thomas JA. Iridium(III)-based minor groove binding complexes as DNA photocleavage agents. Dalton Trans 2024; 53:7282-7291. [PMID: 38466178 DOI: 10.1039/d4dt00171k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Transition metal complexes containing the qtpy ligand (2':4,4'':4',4'''-quaterpyridyl) are known to be DNA intercalators or minor groove binders. In this study, new tricationic iridium(III) complexes of qtpy are reported. Both [Ir(bpy)2(qtpy)]3+1 and [Ir(phen)2(qtpy)]3+2 display good water solubility as chloride salts. The complexes possess high-energy excited states, which are quenched in the presence of duplex DNA and even by the mononucleotides guanosine monophosphate and adenosine monophosphate. Further studies reveal that although the complexes bind to quadruplex DNA, they display a preference for duplex structures, which are bound with an order of magnitude higher affinities than their isostructural dicationic RuII-analogues. Detailed molecular dynamics simulations confirm that the complexes are groove binders through the insertion of, predominantly, the qtpy ligand into the minor groove. Photoirradiation of 1 in the presence of plasmid DNA confirms that this class of complexes can function as synthetic photonucleases by cleaving DNA.
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Affiliation(s)
- Stephen O Aderinto
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, UK.
| | - Torsten John
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Abdulmujeeb Onawole
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | | | - Jim A Thomas
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, UK.
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5
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Berner A, Das RN, Bhuma N, Golebiewska J, Abrahamsson A, Andréasson M, Chaudhari N, Doimo M, Bose PP, Chand K, Strömberg R, Wanrooij S, Chorell E. G4-Ligand-Conjugated Oligonucleotides Mediate Selective Binding and Stabilization of Individual G4 DNA Structures. J Am Chem Soc 2024; 146:6926-6935. [PMID: 38430200 PMCID: PMC10941181 DOI: 10.1021/jacs.3c14408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/03/2024]
Abstract
G-quadruplex (G4) DNA structures are prevalent secondary DNA structures implicated in fundamental cellular functions, such as replication and transcription. Furthermore, G4 structures are directly correlated to human diseases such as cancer and have been highlighted as promising therapeutic targets for their ability to regulate disease-causing genes, e.g., oncogenes. Small molecules that bind and stabilize these structures are thus valuable from a therapeutic perspective and helpful in studying the biological functions of the G4 structures. However, there are hundreds of thousands of G4 DNA motifs in the human genome, and a long-standing problem in the field is how to achieve specificity among these different G4 structures. Here, we developed a strategy to selectively target an individual G4 DNA structure. The strategy is based on a ligand that binds and stabilizes G4s without selectivity, conjugated to a guide oligonucleotide, that specifically directs the G4-Ligand-conjugated oligo (GL-O) to the single target G4 structure. By employing various biophysical and biochemical techniques, we show that the developed method enables the targeting of a unique, specific G4 structure without impacting other off-target G4 formations. Considering the vast amount of G4s in the human genome, this represents a promising strategy to study the presence and functions of individual G4s but may also hold potential as a future therapeutic modality.
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Affiliation(s)
- Andreas Berner
- Department
of Medical Biochemistry and Biophysics, Umeå University, Umeå 901 87, Sweden
| | | | - Naresh Bhuma
- Department
of Chemistry, Umeå University, Umeå 901 87, Sweden
| | | | | | - Måns Andréasson
- Department
of Chemistry, Umeå University, Umeå 901 87, Sweden
| | - Namrata Chaudhari
- Department
of Medical Biochemistry and Biophysics, Umeå University, Umeå 901 87, Sweden
| | - Mara Doimo
- Department
of Medical Biochemistry and Biophysics, Umeå University, Umeå 901 87, Sweden
| | - Partha Pratim Bose
- Department
of Biosciences and Nutrition, Karolinska
Institutet, Neo, Huddinge 141 57, Sweden
| | - Karam Chand
- Department
of Chemistry, Umeå University, Umeå 901 87, Sweden
| | - Roger Strömberg
- Department
of Biosciences and Nutrition, Karolinska
Institutet, Neo, Huddinge 141 57, Sweden
| | - Sjoerd Wanrooij
- Department
of Medical Biochemistry and Biophysics, Umeå University, Umeå 901 87, Sweden
| | - Erik Chorell
- Department
of Chemistry, Umeå University, Umeå 901 87, Sweden
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6
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Muraoka Y, Muramoto J, Yasuhara Y, Kawatake M, Sakamoto T. Near-Infrared Fluorescent Switch-On Probe for Guanine-Quadruplex Imaging with Extremely Large Stokes Shift. Anal Chem 2023; 95:17162-17165. [PMID: 37955574 DOI: 10.1021/acs.analchem.3c04318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
To visualize the guanine-quadruplex (G4) nucleic acids in cells or in biological tissues, near-infrared (NIR) fluorescent probes that can respond specifically to G4 nucleic acids are required. Herein, an NIR fluorescence switch-on probe for G4 imaging having higher selectivity and extremely large Stokes shift (ca. 220 nm) was successfully developed by the modification of our original tripodal quinone-cyanine fluorescent dye. The target binding-induced intramolecular stacking interaction of the probe might cause red shifting of the fluorescence emission. The NIR fluorescence switch-on probe developed here might contribute largely to revealing the behaviors of G4 nucleic acids not only in cells but also in biological tissues.
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Affiliation(s)
- Yuka Muraoka
- Graduate School of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Junya Muramoto
- Graduate School of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Yu Yasuhara
- Faculty of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Mayuko Kawatake
- Faculty of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Takashi Sakamoto
- Graduate School of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
- Faculty of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
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7
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Barr J, Colpaert G, Cadoni E, Madder A. Furan-based (photo)oxidation reactions and their application in nucleic acid and protein targeting. Methods 2023; 218:189-197. [PMID: 37597698 DOI: 10.1016/j.ymeth.2023.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 08/08/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023] Open
Abstract
Oligonucleotides (ODNs) find applications as diagnostic and therapeutic tools due to their unique ability to interact, thanks to Watson-Crick base pairing, with a specific DNA or RNA target strand. Although most of the tools available today rely on mere hydrogen bond formation, chemical modifications to enable covalent interstrand-crosslinking (ICL) have been reported, and are gaining a place under the spotlight as they potentially offer a series of advantages over the state of the art, including a higher potency and selectivity. This methodological paper focuses on the use of a pro-reactive furan moiety and its subsequent oxidation for applications in ODN targeting. The design of effective capture and targeting probes to ensure high ICL yields is discussed and the mechanisms underlying the (photo)chemical oxidation of furan are explained. Furthermore, examples of furan-containing DNAs designed for different applications, including DNA-DNA or DNA-RNA ICL and DNA-peptide/protein targeting, are provided. The paper highlights the advantages of using different oxidative chemical triggers, such as N-bromosuccinimide or singlet oxygen, to offer additional selectivity control over the ICL reaction.
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Affiliation(s)
- Jack Barr
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Gertjan Colpaert
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium.
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium.
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8
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De Paepe L, Cadoni E, Manicardi A, Madder A. Furan-modified PNA probes for covalent targeting and ligation of nucleic acids. Methods 2023; 218:210-223. [PMID: 37604247 DOI: 10.1016/j.ymeth.2023.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/08/2023] [Accepted: 08/16/2023] [Indexed: 08/23/2023] Open
Abstract
While natural oligonucleotides (ONs) are increasingly used as therapeutic and diagnostic tools, they still face certain challenges such as low resistance to enzymatic degradation, potential immunogenicity, and delivery issues, which can limit their applications. Peptide Nucleic Acids (PNAs) are promising alternatives due to their high affinity for DNA and RNA, the high resistance to enzymatic degradation, and the easy introduction of a wide range of potential modifications. Chemical modifications that enable the covalent targeting of specific DNA and RNA strands offer additional advantages, including enhanced potency. The current study focuses on the utilization of furan-PNAs as pro-reactive probe systems and their applications to DNA and RNA targeting. Specifically, in this methodological paper, we provide practical insights into the design, synthesis, and application of furan-containing PNA probes for achieving efficient PNA-DNA and PNA-RNA interstrand crosslinking (ICL), as well as ON-templated PNA-PNA ligation systems. Furthermore, we discuss the applications of these probes in targeting DNA secondary structures, such as G-quadruplexes and i-motifs, target pull-down assays, and on-surface detection.
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Affiliation(s)
- Lessandro De Paepe
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Alex Manicardi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, 17/A, I-43124 Parma, Italy.
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium.
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