1
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Sviben I, Glavaš M, Erben A, Bachelart T, Pavlović Saftić D, Piantanida I, Basarić N. Dipeptides Containing Pyrene and Modified Photochemically Reactive Tyrosine: Noncovalent and Covalent Binding to Polynucleotides. Molecules 2023; 28:7533. [PMID: 38005255 PMCID: PMC10672942 DOI: 10.3390/molecules28227533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Dipeptides 1 and 2 were synthesized from unnatural amino acids containing pyrene as a fluorescent label and polynucleotide binding unit, and modified tyrosine as a photochemically reactive unit. Photophysical properties of the peptides were investigated by steady-state and time-resolved fluorescence. Both peptides are fluorescent (Φf = 0.3-0.4) and do not show a tendency to form pyrene excimers in the concentration range < 10-5 M, which is important for their application in the fluorescent labeling of polynucleotides. Furthermore, both peptides are photochemically reactive and undergo deamination delivering quinone methides (QMs) (ΦR = 0.01-0.02), as indicated from the preparative photomethanolysis study of the corresponding N-Boc protected derivatives 7 and 8. Both peptides form stable complexes with polynucleotides (log Ka > 6) by noncovalent interactions and similar affinities, binding to minor grooves, preferably to the AT reach regions. Peptide 2 with a longer spacer between the fluorophore and the photo-activable unit undergoes a more efficient deamination reaction, based on the comparison with the N-Boc protected derivatives. Upon light excitation of the complex 2·oligoAT10, the photo-generation of QM initiates the alkylation, which results in the fluorescent labeling of the oligonucleotide. This study demonstrated, as a proof of principle, that small molecules can combine dual forms of fluorescent labeling of polynucleotides, whereby initial addition of the dye rapidly forms a reversible high-affinity noncovalent complex with ds-DNA/RNA, which can be, upon irradiation by light, converted to the irreversible (covalent) form. Such a dual labeling ability of a dye could have many applications in biomedicinal sciences.
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Affiliation(s)
| | | | | | | | | | - Ivo Piantanida
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (I.S.); (M.G.); (A.E.); (T.B.); (D.P.S.)
| | - Nikola Basarić
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (I.S.); (M.G.); (A.E.); (T.B.); (D.P.S.)
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2
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Nagatsugi F, Onizuka K. Selective Chemical Modification to the Higher-Order Structures of Nucleic Acids. CHEM REC 2023; 23:e202200194. [PMID: 36111635 DOI: 10.1002/tcr.202200194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/31/2022] [Indexed: 11/06/2022]
Abstract
DNA and RNA can adopt a variety of stable higher-order structural motifs, including G-quadruplex (G4 s), mismatches, and bulges. Many of these secondary structures are closely related to the regulation of gene expression. Therefore, the higher-order structure of nucleic acids is one of the candidate therapeutic targets, and the development of binding molecules targeting the higher-order structure of nucleic acids has been pursued vigorously. Furthermore, as one of the methodologies for detecting the higher-order structures of these nucleic acids, developing techniques for the selective chemical modification of the higher-order structures of nucleic acids is also underway. In this personal account, we focus on the following higher-order structures of nucleic acids, double-stranded DNA containing the abasic site, T-T/U-U mismatch structure, and G-quadruplex structure, and describe the development of molecules that bind to and chemically modify these structures.
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Affiliation(s)
- 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
| | - 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
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3
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Chen Y, Onizuka K, Hazemi ME, Nagatsugi F. Reactivity Modulation of Reactive OFF–ON Type G-Quadruplex Alkylating Agents. Bioconjug Chem 2022; 33:2097-2102. [DOI: 10.1021/acs.bioconjchem.2c00458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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
| | - Madoka E. Hazemi
- 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
| | - 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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4
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Photodehydration mechanisms of quinone methide formation from 2-naphthol derivatives. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2022.114171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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5
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Lena A, Benassi A, Stasi M, Saint‐Pierre C, Freccero M, Gasparutto D, Bombard S, Doria F, Verga D. Photoactivatable V-Shaped Bifunctional Quinone Methide Precursors as a New Class of Selective G-quadruplex Alkylating Agents. Chemistry 2022; 28:e202200734. [PMID: 35441438 PMCID: PMC9322314 DOI: 10.1002/chem.202200734] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Indexed: 12/22/2022]
Abstract
Combining the selectivity of G-quadruplex (G4) ligands with the spatial and temporal control of photochemistry is an emerging strategy to elucidate the biological relevance of these structures. In this work, we developed six novel V-shaped G4 ligands that can, upon irradiation, form stable covalent adducts with G4 structures via the reactive intermediate, quinone methide (QM). We thoroughly investigated the photochemical properties of the ligands and their ability to generate QMs. Subsequently, we analyzed their specificity for various topologies of G4 and discovered a preferential binding towards the human telomeric sequence. Finally, we tested the ligand ability to act as photochemical alkylating agents, identifying the covalent adducts with G4 structures. This work introduces a novel molecular tool in the chemical biology toolkit for G4s.
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Affiliation(s)
- Alberto Lena
- Department of ChemistryUniversity of PaviaViale Taramelli 1027100PaviaItaly
| | - Alessandra Benassi
- Department of ChemistryUniversity of PaviaViale Taramelli 1027100PaviaItaly
| | - Michele Stasi
- Department of ChemistryUniversity of PaviaViale Taramelli 1027100PaviaItaly
- Present Address: Department of ChemistryTechnical University of MunichLichtenbergstraße 485748GarchingGermany
| | | | - Mauro Freccero
- Department of ChemistryUniversity of PaviaViale Taramelli 1027100PaviaItaly
| | - Didier Gasparutto
- University Grenoble AlpesCEACNRSIRIGSyMMES-UMR581938054GrenobleFrance
| | - Sophie Bombard
- CNRS UMR9187INSERM U1196Institut CuriePSL Research University91405OrsayFrance
- CNRS UMR9187INSERM U1196Université Paris-Saclay91405OrsayFrance
| | - Filippo Doria
- Department of ChemistryUniversity of PaviaViale Taramelli 1027100PaviaItaly
| | - Daniela Verga
- CNRS UMR9187INSERM U1196Institut CuriePSL Research University91405OrsayFrance
- CNRS UMR9187INSERM U1196Université Paris-Saclay91405OrsayFrance
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6
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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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7
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Ribaudo G, Ongaro A, Oselladore E, Memo M, Gianoncelli A. Combining Electrospray Mass Spectrometry (ESI-MS) and Computational Techniques in the Assessment of G-Quadruplex Ligands: A Hybrid Approach to Optimize Hit Discovery. J Med Chem 2021; 64:13174-13190. [PMID: 34510895 PMCID: PMC8474113 DOI: 10.1021/acs.jmedchem.1c00962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
![]()
Guanine-rich sequences
forming G-quadruplexes (GQs) are present
in several genomes, ranging from viral to human. Given their peculiar
localization, the induction of GQ formation or GQ stabilization with
small molecules represents a strategy for interfering with crucial
biological functions. Investigating the recognition event at the molecular
level, with the aim of fully understanding the triggered pharmacological
effects, is challenging. Native electrospray ionization mass spectrometry
(ESI-MS) is being optimized to study these noncovalent assemblies.
Quantitative parameters retrieved from ESI-MS studies, such as binding
affinity, the equilibrium binding constant, and sequence selectivity,
will be overviewed. Computational experiments supporting the ESI-MS
investigation and boosting its efficiency in the search for GQ ligands
will also be discussed with practical examples. The combination of
ESI-MS and in silico techniques in a hybrid high-throughput-screening
workflow represents a valuable tool for the medicinal chemist, providing
data on the quantitative and structural aspects of ligand–GQ
interactions.
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Affiliation(s)
- Giovanni Ribaudo
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Alberto Ongaro
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Erika Oselladore
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Maurizio Memo
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Alessandra Gianoncelli
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
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8
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Erben A, Sviben I, Mihaljević B, Piantanida I, Basarić N. Non-Covalent Binding of Tripeptides-Containing Tryptophan to Polynucleotides and Photochemical Deamination of Modified Tyrosine to Quinone Methide Leading to Covalent Attachment. Molecules 2021; 26:molecules26144315. [PMID: 34299591 PMCID: PMC8306964 DOI: 10.3390/molecules26144315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 12/01/2022] Open
Abstract
A series of tripeptides TrpTrpPhe (1), TrpTrpTyr (2), and TrpTrpTyr[CH2N(CH3)2] (3) were synthesized, and their photophysical properties and non-covalent binding to polynucleotides were investigated. Fluorescent Trp residues (quantum yield in aqueous solvent ΦF = 0.03–0.06), allowed for the fluorometric study of non-covalent binding to DNA and RNA. Moreover, high and similar affinities of 2×HCl and 3×HCl to all studied double stranded (ds)-polynucleotides were found (logKa = 6.0–6.8). However, the fluorescence spectral responses were strongly dependent on base pair composition: the GC-containing polynucleotides efficiently quenched Trp emission, at variance to AT- or AU-polynucleotides, which induced bisignate response. Namely, addition of AT(U) polynucleotides at excess over studied peptide induced the quenching (attributed to aggregation in the grooves of polynucleotides), whereas at excess of DNA/RNA over peptide the fluorescence increase of Trp was observed. The thermal denaturation and circular dichroism (CD) experiments supported peptides binding within the grooves of polynucleotides. The photogenerated quinone methide (QM) reacts with nucleophiles giving adducts, as demonstrated by the photomethanolysis (quantum yield ΦR = 0.11–0.13). Furthermore, we have demonstrated photoalkylation of AT oligonucleotides by QM, at variance to previous reports describing the highest reactivity of QMs with the GC reach regions of polynucleotides. Our investigations show a proof of principle that QM precursor can be imbedded into a peptide and used as a photochemical switch to enable alkylation of polynucleotides, enabling further applications in chemistry and biology.
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Affiliation(s)
- Antonija Erben
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia; (A.E.); (I.S.); (I.P.)
| | - Igor Sviben
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia; (A.E.); (I.S.); (I.P.)
| | - Branka Mihaljević
- Department of Material Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia;
| | - Ivo Piantanida
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia; (A.E.); (I.S.); (I.P.)
| | - Nikola Basarić
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia; (A.E.); (I.S.); (I.P.)
- Correspondence:
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9
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Photochemical Reactivity of Naphthol-Naphthalimide Conjugates and Their Biological Activity. Molecules 2021; 26:molecules26113355. [PMID: 34199541 PMCID: PMC8199699 DOI: 10.3390/molecules26113355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/21/2021] [Accepted: 05/28/2021] [Indexed: 11/17/2022] Open
Abstract
Quinone methide precursors 1a–e, with different alkyl linkers between the naphthol and the naphthalimide chromophore, were synthesized. Their photophysical properties and photochemical reactivity were investigated and connected with biological activity. Upon excitation of the naphthol, Förster resonance energy transfer (FRET) to the naphthalimide takes place and the quantum yields of fluorescence are low (ΦF ≈ 10−2). Due to FRET, photodehydration of naphthols to QMs takes place inefficiently (ΦR ≈ 10−5). However, the formation of QMs can also be initiated upon excitation of naphthalimide, the lower energy chromophore, in a process that involves photoinduced electron transfer (PET) from the naphthol to the naphthalimide. Fluorescence titrations revealed that 1a and 1e form complexes with ct-DNA with moderate association constants Ka ≈ 105–106 M−1, as well as with bovine serum albumin (BSA) Ka ≈ 105 M−1 (1:1 complex). The irradiation of the complex 1e@BSA resulted in the alkylation of the protein, probably via QM. The antiproliferative activity of 1a–e against two human cancer cell lines (H460 and MCF 7) was investigated with the cells kept in the dark or irradiated at 350 nm, whereupon cytotoxicity increased, particularly for 1e (>100 times). Although the enhancement of this activity upon UV irradiation has no imminent therapeutic application, the results presented have importance in the rational design of new generations of anticancer phototherapeutics that absorb visible light.
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10
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Onizuka K, Ganbold E, Ma Y, Sasaki S, Hazemi ME, Chen Y, Sato N, Ozawa M, Nagasawa K, Nagatsugi F. Selective alkylation of parallel G-quadruplex structure. Org Biomol Chem 2021; 19:2891-2894. [PMID: 33570069 DOI: 10.1039/d0ob02365e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The selective alkylation of nucleic acids is important for a medicinal approach and biological study. We now report a novel selective alkylation of the parallel G-quadruplex structure using the conjugate of the macrocyclic hexaoxazole L2G2-6OTD-1M1PA and vinyl-quinazolinone-S(O)Me (6OTD-VQ-S(O)Me).
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Affiliation(s)
- Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.
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11
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Affiliation(s)
- Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
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12
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Onizuka K, Hazemi ME, Sato N, Tsuji GI, Ishikawa S, Ozawa M, Tanno K, Yamada K, Nagatsugi F. Reactive OFF-ON type alkylating agents for higher-ordered structures of nucleic acids. Nucleic Acids Res 2020; 47:6578-6589. [PMID: 31188442 PMCID: PMC6649768 DOI: 10.1093/nar/gkz512] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/15/2019] [Accepted: 05/30/2019] [Indexed: 01/02/2023] Open
Abstract
Higher-ordered structure motifs of nucleic acids, such as the G-quadruplex (G-4), mismatched and bulge structures, are significant research targets because these structures are involved in genetic control and diseases. Selective alkylation of these higher-order structures is challenging due to the chemical instability of the alkylating agent and side-reactions with the single- or double-strand DNA and RNA. We now report the reactive OFF-ON type alkylating agents, vinyl-quinazolinone (VQ) precursors with a sulfoxide, thiophenyl or thiomethyl group for the OFF-ON control of the vinyl reactivity. The stable VQ precursors conjugated with aminoacridine, which bind to the G-4 DNA, selectively reacted with a T base on the G-4 DNA in contrast to the single- and double-strand DNA. Additionally, the VQ precursor reacted with the T or U base in the AP-site, G-4 RNA and T-T mismatch structures. These VQ precursors would be a new candidate for the T or U specific alkylation in the higher-ordered structures of nucleic acids.
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Affiliation(s)
- 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
| | - Madoka E Hazemi
- 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
| | - Norihiro Sato
- 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
| | - Gen-Ichiro Tsuji
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Shunya Ishikawa
- 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
| | - Mamiko Ozawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Kousuke Tanno
- 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
| | - Ken Yamada
- 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
| | - 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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13
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Ongaro A, Ribaudo G, Braud E, Ethève-Quelquejeu M, De Franco M, Garbay C, Demange L, Gresh N, Zagotto G. Design and synthesis of a peptide derivative of ametantrone targeting the major groove of the d(GGCGCC) 2palindromic sequence. NEW J CHEM 2020. [DOI: 10.1039/c9nj03817e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the synthesis of a peptide derivative of antitumor anthraquinones, designed to target GC-rich palindromic sequences. It has micromolar activities on three cancer cell lines and is fifty times less toxic than mitoxantrone on a healthy line.
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Affiliation(s)
- Alberto Ongaro
- Department of Molecular and Translational Medicine
- Division of Pharmacology
- University of Brescia
- 25123 Brescia
- Italy
| | - Giovanni Ribaudo
- Department of Molecular and Translational Medicine
- Division of Pharmacology
- University of Brescia
- 25123 Brescia
- Italy
| | - Emmanuelle Braud
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques
- Team “Chemistry of RNAs, nucleosides
- peptides and heterocycles” Université de Paris
- CNRS UMR 8601
- Paris
| | - Mélanie Ethève-Quelquejeu
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques
- Team “Chemistry of RNAs, nucleosides
- peptides and heterocycles” Université de Paris
- CNRS UMR 8601
- Paris
| | - Michele De Franco
- Department of Pharmaceutical and Pharmacological Sciences
- University of Padova
- 35131 Padova
- Italy
| | - Christiane Garbay
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques
- Team “Chemistry of RNAs, nucleosides
- peptides and heterocycles” Université de Paris
- CNRS UMR 8601
- Paris
| | - Luc Demange
- Université de Paris
- CiTCoM
- UMR 8038 CNRS
- Faculté de Pharmacie
- F-75006 Paris
| | - Nohad Gresh
- Laboratoire de Chimie Théorique
- UMR 7616 CNRS
- Sorbonne Université
- Paris
- France
| | - Giuseppe Zagotto
- Department of Pharmaceutical and Pharmacological Sciences
- University of Padova
- 35131 Padova
- Italy
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14
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Doria F, Salvati E, Pompili L, Pirota V, D'Angelo C, Manoli F, Nadai M, Richter SN, Biroccio A, Manet I, Freccero M. Dyads of G‐Quadruplex Ligands Triggering DNA Damage Response and Tumour Cell Growth Inhibition at Subnanomolar Concentration. Chemistry 2019; 25:11085-11097. [DOI: 10.1002/chem.201900766] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/18/2019] [Indexed: 02/05/2023]
Affiliation(s)
- Filippo Doria
- Department of ChemistryUniversity of Pavia V. le Taramelli 10 27100 Pavia Italy
| | - Erica Salvati
- Oncogenomic and Epigenetic UnitIRCCS Regina Elena National Cancer Institute Via Elio Chianes 53 00144 Rome Italy
- Present address: Institute of Molecular Biology and Pathology (IBPM)National Research Council (CNR) Via degli Apuli 4 00185 Rome Italy
| | - Luca Pompili
- Oncogenomic and Epigenetic UnitIRCCS Regina Elena National Cancer Institute Via Elio Chianes 53 00144 Rome Italy
| | - Valentina Pirota
- Department of ChemistryUniversity of Pavia V. le Taramelli 10 27100 Pavia Italy
| | - Carmen D'Angelo
- Oncogenomic and Epigenetic UnitIRCCS Regina Elena National Cancer Institute Via Elio Chianes 53 00144 Rome Italy
| | - Francesco Manoli
- Institute for Organic Synthesis and Photoreactivity (ISOF)National Research Council (CNR) Via P. Gobetti 101 40129 Bologna Italy
| | - Matteo Nadai
- Department of Molecular MedicineUniversity of Padua Via Gabelli 63 35121 Padua Italy
| | - Sara N. Richter
- Department of Molecular MedicineUniversity of Padua Via Gabelli 63 35121 Padua Italy
| | - Annamaria Biroccio
- Oncogenomic and Epigenetic UnitIRCCS Regina Elena National Cancer Institute Via Elio Chianes 53 00144 Rome Italy
| | - Ilse Manet
- Institute for Organic Synthesis and Photoreactivity (ISOF)National Research Council (CNR) Via P. Gobetti 101 40129 Bologna Italy
| | - Mauro Freccero
- Department of ChemistryUniversity of Pavia V. le Taramelli 10 27100 Pavia Italy
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15
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Sambol M, Ester K, Landgraf S, Mihaljević B, Cindrić M, Kralj M, Basarić N. Competing photochemical reactions of bis-naphthols and their photoinduced antiproliferative activity. Photochem Photobiol Sci 2019; 18:1197-1211. [PMID: 30820496 DOI: 10.1039/c8pp00532j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The photophysical properties and photochemical reactivities of a series of bis-naphthols 4a-4e and bis-anthrols 5a and 5e were investigated by preparative irradiation in CH3OH, fluorescence spectroscopy and laser flash photolysis (LFP). Methanolysis taking place via photodehydration (bis-naphthols: ΦR = 0.04-0.05) is in competition with symmetry breaking charge separation (SB-CS). The SB-CS gave rise to radical ions that were detected for 4a and 4e by LFP. Photodehydration gave quinone methides (QMs) that were also detected by LFP (λmax = 350 nm, τ ≈ 1-2 ms). In the aqueous solvent, excited state proton transfer (ESPT) competes with the abovementioned processes, giving rise to naphtholates, but the process is inefficient and can only be observed in the buffered aqueous solution at pH > 7. Since the dehydration of bis-naphthols delivers QMs, their potential antiproliferative activity was investigated by an MTT test on three human cancer cell lines (NCI-H1299, lung carcinoma; MCF-7, breast adenocarcinoma; and SUM159, pleomorphic breast carcinoma). Cells were treated with 4 or 5 with or without irradiation (350 nm). An enhancement of the activity (up to 10-fold) was observed upon irradiation, which may be associated with QM formation. However, these QMs do not cross-link DNA. The activity is most likely associated with the alkylation of proteins present in the cell cytoplasm, as evidenced by photoinduced alkylation of bovine and human serum albumins by 4a.
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Affiliation(s)
- Matija Sambol
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia.
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16
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O'Hagan MP, Morales JC, Galan MC. Binding and Beyond: What Else Can G-Quadruplex Ligands Do? European J Org Chem 2019. [DOI: 10.1002/ejoc.201900692] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | - Juan C. Morales
- Instituto de Parasitología y Biomedicina “López Neyra”; Consejo Superior de Investigaciones Científicas (CSIC); PTS Granada; Avenida del Conocimiento 17 18016 Armilla, Granada Spain
| | - M. Carmen Galan
- School of Chemistry; University of Bristol; Cantock's Close BS8 1TS UK
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17
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Ma J, Šekutor M, Škalamera Đ, Basarić N, Phillips DL. Formation of Quinone Methides by Ultrafast Photodeamination: A Spectroscopic and Computational Study. J Org Chem 2019; 84:8630-8637. [PMID: 31244153 DOI: 10.1021/acs.joc.9b01085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Formation of quinone methides (QMs) by photoelimination of an ammonium salt from cresol derivatives was investigated by femtosecond transient absorption spectroscopy (fs-TA) and computationally by time-dependent density functional theory using the PCM(water)/(TD-)B3LYP/6-311++G(d,p) level of theory. The photoelimination takes place in an adiabatic ultrafast reaction on the S1 potential energy surface delivering the corresponding QMs(S1), which were detected by fs-TA. Computations predicted a high-energy cation intermediate in the pathway between the Franck-Condon state of a monoammonium salt and the corresponding QM(S1) that was not detected by fs-TA. On the other hand, elimination from a disalt in H2O takes place in one step, giving directly the QM(S1). The combined experimental and theoretical investigation fully disclosed the formation of QMs by the deamination reaction mechanism, which is important in the application of cresols or similar molecules in biological systems.
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Affiliation(s)
- Jiani Ma
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science , Northwest University , Xi'an 710065 , P. R. China
| | - Marina Šekutor
- Department of Organic Chemistry and Biochemistry , Ruđer Bošković Institute , Bijenička cesta 54 , 10 000 Zagreb , Croatia
| | - Đani Škalamera
- Department of Organic Chemistry and Biochemistry , Ruđer Bošković Institute , Bijenička cesta 54 , 10 000 Zagreb , Croatia
| | - Nikola Basarić
- Department of Organic Chemistry and Biochemistry , Ruđer Bošković Institute , Bijenička cesta 54 , 10 000 Zagreb , Croatia
| | - David Lee Phillips
- Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , Hong Kong S.A.R. , P. R. China
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18
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Ribaudo G, Ongaro A, Zorzan M, Pezzani R, Redaelli M, Zagotto G, Memo M, Gianoncelli A. Investigation of the molecular reactivity of bioactive oxiranylmethyloxy anthraquinones. Arch Pharm (Weinheim) 2019; 352:e1900030. [DOI: 10.1002/ardp.201900030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Giovanni Ribaudo
- Department of Pharmaceutical and Pharmacological SciencesUniversity of PadovaPadova Italy
| | - Alberto Ongaro
- Department of Molecular and Translational MedicineUniversity of BresciaBrescia Italy
| | - Maira Zorzan
- Department of Molecular Medicine (DMM)University of PadovaPadova Italy
| | | | - Marco Redaelli
- Department of Pharmaceutical and Pharmacological SciencesUniversity of PadovaPadova Italy
| | - Giuseppe Zagotto
- Department of Pharmaceutical and Pharmacological SciencesUniversity of PadovaPadova Italy
| | - Maurizio Memo
- Department of Molecular and Translational MedicineUniversity of BresciaBrescia Italy
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19
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Naphthalene Diimides as Multimodal G-Quadruplex-Selective Ligands. Molecules 2019; 24:molecules24030426. [PMID: 30682828 PMCID: PMC6384834 DOI: 10.3390/molecules24030426] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/11/2019] [Accepted: 01/22/2019] [Indexed: 02/03/2023] Open
Abstract
G-quadruplexes are four-stranded nucleic acids structures that can form in guanine-rich sequences. Following the observation that G-quadruplexes are particularly abundant in genomic regions related to cancer, such as telomeres and oncogenes promoters, several G-quadruplex-binding molecules have been developed for therapeutic purposes. Among them, naphthalene diimide derivatives have reported versatility, consistent selectivity and high affinity toward the G-quadruplex structures. In this review, we present the chemical features, synthesis and peculiar optoelectronic properties (absorption, emission, redox) that make naphtalene diimides so versatile for biomedical applications. We present the latest developments on naphthalene diimides as G-quadruplex ligands, focusing on their ability to bind G-quadruplexes at telomeres and oncogene promoters with consequent anticancer activity. Their different binding modes (reversible versus irreversible/covalent) towards G-quadruplexes and their additional use as antimicrobial agents are also presented and discussed.
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20
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Yan Z, Du L, Lan X, Zhang X, Phillips DL. Time-resolved spectroscopic and density functional theory investigation of the influence of the leaving group on the generation of a binol quinone methide. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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21
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Saha A, Bombard S, Granzhan A, Teulade-Fichou MP. Probing of G-Quadruplex Structures via Ligand-Sensitized Photochemical Reactions in BrU-Substituted DNA. Sci Rep 2018; 8:15814. [PMID: 30361545 PMCID: PMC6202380 DOI: 10.1038/s41598-018-34141-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/12/2018] [Indexed: 01/18/2023] Open
Abstract
We studied photochemical reactions of BrU-substituted G-quadruplex (G4) DNA substrates with two pyrene-substituted polyazamacrocyclic ligands, M-1PY and M-2PY. Both ligands bind to and stabilize G4-DNA structures without altering their folding topology, as demonstrated by FRET-melting experiments, fluorimetric titrations and CD spectroscopy. Notably, the bis-pyrene derivative (M-2PY) behaves as a significantly more affine and selective G4 ligand, compared with its mono-pyrene counterpart (M-1PY) and control compounds. Upon short UVA irradiation (365 nm) both ligands, in particular M-2PY, efficiently sensitize photoreactions at BrU residues incorporated in G4 structures and give rise to two kinds of photoproducts, namely DNA strand cleavage and covalent ligand-DNA photoadducts. Remarkably, the photoinduced strand cleavage is observed exclusively with G4 structures presenting BrU residues in lateral or diagonal loops, but not with parallel G4-DNA structures presenting only propeller loops. In contrast, the formation of fluorescent photoadducts is observed with all BrU-substituted G4-DNA substrates, with M-2PY giving significantly higher yields (up to 27%) than M-1PY. Both ligand-sensitized photoreactions are specific to BrU-modified G4-DNA structures with respect to double-stranded or stem-loop substrates. Thus, ligand-sensitized photoreactions with BrU-substituted G4-DNA may be exploited (i) as a photochemical probe, allowing "photofootprinting" of G4 folding topologies in vitro and (ii) for covalent trapping of G4 structures as photoadducts with pyrene-substituted ligands.
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Affiliation(s)
- Abhijit Saha
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405, Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris Saclay, 91405, Orsay, France
| | - Sophie Bombard
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405, Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris Saclay, 91405, Orsay, France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405, Orsay, France. .,CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris Saclay, 91405, Orsay, France.
| | - Marie-Paule Teulade-Fichou
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405, Orsay, France. .,CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris Saclay, 91405, Orsay, France.
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22
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Škalamera Đ, Antol I, Mlinarić-Majerski K, Vančik H, Phillips DL, Ma J, Basarić N. Ultrafast Adiabatic Photodehydration of 2-Hydroxymethylphenol and the Formation of Quinone Methide. Chemistry 2018; 24:9426-9435. [PMID: 29677402 DOI: 10.1002/chem.201801543] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Indexed: 12/13/2022]
Abstract
The photochemical reactivity of 2-hydroxymethylphenol (1) was investigated experimentally by photochemistry under cryogenic conditions, by detecting reactive intermediates by IR spectroscopy, and by using nanosecond and femtosecond transient absorption spectroscopic methods in solution at room temperature. In addition, theoretical studies were performed to facilitate the interpretation of the experimental results and also to simulate the reaction pathway to obtain a better understanding of the reaction mechanism. The main finding of this work is that photodehydration of 1 takes place in an ultrafast adiabatic photochemical reaction without any clear intermediate, delivering quinone methide (QM) in the excited state. Upon photoexcitation to a higher vibrational level of the singlet excited state, 1 undergoes vibrational relaxation leading to two photochemical pathways, one by which synchronous elimination of H2 O gives QM 2 in its S1 state and the other by which homolytic cleavage of the phenolic O-H bond produces a phenoxyl radical (S0 ). Both are ultrafast processes that occur within a picosecond. The excited state of QM 2 (S1 ) probably deactivates to S0 through a conical intersection to give QM 2 (S0 ), which subsequently delivers benzoxete 4. Elucidation of the reaction mechanisms for the photodehydration of phenols by which QMs are formed is important to tune the reactivity of QMs with DNA and proteins for the potential application of QMs in medicine as therapeutic agents.
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Affiliation(s)
- Đani Škalamera
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia.,Department of Organic Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia
| | - Ivana Antol
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia
| | - Kata Mlinarić-Majerski
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia
| | - Hrvoj Vančik
- Department of Organic Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia
| | - David Lee Phillips
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong S.A.R., P.R. China
| | - Jiani Ma
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of, Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, P.R. China
| | - Nikola Basarić
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia
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23
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Bifunctional cross-linking approaches for mass spectrometry-based investigation of nucleic acids and protein-nucleic acid assemblies. Methods 2018; 144:64-78. [PMID: 29753003 DOI: 10.1016/j.ymeth.2018.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/30/2018] [Accepted: 05/04/2018] [Indexed: 12/13/2022] Open
Abstract
With the goal of expanding the very limited toolkit of cross-linking agents available for nucleic acids and their protein complexes, we evaluated the merits of a wide range of bifunctional agents that may be capable of reacting with the functional groups characteristic of these types of biopolymers. The survey specifically focused on the ability of test reagents to produce desirable inter-molecular conjugates, which could reveal the identity of interacting components and the position of mutual contacts, while also considering a series of practical criteria for their utilization as viable nucleic acid probes. The survey employed models consisting of DNA, RNA, and corresponding protein complexes to mimic as close as possible typical applications. Denaturing polyacrylamide gel electrophoresis (PAGE) and mass spectrometric (MS) analyses were implemented in concert to monitor the formation of the desired conjugates. In particular, the former was used as a rapid and inexpensive tool for the efficient evaluation of cross-linker activity under a broad range of experimental conditions. The latter was applied after preliminary rounds of reaction optimization to enable full-fledged product characterization and, more significantly, differentiation between mono-functional and intra- versus inter-molecular conjugates. This information provided the feedback necessary to further optimize reaction conditions and explain possible outcomes. Among the reagents tested in the study, platinum complexes and nitrogen mustards manifested the most favorable characteristics for practical cross-linking applications, whereas other compounds provided inferior yields, or produced rather unstable conjugates that did not survive the selected analytical conditions. The observed outcomes will help guide the selection of the most appropriate cross-linking reagent for a specific task, whereas the experimental conditions described here will provide an excellent starting point for approaching these types of applications. As a whole, the results of the survey clearly emphasize that finding a universal reagent, which may afford excellent performance with all types of nucleic acid substrates, will require extending the exploration beyond the traditional chemistries employed to modify the constitutive functional groups of these vital biopolymers.
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24
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Ruggiero E, Richter SN. G-quadruplexes and G-quadruplex ligands: targets and tools in antiviral therapy. Nucleic Acids Res 2018; 46:3270-3283. [PMID: 29554280 PMCID: PMC5909458 DOI: 10.1093/nar/gky187] [Citation(s) in RCA: 270] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/27/2018] [Accepted: 03/02/2018] [Indexed: 12/13/2022] Open
Abstract
G-quadruplexes (G4s) are non-canonical nucleic acids secondary structures that form within guanine-rich strands of regulatory genomic regions. G4s have been extensively described in the human genome, especially in telomeres and oncogene promoters; in recent years the presence of G4s in viruses has attracted increasing interest. Indeed, G4s have been reported in several viruses, including those involved in recent epidemics, such as the Zika and Ebola viruses. Viral G4s are usually located in regulatory regions of the genome and implicated in the control of key viral processes; in some cases, they have been involved also in viral latency. In this context, G4 ligands have been developed and tested both as tools to study the complexity of G4-mediated mechanisms in the viral life cycle, and as therapeutic agents. In general, G4 ligands showed promising antiviral activity, with G4-mediated mechanisms of action both at the genome and transcript level. This review aims to provide an updated close-up of the literature on G4s in viruses. The current state of the art of G4 ligands in antiviral research is also reported, with particular focus on the structural and physicochemical requirements for optimal biological activity. The achievements and the to-dos in the field are discussed.
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Affiliation(s)
- Emanuela Ruggiero
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, Padua 35121, Italy
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25
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Doria F, Nadai M, Zuffo M, Perrone R, Freccero M, Richter SN. A red-NIR fluorescent dye detecting nuclear DNA G-quadruplexes: in vitro analysis and cell imaging. Chem Commun (Camb) 2018; 53:2268-2271. [PMID: 28149992 PMCID: PMC5471928 DOI: 10.1039/c6cc08492c] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Light-up of nuclear G-quadruplex DNA in cells by an aggregating and red/NIR emitting dye.
Aggregation, red-NIR emission and light-up upon nucleic acid G-quadruplex binding have been investigated for a prototype core-extended naphthalene diimide, which is capable of fast cellular entry and nucleolar localization. Both high-level colocalization with an anti-G-quadruplex antibody and nucleolin displacement reveal that the compound targets and thus makes visible nuclear DNA G-quadruplexes.
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Affiliation(s)
- F Doria
- Dept. of Chemistry, University of Pavia, V.le Taramelli 10, 27100 Pavia, Italy.
| | - M Nadai
- Dept. of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy.
| | - M Zuffo
- Dept. of Chemistry, University of Pavia, V.le Taramelli 10, 27100 Pavia, Italy.
| | - R Perrone
- Dept. of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy.
| | - M Freccero
- Dept. of Chemistry, University of Pavia, V.le Taramelli 10, 27100 Pavia, Italy.
| | - S N Richter
- Dept. of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy.
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26
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Zhou J, Wang ML, Gao X, Jiang GF, Zhou YG. Bifunctional squaramide-catalyzed synthesis of chiral dihydrocoumarins via ortho-quinone methides generated from 2-(1-tosylalkyl)phenols. Chem Commun (Camb) 2018; 53:3531-3534. [PMID: 28289737 DOI: 10.1039/c7cc01072a] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A bifunctional squaramide-catalyzed reaction of azlactones with o-quinone methides in situ generated from 2-(1-tosylalkyl)-phenols has been successfully developed under basic conditions, providing an efficient and mild access to chiral dihydrocoumarins bearing adjacent tertiary and quaternary stereogenic centers in high yields with excellent diastereo- and enantioselectivities.
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Affiliation(s)
- Ji Zhou
- State Key Lab of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China. and State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China.
| | - Mao-Lin Wang
- State Key Lab of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Xiang Gao
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China.
| | - Guo-Fang Jiang
- State Key Lab of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China.
| | - Yong-Gui Zhou
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China.
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27
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Sato N, Takahashi S, Tateishi-Karimata H, Hazemi ME, Chikuni T, Onizuka K, Sugimoto N, Nagatsugi F. Alkylating probes for the G-quadruplex structure and evaluation of the properties of the alkylated G-quadruplex DNA. Org Biomol Chem 2018; 16:1436-1441. [PMID: 29412214 DOI: 10.1039/c7ob03179c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The G-quadruplex structure has been found in biologically significant regions of the genomic DNA, including the telomere and promoter regions, and is known to play an important role in a number of biological processes. In this paper, we report the development of alkylating probes for the G-quadruplex structure and evaluation of the properties of the modified G-quadruplex structure.
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Affiliation(s)
- Norihiro Sato
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi, 980-8577, Japan.
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28
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Zhou J, Huang WJ, Jiang GF. Synthesis of Chiral Pyrazolone and Spiropyrazolone Derivatives through Squaramide-Catalyzed Reaction of Pyrazolin-5-ones with o-Quinone Methides. Org Lett 2018; 20:1158-1161. [DOI: 10.1021/acs.orglett.8b00025] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ji Zhou
- State Key Lab of Chemo/Biosensing and
Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Wen-Jun Huang
- State Key Lab of Chemo/Biosensing and
Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Guo-Fang Jiang
- State Key Lab of Chemo/Biosensing and
Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
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29
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Husak A, Noichl BP, Šumanovac Ramljak T, Sohora M, Škalamera Đ, Budiša N, Basarić N. Photochemical formation of quinone methides from peptides containing modified tyrosine. Org Biomol Chem 2018; 14:10894-10905. [PMID: 27812591 DOI: 10.1039/c6ob02191c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We have demonstrated that quinone methide (QM) precursors can be introduced in the peptide structure and used as photoswitchable units for peptide modifications. QM precursor 1 was prepared from protected tyrosine in the Mannich reaction, and further used as a building block in peptide synthesis. Moreover, peptides containing tyrosine can be transformed into a photoactivable QM precursor by the Mannich reaction which can afford monosubstituted derivatives 2 or bis-substituted derivatives 3. Photochemical reactivity of modified tyrosine 1 and dipeptides 2 and 3 was studied by preparative irradiation in CH3OH where photodeamination and photomethanolysis occur. QM precursors incorporated in peptides undergo photomethanolysis with quantum efficiency ΦR = 0.1-0.2, wherein the peptide backbone does not affect their photochemical reactivity. QMs formed from dipeptides were detected by laser flash photolysis (λmax ≈ 400 nm, τ = 100 μs-20 ms) and their reactivity with nucleophiles was studied. Consequently, QM precursors derived from tyrosine can be a part of the peptide backbone which can be transformed into QMs upon electronic excitation, leading to the reactions of peptides with different reagents. This proof of principle showing the ability to photochemically trigger peptide modifications and interactions with other molecules can have numerous applications in organic synthesis, materials science, biology and medicine.
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Affiliation(s)
- Antonija Husak
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia.
| | - Benjamin P Noichl
- Institute for Chemistry, Technical University Berlin, Müller-Breslau-Str. 10, 10623 Berlin, Germany
| | - Tatjana Šumanovac Ramljak
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia.
| | - Margareta Sohora
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia.
| | - Đani Škalamera
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia.
| | - Nediljko Budiša
- Institute for Chemistry, Technical University Berlin, Müller-Breslau-Str. 10, 10623 Berlin, Germany
| | - Nikola Basarić
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia.
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30
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Li Y, Liu T, Liang C. Mechanisms and stereoselectivities of NHC-catalyzed [4 + 2] cycloaddition reaction between phenylacetic acid and o-quinone methide: A computational investigation. MOLECULAR CATALYSIS 2017. [DOI: 10.1016/j.mcat.2017.08.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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31
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Škalamera Đ, Mlinarić-Majerski K, Martin Kleiner I, Kralj M, Oake J, Wan P, Bohne C, Basarić N. Photochemical Formation of Anthracene Quinone Methide Derivatives. J Org Chem 2017; 82:6006-6021. [PMID: 28534631 DOI: 10.1021/acs.joc.6b02735] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Anthrols 2-7 were synthesized and their photochemical reactivity investigated by irradiations in aq CH3OH. Upon excitation with visible light (λ > 400 nm) in methanolic solutions, they undergo photodehydration or photodeamination and deliver methyl ethers, most probably via quinone methides (QMs), with methanolysis quantum efficiencies ΦR = 0.02-0.3. Photophysical properties of 2-7 were determined by steady-state fluorescence and time-correlated single photon counting. Generally, anthrols 2-7 are highly fluorescent in aprotic solvents (ΦF = 0.5-0.9), whereas in aqueous solutions the fluorescence is quenched due to excited-state proton transfer (ESPT) to solvent. The exception is amine 4 that undergoes excited-state intramolecular proton transfer (ESIPT) in neat CH3CN where photodeamination is probably coupled to ESIPT. Photodehydration may take place via ESIPT (or ESPT) that is coupled to dehydration or via a hitherto undisclosed pathway that involves photoionization and deprotonation of radical cation, followed by homolytic cleavage of the alcohol OH group from the phenoxyl radical. QMs were detected by laser flash photolysis and their reactivity with nucleophiles investigated. Biological investigation of 2-5 on human cancer cell lines showed enhancement of antiproliferative effect upon exposure of cells to irradiation by visible light, probably due to formation of electrophilic species such as QMs.
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Affiliation(s)
| | | | | | | | - Jessy Oake
- Department of Chemistry, University of Victoria , Box 1700 STN CSC, Victoria BC V8W 2Y2, Canada
| | - Peter Wan
- Department of Chemistry, University of Victoria , Box 1700 STN CSC, Victoria BC V8W 2Y2, Canada
| | - Cornelia Bohne
- Department of Chemistry, University of Victoria , Box 1700 STN CSC, Victoria BC V8W 2Y2, Canada
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32
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Narayana Reddy P, Padmaja P, Ramana Reddy B, Singh Jadav S. Synthesis, in vitro antiproliferative activity, antioxidant activity and molecular modeling studies of new carbazole Mannich bases. Med Chem Res 2017. [DOI: 10.1007/s00044-017-1927-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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Street STG, Chin DN, Hollingworth GJ, Berry M, Morales JC, Galan MC. Divalent Naphthalene Diimide Ligands Display High Selectivity for the Human Telomeric G-quadruplex in K + Buffer. Chemistry 2017; 23:6953-6958. [PMID: 28257554 PMCID: PMC5485019 DOI: 10.1002/chem.201700140] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Indexed: 01/09/2023]
Abstract
Selective G‐quadruplex ligands offer great promise for the development of anti‐cancer therapies. A novel series of divalent cationic naphthalene diimide ligands that selectively bind to the hybrid form of the human telomeric G‐quadruplex in K+ buffer are described herein. We demonstrate that an imidazolium‐bearing mannoside‐conjugate is the most selective ligand to date for this quadruplex against several other quadruplex and duplex structures. We also show that a similarly selective methylpiperazine‐bearing ligand was more toxic to HeLa cancer cells than doxorubicin, whilst exhibiting three times less toxicity towards fetal lung fibroblasts WI‐38.
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Affiliation(s)
- Steven T G Street
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Donovan N Chin
- Novartis Institutes for Biomedical Research, 250 Massachusetts Ave., Cambridge, Massachusetts, 02139, USA
| | | | - Monica Berry
- School of Physics, University of Bristol, HH Wills Physics Laboratory, Bristol, BS8 1TL, UK
| | - Juan C Morales
- Instituto de Parasitología y Biomedicina, Avenida del Conocimiento, s/n, 18016, Armilla, Granada, Spain
| | - M Carmen Galan
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
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34
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Wu B, Yu Z, Gao X, Lan Y, Zhou YG. Regioselective α-Addition of Deconjugated Butenolides: Enantioselective Synthesis of Dihydrocoumarins. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700437] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Bo Wu
- State Key Laboratory of Catalysis; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian 116023 P.R. China
| | - Zhaoyuan Yu
- School of Chemistry and Chemical Engineering; Chongqing University; Chongqing 400030 P.R. China
| | - Xiang Gao
- State Key Laboratory of Catalysis; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian 116023 P.R. China
| | - Yu Lan
- School of Chemistry and Chemical Engineering; Chongqing University; Chongqing 400030 P.R. China
| | - Yong-Gui Zhou
- State Key Laboratory of Catalysis; Dalian Institute of Chemical Physics; Chinese Academy of Sciences; Dalian 116023 P.R. China
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35
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Wu B, Yu Z, Gao X, Lan Y, Zhou YG. Regioselective α-Addition of Deconjugated Butenolides: Enantioselective Synthesis of Dihydrocoumarins. Angew Chem Int Ed Engl 2017; 56:4006-4010. [PMID: 28247568 DOI: 10.1002/anie.201700437] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Indexed: 11/08/2022]
Abstract
The enantioselective α-addition of deconjugated butenolides has rarely been exploited, in contrast to the well-studied γ-addition of deconjugated butenolides. In this study, an unprecedented asymmetric α-addition/transesterification of deconjugated butenolides with ortho-quinone methides generated in situ afforded a series of functionalized 3,4-dihydrocoumarins containing two contiguous stereogenic centers with excellent diastereo- and enantioselectivity. DFT calculations suggested that the rarely observed regioselectivity was due to the distortion energy that resulted from the interaction between the nucleophilic dienolate and the electrophilic ortho-quinone methide.
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Affiliation(s)
- Bo Wu
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P.R. China
| | - Zhaoyuan Yu
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400030, P.R. China
| | - Xiang Gao
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P.R. China
| | - Yu Lan
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400030, P.R. China
| | - Yong-Gui Zhou
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, P.R. China
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36
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Abstract
The nitrosocarbonyls (R-CONO) are highly reactive species and remarkable intermediates toward different synthetic targets. This review will cover a research area whose impact in current organic synthesis is constantly increasing in the chemical community. This review represents the first and comprehensive picture on the generation and trapping of nitrosocarbonyls and is solidly built on more than 380 papers. Six different classes of key starting materials such as hydroxamic acids, N-hydroxy carbamates, N-hydroxyureas, nitrile oxides, and 1,2,4-oxadiazole-4-oxides were highlighted. The content of the review surveys all the methods to generate the nitrosocarbonyls through different approaches (oxidative, thermal, photochemical, catalytic, aerobic, and the less common ones) in the light of efficiency, yields, and mildness. The most successful trapping agents employed to catch these fleeting intermediates are reviewed, exploiting their superior dienophilic, enophilic, and electrophilic power. The work is completed by paragraphs dedicated to the detection of the intermediates, theoretical studies, and insights about the challenges and future directions for the field.
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Affiliation(s)
- Misal Giuseppe Memeo
- Dipartimento di Chimica, Università degli Studi di Pavia , Viale Taramelli 12, 27100 Pavia, Italy
| | - Paolo Quadrelli
- Dipartimento di Chimica, Università degli Studi di Pavia , Viale Taramelli 12, 27100 Pavia, Italy
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37
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Arévalo-Ruiz M, Doria F, Belmonte-Reche E, De Rache A, Campos-Salinas J, Lucas R, Falomir E, Carda M, Pérez-Victoria JM, Mergny JL, Freccero M, Morales JC. Synthesis, Binding Properties, and Differences in Cell Uptake of G-Quadruplex Ligands Based on Carbohydrate Naphthalene Diimide Conjugates. Chemistry 2017; 23:2157-2164. [PMID: 27925323 DOI: 10.1002/chem.201604886] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Indexed: 11/06/2022]
Abstract
The G-quadruplexes (G4s) are currently being explored as therapeutic targets in cancer and other pathologies. Six carbohydrate naphthalene diimide conjugates (carb-NDIs) have been synthesized as G4 ligands to investigate their potential selectivity in G4 binding and cell penetration. Carb-NDIs have shown certain selectivity for G4 structures against DNA duplexes, but different sugar moieties do not induce a preference for a specific G4 topology. Interestingly, when monosaccharides were attached through a short ethylene linker to the NDI scaffold, their cellular uptake was two- to threefold more efficient than that when the sugar was directly attached through its anomeric position. Moreover, a correlation between more efficient cell uptake of these carb-NDIs and their higher toxicity in cancerous cell lines has been observed. Carb-NDIs seem to be mainly translocated into cancer cells through glucose transporters (GLUT), of which GLUT4 plays a major role.
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Affiliation(s)
- Matilde Arévalo-Ruiz
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud, Avenida del Conocimiento, s/n, 18016, Armilla, Granada, Spain
| | - Filippo Doria
- Department of Chemistry, University of Pavia, V.le Taramelli 10, 27100, Pavia, Italy
| | - Efres Belmonte-Reche
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud, Avenida del Conocimiento, s/n, 18016, Armilla, Granada, Spain
| | - Aurore De Rache
- Institut Européen de Chimie Biologie (IECB), ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR5320, 2, rue Robert Escarpit, Pessac, France
| | - Jenny Campos-Salinas
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud, Avenida del Conocimiento, s/n, 18016, Armilla, Granada, Spain
| | - Ricardo Lucas
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud, Avenida del Conocimiento, s/n, 18016, Armilla, Granada, Spain
| | - Eva Falomir
- Department of Inorganic and Organic Chemistry, University Jaume I, 12071, Castellón, Spain
| | - Miguel Carda
- Department of Inorganic and Organic Chemistry, University Jaume I, 12071, Castellón, Spain
| | - José María Pérez-Victoria
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud, Avenida del Conocimiento, s/n, 18016, Armilla, Granada, Spain
| | - Jean-Louis Mergny
- Institut Européen de Chimie Biologie (IECB), ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR5320, 2, rue Robert Escarpit, Pessac, France
| | - Mauro Freccero
- Department of Chemistry, University of Pavia, V.le Taramelli 10, 27100, Pavia, Italy
| | - Juan Carlos Morales
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud, Avenida del Conocimiento, s/n, 18016, Armilla, Granada, Spain
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38
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Cao Q, Li Y, Freisinger E, Qin PZ, Sigel RKO, Mao ZW. G-quadruplex DNA targeted metal complexes acting as potential anticancer drugs. Inorg Chem Front 2017. [DOI: 10.1039/c6qi00300a] [Citation(s) in RCA: 174] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This review summarizes the recent development of G4 DNA targeted metal complexes and discusses their potential as anticancer drugs.
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Affiliation(s)
- Qian Cao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou 510275
- China
| | - Yi Li
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou 510275
- China
| | - Eva Freisinger
- University of Zurich
- Department of Chemistry
- CH-8057 Zurich
- Switzerland
| | - Peter Z. Qin
- Department of Chemistry
- University of Southern California
- Los Angeles
- USA
| | | | - Zong-Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou 510275
- China
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39
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Du L, Zhang X, Xue J, Tang W, Li MD, Lan X, Zhu J, Zhu R, Weng Y, Li YL, Phillips DL. Influence of Water in the Photogeneration and Properties of a Bifunctional Quinone Methide. J Phys Chem B 2016; 120:11132-11141. [PMID: 27723330 DOI: 10.1021/acs.jpcb.6b08705] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Quinone methides (QM) are crucial reactive species in molecular biology and organic chemistry, with little known regarding the mechanism(s) for the generation of short-lived reactive QM intermediates from relevant precursors in aqueous solutions. In this study, several time-resolved spectroscopy methods were used to directly examine the photophysics and photochemical pathways of 1,1'-(2,2'-dihydroxy-1,1'-binaphthyl-6,6'-diyl)bis(N,N,N-trimethylmethanaminium) bromide (BQMP-b) from initial photoexcitation to the generation of the key reactive binol QM intermediate (BQM) in aqueous solution. The fluorescence of BQMP-b is effectively quenched with a small amount of water, which suggests an excited state intramolecular proton transfer (ESIPT) occurs. The kinetics isotope effects observed in femtosecond and nanosecond time-resolved transient absorption experiments provide evidence for the participation of water molecules in the BQMP-b singlet excited state ESIPT process and in the subsequent -HNMe3+ group release and ground state intramolecular proton transfer that give rise to production of the reactive BQM intermediate. Nanosecond time-resolved resonance Raman (ns-TR3) measurements were also employed to investigate the structure and properties of several intermediates, including the key reactive BQM in aqueous solution. The ns-TR3 and density functional theory (DFT) computational results were compared, and this indicates the binol moiety and water molecules both have important roles in the characteristics and structure of the key reactive BQM intermediate produced from BQMP-b. The results presented here also provide new benchmark characterization of bifunctional quinone methide intermediates that can be utilized to guide direct time-resolved spectroscopic study of the alkylation and interstrand cross-linking reactions of quinone methides with DNA in the future.
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Affiliation(s)
- Lili Du
- Department of Chemistry, University of Hong Kong , Pokfulam Road, Hong Kong S.A.R., P. R. China
| | - Xiting Zhang
- Department of Chemistry, University of Hong Kong , Pokfulam Road, Hong Kong S.A.R., P. R. China
| | - Jiadan Xue
- Department of Chemistry, Zhejiang Sci-Tech University , Hangzhou 310018, P. R. China
| | - WenJian Tang
- School of Pharmacy, Anhui Medical University , Meishan Road 81, Hefei 230032, P.R. China
| | - Ming-De Li
- Department of Chemistry, University of Hong Kong , Pokfulam Road, Hong Kong S.A.R., P. R. China
| | - Xin Lan
- Department of Chemistry, University of Hong Kong , Pokfulam Road, Hong Kong S.A.R., P. R. China
| | - Jiangrui Zhu
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences , Beijing 100190, P. R. China
| | - Ruixue Zhu
- Department of Chemistry, University of Hong Kong , Pokfulam Road, Hong Kong S.A.R., P. R. China
| | - Yuxiang Weng
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences , Beijing 100190, P. R. China
| | - Yun-Liang Li
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences , Beijing 100190, P. R. China
| | - David Lee Phillips
- Department of Chemistry, University of Hong Kong , Pokfulam Road, Hong Kong S.A.R., P. R. China
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40
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Doria F, Nadai M, Costa G, Sattin G, Gallati C, Bergamaschi G, Moraca F, Alcaro S, Freccero M, Richter SN. Extended Naphthalene Diimides with Donor/Acceptor Hydrogen-Bonding Properties Targeting G-Quadruplex Nucleic Acids. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600757] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Filippo Doria
- Department of Chemistry; University of Pavia; v.le Taramelli 10 27100 Pavia Italy
| | - Matteo Nadai
- Department of Molecular Medicine; University of Padua; via Gabelli 63 35121 Padua Italy
| | - Giosuè Costa
- Dipartimento di Scienze della Salute Università degli Studi “Magna Graecia” di Catanzaro Campus “Salvatore Venuta”; Viale Europa 88100 Catanzaro Italy
| | - Giovanna Sattin
- Department of Molecular Medicine; University of Padua; via Gabelli 63 35121 Padua Italy
| | - Caroline Gallati
- Department of Chemistry; University of Pavia; v.le Taramelli 10 27100 Pavia Italy
| | - Greta Bergamaschi
- Department of Chemistry; University of Pavia; v.le Taramelli 10 27100 Pavia Italy
| | - Federica Moraca
- Dipartimento di Scienze della Salute Università degli Studi “Magna Graecia” di Catanzaro Campus “Salvatore Venuta”; Viale Europa 88100 Catanzaro Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute Università degli Studi “Magna Graecia” di Catanzaro Campus “Salvatore Venuta”; Viale Europa 88100 Catanzaro Italy
| | - Mauro Freccero
- Department of Chemistry; University of Pavia; v.le Taramelli 10 27100 Pavia Italy
| | - Sara N. Richter
- Department of Molecular Medicine; University of Padua; via Gabelli 63 35121 Padua Italy
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41
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Morel E, Poyer F, Vaslin L, Bombard S, Teulade-Fichou MP. Photoactivatable platinum(II) terpyridine derivatives for G-quadruplex DNA double anchoring. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.02.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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42
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Wang Y, Lin Z, Fan H, Peng X. Photoinduced DNA Interstrand Cross-Link Formation by Naphthalene Boronates via a Carbocation. Chemistry 2016; 22:10382-6. [DOI: 10.1002/chem.201601504] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Yibin Wang
- Department of Chemistry and Biochemistry; University of Wisconsin Milwaukee; 3210 N. Cramer St. Milwaukee WI 53211 USA
| | - Zechao Lin
- Department of Chemistry and Biochemistry; University of Wisconsin Milwaukee; 3210 N. Cramer St. Milwaukee WI 53211 USA
| | - Heli Fan
- Department of Chemistry and Biochemistry; University of Wisconsin Milwaukee; 3210 N. Cramer St. Milwaukee WI 53211 USA
| | - Xiaohua Peng
- Department of Chemistry and Biochemistry; University of Wisconsin Milwaukee; 3210 N. Cramer St. Milwaukee WI 53211 USA
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43
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Doria F, Lena A, Bargiggia R, Freccero M. Conjugation, Substituent, and Solvent Effects on the Photogeneration of Quinone Methides. J Org Chem 2016; 81:3665-73. [DOI: 10.1021/acs.joc.6b00331] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Filippo Doria
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli
10, 27100 Pavia, Italy
| | - Alberto Lena
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli
10, 27100 Pavia, Italy
| | - Riccardo Bargiggia
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli
10, 27100 Pavia, Italy
| | - Mauro Freccero
- Dipartimento di Chimica, Università di Pavia, V.le Taramelli
10, 27100 Pavia, Italy
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44
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Virgilio A, Esposito V, Mayol L, Giancola C, Petraccone L, Galeone A. The oxidative damage to the human telomere: effects of 5-hydroxymethyl-2'-deoxyuridine on telomeric G-quadruplex structures. Org Biomol Chem 2016; 13:7421-9. [PMID: 25997822 DOI: 10.1039/c5ob00748h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
As part of the genome, human telomeric regions can be damaged by the chemically reactive molecules responsible for oxidative DNA damage. Considering that G-quadruplex structures have been proven to occur in human telomere regions, several studies have been devoted to investigating the effect of oxidation products on the properties of these structures. However only investigations concerning the presence in G-quadruplexes of the main oxidation products of deoxyguanosine and deoxyadenosine have appeared in the literature. Here, we investigated the effects of 5-hydroxymethyl-2'-deoxyuridine (5-hmdU), one of the main oxidation products of T, on the physical-chemical properties of the G-quadruplex structures formed by two human telomeric sequences. Collected calorimetric, circular dichroism and electrophoretic data suggest that, in contrast to most of the results on other damage, the replacement of a T with a 5-hmdU results in only negligible effects on structural stability. Reported results and other data from literature suggest a possible protecting effect of the loop residues on the other parts of the G-quadruplexes.
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Affiliation(s)
- Antonella Virgilio
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Via D. Montesano 49, I-80131 Napoli, Italy.
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45
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Kralj M, Uzelac L, Wang YH, Wan P, Tireli M, Mlinarić-Majerski K, Piantanida I, Basarić N. Enhancement of antiproliferative activity by phototautomerization of anthrylphenols. Photochem Photobiol Sci 2016; 14:1082-92. [PMID: 25850014 DOI: 10.1039/c5pp00099h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
An antiproliferative investigation was conducted on 3 human cancer cell lines, HCT 116 (colon), MCF-7 (breast), and H 460 (lung), on a series of 4 anthrylphenols in the dark and upon exposure to light (350 nm). 9-(2-Hydroxyphenyl)anthracene (1) moderately inhibited proliferation, but irradiation considerably enhanced the effect. The other anthracenes 4–6 exhibited antiproliferative activity in the dark, which was not enhanced upon irradiation. The enhancement of the antiproliferative effect on the irradiation of 1 was rationalized as being due to the formation of quinone methide (QM 2) by excited state proton transfer. QM 2 acts as an electrophilic species capable of reacting with biological molecules. Although QM 2 reacts with nucleotides, the adducts could not be isolated. On the contrary, cysteine adduct 8 was isolated and characterized, whereas the adducts with glycine, serine and tripeptide glutathione were characterized by MS. Non-covalent binding of 1 to DNA and bovine serum albumin was demonstrated by UV-vis, fluorescence and CD spectroscopy. However, a straightforward conclusion regarding the DNA or protein alkylating (damaging) ability of 2 could not be drawn. The results obtained by the irradiation of 1 in the presence of DNA, amino acids and peptides, cell cycle perturbation analysis, and in vitro translation of GFP suggest that the effect is not only due to the damage of DNA but also due to the impact on the cellular proteins. Considering that to date all QM agents were assumed to target DNA dominantly, this is an important finding with an impact on the further development of anticancer agents based on QMs.
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Affiliation(s)
- Marijeta Kralj
- Department of Molecular Medicine, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia.
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46
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Salvati E, Doria F, Manoli F, D'Angelo C, Biroccio A, Freccero M, Manet I. A bimodal fluorescent and photocytotoxic naphthalene diimide for theranostic applications. Org Biomol Chem 2016; 14:7238-49. [DOI: 10.1039/c6ob00987e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe the bimodal activity of a water-soluble tetracationic naphthalene diimide as red light emitter for fluorescence imaging, including fluorescence-lifetime imaging, and singlet oxygen photosensitizer, inducing photocytotoxicity in cancer cells.
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Affiliation(s)
- Erica Salvati
- Oncogenomic and Epigenetic Unit
- Regina Elena National Cancer Institute
- 53 Rome
- Italy
| | - Filippo Doria
- Dipartimento di Chimica
- Università di Pavia
- 27100 Pavia
- Italy
| | - Francesco Manoli
- Istituto per la Sintesi Organica e la Fotoreattività
- Consiglio Nazionale delle Ricerche
- 40129 Bologna
- Italy
| | - Carmen D'Angelo
- Oncogenomic and Epigenetic Unit
- Regina Elena National Cancer Institute
- 53 Rome
- Italy
| | - Annamaria Biroccio
- Oncogenomic and Epigenetic Unit
- Regina Elena National Cancer Institute
- 53 Rome
- Italy
| | - Mauro Freccero
- Dipartimento di Chimica
- Università di Pavia
- 27100 Pavia
- Italy
| | - Ilse Manet
- Istituto per la Sintesi Organica e la Fotoreattività
- Consiglio Nazionale delle Ricerche
- 40129 Bologna
- Italy
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47
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Wu B, Gao X, Yan Z, Chen MW, Zhou YG. C–H Oxidation/Michael Addition/Cyclization Cascade for Enantioselective Synthesis of Functionalized 2-Amino-4H-chromenes. Org Lett 2015; 17:6134-7. [DOI: 10.1021/acs.orglett.5b03148] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bo Wu
- State
Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Xiang Gao
- State
Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Zhong Yan
- State
Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Mu-Wang Chen
- State
Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Yong-Gui Zhou
- State
Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- State
Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, P. R. China
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48
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Chen CH, Hu TH, Huang TC, Chen YL, Chen YR, Cheng CC, Chen CT. Delineation of G-Quadruplex Alkylation Sites Mediated by 3,6-Bis(1-methyl-4-vinylpyridinium iodide)carbazole-Aniline Mustard Conjugates. Chemistry 2015; 21:17379-90. [PMID: 26769627 DOI: 10.1002/chem.201502595] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Indexed: 11/12/2022]
Abstract
A new G-quadruplex (G-4)-directing alkylating agent BMVC-C3M was designed and synthesized to integrate 3,6-bis(1-methyl-4-vinylpyridinium iodide)carbazole (BMVC) with aniline mustard. Various telomeric G-4 structures (hybrid-2 type and antiparallel) and an oncogene promoter, c-MYC (parallel), were constructed to react with BMVC-C3M, yielding 35 % alkylation yield toward G-4 DNA over other DNA categories (<6 %) and high specificity under competition conditions. Analysis of the intact alkylation adducts by electrospray ionization mass spectroscopy (ESI-MS) revealed the stepwise DNA alkylation mechanism of aniline mustard for the first time. Furthermore, the monoalkylation sites and intrastrand cross-linking sites were determined and found to be dependent on G-4 topology based on the results of footprinting analysis in combination with mass spectroscopic techniques and in silico modeling. The results indicated that BMVC-C3M preferentially alkylated at A15 (H26), G12 (H24), and G2 (c-MYC), respectively, as monoalkylated adducts and formed A15-C3M-A21 (H26), G12-C3M-G4 (H24), and G2-C3M-G4/G17 (c-MYC), respectively, as cross-linked dialkylated adducts. Collectively, the stability and site-selective cross-linking capacity of BMVC-C3M provides a credible tool for the structural and functional characterization of G-4 DNAs in biological systems.
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Affiliation(s)
- Chien-Han Chen
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan (R.O.C.), Fax: (+886) 2-23636359
| | - Tsung-Hao Hu
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan (R.O.C.), Fax: (+886) 2-23636359
| | - Tzu-Chiao Huang
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan (R.O.C.), Fax: (+886) 2-23636359
| | - Ying-Lan Chen
- Agricultural Biotechnology Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Taipei, 11529 Taiwan (R.O.C.).,Institute of Plant Biology and Department of Life Science, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan (R.O.C.)
| | - Yet-Ran Chen
- Agricultural Biotechnology Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Taipei, 11529 Taiwan (R.O.C.)
| | - Chien-Chung Cheng
- Department of Applied Chemistry, Chia-Yi University, No. 300, Xuefu Road, Chiayi City, 60004 Taiwan (R.O.C.), Fax: (+886) 5-2717901.
| | - Chao-Tsen Chen
- Department of Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan (R.O.C.), Fax: (+886) 2-23636359.
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49
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Škalamera Đ, Bohne C, Landgraf S, Basarić N. Photodeamination Reaction Mechanism in Aminomethyl p-Cresol Derivatives: Different Reactivity of Amines and Ammonium Salts. J Org Chem 2015; 80:10817-28. [PMID: 26461794 DOI: 10.1021/acs.joc.5b01991] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Derivatives of p-cresol 1-4 were synthesized, and their photochemical reactivity, acid-base, and photophysical properties were investigated. The photoreactivity of amines 1 and 3 is different from that for the corresponding ammonium salts 2 and 4. All compounds have low fluorescence quantum yields because the excited states undergo deamination reactions, and for all cresols the formation of quinone methides (QMs) was observed by laser flash photolysis. The reactivity observed is a consequence of the higher acidity of the S1 states of these p-cresols and the ability for excited-state intramolecular proton transfer (ESIPT) to occur in the case of 1 and 3, but not for salts 2 and 4. In aqueous solvent, deamination depends largely on the prototropic form of the molecule. The most efficient deamination takes place when monoamine is in the zwitterionic form (pH 9-11) or diamine is in the monocationic form (pH 7-9). QM1, QM3, and QM4 react with nucleophiles, and QM1 exhibits a shorter lifetime when formed from 1 (τ in CH3CN = 5 ms) than from 2 (τ in CH3CN = 200 ms) due to the reaction with eliminated dimethylamine, which acts as a nucleophile in the case of QM1. Bifunctional QM4 undergoes two types of reactions with nucleophiles, giving adducts or new QM species. The mechanistic diversity uncovered is of significance to biological systems, such as for the use of bifunctional QMs to achieve DNA cross-linking.
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Affiliation(s)
- Đani Škalamera
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute , Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Cornelia Bohne
- Department of Chemistry, University of Victoria , Box 3065 STN CSC, Victoria, BC V8W 3 V6, Canada
| | - Stephan Landgraf
- Institute of Physical and Theoretical Chemistry, Graz University of Technology , Stremayrgasse 9, A-8010 Graz, Austria
| | - Nikola Basarić
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute , Bijenička cesta 54, 10 000 Zagreb, Croatia
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50
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Laughlin S, Wilson WD. May the Best Molecule Win: Competition ESI Mass Spectrometry. Int J Mol Sci 2015; 16:24506-31. [PMID: 26501262 PMCID: PMC4632762 DOI: 10.3390/ijms161024506] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 09/18/2015] [Accepted: 10/09/2015] [Indexed: 02/07/2023] Open
Abstract
Electrospray ionization mass spectrometry has become invaluable in the characterization of macromolecular biological systems such as nucleic acids and proteins. Recent advances in the field of mass spectrometry and the soft conditions characteristic of electrospray ionization allow for the investigation of non-covalent interactions among large biomolecules and ligands. Modulation of genetic processes through the use of small molecule inhibitors with the DNA minor groove is gaining attention as a potential therapeutic approach. In this review, we discuss the development of a competition method using electrospray ionization mass spectrometry to probe the interactions of multiple DNA sequences with libraries of minor groove binding molecules. Such an approach acts as a high-throughput screening method to determine important information including the stoichiometry, binding mode, cooperativity, and relative binding affinity. In addition to small molecule-DNA complexes, we highlight other applications in which competition mass spectrometry has been used. A competitive approach to simultaneously investigate complex interactions promises to be a powerful tool in the discovery of small molecule inhibitors with high specificity and for specific, important DNA sequences.
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Affiliation(s)
- Sarah Laughlin
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA.
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA.
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