1
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Chen Y, Onizuka K, Nagatsugi F. Michael addition-activated alkylation of G-quadruplex DNA with methylamine-protected vinyl-quinazolinone derivatives. Bioorg Med Chem Lett 2024; 109:129855. [PMID: 38908766 DOI: 10.1016/j.bmcl.2024.129855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/11/2024] [Accepted: 06/19/2024] [Indexed: 06/24/2024]
Abstract
The role of G-quadruplex (G4) in cellular processes can be investigated by the covalent modification of G4-DNA using alkylating reagents. Controllable alkylating reagents activated by external stimuli can react elegantly and selectively. Herein, we report a chemical activation system that can significantly boost the reaction rate of methylamine-protected vinyl-quinazolinone (VQ) derivative for the alkylation of G4-DNA. The two screened activators can transform low-reactive VQ-NHR' to highly reactive intermediates following the Michael addition mechanism. This approach expands the toolbox of activable G4 alkylating reagents.
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Affiliation(s)
- Yutong Chen
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan; Division for the Establishment of Frontier Sciences of Organization for Advanced Studies, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan.
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2
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Guo Y, Ge L, Phillips DL, Ma J, Fang Y. Different Reaction Mechanisms Triggered by the Meta Effect: Photoinduced Generation of Quinone Methides from Hydroxybiphenyl Derivatives. J Phys Chem Lett 2024; 15:8569-8576. [PMID: 39140706 DOI: 10.1021/acs.jpclett.4c01875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
A series of sterically congested quinone methides (QMs) exhibit photoinduced antiproliferative activity against some human cancer cell lines. To elucidate the structure-reactivity relationship and details of mechanisms of the photogeneration of sterically congested QMs, we chose phenylphenol derivatives 1-3 as QM precursors and investigated their photodehydration processes in aqueous solutions using ultrafast spectroscopy and theoretical computations. We found that meta derivatives 1 and 2 undergo water-mediated excited-state proton transfer (ESPT) from the phenol OH, followed by expulsion of the OH- to form QMs. By comparison, para derivative 3 proceeds via water-mediated ESPT from H2O to benzyl alcohol coupled with dehydration as the first step, delivering a cation intermediate, which further deprotonates to yield QM. Such results would help chemists understand more about the meta effects in photochemistry and about ESPT and would help synthetic chemists design sterically congested QM precursors with extraordinary reactivities and expand applications of QMs in biological and medical systems.
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Affiliation(s)
- Yan Guo
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Lingfeng Ge
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - David Lee Phillips
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong S.A.R. 999077, P. R. China
| | - Jiani Ma
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Yu Fang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
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3
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Majhi A, Venkateswarlu K, Sasikumar P. Coumarin Based Fluorescent Probe for Detecting Heavy Metal Ions. J Fluoresc 2024; 34:1453-1483. [PMID: 37581754 DOI: 10.1007/s10895-023-03372-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/25/2023] [Indexed: 08/16/2023]
Abstract
Heavy metals such as Iron, Copper, and Zinc are micro-essential trace metal and involve animportant biological role, but it quickly turns toxic at exceeding the permissible limit, causing gastrointestinal irritation, liver, bone, and kidney damage, as well as disorders including Wilson's, Parkinson's, and Alzheimer's. It is important to detect the metal ions as well as their concentration quickly and affordable cost using organic probes. Among the organic probes,the coumarin fluorescent probe shows a very prominent candidate with heavy metal ions. Therefore, in the present review, we reviewed the very recent literature the identify the heavy metals using modified coumarin fluorescent probes. Readers will get information quickly about the method of preparation of modified coumarin core and their use as fluorescent probes with heavy metals using absorption and emission spectroscopic methods along with the probable mechanistic pathway of detection.
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Affiliation(s)
- Anjoy Majhi
- Department of Chemistry, Presidency University, 86/1 College Street, Kolkata, West Bengal, 700073, India.
| | - Katta Venkateswarlu
- Laboratory for Synthetic and Natural Products Chemistry, Department of Chemistry, Yogi Vemana University, Kadapa, 516005, India
| | - Palani Sasikumar
- Department of Chemistry, Presidency University, 86/1 College Street, Kolkata, West Bengal, 700073, India.
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4
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Nadai M, Doria F, Frasson I, Perrone R, Pirota V, Bergamaschi G, Freccero M, Richter SN. Naphthalene Diimide-Tetraazacycloalkane Conjugates Are G-Quadruplex-Based HIV-1 Inhibitors with a Dual Mode of Action. ACS Infect Dis 2024; 10:489-499. [PMID: 38175706 PMCID: PMC10862543 DOI: 10.1021/acsinfecdis.3c00453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/06/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024]
Abstract
Human immunodeficiency virus 1 (HIV-1) therapeutic regimens consist of three or more drugs targeting different steps of the viral life cycle to limit the emergence of viral resistance. In line with the multitargeting strategy, here we conjugated a naphthalene diimide (NDI) moiety with a tetraazacycloalkane to obtain novel naphthalene diimide (NDI)-tetraazacycloalkane conjugates. The NDI inhibits the HIV-1 promoter activity by binding to LTR G-quadruplexes, and the tetraazacycloalkane mimics AMD3100, which blocks HIV entry into cells by interfering with the CXCR4 coreceptor. We synthesized, purified, and tested the metal-free NDI-tetraazacycloalkane conjugate and the two derived metal-organic complexes (MOCs) that incorporate Cu2+ and Zn2+. The NDI-MOCs showed enhanced binding to LTR G4s as assessed by FRET and CD assays in vitro. They also showed enhanced activity in cells where they dose-dependently reduced LTR promoter activity and inhibited viral entry only of the HIV-1 strain that exploited the CXCR4 coreceptor. The time of addition assay confirmed the dual targeting at the different HIV-1 steps. Our results indicate that the NDI-MOC conjugates can simultaneously inhibit viral entry, by targeting the CXCR4 coreceptor, and LTR promoter activity, by stabilizing the LTR G-quadruplexes. The approach of combining multiple targets in a single compound may streamline treatment regimens and improve the overall patient outcomes.
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Affiliation(s)
- Matteo Nadai
- Department
of Molecular Medicine, University of Padua, Via Gabelli 63, 35121 Padua, Italy
| | - Filippo Doria
- Department
of Chemistry, University of Pavia, V.le Taramelli 10, 27100 Pavia, Italy
| | - Ilaria Frasson
- Department
of Molecular Medicine, University of Padua, Via Gabelli 63, 35121 Padua, Italy
| | - Rosalba Perrone
- Buck
Institute for Research on Aging, Novato, California 94945, United States
| | - Valentina Pirota
- Department
of Chemistry, University of Pavia, V.le Taramelli 10, 27100 Pavia, Italy
| | - Greta Bergamaschi
- National
Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche
“Giulio Natta” (SCITEC–CNR), Via Mario Bianco 9, 20131 Milano, 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
- Microbiology
and Virology Unit, Padua University Hospital, 35121 Padua, Italy
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5
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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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6
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Clowes SR, Ali Y, Astley OR, Răsădean DM, Pantoş GD. The Influence of Chirality on the β-Amino-Acid Naphthalenediimides/G-Quadruplex DNA Interaction. Molecules 2023; 28:7291. [PMID: 37959711 PMCID: PMC10647805 DOI: 10.3390/molecules28217291] [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: 09/05/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
G-quadruplexes (G4s) have been identified as a potential alternative chemotherapy target. A series of eight β-amino acid derived naphthalenediimides (NDI) were screened against a series of oncogenic G4 sequences: c-KIT1, h-TELO, and TBA. Three sets of enantiomers were investigated to further our understanding of the effect of point chirality on G4 stabilisation. Enantioselective binding behaviour was observed with both c-KIT1 and h-TELO. Docking studies using GNINA and UV-vis titrations were employed to better understand this selective binding behaviour.
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Affiliation(s)
| | | | | | | | - G. Dan Pantoş
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
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7
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Cadoni E, De Paepe L, Colpaert G, Tack R, Waegeman D, Manicardi A, Madder A. A red light-triggered chemical tool for sequence-specific alkylation of G-quadruplex and I-motif DNA. Nucleic Acids Res 2023; 51:4112-4125. [PMID: 36971129 PMCID: PMC10201448 DOI: 10.1093/nar/gkad189] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/03/2023] [Accepted: 03/12/2023] [Indexed: 08/21/2023] Open
Abstract
The importance of non-canonical DNA structures such as G-quadruplexes (G4) and intercalating-motifs (iMs) in the fine regulation of a variety of cellular processes has been recently demonstrated. As the crucial roles of these structures are being unravelled, it is becoming more and more important to develop tools that allow targeting these structures with the highest possible specificity. While targeting methodologies have been reported for G4s, this is not the case for iMs, as evidenced by the limited number of specific ligands able to bind the latter and the total absence of selective alkylating agents for their covalent targeting. Furthermore, strategies for the sequence-specific covalent targeting of G4s and iMs have not been reported thus far. Herein, we describe a simple methodology to achieve sequence-specific covalent targeting of G4 and iM DNA structures based on the combination of (i) a peptide nucleic acid (PNA) recognizing a specific sequence of interest, (ii) a pro-reactive moiety enabling a controlled alkylation reaction, and (iii) a G4 or iM ligand orienting the alkylating warhead to the reactive residues. This multi-component system allows for the targeting of specific G4 or iM sequences of interest in the presence of competing DNA sequences and under biologically relevant conditions.
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Affiliation(s)
- Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Lessandro De Paepe
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Gertjan Colpaert
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Ruben Tack
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Dries Waegeman
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Alex Manicardi
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
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8
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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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9
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Holden L, Gkika KS, Burke CS, Long C, Keyes TE. Selective, Disruptive Luminescent Ru(II) Polypyridyl Probes of G-Quadruplex. Inorg Chem 2023; 62:2213-2227. [PMID: 36703307 PMCID: PMC9906756 DOI: 10.1021/acs.inorgchem.2c03903] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Sensors capable of transducing G-quadruplex DNA binding are important both in solution and for imaging and interrogation in cellulo. Ru(II)-based light switches incorporating dipyridylphenazine (dppz) ligands are effective probes for recognition and imaging of DNA and its polymorphs including G-quadruplex, although selectivity is a limitation. While the majority of Ru(II)-based light switches reported to date, stabilize the quadruplex, imaging/theranostic probes that can disrupt G4s are of potentially enormous value in study and therapy for a range of disease states. We report here, on a Ru(II) complex (Ru-PDC3) that assembles the light switch capability of a Ru(II) dipyridylphenazine complex with the well-known G4-selective ligand Phen-DC3, into a single structure. The complex shows the anticipated light switch effect and strong affinity for G4 structures. Affinity depended on the G4 topology and sequence, but across all structures bar one, it was roughly an order of magnitude greater than for duplex or single-stranded DNA. Moreover, photophysical and Raman spectral data showed clear discrimination between duplex DNA and G4-bound structures offering the prospect of discrimination in imaging as well as in solution. Crucially, unlike the constituent components of the probe, Ru-PDC3 is a powerful G4 disrupter. From circular dichroism (CD), a reduction of ellipticity of the G4 between 70 and 95% was observed depending on topology and in many cases was accompanied by an induced CD signal for the metal complex. The extent of change in ellipticity is amongst the largest reported for small-molecule ligand G4 binding. While a promising G4 probe, without modification, the complex is fully water-soluble and readily permeable to live cells.
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10
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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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11
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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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12
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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] [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 Chemistry, University of Pavia, Viale Taramelli 10, 27100, Pavia, Italy
| | - Alessandra Benassi
- Department of Chemistry, University of Pavia, Viale Taramelli 10, 27100, Pavia, Italy
| | - Michele Stasi
- Department of Chemistry, University of Pavia, Viale Taramelli 10, 27100, Pavia, Italy.,Present Address: Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | | | - Mauro Freccero
- Department of Chemistry, University of Pavia, Viale Taramelli 10, 27100, Pavia, Italy
| | - Didier Gasparutto
- University Grenoble Alpes, CEA, CNRS, IRIG, SyMMES-UMR5819, 38054, Grenoble, France
| | - Sophie Bombard
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405, Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris-Saclay, 91405, Orsay, France
| | - Filippo Doria
- Department of Chemistry, University of Pavia, Viale Taramelli 10, 27100, Pavia, Italy
| | - Daniela Verga
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405, Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris-Saclay, 91405, Orsay, France
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13
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Cagirici HB, Budak H, Sen TZ. G4Boost: a machine learning-based tool for quadruplex identification and stability prediction. BMC Bioinformatics 2022; 23:240. [PMID: 35717172 PMCID: PMC9206279 DOI: 10.1186/s12859-022-04782-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/09/2022] [Indexed: 11/10/2022] Open
Abstract
Background G-quadruplexes (G4s), formed within guanine-rich nucleic acids, are secondary structures involved in important biological processes. Although every G4 motif has the potential to form a stable G4 structure, not every G4 motif would, and accurate energy-based methods are needed to assess their structural stability. Here, we present a decision tree-based prediction tool, G4Boost, to identify G4 motifs and predict their secondary structure folding probability and thermodynamic stability based on their sequences, nucleotide compositions, and estimated structural topologies.
Results G4Boost predicted the quadruplex folding state with an accuracy greater then 93% and an F1-score of 0.96, and the folding energy with an RMSE of 4.28 and R2 of 0.95 only by the means of sequence intrinsic feature. G4Boost was successfully applied and validated to predict the stability of experimentally-determined G4 structures, including for plants and humans. Conclusion G4Boost outperformed the three machine-learning based prediction tools, DeepG4, Quadron, and G4RNA Screener, in terms of both accuracy and F1-score, and can be highly useful for G4 prediction to understand gene regulation across species including plants and humans. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04782-z.
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Affiliation(s)
- H Busra Cagirici
- US Department of Agriculture - Agricultural Research Service, Crop Improvement Genetics Research Unit, Western Regional Research Center, 800 Buchanan St, Albany, CA, 94710, USA
| | | | - Taner Z Sen
- US Department of Agriculture - Agricultural Research Service, Crop Improvement Genetics Research Unit, Western Regional Research Center, 800 Buchanan St, Albany, CA, 94710, USA.
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14
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Ali K, Mishra P, Kumar A, Reddy DN, Chowdhury S, Panda G. Reactivity vs. selectivity of quinone methides: synthesis of pharmaceutically important molecules, toxicity and biological applications. Chem Commun (Camb) 2022; 58:6160-6175. [PMID: 35522910 DOI: 10.1039/d2cc00838f] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Quinone methides (QMs) are considered to be highly reactive intermediates because of their aromatization both in chemical and biological systems. Being highly accessible, quinone methides (QMs) have been widely exploited and their concurrent use has been manifested for the synthesis of tertiary and quaternary carbon centers of bioactives, drugs and drug-like molecules. In this feature article, the synthetic routes, structure-reactivity relationships and synthetic applications of quinone methides are discussed. Formation of the intermediates during bioactivation of different chemical entities and possible chemical manifestations leading to their toxicity in biological systems are also covered.
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Affiliation(s)
- Kasim Ali
- Medicinal & Process Chemistry Division, CSIR-Central Drug Research Institute, Jankipuram Extension, Sector 10, Lucknow 226031, UP, India. .,Academy of Scientific & Industrial Research (AcSIR), Ghaziabad, Uttar Pradesh-201 002, India
| | - Prajjval Mishra
- Medicinal & Process Chemistry Division, CSIR-Central Drug Research Institute, Jankipuram Extension, Sector 10, Lucknow 226031, UP, India.
| | - Awnish Kumar
- Medicinal & Process Chemistry Division, CSIR-Central Drug Research Institute, Jankipuram Extension, Sector 10, Lucknow 226031, UP, India.
| | - Damodara N Reddy
- Medicinal & Process Chemistry Division, CSIR-Central Drug Research Institute, Jankipuram Extension, Sector 10, Lucknow 226031, UP, India. .,Academy of Scientific & Industrial Research (AcSIR), Ghaziabad, Uttar Pradesh-201 002, India
| | - Sushobhan Chowdhury
- Medicinal & Process Chemistry Division, CSIR-Central Drug Research Institute, Jankipuram Extension, Sector 10, Lucknow 226031, UP, India.
| | - Gautam Panda
- Medicinal & Process Chemistry Division, CSIR-Central Drug Research Institute, Jankipuram Extension, Sector 10, Lucknow 226031, UP, India. .,Academy of Scientific & Industrial Research (AcSIR), Ghaziabad, Uttar Pradesh-201 002, India
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15
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Yu D, Fan H, Sun J, Xue L, Wang L, Jia Y, Tian J, Sun H. Phenyl Selenide-Based Precursors as Hydrogen Peroxide Inducible DNA Interstrand Cross-Linkers. Chembiochem 2022; 23:e202200086. [PMID: 35224848 DOI: 10.1002/cbic.202200086] [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: 02/08/2022] [Revised: 02/26/2022] [Indexed: 11/10/2022]
Abstract
DNA interstrand crosslinks (ICLs) are highly toxic DNA lesions, and induce cell death by blocking DNA strands separation. Most developed ICL agents, aiming to kill cancer cells, also generate adverse side effects to normal cells. H2O2-inducible DNA ICL agents are highly selective to target cancer cells, as the concentration of H2O2 is higher in cancer cells than normal cells. Previous studies focus on arylboronate-based precursors, reacting with H2O2 to generate reactive quinone methides (QMs) crosslinking DNA. Here we explore phenyl selenide-based precursors 1-3 as H2O2-inducible DNA ICL agents. The precursors 1-3 can be activated by H2O2 to generate the good benzylic leaving group and promote production of reactive QMs to crosslink DNA. Moreover, the DNA cross-linking ability is enhanced by the introduction of substituents in the para position of the phenolic hydroxyl group. From the substituents explored (H, OMe, F), the introduction of electron donating group (OMe) shows a pronounced elevating effect. Further mechanistic studies at the molecular and DNA levels confirm alkylation sites located mainly at dAs, dCs and dGs in DNA. Additionally, cellular experiments reveal that agents 1-3 exhibit higher cytotoxicity toward H1299 human lung cancer cells compared to clinically used drugs, by inducing cellular DNA damage, apoptosis and G0/G1 cell cycle arrest. This study provides a strategy to develop H2O2-inducible DNA interstrand cross-linkers.
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Affiliation(s)
- Dehao Yu
- Tianjin Medical University, Pharmacy, 22 Qixiangtai Road, Heping District, 300070, Tianjin, CHINA
| | - Heli Fan
- Tianjin Medical University, Pharmacy, 22 Qixiangtai Road, Heping District, 300070, Tianjin, CHINA
| | - Jing Sun
- Tianjin Medical University, Pharmacy, 22 Qixiangtai Road, Heping District, 300070, Tianjin, CHINA
| | - Li Xue
- Tianjin Medical University, Pharmacy, 22 Qixiangtai Road, Heping District, 300070, Tianjin, CHINA
| | - Luo Wang
- Tianjin Medical University, Pharmacy, 22 Qixiangtai Road, Heping District, 300070, Tianjin, CHINA
| | - Yuanyuan Jia
- Tianjin Medical University, Pharmacy, 22 Qixiangtai Road, Heping District, 300070, Tianjin, CHINA
| | - Junyu Tian
- Tianjin Medical University, Pharmacy, 22 Qixiangtai Road, Heping District, 300070, Tianjin, CHINA
| | - Huabing Sun
- Tianjin Medical University, Pharmacy, 22 Qixiangtai Road, 300070, Tianjin, CHINA
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16
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A fluorescent molecular rotor for the selective detection of the hybrid-conformation 22AG G-Quadruplex. Bioorg Med Chem Lett 2022; 55:128462. [PMID: 34813881 DOI: 10.1016/j.bmcl.2021.128462] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 01/07/2023]
Abstract
G-quadruplex (G4) DNA plays a vital role in myriad biological process and is linked to several human diseases, including Alzheimer's disease. Probing G4s with fluorescent probes can provide a better understanding their mechanisms of action and of their roles in Nature. In this study we developed a quinolinium-vinylaniline molecular rotor probe, featuring a diethylaminosalicylaldehyde unit that could discriminate the hybrid-22AG G4 sequence selectively amongst other G4 sequences. This probe underwent a significant red-shift upon binding to the target G4 (broad 575 nm → sharp 630 nm) with enhanced fluorescence (up to 14-fold). We suspect that the vinylaniline unit of the molecular rotor, when bound to the hybrid-22 A G4, experienced restricted rotation, thereby undergoing enhanced intramolecular charge transfer. The presence of the diethylaminosalicylaldehyde moiety appeared to play a major role in the enhanced selectivity toward the 22AG G4.
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17
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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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18
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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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19
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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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20
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Fan H, Sun H, Zhang Q, Peng X. Photoinduced DNA Interstrand Cross-Linking by 1,1'-Biphenyl Analogues: Substituents and Leaving Groups Combine to Determine the Efficiency of Cross-Linker. Chemistry 2021; 27:5215-5224. [PMID: 33440025 DOI: 10.1002/chem.202005064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/05/2021] [Indexed: 11/11/2022]
Abstract
Two series of 1,1'-biphenyl analogues with various leaving groups (L=OAc, OCH3 , OCHCH=CH2 , OCH2 Ph, SPh, SePh, and Ph3 P+ ) were synthesized. Their reactivity towards DNA and the reaction mechanism were investigated by determining DNA interstrand cross-link (ICL) efficiency, radical and carbocation formation, and the cross-linking reaction sites. All compounds induced DNA ICL formation upon 350 nm irradiation via a carbocation that was generated from oxidation of the corresponding free radicals. The ICL efficiency and the reaction rate strongly depended on the combined effect of the leaving group and the substituent. Among all compounds tested, the high ICL efficiency (30-43 %) and fast reaction rate were observed with compounds carrying a nitrophenyl group and acetate (2 a), ether (2 b and 2 c), or triphenylphosphonium salt (2 g) as leaving groups. Most compounds with a 4-methoxybenzene group showed similar DNA ICL efficiency (≈30 %) with a slow DNA cross-linking reaction rate. Both cation trapping and free radical trapping adducts were detected in the photo activation process of these compounds, which provided direct evidence for the proposed mechanism. Heat stability study in combination with sequence study suggested that these photo-generated benzyl cations alkylate DNA at dG, dA, and dC sites.
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Affiliation(s)
- Heli Fan
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, Wisconsin, 53211, USA.,School of Pharmacy, Tianjin Medical University, 300070, Tianjin, P. R. China
| | - Huabing Sun
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, Wisconsin, 53211, USA.,School of Pharmacy, Tianjin Medical University, 300070, Tianjin, P. R. China
| | - Qi Zhang
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, Wisconsin, 53211, USA
| | - Xiaohua Peng
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, Wisconsin, 53211, USA
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21
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Zhirov AM, Kovalev DA, Ulshina DV, Pisarenko SV, Demidov OP, Borovlev IV. Diazapyrenes: interaction with nucleic acids and biological activity. Chem Heterocycl Compd (N Y) 2020; 56:674-693. [PMID: 32836316 PMCID: PMC7366485 DOI: 10.1007/s10593-020-02717-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/26/2019] [Indexed: 12/22/2022]
Abstract
The review summarizes data on the practical aspects of the interaction of nucleic acids with diazapyrene derivatives. The information on biological activity is given and the probable mechanisms underlying the action of diazapyrenes are analyzed. It contains 119 references.
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Affiliation(s)
- Andrey M. Zhirov
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Dmitry A. Kovalev
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Diana V. Ulshina
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Sergey V. Pisarenko
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Oleg P. Demidov
- North Caucasus Federal University, 1a Pushkina St, Stavropol, 355017 Russia
| | - Ivan V. Borovlev
- North Caucasus Federal University, 1a Pushkina St, Stavropol, 355017 Russia
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22
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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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23
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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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24
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Shukla J, Mukhopadhyay P. Synthesis of Functionalized Naphthalene Diimides and their Redox Properties. European J Org Chem 2019. [DOI: 10.1002/ejoc.201901390] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Jyoti Shukla
- School of Physical Sciences; Jawaharlal Nehru University; New Delhi India
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25
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Affiliation(s)
- Dattatraya H. Dethe
- Department of Chemistry, Indian Institute of Technology, Kanpur 208016, India
| | - Boda VijayKumar
- Department of Chemistry, Indian Institute of Technology, Kanpur 208016, India
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26
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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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27
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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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28
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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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29
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Minard A, Liano D, Wang X, Di Antonio M. The unexplored potential of quinone methides in chemical biology. Bioorg Med Chem 2019; 27:2298-2305. [PMID: 30955994 DOI: 10.1016/j.bmc.2019.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/29/2019] [Accepted: 04/01/2019] [Indexed: 11/16/2022]
Abstract
Quinone methides (QMs) are transient reactive species that can be efficiently generated from stable precursors under a variety of biocompatible conditions. Due to their electrophilic nature, QMs have been widely explored as cross-linking agents of DNA and proteins under physiological conditions. However, QMs also have a diene character and can irreversibly react via Diels-Alder reaction with electron-rich dienophiles. This particular reactivity has been recently exploited to label biomolecules with fluorophores in living cells. QMs are characterised by two unique properties that make them ideal candidates for chemical biology applications: i) they can be efficiently generated in situ from very stable precursors by means of bio-orthogonal protocols ii) they are reversible cross-linking agents, making them suitable for "catch and release" target-enrichment experiments. Nevertheless, there are only few examples reported to date that truly take advantage of QMs unique chemistry in the context of chemical-biology assay development. In this review, we will examine the most relevant examples that illustrate the benefit of using QMs for chemical biology purposes and we will anticipate novel approaches to further their applications in biologically relevant contexts.
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Affiliation(s)
- Aisling Minard
- Imperial College London, Department of Chemistry, Molecular Science Research Hub, Wood Lane, W12 0BZ London, UK
| | - Denise Liano
- Imperial College London, Department of Chemistry, Molecular Science Research Hub, Wood Lane, W12 0BZ London, UK
| | - Xiaofan Wang
- Imperial College London, Department of Chemistry, Molecular Science Research Hub, Wood Lane, W12 0BZ London, UK
| | - Marco Di Antonio
- Imperial College London, Department of Chemistry, Molecular Science Research Hub, Wood Lane, W12 0BZ London, UK.
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30
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Dethe DH, B VK, Maiti R. Biomimetic total syntheses of chromane meroterpenoids, guadials B and C, guapsidial A and psiguajadial D. Org Biomol Chem 2019; 16:4793-4796. [PMID: 29931003 DOI: 10.1039/c8ob01092g] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The first biomimetic total syntheses of chromane meroterpenoids, guadials B and C, guapsidial A and psiguajadial D have been completed. The key synthetic transformation involves an efficient and high yielding hetero-Diels-Alder reaction. The two structurally isomeric natural products, guadials B and C, were obtained from a common o-quinone methide in the separate reactions with α-pinene and β-pinene, respectively. The two regioisomeric natural products, guapsidial A and psiguajadial D, were achieved in a single chemical operation.
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Affiliation(s)
- Dattatraya H Dethe
- Department of Chemistry, Indian Institute of Technology, Kanpur, 208016, India.
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31
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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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32
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Ng AWH, Au‐Yeung HY. Molecular Links and Knots from Naphthalenediimide: A Balance of Weak Interactions. Chem Asian J 2019; 14:1602-1612. [DOI: 10.1002/asia.201801681] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Antony Wing Hung Ng
- Department of ChemistryThe University of Hong Kong Pokfulam Road Hong Kong P. R. China
| | - Ho Yu Au‐Yeung
- Department of ChemistryThe University of Hong Kong Pokfulam Road Hong Kong P. R. China
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33
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Tuo W, Bouquet J, Taran F, Le Gall T. A FRET probe for the detection of alkylating agents. Chem Commun (Camb) 2019; 55:8655-8658. [DOI: 10.1039/c9cc04391h] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A fluorogenic FRET probe allows efficient detection of toxic alkylating agents through a self-immolative reaction.
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Affiliation(s)
- Wei Tuo
- CEA-Université Paris-Saclay
- Institut Joliot
- Service de Chimie Bioorganique et de Marquage
- 91191 Gif-sur-Yvette
- France
| | - Jaufret Bouquet
- CEA-Université Paris-Saclay
- Institut Joliot
- Service de Chimie Bioorganique et de Marquage
- 91191 Gif-sur-Yvette
- France
| | - Frédéric Taran
- CEA-Université Paris-Saclay
- Institut Joliot
- Service de Chimie Bioorganique et de Marquage
- 91191 Gif-sur-Yvette
- France
| | - Thierry Le Gall
- CEA-Université Paris-Saclay
- Institut Joliot
- Service de Chimie Bioorganique et de Marquage
- 91191 Gif-sur-Yvette
- France
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34
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Xu Y, Wei H, Chen J, Gao K. A thiol-inducible and quick-response DNA cross-linking agent. Bioorg Med Chem Lett 2019; 29:281-283. [DOI: 10.1016/j.bmcl.2018.11.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/14/2018] [Accepted: 11/18/2018] [Indexed: 12/11/2022]
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35
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Yan Z, Du L, Lan X, Li Y, Wang W, Phillips DL. Time-Resolved Spectroscopic and Density Functional Theory Investigation of the Photogeneration of a Bifunctional Quinone Methide in Neutral and Basic Aqueous Solutions. Molecules 2018; 23:E3102. [PMID: 30486443 PMCID: PMC6321171 DOI: 10.3390/molecules23123102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/20/2018] [Accepted: 11/23/2018] [Indexed: 01/01/2023] Open
Abstract
Binol quinone methides (BQMs) can be generated from 1,1'-(2,2'-dihydroxy-1,1'-binaphthyl-6,6'-diyl)bis(N,N,N-trimethylmethanamiuium) bromide (BQMP-b) in a 1:1 MeCN:H₂O mixed solution via a ground state intramolecular proton transfer (GSIPT), as mentioned in our previously reported studies. Here, the photoreaction of BQMP-b in neutral and basic aqueous solution (pH = 7, 10, 12) was investigated to explore the possible mechanisms and the key intermediates produced in the process of the photoreaction and to examine whether they are different from those in a neutral mild-mixed MeCN:H₂O solution. The studies were conducted using femtosecond transient absorption (fs-TA), nanosecond transient absorption (ns-TA), and nanosecond time-resolved resonance Raman spectroscopy (ns-TR³) in conjunction with results from density functional theory (DFT) computations. The results showed that BQMP-b was deprotonated initially and produced BQMs species more effectively through an E1bc elimination reaction in a strong basic aqueous condition (pH = 12), which differed from the reaction pathway that took place in the solution with pH = 7 or 10. A related single naphthol ring molecule 1-(6-hydroxynaphthalen-2-yl)-N,N,N-trimethylmethanaminium bromide (QMP-b) that did not contain a second naphthol ring was also investigated. The related reaction mechanisms are elucidated in this work, and it is briefly discussed how the mechanisms vary as a function of aqueous solution pH conditions.
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Affiliation(s)
- Zhiping Yan
- Department of Chemistry, The University of Hong Kong, Hong Kong, China.
| | - Lili Du
- Department of Chemistry, The University of Hong Kong, Hong Kong, China.
| | - Xin Lan
- Department of Chemistry, The University of Hong Kong, Hong Kong, China.
| | - Yuanchun Li
- Department of Chemistry, The University of Hong Kong, Hong Kong, China.
| | - Wenchao Wang
- Department of Chemistry, The University of Hong Kong, Hong Kong, China.
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36
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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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37
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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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38
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Chen W, Fan H, Balakrishnan K, Wang Y, Sun H, Fan Y, Gandhi V, Arnold LA, Peng X. Discovery and Optimization of Novel Hydrogen Peroxide Activated Aromatic Nitrogen Mustard Derivatives as Highly Potent Anticancer Agents. J Med Chem 2018; 61:9132-9145. [PMID: 30247905 DOI: 10.1021/acs.jmedchem.8b00559] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We describe several new aromatic nitrogen mustards with various aromatic substituents and boronic esters that can be activated with H2O2 to efficiently cross-link DNA. In vitro studies demonstrated the anticancer potential of these compounds at lower concentrations than those of other clinically used chemotherapeutics, such as melphalan and chlorambucil. In particular, compound 10, bearing an amino acid ester chain, is selectively cytotoxic toward breast cancer and leukemia cells that have inherently high levels of reactive oxygen species. Importantly, 10 was 10-14-fold more efficacious than melphalan and chlorambucil for triple-negative breast-cancer (TNBC) cells. Similarly, 10 is more toxic toward primary chronic-lymphocytic-leukemia cells than either chlorambucil or the lead compound, 9. The introduction of an amino acid side chain improved the solubility and permeability of 10. Furthermore, 10 inhibited the growth of TNBC tumors in xenografted mice without obvious signs of general toxicity, making this compound an ideal drug candidate for clinical development.
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Affiliation(s)
- Wenbing Chen
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery , University of Wisconsin, Milwaukee , 3210 North Cramer Street , Milwaukee , Wisconsin 53211 , United States
| | - Heli Fan
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery , University of Wisconsin, Milwaukee , 3210 North Cramer Street , Milwaukee , Wisconsin 53211 , United States
| | - Kumudha Balakrishnan
- Department of Experimental Therapeutics , MD Anderson Cancer Center , Houston , Texas 77030 , United States
| | | | | | | | - Varsha Gandhi
- Department of Experimental Therapeutics , MD Anderson Cancer Center , Houston , Texas 77030 , United States
| | - Leggy A Arnold
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery , University of Wisconsin, Milwaukee , 3210 North Cramer Street , Milwaukee , Wisconsin 53211 , United States
| | - Xiaohua Peng
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery , University of Wisconsin, Milwaukee , 3210 North Cramer Street , Milwaukee , Wisconsin 53211 , United States
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39
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Basha RS, Chen CW, Reddy DM, Lee CF. Iodine-Mediated Direct Generation of o-Quinone Methides at Room Temperature: A Facile Protocol for the Synthesis of ortho-Hydroxybenzyl Thioethers. Chem Asian J 2018; 13:2475-2483. [PMID: 29624908 DOI: 10.1002/asia.201800233] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 03/29/2018] [Indexed: 01/11/2023]
Abstract
An iodine-mediated preparation of ortho-quinone methides (o-QMs) from ortho-hydroxybenzyl alcohols by a C-O bond scission strategy is described. The in situ generated o-QMs were then employed for C-S bond formation by thio-Michael addition of thiols to provide the ortho-hydroxybenzyl thioethers (o-HBT) in moderate to excellent yields.
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Affiliation(s)
- R Sidick Basha
- Department of Chemistry, National Chung Hsing University (NCHU), Taichung, Taiwan, 402, R.O.C
| | - Chia-Wei Chen
- Department of Chemistry, National Chung Hsing University (NCHU), Taichung, Taiwan, 402, R.O.C
| | | | - Chin-Fa Lee
- Department of Chemistry, National Chung Hsing University (NCHU), Taichung, Taiwan, 402, R.O.C.,Research Center for Sustainable Energy and Nanotechnology, (NCHU), Taichung, Taiwan, 402, R.O.C.,Innovation and Development Center of Sustainable Agriculture, (NCHU), Taichung, Taiwan, 402, R.O.C
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40
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Lin Z, Fan H, Zhang Q, Peng X. Design, Synthesis, and Characterization of Binaphthalene Precursors as Photoactivated DNA Interstrand Cross-Linkers. J Org Chem 2018; 83:8815-8826. [PMID: 29929368 DOI: 10.1021/acs.joc.8b00642] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Most recently, alkylation via photogenerated carbocations has been identified as a novel mechanism for photoinduced DNA interstrand cross-link (ICL) formation by bifunctional aryl compounds. However, most compounds showed a low efficiency for DNA cross-linking. Here, we have developed a series of new 1,1'-binaphthalene analogues that efficiently form DNA ICLs upon 350 nm irradiation via generated 2-naphthalenylmethyl cations. The DNA cross-linking efficiency depends on the substituents at position 4 of the naphthalene moiety as well as the leaving groups. Compounds with NO2, Ph, H, Br, or OMe substituents led to 2-4 times higher DNA ICL yields than those with a boronate ester group. Compounds with trimethylammonium salt as a leaving group showed slightly better cross-linking efficiency than those with bromo as a leaving group. Some of these compounds showed a better cross-linking efficiency than that of traditional alkylating agents, such as nitrogen mustard analogues or quinone methide precursors. These highly efficient photoactivated carbocation precursors allow determination and characterization of the adducts formed between the photogenerated naphthalenyl cations and four natural nucleosides, indicating that the alkylation sites for these naphthalene analogues are dG, dA, and dC.
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Affiliation(s)
- Zechao Lin
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery , University of Wisconsin-Milwaukee , 3210 North Cramer Street , Milwaukee , Wisconsin 53211 , United States
| | - Heli Fan
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery , University of Wisconsin-Milwaukee , 3210 North Cramer Street , Milwaukee , Wisconsin 53211 , United States
| | - Qi Zhang
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery , University of Wisconsin-Milwaukee , 3210 North Cramer Street , Milwaukee , Wisconsin 53211 , United States
| | - Xiaohua Peng
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery , University of Wisconsin-Milwaukee , 3210 North Cramer Street , Milwaukee , Wisconsin 53211 , United States
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41
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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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42
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Hazemi ME, Onizuka K, Kobayashi T, Usami A, Sato N, Nagatsugi F. Vinyldiaminotriazine-acridine conjugate as G-quadruplex alkylating agent. Bioorg Med Chem 2018; 26:3551-3558. [PMID: 29807700 DOI: 10.1016/j.bmc.2018.05.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 05/18/2018] [Accepted: 05/19/2018] [Indexed: 10/16/2022]
Abstract
Higher-order structures of nucleic acids have become widely noted for their biological consequences and the discovery of an alkylating small molecule for these structures has been of interest due to its therapeutic potential. We previously developed the vinyldiaminotriazine (VDAT)-acridine conjugate as a T-T mismatch alkylating agent. In this report, we focused on the finding of the alkylation to the G-quadruplex (G4) DNA with VDAT-acridine conjugates. The VDAT-acridine conjugates exhibited a considerable alkylation ability to G4 under mild conditions. Moreover, the investigation of properties with the alkylated G4 revealed that alkylation by this conjugate significantly increased the stability of the G4 structure. This study provides a starting point in the further development of selective G4 alkylating small molecules.
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Affiliation(s)
- Madoka E Hazemi
- 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
| | - Tomohito Kobayashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Akira Usami
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Norihiro Sato
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.
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43
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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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44
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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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45
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Weißenstein A, Grande V, Saha-Möller CR, Würthner F. Water-soluble naphthalene diimides: synthesis, optical properties, and colorimetric detection of biogenic amines. Org Chem Front 2018. [DOI: 10.1039/c8qo00611c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Biocompatible water-soluble naphthalene diimides (NDIs) were synthesized and a core-dichlorinated NDI was shown to detect primary amines and biogenic diamines.
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Affiliation(s)
| | - Vincenzo Grande
- Center for Nanosystems Chemistry (CNC)
- Universität Würzburg
- 97074 Würzburg
- Germany
| | | | - Frank Würthner
- Institut für Organische Chemie
- Universität Würzburg
- 97074 Würzburg
- Germany
- Center for Nanosystems Chemistry (CNC)
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46
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Nikolić D, Macias C, Lankin DC, van Breemen RB. Collision-induced dissociation of phenethylamides: role of ion-neutral complexes. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:1385-1395. [PMID: 28558170 PMCID: PMC5555735 DOI: 10.1002/rcm.7915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 04/21/2017] [Accepted: 05/25/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Phenethylamides are a large group of naturally occurring molecules found both in the plant and animal kingdoms. In addition, they are used as intermediates for the synthesis of pharmaceutically important dihydro- and tetrahydroisoquinolines. To enable efficient characterization of this class of molecules, a detailed mass spectrometric fragmentation study of a broad series of analogs was carried out. METHODS The test compounds were synthesized using standard methods for amide bond formation. Low-energy high-resolution tandem mass spectra were acquired on a hybrid quadrupole/time-of-flight mass spectrometer using positive ion electrospray ionization. RESULTS A total of 26 analogs were investigated in the study. Fragmentation of phenethylamides was found to proceed via intermediate ion-neutral complexes. The complexes can break down via multiple pathways including dissociation, proton transfer, Friedel-Crafts acylation, and single electron transfer. The relative contribution of each of these pathways strongly depends on the structure of the coupling amine and acid. CONCLUSIONS A general scheme for the fragmentation of phenethylamides was developed. This study further extends the knowledge base of the ion-neutral complex by discovering Friedel-Crafts acylation as a novel reaction. The strong influence of minor structural modifications on the fragmentation patterns highlights the importance of testing many analogs in order to fully predict a fragmentation pattern of a particular class of molecules.
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Affiliation(s)
- Dejan Nikolić
- Corresponding Author: Dejan Nikolić, Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612-7231, Telephone (312) 413-5867, FAX (312) 996-7107,
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Perrone R, Lavezzo E, Riello E, Manganelli R, Palù G, Toppo S, Provvedi R, Richter SN. Mapping and characterization of G-quadruplexes in Mycobacterium tuberculosis gene promoter regions. Sci Rep 2017; 7:5743. [PMID: 28720801 PMCID: PMC5515968 DOI: 10.1038/s41598-017-05867-z] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/02/2017] [Indexed: 12/04/2022] Open
Abstract
Mycobacterium tuberculosis is the causative agent of tuberculosis (TB), one of the top 10 causes of death worldwide in 2015. The recent emergence of strains resistant to all current drugs urges the development of compounds with new mechanisms of action. G-quadruplexes are nucleic acids secondary structures that may form in G-rich regions to epigenetically regulate cellular functions. Here we implemented a computational tool to scan the presence of putative G-quadruplex forming sequences in the genome of Mycobacterium tuberculosis and analyse their association to transcription start sites. We found that the most stable G-quadruplexes were in the promoter region of genes belonging to definite functional categories. Actual G-quadruplex folding of four selected sequences was assessed by biophysical and biomolecular techniques: all molecules formed stable G-quadruplexes, which were further stabilized by two G-quadruplex ligands. These compounds inhibited Mycobacterium tuberculosis growth with minimal inhibitory concentrations in the low micromolar range. These data support formation of Mycobacterium tuberculosis G-quadruplexes in vivo and their potential regulation of gene transcription, and prompt the use of G4 ligands to develop original antitubercular agents.
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Affiliation(s)
- Rosalba Perrone
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy
| | - Enrico Lavezzo
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy
| | - Erika Riello
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy
| | - Riccardo Manganelli
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy
| | - Stefano Toppo
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy.
| | - Roberta Provvedi
- Department of Biology, University of Padua, via Ugo Bassi 58/b, 35121, Padua, Italy.
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy.
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Liu HY, Chen AC, Yin QK, Li Z, Huang SM, Du G, He JH, Zan LP, Wang SK, Xu YH, Tan JH, Ou TM, Li D, Gu LQ, Huang ZS. New Disubstituted Quindoline Derivatives Inhibiting Burkitt's Lymphoma Cell Proliferation by Impeding c-MYC Transcription. J Med Chem 2017; 60:5438-5454. [PMID: 28603988 DOI: 10.1021/acs.jmedchem.7b00099] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The c-MYC oncogene is overactivated during Burkitt's lymphoma pathogenesis. Targeting c-MYC to inhibit its transcriptional activity has emerged as an effective anticancer strategy. We synthesized four series of disubstituted quindoline derivatives by introducing the second cationic amino side chain and 5-N-methyl group based on a previous study of SYUIQ-5 (1) as c-MYC promoter G-quadruplex ligands. The in vitro evaluations showed that all new compounds exhibited higher stabilities and binding affinities, and most of them had better selectivity (over duplex DNA) for the c-MYC G-quadruplex compared to 1. Moreover, the new ligands prevented NM23-H2, a transcription factor, from effectively binding to the c-MYC G-quadruplex. Further studies showed that the selected ligand, 7a4, down-regulated c-MYC transcription by targeting promoter G-quadruplex and disrupting the NM23-H2/c-MYC interaction in RAJI cells. 7a4 could inhibit Burkitt's lymphoma cell proliferation through cell cycle arrest and apoptosis and suppress tumor growth in a human Burkitt's lymphoma xenograft.
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Affiliation(s)
- Hui-Yun Liu
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Ai-Chun Chen
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Qi-Kun Yin
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Zeng Li
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Su-Mei Huang
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Gang Du
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Jin-Hui He
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Li-Peng Zan
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Shi-Ke Wang
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Yao-Hao Xu
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Jia-Heng Tan
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Tian-Miao Ou
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Ding Li
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Lian-Quan Gu
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Zhi-Shu Huang
- Institute of Medicinal Chemistry, School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
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Sur S, Tiwari V, Sinha D, Kamran MZ, Dubey KD, Suresh Kumar G, Tandon V. Naphthalenediimide-Linked Bisbenzimidazole Derivatives as Telomeric G-Quadruplex-Stabilizing Ligands with Improved Anticancer Activity. ACS OMEGA 2017; 2:966-980. [PMID: 30023623 PMCID: PMC6044781 DOI: 10.1021/acsomega.6b00523] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 02/28/2017] [Indexed: 05/22/2023]
Abstract
Human telomeric G-quadruplex DNA stabilization has emerged as an exciting novel approach for anticancer drug development. In the present study, we have designed and synthesized three C2-symmetric bisubstituted bisbenzimidazole naphthalenediimide (NDI) ligands, ALI-C3 , BBZ-ARO, and BBZ-AROCH2 , which stabilize human telomeric G-quadruplex DNA with high affinity. Herein, we have studied the binding affinities and thermodynamic contributions of each of these molecules with G-quadruplex DNA and compared the same to those of the parent NDI analogue, BMSG-SH-3. Results of fluorescence resonance energy transfer and surface plasmon resonance demonstrate that these ligands have a higher affinity for G4-DNA over duplex DNA and induce the formation of a G-quadruplex. The binding equilibrium constants obtained from the microcalorimetry studies of BBZ-ARO, ALI-C3 , and BBZ-AROCH2 were 8.47, 6.35, and 3.41 μM, respectively, with h-telo 22-mer quadruplex. These showed 10 and 100 times lower binding affinity with h-telo 12-mer and duplex DNA quadruplexes, respectively. Analysis of the thermodynamic parameters obtained from the microcalorimetry study suggests that interactions were most favorable for BBZ-ARO among all of the synthesized compounds. The ΔGfree obtained from molecular mechanics Poisson-Boltzmann surface area calculations of molecular dynamics (MD) simulation studies suggest that BBZ-ARO interacted strongly with G4-DNA. MD simulation results showed the highest hydrogen bond occupancy and van der Waals interactions were between the side chains of BBZ-ARO and the DNA grooves. A significant inhibition of telomerase activity (IC50 = 4.56 μM) and induced apoptosis in cancer cell lines by BBZ-ARO suggest that this molecule has the potential to be developed as an anticancer agent.
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Affiliation(s)
- Souvik Sur
- Chemical
Biology Laboratory, Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Vinod Tiwari
- Chemical
Biology Laboratory, Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Devapriya Sinha
- Chemical
Biology Laboratory, Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Mohammad Zahid Kamran
- Special
Center for Molecular Medicine, Jawaharlal
Nehru University, New Delhi 110067, India
| | | | - Gopinatha Suresh Kumar
- Biophysical
Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Vibha Tandon
- Chemical
Biology Laboratory, Department of Chemistry, University of Delhi, Delhi 110007, India
- Special
Center for Molecular Medicine, Jawaharlal
Nehru University, New Delhi 110067, India
- E-mail: , . Phone: 91-11-26741640; 91-11-26708783
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Hydrogen peroxide activated quinone methide precursors with enhanced DNA cross-linking capability and cytotoxicity towards cancer cells. Eur J Med Chem 2017; 133:197-207. [PMID: 28388522 DOI: 10.1016/j.ejmech.2017.03.041] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 02/24/2017] [Accepted: 03/22/2017] [Indexed: 11/21/2022]
Abstract
Quinone methide (QM) formation induced by endogenously generated H2O2 is attractive for biological and biomedical applications. To overcome current limitations due to low biological activity of H2O2-activated QM precursors, we are introducing herein several new arylboronates with electron donating substituents at different positions of benzene ring and/or different neutral leaving groups. The reaction rate of the arylboronate esters with H2O2 and subsequent bisquinone methides formation and DNA cross-linking was accelerated with the application of Br as a leaving group instead of acetoxy groups. Additionally, a donating group placed meta to the nascent exo-methylene group of the quinone methide greatly improves H2O2-induced DNA interstrand cross-link formation as well as enhances the cellular activity. Multiple donating groups decrease the stability and DNA cross-linking capability, which lead to low cellular activity. A cell-based screen demonstrated that compounds 2a and 5a with a OMe or OH group dramatically inhibited the growth of various tissue-derived cancer cells while normal cells were less affected. Induction of H2AX phosphorylation by these compounds in CLL lymphocytes provide evidence for a correlation between cell death and DNA damage. The compounds presented herein showed potent anticancer activities and selectivity, which represent a novel scaffold for anticancer drug development.
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