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Photochemical synthesis, intercalation with DNA and antitumor evaluation in vitro of benzo[d]thiazolo[3,2-a]quinolin-10-ium derivatives. Bioorg Chem 2021; 115:105267. [PMID: 34426158 DOI: 10.1016/j.bioorg.2021.105267] [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: 05/28/2021] [Revised: 07/18/2021] [Accepted: 08/09/2021] [Indexed: 11/23/2022]
Abstract
A new anticancer benzo[d]thiazolo[3,2-a]quinolin-10-ium derivatives were synthesized and characterized. Anticancer evaluation in vitro against four cancer cell lines including adenocarcinomic human alveolar basal epithelial cells (A549), hepatocellular carcinoma (HepG2), prostate cancer (PC3) and breast cancer (MCF7) indicated that some of prepared compounds shows higher selectivity in comparison with doxorubicin. DNA interaction studies by optical, CD, NMR spectroscopies showed the high affinity of benzothiazole ligands towards the dsDNA. The ligand-DNA interaction occurs through the intercalation of benzo[d]thiazolo[3,2-a]quinolin-10-ium derivatives with nucleic acid. The investigation of formed ligand - DNA complexes by docking and molecular dynamic calculations was applied for analysis of the relationship between structure and anticancer activity. The results suggested that benzo[d]thiazolo[3,2-a]quinolin-10-ium derivatives might serve as a novel scaffold for the future development to new antitumor agents.
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Kiss E, Mirzahosseini A, Hubert Á, Ambrus A, Őrfi L, Horváth P. DNA binding of sunitinib: Spectroscopic evidence via circular dichroism and nuclear magnetic resonance. J Pharm Biomed Anal 2017; 150:355-361. [PMID: 29287262 DOI: 10.1016/j.jpba.2017.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/30/2017] [Accepted: 12/02/2017] [Indexed: 10/18/2022]
Abstract
Sunitinib is a non-selective tyrosine kinase inhibitor, but in its chemical structure there can be discovered certain features, which suggest the ability to bind to DNA. These elements are the planar aromatic system and the tertiary amine function, which is protonated at the pH of the organism. In this study, the binding of the drug sunitinib to DNA was investigated using circular dichroism (CD), 1H NMR and UV spectroscopies, along with CD melting. For these studies DNA was isolated from calf thymus (CT), salmon fish sperm (SS), and chicken erythrocyte (CE), however for our purposes an artificially constructed and highly purified plasmid DNA (pUC18) preparation proved to be the most suitable. DNA binding of the drug was confirmed by shifts in the characteristic CD bands of the DNA, the appearance of an induced CD (ICD) signal in the upper absorption region of sunitinib (300 nm-500 nm), and the evidence from CD melting studies and the NMR. Based on the CD and NMR measurements, it can be assumed that sunitinib has a multiple-step binding mechanism.
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Affiliation(s)
- Eszter Kiss
- Department of Pharmaceutical Chemistry, Semmelweis University, 1092 Budapest, Hőgyes Endre utca. 9, Hungary.
| | - Arash Mirzahosseini
- Department of Pharmaceutical Chemistry, Semmelweis University, 1092 Budapest, Hőgyes Endre utca. 9, Hungary.
| | - Ágnes Hubert
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, 1094 Budapest, Tűzoltó utca 37-47, Hungary.
| | - Attila Ambrus
- Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, 1094 Budapest, Tűzoltó utca 37-47, Hungary.
| | - László Őrfi
- Department of Pharmaceutical Chemistry, Semmelweis University, 1092 Budapest, Hőgyes Endre utca. 9, Hungary.
| | - Péter Horváth
- Department of Pharmaceutical Chemistry, Semmelweis University, 1092 Budapest, Hőgyes Endre utca. 9, Hungary.
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Berdnikova DV, Aliyeu TM, Paululat T, Fedorov YV, Fedorova OA, Ihmels H. DNA–ligand interactions gained and lost: light-induced ligand redistribution in a supramolecular cascade. Chem Commun (Camb) 2015; 51:4906-9. [DOI: 10.1039/c5cc01025j] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Controlled DNA binding: a photoresponsive ligand is made to migrate from cyclodextrin to double-stranded DNA upon irradiation and is eventually extracted from the nucleic acid by cucurbituril.
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Affiliation(s)
- Daria V. Berdnikova
- Department Chemie–Biologie
- Organische Chemie II
- Universität Siegen
- 57068 Siegen
- Germany
| | - Tseimur M. Aliyeu
- A. N. Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- 119991 Moscow
- Russia
| | - Thomas Paululat
- Department Chemie–Biologie
- Organische Chemie II
- Universität Siegen
- 57068 Siegen
- Germany
| | - Yuri V. Fedorov
- A. N. Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- 119991 Moscow
- Russia
| | - Olga A. Fedorova
- A. N. Nesmeyanov Institute of Organoelement Compounds
- Russian Academy of Sciences
- 119991 Moscow
- Russia
| | - Heiko Ihmels
- Department Chemie–Biologie
- Organische Chemie II
- Universität Siegen
- 57068 Siegen
- Germany
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Hennig M, Munzarova ML, Bermel W, Scott LG, Sklenar V, Williamson JR. Measurement of long-range 1H-19F scalar coupling constants and their glycosidic torsion dependence in 5-fluoropyrimidine-substituted RNA. J Am Chem Soc 2007; 128:5851-8. [PMID: 16637654 PMCID: PMC2556634 DOI: 10.1021/ja060165t] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Long-range scalar 5J(H1',F) couplings were observed in 5-fluoropyrimidine-substituted RNA. We developed a novel S3E-19F-alpha,beta-edited NOESY experiment for quantitation of these long-range scalar 5J(H1',F) couplings, where the J-couplings can be extracted from inspection of intraresidual (H1',H6) NOE cross-peaks. Quantum chemical calculations were exploited to investigate the relation between scalar couplings and conformations around the glycosidic bond in oligonucleotides. The theoretical dependence of the observed 5J(H1',F) couplings on the torsion angle chi can be described by a generalized Karplus relationship. The corresponding density functional theory (DFT) analysis is outlined. Additional NMR experiments facilitating the resonance assignments of 5-fluoropyrimidine-substituted RNAs are described, and chemical shift changes due to altered shielding in the presence of fluorine-19 (19F) are presented.
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Affiliation(s)
- Mirko Hennig
- Department of Molecular Biology and The Skaggs Institute of Chemical Biology, The Scripps Research Institute, MB 33, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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Hennig M, Scott LG, Sperling E, Bermel W, Williamson JR. Synthesis of 5-fluoropyrimidine nucleotides as sensitive NMR probes of RNA structure. J Am Chem Soc 2007; 129:14911-21. [PMID: 17990877 DOI: 10.1021/ja073825i] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzymatic synthesis methods for the fluorinated 5'-triphosphate analogues 5F-UTP and 5F-CTP have been developed to facilitate 19F-labeling of RNAs for biophysical studies. HIV-2 TAR RNAs were synthesized using these analogues by in vitro transcription reactions using T7 RNA polymerase. The uniform incorporation of 5F-U or 5F-C analogues into HIV-2 TAR RNA transcripts does not significantly alter the RNA structure or thermodynamic stability. Fluorine observed homonuclear 19F-19F and heteronuclear 19F-1H NOE experiments providing selective distance information are presented and discussed. The availability of efficient synthesis of 5F-UTP, and for the first time, 5F-CTP, will facilitate the use of 5F-labeled RNAs in structural, ligand binding, and dynamic studies of RNAs using the advantages of 19F-labeling.
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Affiliation(s)
- Mirko Hennig
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 173 Ashley Avenue, P.O. Box 250509, Charleston, South Carolina 29425, USA.
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Bocian W, Kawecki R, Bednarek E, Sitkowski J, Pietrzyk A, Williamson MP, Hansen PE, Kozerski L. Multiple binding modes of the camptothecin family to DNA oligomers. Chemistry 2006; 10:5776-87. [PMID: 15472946 DOI: 10.1002/chem.200305624] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The binding constants of camptothecin, topotecan and its lactone ring-opened carboxylate derivative to DNA octamers were measured by UV and NMR spectroscopy. The self-association of topotecan (TPT) was also measured. The carboxylate form of TPT binds in the same way as the lactone, but more weakly. Titration of TPT into d(GCGATCGC)2 shows a preferred location stacked onto the terminal G1 base. However, the intermolecular NOEs cannot be reconciled with a single conformation of the complex, and suggest a model of a limited number of conformations in fast exchange. MD calculations on four pairs of starting structures with TPT stacked onto the G1-C8 base pair in different orientations were therefore performed. The use of selected experimental "docking" restraints yielded ten MD trajectories covering a wide conformational space. From a combination of calculated free energies, NOEs and chemical shifts, some of the structures produced could be eliminated, and it is concluded that the data are consistent with two major families of conformations in fast exchange. One of these is the conformation found in a crystal of a TPT/DNA/topoisomerase I ternary complex [Proc. Natl. Acad. Sci. USA 2002, 99, 15 387-15 392].
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Affiliation(s)
- Wojciech Bocian
- National Institute of Public Health, 00-725 Warszawa, Chełmska 30/34, Poland
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Jähnchen J, Purwanto MGM, Weisz K. NMR studies on self-complementary oligonucleotides conjugated with methylene blue. Biopolymers 2006; 79:335-43. [PMID: 16130129 DOI: 10.1002/bip.20363] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A carboxyl-functionalized methylene blue (MB) derivative was synthesized and covalently coupled to three CG-rich self-complementary 2'-deoxyoligonucleotides at their 5'-end. Thermodynamic and structural details about the interactions between the dye and oligonucleotide duplexes were investigated employing ultraviolet (UV) melting and (1)H nuclear magnetic resonance (NMR) experiments. In contrast to previous findings on MB binding, no specific intercalation or binding in the minor or major groove of the double helix was found in a 100 mM NaCl buffer. Rather, proton chemical shift changes in the conjugates provide ample evidence for weak dye-DNA interactions largely through external MB stacking on the terminal base pairs.
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Affiliation(s)
- Judith Jähnchen
- Institut für Chemie und Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Soldmannstrasse 16, D-17489 Greifswald, Germany
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Scott LG, Geierstanger BH, Williamson JR, Hennig M. Enzymatic synthesis and 19F NMR studies of 2-fluoroadenine-substituted RNA. J Am Chem Soc 2005; 126:11776-7. [PMID: 15382896 DOI: 10.1021/ja047556x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The production of isotopically labeled RNA remains critical to current NMR structural studies. One approach to obtain simple NMR spectra is to label with a nucleus that is not naturally occurring in RNA. Fluorine-19 can serve as a sensitive site-specific probe upon incorporation into RNA. Here we report the efficient in vitro enzymatic synthesis of 2-fluoroadenosine-5'-triphosphate and its incorporation into the HIV-2 transactivation region (TAR) of RNA by DNA template-directed transcription using phage T7 RNA polymerase. We provide unequivocal evidence for this 19F-substituted base analogue capability to selectively interact with uracil, forming 2F-A-U base pairs in RNA. The introduction of a 2-fluoroadenyl substitution is relatively nonperturbing and provides us with uniquely positioned, sensitive NMR reporter groups to monitor structural changes in the local RNA environment.
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Affiliation(s)
- Lincoln G Scott
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, MB33, La Jolla, California 92037, USA
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Véliz EA, Stephens OM, Beal PA. Synthesis and analysis of RNA containing 6-trifluoromethylpurine ribonucleoside. Org Lett 2001; 3:2969-72. [PMID: 11554820 DOI: 10.1021/ol016295i] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the synthesis of a 5'-DMT-2'-TBDMS-protected phosphoramidite of 6-trifluoromethylpurine ribonucleoside ((TFM)P) and its use in the site-specific incorporation of 6-trifluoromethylpurine into RNA. Properties of (TFM)P-substituted RNA suggest it will be valuable in the study of RNA structure and the binding of RNA-modifying enzymes, particularly the RNA-editing adenosine deaminases. Reaction: see text.
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Affiliation(s)
- E A Véliz
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
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Abstract
The DNA-binding properties of many ligands can be rationalized on the basis of their structural and electronic complementarity with the functional groups present in the minor and major grooves of particular DNA sequences. Specific hydrogen bonding patterns are particularly useful for the purpose of sequence recognition. Less obvious, however, is the influence of base composition on the conformational preferences of individual base steps and on the binding of intercalating moieties which become sandwiched between contiguous base pairs. Improved knowledge of stacking interactions may lead to a better understanding of the architecture and inherent flexibility of particular DNA sequences and may provide insight into the principles that dictate the structural changes and specificity patterns observed in the binding of some intercalating ligands to DNA.
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Affiliation(s)
- F Gago
- Departamento de Farmacología, Universidad de Alcalá, Madrid, Spain
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Abstract
Gene therapy is an emerging field that has reached the early clinical stages of development for some disease states. However, the demonstration of safety in animals and the introduction of gene-based formulations in humans hides the fact that numerous developmental and basic research questions remain. This article highlights progress and emerging issues in the area of liposome-based non-viral gene delivery. The colloidal nature of these formulations render them complicated at the physico-chemical and biological levels. Instrumentation and methodologies need to be developed to better understand the subtleties of plasmid DNA, complexing agents, delivery mode and the route of entry into the cell and the nucleus. Major hurdles to entry include membrane binding, endosomal release, nuclear uptake and decomplexation. Each 'stage' is poorly understood but numerous approaches are being directed to increase cellular delivery. These research efforts, coupled with sensible formulation research and a multi-disciplinary, long-term effort, are necessary for success.
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