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San Y, Sun J, Wang H, Jin ZH, Gao HJ. Synthesis of 1,8-Naphthyridines by the Ionic Liquid-Catalyzed Friedlander Reaction and Application in Corrosion Inhibition. ACS OMEGA 2021; 6:28063-28071. [PMID: 34723006 PMCID: PMC8552317 DOI: 10.1021/acsomega.1c04103] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 10/05/2021] [Indexed: 06/13/2023]
Abstract
A several of basic ionic liquids (ILs) were synthesized as green solvents and catalysts for the preparation of 1,8-naphthyridyl derivatives via the Friedlander reaction. [Bmmim][Im] exhibited remarkable catalytic activity to achieve the synthetic targets, and the reaction conditions were optimized. The model product 2,3-diphenyl-1,8-naphthyridine (1,8-Nap), with carboxyethylthiosuccinic acid (CETSA) to form an IL corrosion inhibitor ([1,8-Nap][CETSA]), and its corrosion inhibition performance for Q235 steel in 1 M HCl were researched by weight loss measurements, and the results showed that the inhibition efficiency was 96.95% when the concentration of [1,8-Nap][CETSA] was 1 mM at 35 °C. The electrochemical test verified that [1,8-Nap][CETSA] acted as a mixed-type inhibitor but mainly exhibited cathodic behavior. The inhibitor adsorbed on the metal surface was further proved by surface topography analysis.
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Affiliation(s)
- Ying San
- Institute of Petrochemical
Technology, Jilin Institute of Chemical
Technology, Jilin 132022, China
| | - Jian Sun
- Institute of Petrochemical
Technology, Jilin Institute of Chemical
Technology, Jilin 132022, China
| | - Hong Wang
- Institute of Petrochemical
Technology, Jilin Institute of Chemical
Technology, Jilin 132022, China
| | - Zhao-Hui Jin
- Institute of Petrochemical
Technology, Jilin Institute of Chemical
Technology, Jilin 132022, China
| | - Hua-Jing Gao
- Institute of Petrochemical
Technology, Jilin Institute of Chemical
Technology, Jilin 132022, China
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2
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Hisama K, Orimoto Y, Pomogaeva A, Nakatani K, Aoki Y. Ab initio multi-level layered elongation method and its application to local interaction analysis between DNA bulge and ligand molecules. J Chem Phys 2021; 155:044110. [PMID: 34340364 DOI: 10.1063/5.0050096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A multi-level layered elongation method was developed for efficiently analyzing the electronic states of local structures in large bio/nano-systems at the full ab initio level of theory. The original elongation method developed during the last three decades in our group has focused on the system in one direction from one terminal to the other terminal to sequentially construct the electronic states of a polymer, called a theoretical synthesis of polymers. In this study, an important region termed the central (C) part is targeted in a large polymer and the remainder are terminal (T) parts. The electronic structures along with polymer elongation are calculated repeatedly from both end T parts to the C central part at the same time. The important C part is treated with large basis sets (high level) and the other regions are treated with small basis sets (low level) in the ab initio theoretical framework. The electronic structures besides the C part can be reused for other systems with different structures at the C part, which renders the method computationally efficient. This multi-level layered elongation method was applied to the investigation on DNA single bulge recognition of small molecules (ligands). The reliability and validity of our approach were examined in comparison with the results obtained by direct calculations using a conventional quantum chemical method for the entire system. Furthermore, stabilization energies by the formation of the complex of bulge DNA and a ligand were estimated with basis set superposition error corrections incorporated into the elongation method.
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Affiliation(s)
- Keisuke Hisama
- Department of Interdisciplinary Engineering Sciences, Chemistry and Materials Science, Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan
| | - Yuuichi Orimoto
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan
| | - Anna Pomogaeva
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Yuriko Aoki
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan
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3
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Murata A, Otabe T, Zhang J, Nakatani K. BzDANP, a Small-Molecule Modulator of Pre-miR-29a Maturation by Dicer. ACS Chem Biol 2016; 11:2790-2796. [PMID: 27536863 DOI: 10.1021/acschembio.6b00214] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We here report the synthesis of novel molecule BzDANP having a three-ring benzo[c][1,8]naphthyridine system, the evaluation of its binding properties to a single nucleotide bulge in RNA duplexes, and BzDANP-induced suppression of pre-miR-29a processing by Dicer. BzDANP showed much increased affinity to the bulged RNAs as compared with the parent molecule DANP, which possesses the same hydrogen-bonding surface as BzDANP but in a two-ring [1,8]naphthyridine system. Melting temperature analysis of bulged RNAs showed that BzDANP most effectively stabilized the C-bulged RNA. Dicer-mediated processing of pre-miR-29a was suppressed by BzDANP in a concentration dependent manner. The presence of the C-bulge at the Dicer cleavage site was effective for the suppression of pre-miR-29a processing by BzDANP. These results demonstrated that the small molecule binding to the bulged site in the vicinity of the Dicer cleavage site could be a potential modulator for the maturation of pre-miRNA.
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Affiliation(s)
- Asako Murata
- Department of Regulatory
Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Takahiro Otabe
- Department of Regulatory
Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Jinhua Zhang
- Department of Regulatory
Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory
Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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Dyubankova N, Froeyen M, Abramov M, Mattelaer HP, Herdewijn P, Lescrinier E. NMR study on the interaction of the conserved CREX 'stem-loop' in the Hepatitis E virus genome with a naphthyridine-based ligand. Org Biomol Chem 2015; 13:9665-72. [PMID: 26264660 DOI: 10.1039/c5ob01381j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A 2-amino-1,8-naphthyridine derivative that is described to bind single guanine bulges in RNA-DNA and RNA-RNA duplexes was synthesized and its interaction with the single G bulge in the conserved CREX of the Hepatitis E Virus (HEV) genome was explored by NMR and molecular modeling. Results indicate that the ligand intercalates in the internal loop, though none of the expected hydrogen bonds with the single G in the bulge could be demonstrated.
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Affiliation(s)
- N Dyubankova
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium.
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Malina J, Hannon MJ, Brabec V. Recognition of DNA bulges by dinuclear iron(II) metallosupramolecular helicates. FEBS J 2014; 281:987-97. [PMID: 24355059 DOI: 10.1111/febs.12696] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Revised: 11/05/2013] [Accepted: 11/25/2013] [Indexed: 12/24/2022]
Abstract
Bulged DNA structures are of general biological significance because of their important roles in a number of biochemical processes. Compounds capable of targeting bulged DNA sequences can be used as probes for studying their role in nucleic acid function, or could even have significant therapeutic potential. The interaction of [Fe(2)L(3)](4+) metallosupramolecular helicates (L = C(25)H(20)N(4)) with DNA duplexes containing bulges has been studied by measurement of the DNA melting temperature and gel electrophoresis. This study was aimed at exploring binding affinities of the helicates for DNA bulges of various sizes and nucleotide sequences. The studies reported herein reveal that both enantiomers of [Fe(2)L(3)](4+) bind to DNA bulges containing at least two unpaired nucleotides. In addition, these helicates show considerably enhanced affinity for duplexes containing unpaired pyrimidines in the bulge and/or pyrimidines flanking the bulge on both sides. We suggest that the bulge creates the structural motif, such as the triangular prismatic pocket formed by the unpaired bulge bases, to accommodate the [Fe(2)L(3)](4+) helicate molecule, and is probably responsible for the affinity for duplexes with a varying number of bulge bases. Our results reveal that DNA bulges represent another example of unusual DNA structures recognized by dinuclear iron(II) ([Fe(2)L(3)](4+)) supramolecular helicates.
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Affiliation(s)
- Jaroslav Malina
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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6
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Wong CH, Richardson SL, Ho YJ, Lucas AMH, Tuccinardi T, Baranger AM, Zimmerman SC. Investigating the binding mode of an inhibitor of the MBNL1·RNA complex in myotonic dystrophy type 1 (DM1) leads to the unexpected discovery of a DNA-selective binder. Chembiochem 2012; 13:2505-9. [PMID: 23097190 DOI: 10.1002/cbic.201200602] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Indexed: 01/12/2023]
Affiliation(s)
- Chun-Ho Wong
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801, USA
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Váradi L, Gray M, Groundwater PW, Hall AJ, James AL, Orenga S, Perry JD, Anderson RJ. Synthesis and evaluation of fluorogenic 2-amino-1,8-naphthyridine derivatives for the detection of bacteria. Org Biomol Chem 2012; 10:2578-89. [DOI: 10.1039/c2ob06986e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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8
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Direct phosphorylation in the synthesis of new bis(phosphorylamino)pyridine ligands. MENDELEEV COMMUNICATIONS 2010. [DOI: 10.1016/j.mencom.2010.06.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Bai LP, Cai Z, Zhao ZZ, Nakatani K, Jiang ZH. Site-specific binding of chelerythrine and sanguinarine to single pyrimidine bulges in hairpin DNA. Anal Bioanal Chem 2008; 392:709-16. [DOI: 10.1007/s00216-008-2302-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2008] [Revised: 06/02/2008] [Accepted: 07/17/2008] [Indexed: 11/30/2022]
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11
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Goswami S, Jana S, Hazra A, Adak AK. One-pot solvent and catalyst-free synthesis of functionalized 1,8-naphthyridines and quinolines by microwave irradiation. J Heterocycl Chem 2007. [DOI: 10.1002/jhet.5570440536] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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12
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Lu SH, Selvi S, Fang JM. Ethynyl-Linked (Pyreno)pyrrole−Naphthyridine and Aniline−Naphthyridine Molecules as Fluorescent Sensors of Guanine via Multiple Hydrogen Bondings. J Org Chem 2006; 72:117-22. [PMID: 17194089 DOI: 10.1021/jo061831b] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
New fluorescent molecular sensors for 9-alkylguanines were constructed by conjugation of 2-acetamido-1,8-naphthyridine with N-Boc-pyrrole, N-Boc-pyreno[2,1-b]pyrrole, or acetanilide moieties via an ethynyl bridge. In combination with the triple hydrogen-bonding motif of 2-acetamidonaphthyridine toward alkylguanine, an additional binding site was provided by the substituent properly located on the pyrrole or aniline ring to enhance the affinity of these receptor molecules. Besides the ESI-MS analyses, the binding events were readily monitored by the absorption and fluorescence changes in the visible region.
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Affiliation(s)
- Shao-Hung Lu
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
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13
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Idutsu Y, Sasaki A, Matsumura S, Toshima K. Molecular design, chemical synthesis, and evaluation of cytosine–carbohydrate hybrids for selective recognition of a single guanine bulged duplex DNA. Bioorg Med Chem Lett 2005; 15:4332-5. [PMID: 16061380 DOI: 10.1016/j.bmcl.2005.06.073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2005] [Revised: 06/11/2005] [Accepted: 06/14/2005] [Indexed: 10/25/2022]
Abstract
The designed cytosine-carbohydrate hybrid molecule selectively recognized and stabilized the bulged duplex DNA possessing the complementary bulged DNA base, guanine, while the nucleotide base itself did not exhibit any such ability. It was also found that the assistance of the carbohydrate to stabilize the interaction between the nucleotide base and the complementally bulge DNA base is very helpful for the selective recognition and stabilization of the single-bulged duplex DNA.
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Affiliation(s)
- Yusuke Idutsu
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
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14
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Tok JBH, Bi L, Saenz M. Specific recognition of napthyridine-based ligands toward guanine-containing bulges in RNA duplexes and RNA–DNA heteroduplexes. Bioorg Med Chem Lett 2005; 15:827-31. [PMID: 15664866 DOI: 10.1016/j.bmcl.2004.10.059] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2004] [Revised: 10/13/2004] [Accepted: 10/15/2004] [Indexed: 11/18/2022]
Abstract
Mismatched bulges in nucleic acid constructs are important in the recognition event between biological molecules. Herein, it is observed that napthyridine dimer 2 is able to specifically bind G-G mismatches in all nucleic acid constructs comprising of RNA-RNA, RNA-DNA and DNA-DNA duplexes. However, the binding affinity of 2 is strongest toward DNA duplex, followed by RNA-DNA heteroduplex and RNA duplex being the weakest binding partner. Nonetheless, this binding behavior suggests that the binding process primarily occurs between the guanine base pairs and the napthyridine moiety, and is independent of the tertiary structure of the nucleic acid duplexes.
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Affiliation(s)
- Jeffrey B-H Tok
- Department of Chemistry, York College and Graduate Center, The City University of New York, 94-20 Guy R. Brewer Blvd., Jamaica, NY 11451, USA.
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15
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Peng T, Murase T, Goto Y, Kobori A, Nakatani K. A new ligand binding to G–G mismatch having improved thermal and alkaline stability. Bioorg Med Chem Lett 2005; 15:259-62. [PMID: 15603935 DOI: 10.1016/j.bmcl.2004.11.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2004] [Revised: 10/28/2004] [Accepted: 10/30/2004] [Indexed: 10/26/2022]
Abstract
Naphthyridine dimer (ND) specially binds to guanine-guanine (G-G) mismatch in duplex DNA. In order to improve the thermal and alkaline stability and binding ability of the ligand, we have examined structural modification of the linker. A new ligand (NNC) possessing 2-amino-1,8-naphthyridines and a carbamate linker is much more thermally stable than ND. The half-life of NNC is 2.5 times longer than that of ND at 80 degrees C. NNC is also much more stable than ND under alkaline conditions. In addition, NNC binds to G-G mismatch more strongly than ND. The improved stability and the binding of NNC to the G-G mismatch would be suitable for the practical use of NNC-immobilized sensor.
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Affiliation(s)
- Tao Peng
- PRESTO, Japan Science and Technology Agency (JST), Kyoto 615-8510, Japan
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16
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Hagihara S, Kumasawa H, Goto Y, Hayashi G, Kobori A, Saito I, Nakatani K. Detection of guanine-adenine mismatches by surface plasmon resonance sensor carrying naphthyridine-azaquinolone hybrid on the surface. Nucleic Acids Res 2004; 32:278-86. [PMID: 14715926 PMCID: PMC373281 DOI: 10.1093/nar/gkh171] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We have discovered a new molecule naphthyridine-azaquinolone hybrid (Npt-Azq) that strongly stabilized the guanine-adenine (G-A) mismatch in duplex DNA. In the presence of Npt-Azq, the melting temperature (T(m)) of 5'-d(CTA ACG GAA TG)-3'/3'-d(GAT TGA CTT AC)-5' containing a single G-A mismatch increased by 15.4 degrees C, whereas fully matched duplex increased its T(m) only by 2.2 degrees C. Npt-Azq was immobilized on the sensor surface for the surface plasmon resonance (SPR) assay to examine SPR detection of duplexes containing a G-A mismatch. Distinct SPR signals were observed when 27mer DNA containing a G-A mismatch was analyzed by the Npt-Azq immobilized sensor surfaces, whereas the signal of the fully matched duplex was approximately 6-fold weaker in intensity. The SPR signals for the G-A mismatch were proportional to the concentration of DNA in a range up to 1 microM, confirming that the SPR signal is in fact due to the binding of the G-A mismatch to Npt-Azq immobilized on the surface. Examination of all 16 G-A mismatches regarding the flanking sequence revealed that the sensor surface reported here is applicable to eight flanking sequences, covering 50% of all possible G-A mismatches.
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Affiliation(s)
- Shinya Hagihara
- Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, Kyoto, Japan
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