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Chen R, Francese R, Wang N, Li F, Sun X, Xu B, Liu J, Liu Z, Donalisio M, Lembo D, Zhou GC. Exploration of novel hexahydropyrrolo[1,2-e]imidazol-1-one derivatives as antiviral agents against ZIKV and USUV. Eur J Med Chem 2023; 248:115081. [PMID: 36623328 DOI: 10.1016/j.ejmech.2022.115081] [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: 10/20/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/05/2023]
Abstract
Zika virus (ZIKV) and Usutu virus (USUV) are two emerging flaviviruses mostly transmitted by mosquitos. ZIKV is associated with microcephaly in newborns and the less-known USUV, with its reported neurotropism and its extensive spread in Europe, represents a growing concern for human health. There is still no approved vaccine or specific antiviral against ZIKV and USUV infections. The main goal of this study is to investigate the anti-ZIKV and anti-USUV activity of a new library of compounds and to preliminarily investigate the mechanism of action of the selected hit compounds in vitro. Two potent anti-ZIKV and anti-USUV agents, namely ZDL-115 and ZDL-116, were discovered, both presenting low cytotoxicity, cell-line independent antiviral activity in the low micromolar range and ability of reducing viral progeny production. The analysis of the structure-activity relationship (SAR) revealed that introduction of 2-deoxyribose to 3-arene was fundamental to enhance the solubility and improve the antiviral action. Additionally, we demonstrated that ZDL-115 and ZDL-116 are significantly active against both viruses when added on cells for at least 24 h prior to viral inoculation or immediately post-infection. The docking analysis showed that ZDL-116 could target the host vitamin D receptor (VDR) and viral proteins. Future experiments will be focused on compound modification to discover analogues that are more potent and on the clarification of the mechanism of action and the specific drug target. The discovery and the development of a novel anti-flavivirus drug will have a significant impact in a context where there are no fully effective antiviral drugs or vaccines for most flaviviruses.
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Affiliation(s)
- Ran Chen
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, Jiangsu, China; Xitaihu Lake Industrial College, Nanjing Tech University, Changzhou, 213149, Jiangsu, China
| | - Rachele Francese
- Laboratory of Molecular Virology and Antiviral Research, Department of Clinical and Biological Sciences, University of Turin, S. Luigi Gonzaga Hospital, 10043 Orbassano, Turin, Italy
| | - Na Wang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Feng Li
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Xia Sun
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Bin Xu
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Jinsong Liu
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Zhuyun Liu
- School of Pharmacy, Taizhou Polytechnic College, Taizhou, 225300, Jiangsu, China
| | - Manuela Donalisio
- Laboratory of Molecular Virology and Antiviral Research, Department of Clinical and Biological Sciences, University of Turin, S. Luigi Gonzaga Hospital, 10043 Orbassano, Turin, Italy
| | - David Lembo
- Laboratory of Molecular Virology and Antiviral Research, Department of Clinical and Biological Sciences, University of Turin, S. Luigi Gonzaga Hospital, 10043 Orbassano, Turin, Italy.
| | - Guo-Chun Zhou
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, Jiangsu, China; Xitaihu Lake Industrial College, Nanjing Tech University, Changzhou, 213149, Jiangsu, China.
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Kishimoto Y, Fujii A, Nakagawa O, Obika S. Enhanced duplex- and triplex-forming ability and enzymatic resistance of oligodeoxynucleotides modified by a tricyclic thymine derivative. Org Biomol Chem 2021; 19:8063-8074. [PMID: 34494641 DOI: 10.1039/d1ob01462e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We designed and synthesized an artificial nucleic acid, [3-(1,2-dihydro-2-oxobenzo[b][1,8]naphthyridine)]-2'-deoxy-D-ribofuranose (OBN), with a tricyclic structure in a nucleobase as a thymidine analog. Oligodeoxynucleotides (ODNs) containing consecutive OBN displayed improved duplex-forming ability with complementary single-stranded (ss) RNA and triplex-forming ability with double-stranded DNA in comparison with ODNs composed of natural thymidine. OBN-modified ODNs also displayed enhanced enzymatic resistance compared with ODNs with natural thymidine and phosphorothioate modification, respectively, due to the structural steric hindrance of the nucleobase. The fluorescence spectra of OBN-modified ODNs showed sufficient fluorescence intensity with ssDNA and ssRNA, which is an advantageous feature for fluorescence imaging techniques of nucleic acids with longer emission wavelengths than bicyclic thymine (bT).
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Affiliation(s)
- Yuki Kishimoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan. .,Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Akane Fujii
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan. .,Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Osamu Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan. .,Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan.,Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahoji, Yamashiro-cho, Tokushima 770-8514, Japan.
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan. .,Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
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Horiba M, Yamaguchi T, Obika S. Synthesis and Properties of Oligonucleotides Having Ethynylphosphonate Linkages. J Org Chem 2020; 85:1794-1801. [PMID: 31867976 DOI: 10.1021/acs.joc.9b01318] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Ethynylphosphonate (EP)-linked thymidine dimers were synthesized via a palladium-catalyzed cross-coupling reaction and successfully incorporated into oligonucleotides. The oligonucleotides containing EP linkages appropriately formed a duplex with their complementary single-stranded RNA (ssRNA) and single-stranded DNA. The oligonucleotides containing both the EP linkages and 2'-O,4'-C-methylene-bridged nucleic acid/locked nucleic acid exhibited strong duplex-forming ability toward the complementary ssRNA. The EP-modified oligonucleotides exhibited higher exonuclease resistances than their natural counterparts. Moreover, one EP modification to a gapmer-type antisense oligonucleotide resulted in a switch of the cleavage site in the target ssRNA. Therefore, the EP modification can be applied for controlling the cleavage site in the RNase H-dependent mechanism.
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Affiliation(s)
- Masahiko Horiba
- Graduate School of Pharmaceutical Sciences , Osaka University , 1-6 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences , Osaka University , 1-6 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences , Osaka University , 1-6 Yamadaoka , Suita , Osaka 565-0871 , Japan
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Temburnikar K, Zhang Z, Seley-Radtke K. Modified synthesis of 3'-O-TBDPS-protected furanoid glycal. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2012; 31:319-27. [PMID: 22444193 DOI: 10.1080/15257770.2012.656212] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Thermolytic cleavage of 3'-OH protected thymidine is the most common method of preparing furanoid glycals. We have observed that glycosidic bond cleavage is more facile when the 5'-OH of thymidine was also protected with a silyl group. Addition of trimethylsilyl chloride facilitated cleavage of the glycosidic bond; thus, both modifications are required for the formation of the furanoid glycal. Investigations into the selective deprotection of 5'-silyl versus 3'-silyl and subsequent glycosidic bond cleavage are reported herein.
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Affiliation(s)
- Kartik Temburnikar
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, USA
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Yang Z, Hutter D, Sheng P, Sismour AM, Benner SA. Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern. Nucleic Acids Res 2006; 34:6095-101. [PMID: 17074747 PMCID: PMC1635279 DOI: 10.1093/nar/gkl633] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To support efforts to develop a ‘synthetic biology’ based on an artificially expanded genetic information system (AEGIS), we have developed a route to two components of a non-standard nucleobase pair, the pyrimidine analog 6-amino-5-nitro-3-(1′-β-D-2′-deoxyribofuranosyl)-2(1H)-pyridone (dZ) and its Watson–Crick complement, the purine analog 2-amino-8-(1′-β-D-2′-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one (dP). These implement the pyDDA:puAAD hydrogen bonding pattern (where ‘py’ indicates a pyrimidine analog and ‘pu’ indicates a purine analog, while A and D indicate the hydrogen bonding patterns of acceptor and donor groups presented to the complementary nucleobases, from the major to the minor groove). Also described is the synthesis of the triphosphates and protected phosphoramidites of these two nucleosides. We also describe the use of the protected phosphoramidites to synthesize DNA oligonucleotides containing these AEGIS components, verify the absence of epimerization of dZ in those oligonucleotides, and report some hybridization properties of the dZ:dP nucleobase pair, which is rather strong, and the ability of each to effectively discriminate against mismatches in short duplex DNA.
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Affiliation(s)
| | | | | | | | - Steven A. Benner
- To whom correspondence should be addressed at Foundation for Applied Molecular Evolution, P.O. Box 13174, Gainesville FL 32604-1174, USA. Tel: +1 352 271 7005; Fax: +1 352 271 7076;
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Joy A, Guler G, Ahmed S, McLaughlin LW, Schuster GB. Polaronic semiconductor behavior of long-range charge transfer in DNA oligomers in solution: controlling barriers to long-distance radical cation migration in DNA with thymine analogs. Faraday Discuss 2006; 131:357-65; discussion 393-402. [PMID: 16512383 DOI: 10.1039/b505550d] [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] [Indexed: 11/21/2022]
Abstract
A series of anthraquinone-linked DNA oligonucleotides was prepared and the efficiency of long-distance radical cation migration was measured. In one set of oligonucleotides, two GG steps are separated by either a TATA or an ATAT bridge. In these two compounds, the efficiency of radical cation migration from GG to GG differs by more than an order of magnitude. Replacement of the thymines in the TATA or ATAT bridges with 3-methyl-2-pyridone (t, a thymine analog) results in the much more efficient radical cation migration across the bridge in both cases. This is attributed to a decrease in the oxidation potential of t to a value below that of A. In contrast, replacement of the thymines in the TATA or ATAT bridges with difluorotoluene (f, a thymine analog with high oxidation potential) does not measurably affect radical cation migration. These findings are readily accommodated by the phonon-assisted polaron-hopping mechanism for long-distance charge transfer in duplex DNA and indicate that DNA in solution behaves as a polaronic semiconductor.
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Affiliation(s)
- Abraham Joy
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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Aly YL, Pedersen EB. Synthesis of a New Furanoid Glycal Auxiliary. MONATSHEFTE FUR CHEMIE 2005. [DOI: 10.1007/s00706-005-0342-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Hutter D, Benner SA. Expanding the genetic alphabet: non-epimerizing nucleoside with the pyDDA hydrogen-bonding pattern. J Org Chem 2004; 68:9839-42. [PMID: 14656120 DOI: 10.1021/jo034900k] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
6-Amino-3-(2'-deoxy-beta-D-ribofuranosyl)-5-nitro-1H-pyridin-2-one (4), a C-glycoside exhibiting the nonstandard pyDDA hydrogen-bonding pattern, was synthesized via Heck coupling. The nitro group greatly enhances the stability of the nucleoside toward acid-catalyzed epimerization without leading to significant deprotonation of the heterocycle at physiological pH. These results make nucleoside 4 a promising candidate for an expanded genetic alphabet.
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Affiliation(s)
- Daniel Hutter
- Department of Chemistry and Department of Anatomy and Cell Biology, University of Florida, Gainesville, Florida 32611-7200
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Kawahara SI, Uchimaru T, Taira K. 2-Pyridone and 3-oxo-1,2,6-thiadiazine-1,1-dioxide derivatives: a new class of hydrogen bond equivalents of uracil. J Comput Aided Mol Des 2003; 17:329-34. [PMID: 14635725 DOI: 10.1023/a:1026133912931] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Hydrogen bond complex stability between adenine (A) and hydrogen bond equivalents of uracil: 2-pyridone derivatives (U(X2O)X) and 3-oxo-1,2,6-thiadiazine-1,1-dioxide derivatives (U(SO2)X) was studied, and as the result, the hydrogen bond energy of U(X2O)X-A and a complex of UX(SO2)X-A, was about 1.5 kcal/mol more stable than that of the corresponding adenine-uracil derivatives complex, respectively. The energy difference between the imide tautomer and enol tautomer was smaller than those of uracil derivatives. U(SO2)F can form a stable complex with A, and its imide tautomer is stable.
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Affiliation(s)
- Shun-ichi Kawahara
- National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, 305-8565, Japan
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Sun Z, Chen D, Lan T, McLaughlin LW. Importance of minor groove functional groups for the stability of DNA duplexes. Biopolymers 2002; 65:211-7. [PMID: 12228926 DOI: 10.1002/bip.10223] [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
Eight oligonucleotide duplexes have been prepared with four pairs of selected complementary pairs of native/analogue heterocyclic bases incorporated at a selected test site. The base pairs vary in the nature of their functionality in the minor groove. Each pair has a minor groove purine amino group present or absent, and correspondingly has a minor grove pyrimidine carbonyl present or absent. Loss of duplex stability is most notable when the minor groove pyrimidine carbonyl is absent although in other respects normal Watson-Crick hydrogen bonding is maintained in these sequences. These differences in stability are discussed in terms of possible variations in minor groove hydration.
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Affiliation(s)
- Zhenhua Sun
- Department of Chemistry, Boston College, 2609 Beacon St., Chestnut Hill, MA 20467, USA
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