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Player MR, Torrence PF. Synthesis and characterization of chimeric 2-5A-DNA oligonucleotides. ACTA ACUST UNITED AC 2008; Chapter 4:Unit 4.4. [PMID: 18428851 DOI: 10.1002/0471142700.nc0404s01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This unit provides protocols for the synthesis and characterization of 2-5A-antisense nucleic acids. These chimeric oligonucleotides consist of 2',5'-phosphodiester-linked oligoadenylates ligated to 3',5'-deoxyribonucleotides and are readily prepared using phosphoramidite chemistry on CPG solid supports. The 3',5'-deoxyribonucleotide functions as the antisense domain to target a given mRNA sequence, while the 2',5'-phosphodiester-linked oligoadenylate serves to locally activate 2-5A-dependent RNase L, causing the targeted sequence to be cleaved.
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Affiliation(s)
- M R Player
- Northern Arizona University, Flagstaff, Arizona, USA
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2
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Prichard MN, Keith KA, Johnson MP, Harden EA, McBrayer A, Luo M, Qiu S, Chattopadhyay D, Fan X, Torrence PF, Kern ER. Selective phosphorylation of antiviral drugs by vaccinia virus thymidine kinase. Antimicrob Agents Chemother 2007; 51:1795-803. [PMID: 17325220 PMCID: PMC1855528 DOI: 10.1128/aac.01447-06] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The antiviral activity of a new series of thymidine analogs was determined against vaccinia virus (VV), cowpox virus (CV), herpes simplex virus, and varicella-zoster virus. Several compounds were identified that had good activity against each of the viruses, including a set of novel 5-substituted deoxyuridine analogs. To investigate the possibility that these drugs might be phosphorylated preferentially by the viral thymidine kinase (TK) homologs, the antiviral activities of these compounds were also assessed using TK-deficient strains of some of these viruses. Some of these compounds were shown to be much less effective in the absence of a functional TK gene in CV, which was unexpected given the high degree of amino acid identity between this enzyme and its cellular homolog. This unanticipated result suggested that the CV TK was important in the mechanism of action of these compounds and also that it might phosphorylate a wider variety of substrates than other type II enzymes. To confirm these data, we expressed the VV TK and human TK1 in bacteria and isolated the purified enzymes. Enzymatic assays demonstrated that the viral TK could efficiently phosphorylate many of these compounds, whereas most of the compounds were very poor substrates for the cellular kinase, TK1. Thus, the specific phosphorylation of these compounds by the viral kinase may be sufficient to explain the TK dependence. This unexpected result suggests that selective phosphorylation by the viral kinase may be a promising new approach in the discovery of highly selective inhibitors of orthopoxvirus replication.
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Affiliation(s)
- Mark N Prichard
- Department of Pediatrics, University of Alabama School of Medicine, Birmingham, AL 35233, USA.
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3
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Zhou L, Thakur CS, Molinaro RJ, Paranjape JM, Hoppes R, Jeang KT, Silverman RH, Torrence PF. Delivery of 2-5A cargo into living cells using the Tat cell penetrating peptide: 2-5A-tat. Bioorg Med Chem 2007; 14:7862-74. [PMID: 16908165 DOI: 10.1016/j.bmc.2006.07.058] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2006] [Accepted: 07/27/2006] [Indexed: 11/22/2022]
Abstract
2',5'-Oligoadenylate tetramer (2-5A) has been chemically conjugated to short HIV-1 Tat peptides to provide 2-5A-tat chimeras. Two different convergent synthetic approaches have been employed to provide such 2-5A-tat bioconjugates. One involved generation of a bioconjugate through reaction of a cysteine terminated Tat peptide with a alpha-chloroacetyl derivative of 2-5A. The second synthetic strategy was based upon a cycloaddition reaction of an azide derivative of 2-5A with a Tat peptide bearing an alkyne function. Either bioconjugate of 2-5A-tat was able to activate human RNase L. The union of 2-5A and Tat peptide provided an RNase L-active chimeric nucleopeptide with the ability to be taken up by cells by virtue of the Tat peptide and to activate RNase L in intact cells. This strategy provides a valuable vehicle for the entry of the charged 2-5A molecule into cells and may provide a means for targeted destruction of HIV RNA in vivo.
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Affiliation(s)
- Longhu Zhou
- Department of Chemistry and Biochemistry, Northern Arizona University, Flagstaff, AZ 86011-5698, USA
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Zhang X, Amer A, Fan X, Balzarini J, Neyts J, De Clercq E, Prichard M, Kern E, Torrence PF. Synthesis and antiviral activities of new acyclic and "double-headed" nucleoside analogues. Bioorg Chem 2006; 35:221-32. [PMID: 17270235 PMCID: PMC4265801 DOI: 10.1016/j.bioorg.2006.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2006] [Revised: 11/20/2006] [Accepted: 11/21/2006] [Indexed: 10/23/2022]
Abstract
To develop an understanding of the structure-activity relationships for the inhibition of orthopoxviruses by nucleoside analogues, a variety of novel chemical entities were synthesized. These included a series of pyrimidine 5-hypermodified acyclic nucleoside analogues based upon recently discovered new leads, and some previously unknown "double-headed" or "abbreviated" nucleosides. None of the synthetic products possessed significant activity against two representative orthopoxviruses; namely, vaccinia virus and cowpox virus. They were also devoid of significant activity against a battery of other DNA and RNA viruses. So far as the results with the orthopoxviruses and herpes viruses, the results may point to the necessity for nucleoside analogues 5'-phosphorylation for antiviral efficacy.
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Affiliation(s)
- Xinying Zhang
- Department of Chemistry and Biochemistry, Northern Arizona University, Flagstaff, AZ 86011-5698, USA
| | - Adel Amer
- Department of Chemistry and Biochemistry, Northern Arizona University, Flagstaff, AZ 86011-5698, USA
| | - Xuesen Fan
- Department of Chemistry and Biochemistry, Northern Arizona University, Flagstaff, AZ 86011-5698, USA
| | - Jan Balzarini
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Johan Neyts
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Mark Prichard
- Department of Pediatrics, University of Alabama School of Medicine, Birmingham, AL, USA
| | - Earl Kern
- Department of Pediatrics, University of Alabama School of Medicine, Birmingham, AL, USA
| | - Paul F. Torrence
- Department of Chemistry and Biochemistry, Northern Arizona University, Flagstaff, AZ 86011-5698, USA
- *Corresponding author. Fax: +1 928 523 8111
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Torrence PF, Fan X, Zhang X, Loiseau PM. Structurally diverse 5-substituted pyrimidine nucleosides as inhibitors of Leishmania donovani promastigotes in vitro. Bioorg Med Chem Lett 2006; 16:5047-51. [PMID: 16879965 DOI: 10.1016/j.bmcl.2006.07.042] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2006] [Revised: 07/11/2006] [Accepted: 07/13/2006] [Indexed: 11/25/2022]
Abstract
The following structurally diverse 5-substituted-2'-deoxyuridine nucleosides displayed potent in vitro antileishmanial activity: 5-formyl, 5-(2,2,-dicyanovinyl)-, 5-(2-cyano-2-ethoxycarbonylvinyl), 5-(2-cyano-2-methoxycarbonylvinyl)-, 5-(2-amino-3-cyano-5-oxo-5,6,7,8-tetrahydro-4H-chromen-4-yl)- and related congeners, and the 5-(3-methyl-5-oxo-1-phenyl-4,5-dihydro-4H-pyrazol-4-ylidene) group.
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Affiliation(s)
- Paul F Torrence
- Department of Chemistry and Biochemistry, Northern Arizona University, Flagstaff, 86011-5698, USA.
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Fan X, Zhang X, Bories C, Loiseau PM, Torrence PF. The Ugi reaction in the generation of new nucleosides as potential antiviral and antileishmanial agents. Bioorg Chem 2006; 35:121-36. [PMID: 16996561 DOI: 10.1016/j.bioorg.2006.08.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2006] [Revised: 08/10/2006] [Accepted: 08/11/2006] [Indexed: 11/17/2022]
Abstract
5-Formyl-2'-deoxyuridine-3',5'-diacetate was converted to a small library of 5-substituted pyrimidine nucleoside N-acylamino acid amides by means of a Ugi multicomponent reaction. The reaction allowed introduction of various substituents at the acyl moiety, at the amino acid alpha-amide group, and at the amino acid carboxyl function. Evaluation of these novel 5-substituted nucleosides against vaccinia virus and cowpox virus provided one compound with discernable activity against cowpox virus but five- to eightfold less active than the Cidofovir standard. More promising activity was seen for the inhibition of Leishmania donovani promastigotes. Several synthetic products showed antileishmanial activity in the 10(-5)M range. When compared to earlier studies demonstrating anti-orthopoxviral and antileishmanial activity of 5-substituted pyrimidine nucleosides, these results imply that the 5-(N-acylamino acid amide)-derivatized pyrimidine nucleosides may possess more steric bulk, greater hydrophobicity, and more flexibility than is compatible with these particular biological activities.
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Affiliation(s)
- Xuesen Fan
- Department of Chemistry and Biochemistry, Northern Arizona University, Flagstaff, AZ 86011-5698, USA
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Fan X, Zhang X, Zhou L, Keith KA, Prichard MN, Kern ER, Torrence PF. Toward orthopoxvirus countermeasures: a novel heteromorphic nucleoside of unusual structure. J Med Chem 2006; 49:4052-4. [PMID: 16821766 PMCID: PMC4298854 DOI: 10.1021/jm060404n] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two privileged drug scaffolds have been hybridized to create the novel heteromorphic nucleoside 5-(2-amino-3-cyano-5-oxo-5,6,7,8-tetrahydro-4H-chromen-4-yl)-1-(2-deoxypentofuranosyl)pyrimidine-2,4(1H,3H)-dione (2). Compound 2 inhibited the replication of two orthopoxviruses, vaccinia virus (VV) (EC(50) = 4.6 +/- 2.0 microM), and cowpox virus (CV) (EC(50) = 2.0 +/- 0.3 microM). Compound 2 exhibited reduced activity against a thymidine kinase (TK) negative strain of CV, implying a requirement for 5'-monophosphorylation for antiorthopoxvirus activity. Compound 2 was efficiently phosphorylated by VV TK, establishing that VV TK is more promiscuous than previously believed.
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Affiliation(s)
| | | | | | | | | | | | - Paul F. Torrence
- To whom correspondence should be addressed. Phone: 928-523-0298. Fax: 928-523-8111.
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Fan X, Zhang X, Zhou L, Keith KA, Kern ER, Torrence PF. Assembling a smallpox biodefense by interrogating 5-substituted pyrimidine nucleoside chemical space. Antiviral Res 2006; 71:201-5. [PMID: 16759713 DOI: 10.1016/j.antiviral.2006.04.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2006] [Accepted: 04/19/2006] [Indexed: 11/20/2022]
Abstract
The nucleoside 5-formyl-2'-deoxyuridine has been used as a starting point for the generation of novel 5-substituted pyrimidine nucleosides that are shown to possess significant antiviral activity against two representative orthopoxviruses, namely vaccinia virus and cowpox virus.
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Affiliation(s)
- Xuesen Fan
- Department of Chemistry and Biochemistry, Northern Arizona University, Flagstaff, AZ 86011, USA
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Fan X, Zhang X, Zhou L, Keith KA, Kern ER, Torrence PF. 5-(Dimethoxymethyl)-2'-deoxyuridine: a novel gem diether nucleoside with anti-orthopoxvirus activity. J Med Chem 2006; 49:3377-82. [PMID: 16722657 PMCID: PMC4262926 DOI: 10.1021/jm0601710] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To provide potential new leads for the treatment of orthopoxvirus infections, the 5-position of the pyrimidine nucleosides have been modified with a gem diether moiety to yield the following new nucleosides: 5-(dimethoxymethyl)-2'-deoxyuridine (2b), 5-(diethoxymethyl)-2'-deoxyuridine (3b), 5-formyl-2'-deoxyuridine ethylene acetal (4b), and 5-formyl-2'-deoxyuridine propylene acetal (5b). These were evaluated in human foreskin fibroblast cells challenged with the vaccinia virus or cowpox virus. Of the four gem diether nucleosides, only the dimethyl gem diether congener showed significant antiviral activity against both viruses. This antiviral activity did not appear to be related to the decomposition to the 5-formyl-2'-deoxyuridine, which was itself devoid of anti-orthopoxvirus activity in these assays. Moreover, at the pH of the in vitro assays, 2b was very stable with a decomposition (to aldehyde) half-life of >15 d. The anti-orthopoxvirus activity of pyrimidine may be favored by the introduction of hydrophilic moieties to the 5-position side chain.
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Affiliation(s)
| | | | | | | | | | - Paul F. Torrence
- To whom correspondence should be addressed. Tel: (928) 523-0298. Fax: (928) 523-8111.
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Fan X, Zhang X, Zhou L, Keith KA, Kern ER, Torrence PF. A pyrimidine–pyrazolone nucleoside chimera with potent in vitro anti-orthopoxvirus activity. Bioorg Med Chem Lett 2006; 16:3224-8. [PMID: 16603351 DOI: 10.1016/j.bmcl.2006.03.043] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2006] [Revised: 03/13/2006] [Accepted: 03/14/2006] [Indexed: 11/30/2022]
Abstract
Synthetic hybridization of two privileged drug scaffolds, pyrazolone on the one hand and pyrimidine nucleoside on the other, resulted in the generation of two novel 5-substituted pyrimidine nucleosides with potent in vitro antiviral activity against two representative orthopoxviruses, vaccinia virus and cowpox virus.
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Affiliation(s)
- Xuesen Fan
- Department of Chemistry and Biochemistry, Northern Arizona University, Flagstaff, AZ 86011, USA
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Zhou L, Amer A, Korn M, Burda R, Balzarini J, De Clercq E, Kern ER, Torrence PF. Synthesis and antiviral activities of 1,2,3-triazole functionalized thymidines: 1,3-dipolar cycloaddition for efficient regioselective diversity generation. Antivir Chem Chemother 2006; 16:375-83. [PMID: 16331842 DOI: 10.1177/095632020501600604] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Efficient regioselective synthesis of nucleoside conjugates was achieved by cycloaddition reaction of azides and alkynes using sodium ascorbate/ CuSO4 system as a catalyst. These 16 novel thymidine analogues were obtained in excellent yields (75-100%), employing mild reaction conditions with a broad scope of structural modification. For the compounds tested, no specific antiviral effects could be witnessed against a broad range of viruses.
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Affiliation(s)
- Longhu Zhou
- Department of Chemistry and Biochemistry, Northern Arizona University, AZ, USA
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Torrence PF, Gupta N, Whitney C, Morrey JD. Evaluation of synthetic oligonucleotides as inhibitors of West Nile virus replication. Antiviral Res 2006; 70:60-5. [PMID: 16540182 DOI: 10.1016/j.antiviral.2006.01.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2005] [Revised: 01/11/2006] [Accepted: 01/11/2006] [Indexed: 11/23/2022]
Abstract
A series of synthetic oligonucleotide phosphorothioate 15-mers were generated against specific sequences in the West Nile virus RNA genome. These antisense oligonucleotides targeted (1) conserved features of the West Nile virus RNA genome that may be expected to lead to inhibition of virus replication since such features play essential roles in the virus lifecycle; (2) G-quartet oligonucleotides with potential facilitated uptake properties and that also targeted conserved sequences among a range of West Nile virus strains. Several formulations with significant in vitro antiviral activity were found. Among the active oligonucleotides were examples that targeted both C-rich RNA sequences of the West Nile RNA genome as well as recognized conserved sequences key to West Nile virus replication. Since the antiviral activity of the latter oligonucleotides diminished upon 2'-O-methyl substitution, it is likely that their activity involves RNase H-catalyzed RNA degradation. One G-rich oligonucleotide that did not target a West Nile virus RNA sequence also was found. These results suggest the potential of antisense strategies for the control of West Nile virus replication if the attendant problem of oligonucleotide delivery can be adequately addressed.
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Affiliation(s)
- Paul F Torrence
- Northern Arizona University, Department of Chemistry and Biochemistry, Bldg 20, Room 125, Box 5698, Flagstaff, AZ 86011, USA.
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Zhou L, Civitello ER, Gupta N, Silverman RH, Molinaro RJ, Anderson DE, Torrence PF. Endowing RNase H-inactive antisense with catalytic activity: 2-5A-morphants. Bioconjug Chem 2005; 16:383-90. [PMID: 15769093 DOI: 10.1021/bc049778q] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A convergent synthetic approach was used to conjugate 2',5'-oligoadenylate (2-5A, p5'A2' [p5'A2'](n)()p5'A) to phosphorodiamidate morpholino oligomers (morphants). To provide requisite quantities of 2-5A starting material, commercially and readily available synthons for solid-phase synthesis were adapted for larger scale solution synthesis. Thus, the tetranucleotide 5'-phosphoryladenylyl(2'-->5')adenylyl(2'-->5')adenylyl(2'-->5')adenosine (p5'A2'p5'A2'](2)p5'A2', tetramer 2-5A, 9) was synthesized starting with 2',3'-O-dibenzoyl-N(6),N(6)-dibenzoyl adenosine prepared from commercially available 5'-O-(4-monomethoxytrityl) adenosine. Coupling with N(6)-benzoyl-5'-O-(4,4'-dimethoxytrityl)-3'-O-(tert-butyldimethylsilyl) adenosine-2'-(N,N-diisopropyl-2-cyanoethyl)phosphoramidite, followed by oxidization and deprotection, generated 5'-deprotected dimer 2-5A. Similar procedures lengthened the chain to form protected tetramer 2-5 A. The title product 9 p5'A(2'p5'A)(3) (tetramer 2-5A) was obtained through phosphorylation of the terminal 5'-hydroxy of the protected tetramer and removal of remaining protecting groups using concentrated ammonium hydroxide-ethanol (3:1, v/v) at 55 degrees C and tetrabutylammonium fluoride (TBAF) in THF at room temperature, respectively. The 2-5A-phosphorodiamidate morpholino antisense chimera 11 (2-5A-morphant) was synthesized by covalently linking an aminolinker-functionalized phosphorodiamidate morpholino oligomer with periodate oxidized 2-5A tetramer (p5'A2'[p5'A2'](2)p5'A). The resulting Schiff base was reduced with cyanoborohydride thereby transforming the ribose of the 2'-terminal nucleotide of 2-5A N-substituted morpholine. RNase L assays demonstrated that this novel 2-5A-antisense chimera had significant biological activity, thereby providing another potential tool for RNA ablation.
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Affiliation(s)
- Longhu Zhou
- Department of Chemistry, Northern Arizona University, Box 5698, Flagstaff, Arizona 86011-5698, USA
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14
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Kalinichenko EN, Podkopaeva TL, Budko EV, Seela F, Dong B, Silverman R, Vepsäläinen J, Torrence PF, Mikhailopulo IA. 3-Deazaadenosine analogues of p5'A2'p5'A2'p5'A: synthesis, stereochemistry, and the roles of adenine ring nitrogen-3 in the interaction with RNase L. Bioorg Med Chem 2005; 12:3637-47. [PMID: 15186848 DOI: 10.1016/j.bmc.2004.04.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2004] [Accepted: 04/15/2004] [Indexed: 11/24/2022]
Abstract
Sequence-specific 3-deazaadenosine (c(3)A)-substituted analogues of trimeric 2',5'-oligoadenylate, p5'A2'p5'A2'p5'A, were synthesized and evaluated for their ability to activate human RNase L (EC 3.1.2.6) aiming at the elucidation of the nitrogen-3 role in this biochemical process. Substitution of either 5'-terminal or 2'-terminal adenosine with c(3)A afforded the respective analogues p5'(c(3)A)2'p5'A2'p5'A and p5'A2'p5'A2'p5'(c(3)A) that were as effective as the natural tetramer itself as activators of RNase L (EC(50)=1nM). In contrast, p5'A2'p5'(c(3)A)2'p5'A showed diminished RNase L activation ability (EC(50)=10nM). The extensive conformational analysis of the c(3)A-substituted core trimers versus the parent natural core trimer by the (1)H and (13)C NMR, and CD spectroscopy displayed close stereochemical similarity between the natural core trimer and (c(3)A)2'p5'A2'p5'A and A2'p5'A2'p5'(c(3)A) analogues, thereby strong evidences for the syn base orientation about the glycosyl bond of the c(3)A residue of the latter were found. On the contrary, an analogue A2'p5'(c(3)A)2'p5'A displayed rather essential deviations from the spatial arrangement of the parent natural core trimer.
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Affiliation(s)
- Elena N Kalinichenko
- Institute of Bioorganic Chemistry, National Academy of Sciences, 220141 Minsk, Belarus
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15
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Abstract
2-5A trimer [5'-monophosphoryladenylyl(2'-5')adenylyl(2'-5')adenosine] activates RNase L. While the 5'-terminal and 2'-terminal adenosine N(6)-amino groups play a key role in binding to and activation of RNase L, the exocyclic amino function of the second adenylate (from the 5'-terminus) plays a relatively minor role in 2-5A's biological activity. To probe the available space proximal to the amino function of the central adenylate of 2-5A trimer during binding to RNase L, a variety of substituents were placed at that position. To accomplish this, the convertible building block 5'-O-dimethoxytrityl-3'-O-(tert-butyldimethylsilyl)-6-(2,4-dinitrophenyl)thioinosine 2'-(2-cyanoethylN,N-diisopropylphosphoramidite) was prepared as a synthon to introduce 6-(2,4-dinitrophenyl)thioinosine into the middle position of the 2-5A trimer during automated synthesis. Post-synthetic treatment with aqueous amines transformed the (2,4-dinitrophenyl)thioinosine into N(6)-substituted adenosines. Assays of these modified trimers for their ability to bind and activate RNase L showed that activation activity could be retained, albeit with some sacrifice compared to unmodified p5'A2'p5'A2'p5'A. Thus, the spatial domain about this N(6)-amino function could be available for modifications to enhance the biological potency of 2-5A analogues and to ligate 2-5A to targeting vehicles such as antisense molecules.
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Affiliation(s)
- Ursula Münch
- Section on Biomedical Chemistry, Laboratory of Medicinal Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0805, USA
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Abstract
Respiratory syncytial virus (RSV) continues as an emerging infectious disease not only among infants and children, but also for the immune-suppressed, hospitalized and the elderly. To date, ribavirin (Virazole) remains the only therapeutic agent approved for the treatment of RSV. The prophylactic administration of palivizumab is problematic and costly. The quest for an efficacious RSV antiviral has produced a greater understanding of the viral fusion process, a new hypothesis for the mechanism of action of ribavirin, and a promising antisense strategy combining the 2'-5' oligoadenylate antisense (2-5A-antisense) approach and RSV genomics.
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Affiliation(s)
- Paul F Torrence
- Department of Chemistry, Northern Arizona University, Flagstaff, Ariz., USA.
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Imai J, Torrence PF. Bis(2,2,2-trichloroethyl) phosphorochloridite as a reagent for the phosphorylation of oligonucleotides: preparation of 5'-phosphorylated 2',5'-oligoadenylates. J Org Chem 2002. [DOI: 10.1021/jo00333a016] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Maggiora L, Chang CCTC, Torrence PF, Mertes MP. 5-Nitro-2'-deoxyuridine 5'-phosphate: a mechanism-based inhibitor of thymidylate synthetase. J Am Chem Soc 2002. [DOI: 10.1021/ja00401a042] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Affiliation(s)
- P F Torrence
- Department of Chemistry, Northern Arizona University, Flagstaff, Arizona 86011, USA
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Fettes KJ, Howard N, Hickman DT, Adah S, Player MR, Torrence PF, Micklefield J. Synthesis and nucleic-acid-binding properties of sulfamide- and 3′-N-sulfamate-modified DNAElectronic supplementary information (ESI) available: typical melting curves obtained from thermal denaturation of modified oligonucleotides with complementary DNA and RNA. See http://www.rsc.org/suppdata/p1/b1/b110603c/. ACTA ACUST UNITED AC 2002. [DOI: 10.1039/b110603c] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Leaman DW, Longano FJ, Okicki JR, Soike KF, Torrence PF, Silverman RH, Cramer H. Targeted therapy of respiratory syncytial virus in African green monkeys by intranasally administered 2-5A antisense. Virology 2002; 292:70-7. [PMID: 11878909 DOI: 10.1006/viro.2001.1213] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Respiratory syncytial virus (RSV) is a leading cause of respiratory disease in infants, young children, immunocompromised patients, and the institutionalized elderly. Previous work had shown that RNase L, an antiviral enzyme of the interferon system, could be recruited to cleave RSV genomic RNA by attaching tetrameric 2prime prime or minute-5prime prime or minute-linked oligoadenylates (2-5A) to an oligonucleotide complementary to repetitive gene-start sequences within the RSV genome (2-5A antisense). A 2prime prime or minute-O-methyl RNA-modified analog of the lead 2-5A anti-RSV chimera is shown here to have enhanced antiviral activity in cell culture studies while also cleaving RSV genomic RNA in an RNase L- and sequence-specific manner. When administered intranasally to RSV-infected African green monkeys, this chimera reduced nasal RSV replication by up to four log(10) units in a dose- and time-dependent manner.
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Affiliation(s)
- Douglas W Leaman
- Ridgeway Biosystems Inc., 9500 Euclid Avenue, NE50, Cleveland, Ohio 44195, USA.
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24
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Abstract
This review describes the application of a natural defense mechanism to develop effective agents for the post-transcriptional control of gene expression. 2-5A is a unique 2',5'-phosphodiester bond linked oligoadenylate, (pp)p5'A2'(p5'A)(n), that is elaborated in virus-infected interferon-treated cells. The 2-5A system is an RNA degradation pathway that is an important mechanistic component of interferon's action against certain viruses. It may also play a role in the anticellular effects of interferon and in general RNA decay. A major player in the 2-5A-system is the latent and constitutive 2-5A-dependent ribonuclease (RNase L) which upon activation by 2-5A, degrades RNA. This RNase L enzyme can be recruited for antisense therapeutics by linking it to an appropriate oligonucleotide targeted to a chosen RNA. Syntheses of 2-5A, its analogues, 2-5A-antisense, and its modifications are detailed herein. Applications of 2-5A-antisense to particular targets such as HIV, PKR, chronic myelogenous leukemia, telomerase, and respiratory syncytical virus are described.
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MESH Headings
- Adenine Nucleotides/chemistry
- Adenine Nucleotides/metabolism
- Animals
- Antineoplastic Agents/pharmacology
- Antiviral Agents/chemistry
- Antiviral Agents/metabolism
- Antiviral Agents/pharmacology
- Apoptosis/drug effects
- Apoptosis/physiology
- Carrier Proteins/chemical synthesis
- Carrier Proteins/chemistry
- Carrier Proteins/metabolism
- Carrier Proteins/pharmacology
- Endoribonucleases/metabolism
- Gene Expression Regulation, Viral/drug effects
- Humans
- Interferons/pharmacology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Oligoribonucleotides/chemistry
- Oligoribonucleotides/metabolism
- Oligoribonucleotides, Antisense/chemical synthesis
- Oligoribonucleotides, Antisense/chemistry
- Oligoribonucleotides, Antisense/metabolism
- Oligoribonucleotides, Antisense/pharmacology
- RNA Viruses/drug effects
- Respiratory Syncytial Viruses/drug effects
- Sequence Homology, Nucleic Acid
- Tumor Cells, Cultured/drug effects
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Affiliation(s)
- S A Adah
- Section on Biomedical Chemistry, Laboratory of Medicinal Chemistry, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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25
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Verheijen JC, Chen L, Bayly SF, Torrence PF, van der Marel GA, van Boom JH. Synthesis and RNAse L binding and activation of a 2-5A-(5')-DNA-(3')-PNA chimera, a novel potential antisense molecule. Nucleosides Nucleotides Nucleic Acids 2000; 19:1821-30. [PMID: 11200276 DOI: 10.1080/15257770008045463] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Fully automated solid-phase synthesis gave access to a hybrid in which 5'-phosphorylated-2'-5'-linked oligoadenylate (2-5A) is connected to the 5'-terminus of DNA which, in turn, is linked at the 3'-end to PNA [2-5A-(5')-DNA-(3')-PNA chimera]. This novel antisense molecule retains full RNase L activation potency while suffering only a slight reduction in binding affinity.
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Affiliation(s)
- J C Verheijen
- Leiden Institute of Chemistry, Gorlaeus Laboratories, The Netherlands
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26
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Abstract
2-5A was conjugated to N-(2-aminoethyl)-glycyl PNA by periodate oxidization, followed by coupling with amino-derivatized PNA and final cyanoborohydride reduction. An adduct of 2-5A pentamer with tetrameric thymine PNA activated RNase L with the same potency as earlier versions of 2-5A-PNA or 2-5A-DNA.
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Affiliation(s)
- Z Wang
- Section on Biomedical Chemistry, Laboratory of Medicinal Chemistry, National Institute of Diabetes and Digestive antd Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0805, USA
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27
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Torrence PF. RSV infections: developments in the search for new drugs. Drug News Perspect 2000; 13:226-33. [PMID: 12937627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Respiratory syncytial virus (RSV) is the major cause of lower respiratory tract infection in infants and young children, and is also a significant threat to other populations including the immunosuppressed, the elderly and those with chronic chest or cardiac disease. To expand the scope of available antiviral drugs, presently limited to ribavirin, a variety of different structural formats have been explored in the past half-dozen years. Interesting leads for future discovery and lead development include a group of biphenyl relatives (represented by CL-387626) that bind the RSV fusion (F) protein; 2-5A-antisense oligonucleotides that target the RSV genomic RNA; Rho A-derived peptides that block Rho A GTPase interaction with RSV fusion (F) protein; and several compounds of presently unknown mechanisms of action, such as benzodithiins.
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Affiliation(s)
- P F Torrence
- Department of Chemistry, Northern Arizona University, Flagstaff, Arizona 86011-5698, USA
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28
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Verheijen JC, van Roon AM, Meeuwenoord NJ, Stuivenberg HR, Bayly SF, Chen L, van der Marel GA, Torrence PF, van Boom JH. Incorporation of a 4-hydroxy-N-acetylprolinol nucleotide analogue improves the 3'-exonuclease stability of 2'-5'-oligoadenylate-antisense conjugates. Bioorg Med Chem Lett 2000; 10:801-4. [PMID: 10782690 DOI: 10.1016/s0960-894x(00)00100-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Incorporation of a 4-hydroxy-N-acetylprolinol nucleotide analogue at the 3'-terminus of DNA or 2-5A-DNA sequences resulted in a significantly enhanced 3'-exonuclease resistance while the affinity for complementary RNA was only slightly decreased. Furthermore, the binding to and activation of human RNase L by thus modified 2-5A-DNA conjugates was not altered as compared to the parent unmodified 2-5A-DNAs.
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Affiliation(s)
- J C Verheijen
- Leiden Institute of Chemistry, Gorlaeus Laboratories, The Netherlands
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29
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Kitade Y, Wakana M, Tsuboi T, Yatome C, Bayly SF, Player MR, Torrence PF. 2-Methyladenosine-Substituted 2',5'-oligoadenylates: conformations, 2-5A binding and catalytic activities with human ribonuclease L. Bioorg Med Chem Lett 2000; 10:329-31. [PMID: 10714492 DOI: 10.1016/s0960-894x(99)00703-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
2-Methyladenosine-substituted analogues of 2-5A, p5'A2'p5'A2'p5'(me2A), p5'(me2A)2'p5'A2'p5'A, and p5'(me2A) 2'p5'(me2A)2'pS'(me2A), were prepared via a modification of a lead ion-catalyzed ligation reaction. These 5'-monophosphates were subsequently converted into the corresponding 5'-triphosphates. Both binding and activation of human recombinant RNase L by various 2-methyladenosine-substituted 2-5A analogues were examined. Among the 2-5A analogues, p5'A2'p5'A2'p5'(me2A) showed the strongest binding affinity and was as effective as 2-5A itself as an activator of RNase L. The CD spectra of both p5'(me2A)2'p5'A2'p5'A and p5'A2'p5'A2'p5'(me2A) were superimposable on that of p5'A2'p5'A2'p5'A, indicative of an anti orientation about the base-glycoside bonds as in naturally occurring 2-5A.
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Affiliation(s)
- Y Kitade
- Department of Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido, Japan.
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30
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Geselowitz DA, Cramer H, Wondrak EM, Player MR, Torrence PF. Fluorescence resonance energy transfer analysis of RNase L-catalyzed oligonucleotide cleavage. Antisense Nucleic Acid Drug Dev 2000; 10:45-51. [PMID: 10726660 DOI: 10.1089/oli.1.2000.10.45] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
A method is described for monitoring the cleavage of an oligoribonucleotide substrate by the 2-5A-dependent RNase L based on fluorescence resonance energy transfer (FRET). The oligoribonucleotide, rC11U2C7, was labeled covalently at its 5'-terminus with fluorescein and at its 3'-terminus with rhodamine to provide a substrate for RNase L. On cleavage, the fluorescence at 538 nm (with 485 nm excitation) increased by a factor of 2.8, allowing real-time quantitation of the reaction progress. The method was performed easily in a 96-well plate format and allowed quantitative high throughput analyses of RNase L activity with different activators.
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Affiliation(s)
- D A Geselowitz
- Laboratory of Medicinal Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Health, Bethesda, MD 20892-0805, USA
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31
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Fettes KJ, Howard N, Hickman DT, Adah SA, Player MR, Torrence PF, Micklefield J. Replacement of the phosphodiester linkage in DNA with sulfamide and 3′-N-sulfamate groups. Chem Commun (Camb) 2000. [DOI: 10.1039/b001586p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Silverman RH, Dong B, Maitra RK, Player MR, Torrence PF. Selective RNA cleavage by isolated RNase L activated with 2-5A antisense chimeric oligonucleotides. Methods Enzymol 1999; 313:522-33. [PMID: 10595377 DOI: 10.1016/s0076-6879(00)13033-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- R H Silverman
- Department of Cancer, Lerner Research Institute, Cleveland Clinic Foundation, Ohio 44195, USA
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33
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Verheijen JC, Bayly SF, Player MR, Torrence PF, van der Marel GA, van Boom JH. 2-5A-PNA complexes: a novel class of antisense compounds. Nucleosides and Nucleotides 1999; 18:1485-6. [PMID: 10474229 DOI: 10.1080/07328319908044761] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
This paper presents the fully automated solid phase synthesis of 2-5A-PNA hybrids. These stable antisense probes cause RNase L mediated hydrolysis of target RNA sequences.
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34
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Cramer H, Geselowitz DA, Torrence PF. Using fluorescence resonance energy transfer (FRET) for measuring 2-5A analogues ability to activate RNase L. Nucleosides Nucleotides 1999; 18:1523-5. [PMID: 10474231 DOI: 10.1080/07328319908044776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The development of a method for measuring the ability of 2-5A analogues to activate the cleavage of an oligoribonucleotide substrate by RNase L is described. This method is based on fluorescence resonance energy transfer. The method is easily performed with 96-well plates, allowing for quantitative high-throughput analyses of 2-5A analogues under different reaction conditions.
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Affiliation(s)
- H Cramer
- Section of Biomedical Chemistry, NIDDK, NIH, Bethesda, MD 20892, USA
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35
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Torrence PF. 2-5A-antisense chimeras: inhibitors of respiratory syncytial virus infection. Curr Opin Mol Ther 1999; 1:307-15. [PMID: 11713795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
A new approach to the chemical control of respiratory syncytial virus infection is reviewed in the context of the biology of the virus and previous treatment approaches. Conjugation of the interferon action mediator, 2',5'-oligoadenylate (2-5A), to antisense agents provides a strategy for the selective ablation of RNA. This application of this technology to respiratory syncytial virus has provided a potent selective inhibitor of virus replication.
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MESH Headings
- 2',5'-Oligoadenylate Synthetase/genetics
- 2',5'-Oligoadenylate Synthetase/metabolism
- Adenine Nucleotides/chemistry
- Adenine Nucleotides/pharmacology
- Adenosine Triphosphate/metabolism
- Antisense Elements (Genetics)/chemistry
- Antisense Elements (Genetics)/pharmacology
- Antiviral Agents/pharmacology
- Child
- Child, Preschool
- Computer Simulation
- Drug Design
- Endoribonucleases/metabolism
- Enzyme Induction
- Humans
- Infant
- Interferons/physiology
- Models, Molecular
- Oligoribonucleotides/chemistry
- Oligoribonucleotides/pharmacology
- RNA, Double-Stranded/antagonists & inhibitors
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/metabolism
- RNA, Viral/antagonists & inhibitors
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Respiratory Syncytial Virus Infections/drug therapy
- Respiratory Syncytial Viruses/drug effects
- Respiratory Syncytial Viruses/genetics
- Respiratory Syncytial Viruses/physiology
- Substrate Specificity
- Virus Replication/drug effects
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Affiliation(s)
- P F Torrence
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0805, USA.
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36
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Cramer H, Player MR, Torrence PF. Discrimination between ribonuclease H- and ribonuclease L-mediated RNA degradation by 2'-O-methylated 2-5A-antisense oligonucleotides. Bioorg Med Chem Lett 1999; 9:1049-54. [PMID: 10230638 DOI: 10.1016/s0960-894x(99)00134-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
2',5'-Oligoadenylate (2-5A) antisense chimeric oligonucleotides were synthesized containing varying 2'-O-methyl-ribonucleotide substitution patterns in the antisense domain. The ability of these composite oligonucleotides to mediate RNase H- and RNase L-catalyzed RNA degradation showed that these two enzymes have different activation requirements.
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Affiliation(s)
- H Cramer
- Section on Biomedical Chemistry, Laboratory of Medicinal Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0805, USA
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37
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Barnard DL, Sidwell RW, Xiao W, Player MR, Adah SA, Torrence PF. 2-5A-DNA conjugate inhibition of respiratory syncytial virus replication: effects of oligonucleotide structure modifications and RNA target site selection. Antiviral Res 1999; 41:119-34. [PMID: 10320045 DOI: 10.1016/s0166-3542(99)00005-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
To define more fully the conditions for 2-5A-antisense inhibition of respiratory syncytial virus (RSV), relationships between 2-5A antisense oligonucleotide structure and the choice of RNA target sites to inhibition of RSV replication have been explored. The lead 2-5A-antisense chimera for this study was the previously reported NIH8281 that targets the RSV M2 RNA. We have confirmed and extended the earlier study by showing that NIH8281 inhibited RSV strain A2 replication in a variety of antiviral assays, including virus yield reduction assays performed in monkey (EC90 = 0.02 microM) and human cells (EC90 = microM). This 2-5A-antisense chimera also inhibited other A strains, B strains and bovine RSV in cytopathic effect inhibition and Neutral Red Assays (EC50 values = 0.1-1.6 microM). The 2'-O-methylation modification of NIH8281 to increase affinity for the complementary RNA and provide nuclease resistance, the introduction of phosphothioate groups in the antisense backbone to enhance resistance to exo- and endonucleases, and the addition of cholesterol to the 3'-terminus of the antisense oligonucleotide to increase cellular uptake, all resulted in loss of activity. Of the antisense chimeras targeting other RSV mRNAs (NS1, NS2, P, M. G, F, and L), only those complementary to L mRNA were inhibitory. These results suggest that lower abundance mRNAs may be the best targets for 2-5A-antisense; moreover, the active 2-5A antisense chimeras in this study may serve as useful guides for the development of compounds with improved stability, uptake and anti-RSV activity.
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Affiliation(s)
- D L Barnard
- Institute For Antiviral Research, Utah State University, Logan 84322-5600, USA
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38
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Abstract
Phosphorothioate oligodeoxyribonucleotides were found to be inhibitors of the 2-5A-dependent RNase L. Inhibitory potency depended upon the chain length of the phosphorothioate oligonucleotide and was dependent on the phosphorothioate substitution pattern, but was not substantially base-dependent.
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Affiliation(s)
- M R Player
- Section on Biomedical Chemistry, Laboratory of Medicinal Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0805, USA
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39
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Abstract
To potentiate the 2-5A (2',5'-oligoadenylate)-antisense and peptide nucleic acid (PNA) approaches to regulation of gene expression, composite molecules were generated containing both 2-5A and PNA moieties. 2-5A-PNA adducts were synthesized using solid-phase techniques. Highly cross-linked polystyrene beads were functionalized with glycine tethered through a p-hydroxymethylbenzoic acid linker and the PNA domain of the chimeric oligonucleotide analogue was added by sequential elongation of the amino terminus with the monomethoxytrityl protected N-(2-aminoethyl)-N-(adenin-1-ylacetyl)glycinate. Transition to the 2-5A domain was accomplished by coupling of the PNA chain to dimethoxytrityl protected N-(2-hydroxyethyl)-N-(adenin-1-ylacetyl)glycinate. Finally, (2-cyanoethyl)-N,N-diisopropyl-4-O-(4,4-dimethoxytrityl)butylphosphor amidite and the corresponding (2-cyanoethyl)-N,N-diisopropylphosphoramidite of 5-O-(4,4'-dimethoxytrityl)-3-O-(tert-butyldimethylsilyl)-N6-benzoyladeno sine were the synthons employed to add the 2 butanediol phosphate linkers and the four 2',5'-linked riboadenylates. The 5'-phosphate moiety was introduced with 2-[[2-(4,4'-dimethoxytrityloxy)ethyl]sulfonyl]ethyl-(2-cyanoethyl) -N,N-diisopropylphosphoramidite. Deprotection with methanolic NH3 and tetraethylammonium fluoride afforded the desired products, 2-SA-pnaA4, 2-5A-pnaA8 and 2-5A-pnaA12. When evaluated for their ability to cause the degradation of two different RNA substrates by the 2-5A-dependent RNase L, these new 2-5A-PNA conjugates were found to be potent RNase L activators. The union of 2-5A and PNA presents fresh opportunities to explore the biological and therapeutic implications of these unique approaches to antisense.
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Affiliation(s)
- J C Verheijen
- Leiden Institute of Chemistry, Gorlaeus Laboratories, The Netherlands
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40
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Kitade Y, Wakana M, Terai SI, Tsuboi T, Nakanishi M, Yatome C, Dong B, Silverman RH, Torrence PF. 2-Bromoadenosine-Substituted 2′,5′-Oligoadenylates Modulate Binding and Activation Abilities of Human Recombinant RNase L. ACTA ACUST UNITED AC 1998. [DOI: 10.1080/07328319808004320] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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41
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Maran A, Waller CF, Paranjape JM, Li G, Xiao W, Zhang K, Kalaycio ME, Maitra RK, Lichtin AE, Brugger W, Torrence PF, Silverman RH. 2',5'-Oligoadenylate-antisense chimeras cause RNase L to selectively degrade bcr/abl mRNA in chronic myelogenous leukemia cells. Blood 1998; 92:4336-43. [PMID: 9834240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
We report an RNA targeting strategy, which selectively degrades bcr/abl mRNA in chronic myelogenous leukemia (CML) cells. A 2', 5'-tetraadenylate activator (2-5A) of RNase L was chemically linked to oligonucleotide antisense directed against either the fusion site or against the translation start sequence in bcr/abl mRNA. Selective degradation of the targeted RNA sequences was demonstrated in assays with purified RNase L and decreases of p210(bcr/abl) kinase activity levels were obtained in the CML cell line, K562. Furthermore, the 2-5A-antisense chimeras suppressed growth of K562, while having substantially reduced effects on the promyelocytic leukemia cell line, HL60. Findings were extended to primary CML cells isolated from bone marrow of patients. The 2-5A-antisense treatments both suppressed proliferation of the leukemia cells and selectively depleted levels of bcr/abl mRNA without affecting levels of beta-actin mRNA, determined by reverse transcriptase-polymerase chain reaction (RT-PCR). The specificity of this approach was further shown with control oligonucleotides, such as chimeras containing an inactive dimeric form of 2-5A, antisense lacking 2-5A, or chimeras with altered sequences including several mismatched nucleotides. The control oligonucleotides had either reduced or no effect on CML cell growth and bcr/abl mRNA levels. These findings show that CML cell growth can be selectively suppressed by targeting bcr/abl mRNA with 2-5A-antisense for decay by RNase L and suggest that these compounds should be further explored for their potential as ex vivo purging agents of autologous hematopoietic stem cell transplants from CML patients.
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MESH Headings
- Adenine Nucleotides/genetics
- Adenine Nucleotides/pharmacology
- Adenine Nucleotides/therapeutic use
- Endoribonucleases/genetics
- Endoribonucleases/pharmacology
- Enzyme Activation/genetics
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Fusion Proteins, bcr-abl/genetics
- Gene Expression Regulation, Neoplastic
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Oligonucleotides, Antisense/genetics
- Oligonucleotides, Antisense/pharmacology
- Oligonucleotides, Antisense/therapeutic use
- Oligoribonucleotides/genetics
- Oligoribonucleotides/pharmacology
- Oligoribonucleotides/therapeutic use
- RNA, Messenger/antagonists & inhibitors
- RNA, Messenger/genetics
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/pharmacology
- Recombinant Fusion Proteins/therapeutic use
- Tumor Cells, Cultured
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Affiliation(s)
- A Maran
- Department of Cancer Biology, The Lerner Research Institute, and Department of Hematology and Oncology, Cleveland Clinic Foundation, Cleveland, OH,USA
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42
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Player MR, Barnard DL, Torrence PF. Potent inhibition of respiratory syncytial virus replication using a 2-5A-antisense chimera targeted to signals within the virus genomic RNA. Proc Natl Acad Sci U S A 1998; 95:8874-9. [PMID: 9671772 PMCID: PMC21170 DOI: 10.1073/pnas.95.15.8874] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The 2-5A system is a recognized mechanistic component of the antiviral action of interferon. Interferon-induced 2-5A synthetase generates 2-5A, which, in turn, activates the latent constitutive RNase L that degrades viral RNA. Chemical conjugation of 2-5A to an antisense oligonucleotide can target the 2-5A-dependent RNase L to the antisense-specified RNA and effect its selective destruction. Such a 2-5A-antisense chimera (NIH351) has been developed that targets a consensus sequence within the respiratory syncytial virus (RSV) genomic RNA. NIH351 was 50- to 90-fold more potent against RSV strain A2 than was ribavirin, the presently approved drug for clinical management of RSV infection. It was similarly active against a variety of RSV strains of both A and B subgroups and possessed a cell culture selectivity index comparable to ribavirin. In addition, the anti-RSV activity of NIH351 was shown to be virus-specific and a result of a true antisense effect, because a scrambled nucleotide sequence in the antisense domain of NIH351 caused a significant decrease in antiviral activity. The 2-5A system's RNase L was implicated in the mechanism of action of NIH351 because a congener with a disabled 2-5A moiety was of greatly reduced anti-RSV effectiveness. These findings represent an innovative approach to the control of RSV replication.
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Affiliation(s)
- M R Player
- Section on Biomedical Chemistry, Laboratory of Medicinal Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0805, USA
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Player MR, Wondrak EM, Bayly SF, Torrence PF. Ribonuclease L, a 2-5A-dependent enzyme: purification to homogeneity and assays for 2-5A binding and catalytic activity. Methods 1998; 15:243-53. [PMID: 9735309 DOI: 10.1006/meth.1998.0628] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
RNase L is a latent endonuclease found in reptiles, birds, and mammals. It is activated by the 2',5'-phosphodiester-linked oligoadenylates called 2-5A and has been implicated in the mechanism of action of interferon, as well as in a variety of other biological phenomena such as apoptosis. Covalent linkage of 2-5A to antisense oligonucleotides permits recruitment of RNase L for enhancement of antisense action. The purification of RNase L described herein and the assays for its detection and activation will help to provide further mechanistic details on how this unique nuclease functions and what its biochemical roles may be. In addition, such assays will facilitate the screening of 2-5A-antisense congeners for exploration of the potential therapeutic applications of RNase L.
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Affiliation(s)
- M R Player
- Laboratory of Medicinal Chemistry, Building 8, Room B2A02, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, 20892-0805, USA
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Abstract
In an attempt to develop a lead for the application of 2-5A-antisense to the targeted destruction of human immunodeficiency virus (HIV) RNA, specific target sequences within the HIV mRNAs were identified by analysis of the theoretical secondary structure. 2-5A-antisense chimeras were chosen against a total of 11 different sequences: three in the gag mRNA, three in the rev mRNA and five in the tat mRNA. 2-5A-antisense chimera synthesis was accomplished using solid-phase phosphoramidite chemistry. These chimeras were evaluated for their activity in a cell-free assay system using purified recombinant human RNase L to effect cleavage of 32P-labelled RNA transcripts of plasmids derived from HIV NL4-3. This screening revealed that of the three 2-5A-antisense chimeras targeted against gag mRNA, only one had significant HIV RNA cleavage activity, approximately 10-fold-reduced compared to the parent 2-5A tetramer and comparable to that reported for the prototypical 2-5A-anti-PKR chimera, targeted against PKR mRNA. The cleavage activity of this chimera was specific, since a scrambled antisense domain chimera and a chimera without the key 5'-monophosphate moiety were both inactive. The 10 other 2-5A-antisense chimeras against tat and rev had significantly less activity. These results imply that HIV gag RNA, like PKR RNA and a model HIV tat-oligoA-vif RNA, can be cleaved using the 2-5A-antisense approach. The results further imply that not all regions of a potential RNA target are accessible to the 2-5A-antisense approach.
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Affiliation(s)
- M R Player
- Laboratory of Medicinal Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0805, USA
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Abstract
The 2-5A system is an RNA degradation pathway that can be induced by the interferons (IFNs). Treatment of cells with IFN activates genes encoding several double-stranded RNA (dsRNA)-dependent synthetases. These enzymes generate 5'-triphosphorylated, 2',5'-phosphodiester-linked oligoadenylates (2-5A) from ATP. The effects of 2-5A in cells are transient since 2-5A is unstable in cells due to the activities of phosphodiesterase and phosphatase. 2-5A activates the endoribonuclease 2-5A-dependent RNase L, causing degradation of single-stranded RNA with moderate specificity. The human 2-5A-dependent RNase is an 83.5 kDa polypeptide that has little, if any, RNase activity, unless 2-5A is present. 2-5A binding to RNase L switches the enzyme from its off-state to its on-state. At least three 2',5'-linked oligoadenylates and a single 5'-phosphoryl group are required for maximal activation of the RNase. Even though the constitutive presence of 2-5A-dependent RNase is observed in nearly all mammalian cell types, cellular amounts of 2-5A-dependent mRNA and activity can increase after IFN treatment. One well-established role of the 2-5A system is as a host defense against some types of viruses. Since virus infection of cells results in the production and secretion of IFNs, and since dsRNA is both a frequent product of virus infection and an activator of 2-5A synthesis, the replication of encephalomyocarditis virus, which produces dsRNA during its life cycle, is greatly suppressed in IFN-treated cells as a direct result of RNA decay by the activated 2-5A-dependent RNase. This review covers the organic chemistry, enzymology, and molecular biology of 2-5A and its associated enzymes. Additional possible biological roles of the 2-5A system, such as in cell growth and differentiation, human immunodeficiency virus replication, heat shock, atherosclerotic plaque, pathogenesis of Type I diabetes, and apoptosis, are presented.
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Affiliation(s)
- M R Player
- Section on Biomedical Chemistry, Laboratory of Medicinal Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0805, USA
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46
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Xiao W, Li G, Player MR, Maitra RK, Waller CF, Silverman RH, Torrence PF. Nuclease-resistant composite 2',5'-oligoadenylate-3', 5'-oligonucleotides for the targeted destruction of RNA: 2-5A-iso-antisense. J Med Chem 1998; 41:1531-9. [PMID: 9554886 DOI: 10.1021/jm970841p] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A new modification of 2-5A-antisense, 2-5A-iso-antisense, has been developed based on a reversal of the direction of the polarity of the antisense domain of a 2-5A-antisense composite nucleic acid. This modification was able to anneal with its target RNA as well as the parental 2-5A-antisense chimera. The 2-5A-iso-antisense oligonucleotide displayed enhanced resistance to degradation by 3'-exonuclease enzyme activity such as that represented by snake venom phosphodiesterase and by that found in human serum. 2-5A-Iso-antisense was able to effect the degradation of a synthetic nontargeted substrate, [5'-32P]pC11U2C7, and two targeted RNAs, PKR and BCR mRNAs, in a cell-free system containing purified recombinant human 2-5A-dependent RNase L. These results demonstrated that the novel structural modification represented by 2-5A-iso-antisense provided a stabilized biologically active formulation of the 2-5A-antisense strategy.
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Affiliation(s)
- W Xiao
- Section on Biomedical Chemistry, Laboratory of Medicinal Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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Player MR, Kalinichenko EN, Podkopaeva TL, Mikhailopulo IA, Seela F, Torrence PF. Dissection of the roles of adenine ring nitrogen (N-1) and exocyclic amino (N-6) moieties in the interaction of 2-5A with RNase L. Biochem Biophys Res Commun 1998; 245:430-4. [PMID: 9571169 DOI: 10.1006/bbrc.1998.8451] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To elucidate further the roles played by the adenine bases in the interaction of RNase L (EC 3.1.2.6) with the 2',5'-oligoadenylate 2-5A, p5'A2'(p5'A2')np5' A, a series of sequence-specific 1-deazaadenosine (c1A)-substituted analogues were synthesized and evaluated for their ability to bind to and activate human RNase L in comparison to earlier reported inosine-substituted congeners of 2-5A. Substitution of only the 5'-terminal adenosine of p5'A2'p5'A2 p5 A with c1A afforded an analogue with strongly diminished RNase L binding and activation ability, while replacement of the second or middle adenosine of p5 A2' p5'A2'p5' A had only a modest effect. In distinct contrast to p5'A2'p5'A2'p5'I, the c1A analogue with the third or 2'-terminal adenosine replacement approached parent p5' A2'p5'A2'p5' A in RNase L activation ability. These results permitted a further dissection of the role of various nucleotidic functional groups in the interaction of 2-5A with RNase L: specifically, that the 5'-terminal adenosine purine N-1 moiety is key for binding to RNase L, while the 2'-terminal adenosine N-6 exocyclic amino group is critical for RNase L activation.
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Affiliation(s)
- M R Player
- Section on Biomedical Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0805, USA
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48
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Abstract
We have developed chromatographic and spectrophotometric assays for determining the degree of thiolation in phosphatase-resistant 5'-monothiophosphate-capped 2-5A-antisense chimeras. Concomitantly, we have explored the reactivity of this 5'-monophosphorothioate moiety with reporter reagents such as 5-iodoacetomidofluorescein and 5,5'-dithiobis(2-nitrobenzoic acid). On the basis of these reactions, analyses for 5'-monothiophosphate-functionalized 2-5A-antisense chimeras were made possible. Kinetic experiments demonstrated that oligonucleotide backbone negative charge could retard mixed disulfide formation in the reaction of 5,5'-dithiobis(2-nitrobenzoic acid) with 5'-monothiophosphorylated 2-5A-antisense chimeras.
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Affiliation(s)
- M R Player
- Section on Biomedical Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0805, USA
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Castelli JC, Hassel BA, Wood KA, Li XL, Amemiya K, Dalakas MC, Torrence PF, Youle RJ. A study of the interferon antiviral mechanism: apoptosis activation by the 2-5A system. J Exp Med 1997; 186:967-72. [PMID: 9294150 PMCID: PMC2199051 DOI: 10.1084/jem.186.6.967] [Citation(s) in RCA: 208] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The 2-5A system contributes to the antiviral effect of interferons through the synthesis of 2-5A and its activation of the ribonuclease, RNase L. RNase L degrades viral and cellular RNA after activation by unique, 2'-5' phosphodiester-linked, oligoadenylates [2-5A, (pp)p5' A2'(P5'A2')]n, n >=2. Because both the 2-5A system and apoptosis can serve as viral defense mechanisms and RNA degradation occurs during both processes, we investigated the potential role of RNase L in apoptosis. Overexpression of human RNase L by an inducible promoter in NIH3T3 fibroblasts decreased cell viability and triggered apoptosis. Activation of endogenous RNase L, specifically with 2-5A or with dsRNA, induced apoptosis. Inhibition of RNase L with a dominant negative mutant suppressed poly (I).poly (C)-induced apoptosis in interferon-primed fibroblasts. Moreover, inhibition of RNase L suppressed apoptosis induced by poliovirus. Thus, increased RNase L levels induced apoptosis and inhibition of RNase L activity blocked viral-induced apoptosis. Apoptosis may be one of the antiviral mechanisms regulated by the 2-5A system.
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Affiliation(s)
- J C Castelli
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
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50
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Abstract
In order to stabilize 2-5A-antisense chimeras to exonucleases, we have synthesized chimeric oligonucleotides in which the last phosphodiester bond at the 3'-terminus of the antisense domain was inverted from the usual 3',5'-linkage to a 3',3'-linkage. The preparation of such analogues was accomplished through standard phosphoramidite chemistry with the use of a controlled pore glass solid support with a nucleoside attached through its 5'-hydroxyl, thereby permitting elongation at the 3'-hydroxyl. The structures of such terminally inverted linkage chimeras of the general formula pA4-[pBu]2-(pdNn3'-3'dN) were corroborated by a combination of snake venom phosphodiesterase digestion in the presence or absence of bacterial alkaline phosphatase. Most characteristically, the presence of the 3'-terminal-inverted phosphodiester linkage produced an unnatural dinucleotide of general composition dN3'p3'dM. These structures could be confirmed by independent synthesis and fast atom bombardment mass spectroscopy (FAB). 2-5A-Antisense chimeras of this structural class, pA4-[pBu]2-(pdNn'3-3'dN), were 5-6-fold more stable than their unmodified congeners, pA4-[pBu]2-(pdN)n, to degradation by a representative phosphodiesterase from snake venom. In 10% human serum, the new 2-5A-antisense chimeras, pA4-[pBu]2-(pdNn3'-3'dN), possessed a half-life that was 28-fold longer than that of the unmodified chimeras. These results provide entry to a second generation of 2-5A-antisense chimeras.
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Affiliation(s)
- G Li
- Section on Biomedical Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0805, USA
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