76
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Allart B, Van Aerschot A, Herdewijn P. 1,5-Anhydro-2-Deoxy-D-Altritol Oligonucleotides as Conformationally Restricted Analogues of Rna. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319808004682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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77
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Verheggen I, Van Aerschot A, Rozenski J, Janssen G, De Clercq E, Herdewijn P. Synthesis of 1,5-Anhydrohexitol Nucleosides as Mimics of AZT, D4T and DDC. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319608002387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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78
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Van Aerschot A. Oligonucleotides as antivirals: dream or realistic perspective? Antiviral Res 2006; 71:307-16. [PMID: 16621039 DOI: 10.1016/j.antiviral.2006.03.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2006] [Revised: 03/10/2006] [Accepted: 03/13/2006] [Indexed: 01/01/2023]
Abstract
Many reports have been published on antiviral activity of synthetic oligonucleotides, targeted to act either by a true antisense effect or via non-sequence specific interactions. This short review will try to evaluate the current status of the field by focusing on the effects as reported for inhibition of either HSV-1, HCMV or HIV-1. Following an introduction with a historical background and a brief discussion on the different types of constructs and mechanisms of action, the therapeutic potential of antisense oligonucleotides as antivirals, as well as possible pitfalls upon their evaluation will be discussed.
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79
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Wu T, Nauwelaerts K, Van Aerschot A, Froeyen M, Lescrinier E, Herdewijn P. Base−Base Interactions in the Minor Groove of Double-Stranded DNA. J Org Chem 2006; 71:5423-31. [PMID: 16839119 DOI: 10.1021/jo052194c] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A method has been developed for the synthesis of bisheaded nucleosides with thymine and adenine base moieties. We have demonstrated that, when incorporated in oligonucleotides, extrahelical A-T base interactions are possible when the bisheaded nucleosides are positioned in opposite strands of the duplex and are separated from each other by one regular base pair.
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80
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Bobkov GV, Brilliantov KV, Mikhailov SN, Rozenski J, Van Aerschot A, Herdewijn P. Synthesis of Oligoribonucleotides Containing Pyrimidine 2'-O-[(Hydroxyalkoxy)methyl]ribonucleosides. ACTA ACUST UNITED AC 2006. [DOI: 10.1135/cccc20060804] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A simple and efficient method for the preparation of pyrimidine 2'-O-[(2-hydroxyethoxy)methyl]ribonucleosides and 2'-O-[(3-hydroxypropoxy)methyl]ribonucleosides has been developed. These modified nucleosides were incorporated into oligoribonucleotides, which were shown to form stable RNA/RNA duplexes.
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81
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Zhou D, Lagoja IM, Van Aerschot A, Herdewijn P. Synthesis of Aminopropyl Phosphonate Nucleosides with Purine and Pyrimidine Bases. ACTA ACUST UNITED AC 2006. [DOI: 10.1135/cccc20060015] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The synthesis and antiviral evaluation of new acyclic phosphonate nucleosides related to HPMPC (Cidofovir) has been described. These aminopropyl phosphonate nucleosides 1-3 have an amino function within either the acyclic chain (series 2 and 3) or as substituent (series 1). Both purine and pyrimidine nucleotide analogues have been synthesized. In contrast to HPMPC the oxygen analogue of 2c, only a weak antiherpes virus activity could be demonstrated for 2b and 2c.
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82
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Gu P, Schepers G, Griebel C, Rozenski J, Gais HJ, Herdewijn P, Van Aerschot A. Enzymatic resolution and base pairing properties of D- and L-cyclohexenyl nucleic acids (CeNA). NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 24:993-8. [PMID: 16248079 DOI: 10.1081/ncn-200060326] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
An enzymatic transesterification reaction afforded large scale resolution of the cyclohexenol precursor needed for preparation of both series of CeNA building blocks. CeNA oligos of "D-like" chirality display a strong and selective interaction with RNA, while preserving RNase H activity, and therefore have potential as antisense constructs. CeNAs of opposite chirality form a self-pairing system on their own.
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83
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Chaltin P, Margineanu A, Marchand D, Van Aerschot A, Rozenski J, De Schryver F, Herrmann A, Müllen K, Juliano R, Fisher MH, Kang H, De Feyter S, Herdewijn P. Delivery of antisense oligonucleotides using cholesterol-modified sense dendrimers and cationic lipids. Bioconjug Chem 2005; 16:827-36. [PMID: 16029024 DOI: 10.1021/bc050022g] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cholesterol modified mono-, di-, and tetrameric oligonucleotides were synthesized and hybridized with antisense oligonucleotides to study their incorporation in cationic liposomes together with the influence of this dendrimeric delivery system on biological activity. Electrostatic interactions seem to play the most important role during complexation with cationic lipids. This oligonucleotide formulation gives a small but significant increase in the inhibition of P-glycoprotein expression in a cellular system.
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84
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Vijgen S, Nauwelaerts K, Wang J, Van Aerschot A, Lagoja I, Herdewijn P. Synthesis and Conformational Analysis of a Ribo-Type Cyclohexenyl Nucleoside. J Org Chem 2005; 70:4591-7. [PMID: 15932294 DOI: 10.1021/jo048037f] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A straightforward approach to a novel class of ribo-type cyclohexenyl nucleosides is described. An electron-demand Diels-Alder reaction forms the key-step of the chosen synthetic pathway. Although the difference is small, conformational analysis using NMR shows that this nucleoside analogue adopts preferentially an 2H3 conformation (S-type), while the "deoxy" cyclohexenyl analogue has a preference for a C3' endo conformation (N-type). Analyses of the conformational equilibrium reveal that, in the given experimental conditions, the difference between adenosine and its cyclohexenyl congener resides in their different DeltaG values; furthermore, in adenosine, the conformational preference is of enthalpic origin, whereas in the cyclohexenyl congener, the conformational preference is of entropic origin.
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85
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Gu P, Schepers G, Rozenski J, Van Aerschot A, Herdewijn P. Base pairing properties of D- and L-cyclohexene nucleic acids (CeNA). Oligonucleotides 2004; 13:479-89. [PMID: 15025914 DOI: 10.1089/154545703322860799] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Cyclohexene nucleic acids (CeNA) with a D-like configuration form very stable self-complementary duplexes and stable duplexes with RNA. An increased duplex stability with Delta T(m)/mod of +1.2 degrees C is observed. The duplex with DNA is less stable. Excellent mismatch discrimination has been observed as well for the duplex with DNA as for the duplex with RNA. The results obtained with mixed CeNA sequences warrant antisense studies with CeNA. The CeNAs of opposite chirality constitute a self-pairing system on their own, resembling L-RNA sequences.
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86
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Wu T, Froeyen M, Schepers G, Mullens K, Rozenski J, Busson R, Van Aerschot A, Herdewijn P. Synthesis and stability of oligonucleotides containing acyclic achiral nucleoside analogues with two base moieties. Org Lett 2004; 6:51-4. [PMID: 14703348 DOI: 10.1021/ol0360647] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[structure: see text] Nucleotide building blocks with two base moieties were synthesized and incorporated into oligonucleotides. One of the two bases is involved in base pairing within the double helix, while the other base is sticking out of the minor groove. This system may be used for presenting sequence information at the outside of the helix.
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87
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Kang H, Fisher MH, Xu D, Miyamoto YJ, Marchand A, Van Aerschot A, Herdewijn P, Juliano RL. Inhibition of MDR1 gene expression by chimeric HNA antisense oligonucleotides. Nucleic Acids Res 2004; 32:4411-9. [PMID: 15316104 PMCID: PMC514393 DOI: 10.1093/nar/gkh775] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2004] [Revised: 07/01/2004] [Accepted: 07/29/2004] [Indexed: 11/14/2022] Open
Abstract
Hexitol nucleic acids (HNAs) are nuclease resistant and provide strong hybridization to RNA. However, there is relatively little information on the biological properties of HNA antisense oligonucleotides. In this study, we compared the antisense effects of a chimeric HNA 'gapmer' oligonucleotide comprising a phosphorothioate central sequence flanked by 5' and 3' HNA sequences to conventional phosphorothioate oligonucleotides and to a 2'-O-methoxyethyl (2'-O-ME) phosphorothioate 'gapmer'. The antisense oligomers each targeted a sequence bracketing the start codon of the message of MDR1, a gene involved in multi-drug resistance in cancer cells. Antisense and control oligonucleotides were delivered to MDR1-expressing cells using transfection with the cationic lipid Lipofectamine 2000. The anti-MDR1 HNA gapmer was substantially more potent than a phosphorothioate oligonucleotide of the same sequence in reducing expression of P-glycoprotein, the MDR1 gene product. HNA and 2'-O-ME gapmers displayed similar potency, but a pure HNA antisense oligonucleotide (lacking the phosphorothioate 'gap') was ineffective, indicating that RNase H activity was likely required. Treatment with anti-MDR1 HNA gapmer resulted in increased cellular accumulation of the drug surrogate Rhodamine 123 that correlated well with the reduced cell surface expression of P-glycoprotein. Thus, HNA gapmers may provide a valuable additional tool for antisense-based investigations and therapeutic approaches.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily B, Member 1/antagonists & inhibitors
- ATP Binding Cassette Transporter, Subfamily B, Member 1/genetics
- ATP Binding Cassette Transporter, Subfamily B, Member 1/metabolism
- Animals
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/metabolism
- Antineoplastic Agents/pharmacology
- Biological Transport/drug effects
- Blotting, Western
- Cell Line
- Flow Cytometry
- Fluorescent Dyes/metabolism
- Gene Expression Regulation
- Mice
- NIH 3T3 Cells
- Oligonucleotides, Antisense/chemistry
- Oligonucleotides, Antisense/metabolism
- Oligonucleotides, Antisense/pharmacology
- Rhodamine 123/metabolism
- Sugar Alcohols/chemistry
- Thionucleotides/chemistry
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88
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Nauwelaerts K, Vastmans K, Froeyen M, Kempeneers V, Rozenski J, Rosemeyer H, Van Aerschot A, Busson R, Lacey JC, Efimtseva E, Mikhailov S, Lescrinier E, Herdewijn P. Cleavage of DNA without loss of genetic information by incorporation of a disaccharide nucleoside. Nucleic Acids Res 2004; 31:6758-69. [PMID: 14627809 PMCID: PMC290278 DOI: 10.1093/nar/gkg911] [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: 11/14/2022] Open
Abstract
A ribose residue inserted between the 3'-OH of one nucleotide and the 5'-phosphate group of the next nucleotide, functions as a site-specific cleavage site within DNA. This extra ribose does not interrupt helix formation and it protects duplex DNA against cleavage by restriction enzymes. Cleavage can be obtained with periodate and all ribose fragments can be removed with sodium hydroxide. As a result of this, an intact natural oligodeoxynucleotide is obtained after ligation reaction, which means that site-specific cleavage and recovering of intact DNA occurs without loss of genetic information.
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89
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Pochet S, Kaminski PA, Van Aerschot A, Herdewijn P, Marlière P. Replication of hexitol oligonucleotides as a prelude to the propagation of a third type of nucleic acid in vivo. C R Biol 2004; 326:1175-84. [PMID: 14746272 DOI: 10.1016/j.crvi.2003.10.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
No backbone motif other than phospho-ribose and phospho-deoxyribose has been found in natural nucleic acids, currently restricting the molecular types of replicable biopolymers to DNA and RNA. With the aim of propagating and expressing a third type of nucleic acid in vivo, we assessed the replicability of polynucleotides with a phospho-hexitol backbone (HNA) in vivo and in vitro. Faithful polymerisation of up to four deoxynucleotides templated by hexitol oligonucleotides was established in vitro using DNA polymerase from Escherichia coli (PolA Klenow exo-fragment) and Thermus aquaticus (Taq polymerase). Condensation of up to three successive hTTPs (hexitol thymidine triphosphate) in responses to a pentameric hexitol template (hA)5 could also be demonstrated in vitro. Such a marginal HNA-dependent HNA polymerase activity of natural polymerases may be evolved in the future to catalyse in vitro amplification of HNA. The transmission of a two-codon-long genetic message carried on a hexameric hexitol template was also established using a selection screen for restoring thymidylate synthase activity in E. coli. These results exemplify the potential that can be explored by converting artificial substrates with natural enzymes in the field of informational polymer synthesis.
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90
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Gu P, Griebel C, Van Aerschot A, Rozenski J, Busson R, Gais HJ, Herdewijn P. Synthesis of enantiomeric-pure cyclohexenyl nucleoside building blocks for oligonucleotide synthesis. Tetrahedron 2004. [DOI: 10.1016/j.tet.2003.12.052] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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91
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Gu P, Morral J, Wang J, Rozenski J, Busson R, Van Aerschot A, De Clercq E, Herdewijn P. Synthesis and biological evaluation of a series of new cyclohexenyl nucleosides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2003; 22:845-7. [PMID: 14565293 DOI: 10.1081/ncn-120022668] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A series of cyclohexenyl nucleosides (1-8) were successfully prepared with moderate yield and their cytotoxicity and antiviral activity were investigated. Among the eight new compounds, only the diaminopurine analogue 8 showed pronounced activity against HSV-1, HSV-2.
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92
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Rozenski J, Vastmans K, Van Aerschot A, Herdewijn P. Evaluation of capillary HPLC/mass spectrometry as an alternative analysis method for gel electrophoresis of oligonucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2003; 22:1513-6. [PMID: 14565455 DOI: 10.1081/ncn-120023023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A method has been developed to monitor the enzymatic incorporation of nucleotides in DNA by electrospray HPLC mass spectrometry. The main advantages of mass spectrometry over electrophoresis are the ability to directly characterize the reaction products and the shorter analysis time.
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93
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Lagoja IM, Pannecouque C, Van Aerschot A, Witvrouw M, Debyser Z, Balzarini J, Herdewijn P, De Clercq E. N-aminoimidazole derivatives inhibiting retroviral replication via a yet unidentified mode of action. J Med Chem 2003; 46:1546-53. [PMID: 12672256 DOI: 10.1021/jm0211117] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis of a series of N-aminoimidazoles (NAIMs) with an uncommon spectrum of antiretroviral activity is described. From a group of 60 closely related molecules, we were able to subdivide the molecules in different groups based on their anti-HIV and anti-SIV activity in vitro: (i) molecules acting on a new, immediate postintegration step, (ii) molecules acting on both postintegration and HIV-1 reverse transcriptase (RT) as NNRTI, and (iii) molecules that mainly act at the HIV-1 RT according to an NNRTI-type mode of action.
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94
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Chaltin P, Borgions F, Van Aerschot A, Herdewijn P. Comparison of library screening techniques used in the development of dsDNA ligands. Bioorg Med Chem Lett 2003; 13:47-50. [PMID: 12467614 DOI: 10.1016/s0960-894x(02)00836-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The gel retardation and FID (fluorescent intercalator displacement) techniques have been compared for the selection of dsDNA binding ligands out of library mixtures. The selection procedure involves the synthesis and screening of unnatural oligopeptide libraries based on an iterative deconvolution procedure. Both methods yield comparable selection results and binding constants for the selected compounds, meaning that they can be considered as complementary in the discovery process of new antigene compounds. Furthermore, a quinazolin-2,4-dione amino acid has been identified as possessing interesting properties for interaction with dsDNA.
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95
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Gu P, Morral J, Wang J, Rozenski J, Busson R, Van Aerschot A, De Clercq E, Herdewijn P. Synthesis and antiviral activity of a series of new cyclohexenyl nucleosides. Antivir Chem Chemother 2003; 14:31-7. [PMID: 12790514 DOI: 10.1177/095632020301400103] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
A series of new cyclohexenyl nucleosides is synthesized by coupling the heterocyclic bases with a protected cyclohexenyl precursor under Mitsunobu conditions. The compounds were evaluated for their antiviral and cytostatic activity. Pronounced activity against herpes simplex virus type 1 and type 2 was observed for the 2,6-diaminopurine analogue.
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96
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Van Aerschot A, Schepers G, Busson R, Rozenski J, Neyts J, De Clercq E, Herdewijn P. Ribavirin derivatives with a hexitol moiety: synthesis and antiviral evaluation. Antivir Chem Chemother 2003; 14:23-30. [PMID: 12790513 DOI: 10.1177/095632020301400102] [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: 12/13/2022] Open
Abstract
Current standard therapy for the treatment of chronic infections with hepatitis C virus consists of combination therapy with (pegylated) interferon-alpha and ribavirin. 1,5-Anhydrohexitol nucleoside analogues are constrained congeners known to mimic the ribonucleoside conformation. Within this series some analogues are endowed with strong antiviral properties, particularly against herpesviruses. The six-membered anhydrohexitol ring was, therefore, combined with the triazolyl carboxamide moiety of ribavirin, thus providing a new series of ribavirin analogues. None of the newly synthesized compounds elicited any substantial antiviral activity, neither against herpes simplex virus type 1 and 2, nor against bovine viral diarrhoea virus (a surrogate for hepatitis C virus) or the yellow fever virus.
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97
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Gritsenko OM, Koudan EV, Mikhailov SN, Ermolinsky BS, Van Aerschot A, Herdewijn P, Gromova ES. Affinity modification of EcoRII DNA methyltransferase by the dialdehyde-substituted DNA duplexes: mapping the enzyme region that interacts with DNA. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2002; 21:753-64. [PMID: 12537018 DOI: 10.1081/ncn-120016478] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Affinity modification of EcoRII DNA methyltransferase (M x EcoRII) by DNA duplexes containing oxidized 2'-O-beta-D-ribofuranosylcytidine (Crib*) or 1-(beta-D-galactopyranosyl)thymine (Tgal*) residues was performed. Cross-linking yields do not change irrespective of whether active Crib* replaces an outer or an inner (target) deoxycytidine within the EcoRII recognition site. Chemical hydrolysis of M x EcoRII in the covalent cross-linked complex with the Tgal*-substituted DNA indicates the region Gly268-Met391 of the methylase that is likely to interact with the DNA sugar-phosphate backbone. Both specific and non-specific DNA interact with the same M x EcoRII region. Our results support the theoretically predicted DNA binding region of M x EcoRII.
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98
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Zhang Z, Chaltin P, Van Aerschot A, Lacey J, Rozenski J, Busson R, Herdewijn P. New dsDNA binding unnatural oligopeptides with pyrimidine selectivity. Bioorg Med Chem 2002; 10:3401-13. [PMID: 12213453 DOI: 10.1016/s0968-0896(02)00268-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Solid phase peptide library screening followed by extension of a lead recognition element for binding to a dsDNA sequence (NF binding site of IL6) using solution phase screening, delivered a new DNA binding peptide, Ac-Arg-Ual-Sar-Chi-Chi-Tal-Arg-CONH2. In the present research, the contribution of the different amino acid side chains to the binding strength of the peptide to dsDNA was investigated using an ethidium bromide displacement test. Based on these results, the lead structure was optimized by deconvolution. Eight new unnatural amino acids were evaluated at two positions of the heptapeptide replacing the Ual-Sar fragment. The strongest dsDNA binding was observed using ([(3-chlorophenyl)methyl]amino)acetic acid (Cbg) and beta-cyclohexyl-l-alanine (Cha) respectively, at those two positions. A 10-fold increase in affinity compared to the Ual-Sar sequence was obtained. Further enhancement of dsDNA binding was obtained with hybrid molecules linking the newly developed peptide fragment to an acridine derivative with a flexible spacer. This resulted in ligands with affinities in the microM range for the dsDNA target (K(d) of 2.1 x 10(-6) M). DNase I footprinting with the newly developed oligopeptide motifs showed the presence of a pronounced pyrimidine specificity, while conjugation to an intercalator seems to redirect the interaction to mixed sequences. This way, new unnatural oligopeptide motifs and hybrid molecules have been developed endowed with different sequence selectivities. The results demonstrate that the unnatural peptide library approach combined with subsequent modification of selected amino acid positions, is very suited for the discovery of novel sequence-specific dsDNA binding ligands.
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99
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Vastmans K, Rozenski J, Van Aerschot A, Herdewijn P. Recognition of HNA and 1,5-anhydrohexitol nucleotides by DNA metabolizing enzymes. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1597:115-22. [PMID: 12009410 DOI: 10.1016/s0167-4838(02)00267-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hexitol nucleic acids (HNA) as well as their 1,5-anhydrohexitol triphosphate building blocks were evaluated for their ability to be recognized by several DNA metabolizing enzymes. It was found that RNA polymerases can recognize the triphosphate of the adenine analogue. However, only the incorporation of a maximum of three consecutive building block analogues was possible under the applied experimental conditions. Terminal transferase was more successful succeeding in the elongation of a DNA primer with a maximum of 15 1,5-anhydrohexitol purine nucleotides. Furthermore, it was observed that the 1,5-anhydroaltritol triphosphate analogue of adenosine was a poor substrate for terminal transferase and that HNA could not act as a primer for this enzyme. Likewise, HNA did not function as a template for restriction enzymes, ligases or methylases.
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100
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Augustyns K, Rozenski J, Van Aerschot A, Janssen G, Herdewijn P. Synthesis of 2,4-dideoxy-.beta.-D-erythro-hexopyranosyl nucleosides. J Org Chem 2002. [DOI: 10.1021/jo00063a013] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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