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Toti K, Renders M, Groaz E, Herdewijn P, Van Calenbergh S. Nucleosides with Transposed Base or 4'-Hydroxymethyl Moieties and Their Corresponding Oligonucleotides. Chem Rev 2015; 115:13484-525. [PMID: 26655745 DOI: 10.1021/acs.chemrev.5b00545] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This review focuses on 4'-hydroxymethyl- or nucleobase-transposed nucleosides, nucleotides, and nucleoside phosphonates, their stereoisomers, and their close analogues. The biological activities of all known 4'-hydroxymethyl- or nucleobase-transposed nucleosides, nucleotides, and nucleoside phosphonates as potential antiviral or anticancer agents are compiled. The routes that have been taken for the chemical synthesis of such nucleoside derivatives are described, with special attention to the innovative strategies. The enzymatic synthesis, base-pairing properties, structure, and stability of oligonucleotides containing nucleobase- or 4'-hydroxymethyl-transposed nucleotides are discussed. The use of oligonucleotides containing nucleobase- or 4'-hydroxymethyl-transposed nucleotides as small oligonucleotide (e.g., human immunodeficiency virus integrase) inhibitors, in applications such as antisense therapy, silencing RNA (siRNA), or aptamer selections, is detailed.
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Affiliation(s)
- Kiran Toti
- Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University , Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Marleen Renders
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven , Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Elisabetta Groaz
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven , Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Piet Herdewijn
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven , Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Serge Van Calenbergh
- Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University , Ottergemsesteenweg 460, 9000 Ghent, Belgium
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Aubert Y, Chassignol M, Roig V, Mbemba G, Weiss J, Meudal H, Mouscadet JF, Asseline U. Synthesis and anti-HIV-1 integrase activity of modified dinucleotides. Eur J Med Chem 2009; 44:5029-44. [PMID: 19796851 DOI: 10.1016/j.ejmech.2009.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2009] [Revised: 06/30/2009] [Accepted: 09/04/2009] [Indexed: 11/18/2022]
Abstract
The synthesis of a series of thirty-eight new modified dinucleotides and dinucleotide conjugate analogues of d-(5')ApC(3') is described. The inhibitory activity of these compounds toward HIV-1 integrase was examined in enzymatic assays using the natural dinucleotide as a reference. Among the compounds, a perylene-dinucleotide conjugate has shown a two micromolar anti-integrase activity due to the presence of both the intercalator and the dinucleotide.
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Affiliation(s)
- Yves Aubert
- Centre de Biophysique Moléculaire CNRS UPR 4301, affiliated with the University of Orléans and with INSERM Rue Charles Sadron, 45071 Orléans Cedex 02, France
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Abstract
One of the three key enzymes encoded by the pol gene of HIV is a M(r) 32 000 protein called HIV integrase. This viral enzyme is involved in the integration of HIV DNA into host chromosomal DNA. There appears to be no functional equivalent of the enzyme in human cells. The biochemical mechanism of integration of HIV DNA into the host cell genome involves a carefully defined sequence of DNA tailoring (3'-processing) and coupling (joining or integration) reactions. In spite of some effort in this area targeted at the discovery of therapeutically useful inhibitors of this viral enzyme, there are no drugs for HIV/AIDS in clinical use where the mechanism of action is inhibition of HIV integrase. Thus, new knowledge on inhibitors of this enzyme is of critical importance in the anti-HIV drug discovery area. The focus of this review will be on several classes of compounds, including nucleotides, dinucleotides, oligonucleotides and miscellaneous small molecules such as heterocyclic systems, natural products, diketo acids and sulfones, that have been discovered as inhibitors of HIV integrase. Special emphasis in the review will be placed on discoveries from my laboratory on HIV integrase inhibitors that are non-natural, nuclease-resistant dinucleotides. Comments on future directions and the prospects for developing integrase inhibitors as therapeutic antiviral agents are discussed.
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Affiliation(s)
- Vasu Nair
- Department of Chemistry, The University of Iowa, Iowa City 52242, USA.
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Brodin P, Pinskaya M, Buckle M, Parsch U, Romanova E, Engels J, Gottikh M, Mouscadet JF. Disruption of HIV-1 integrase-DNA complexes by short 6-oxocytosine-containing oligonucleotides. Biochemistry 2002; 41:1529-38. [PMID: 11814346 DOI: 10.1021/bi015732y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We recently found that oligonucleotides containing the 6-oxocytosine heterocyclic base are efficient inhibitors of the HIV-1 integrase in vitro [Brodin, P., et al. (2001) Nucleosides Nucleotides Nucleic Acids 20, 481-486]. In this report, we demonstrate that the inhibition arises from a noncompetitive mechanism in which the modified oligonucleotide attacks the integrase-DNA complex, leading to its active disruption. This conclusion is based on the following results. First, despite the fact that the respective affinities of a 6-oxocytosine-containing oligonucleotide and of its nonmodified counterpart for integrase were identical, only the modified compound inhibited the enzyme activities. Second, DNA binding and UV cross-linking assays indicated that the 6-oxocytosine-containing oligonucleotide prevented the formation of a stable integrase-DNA complex. Third, the kinetics of the dissociation of the integrase-DNA complex were dramatically accelerated in the presence of the modified ODN, whereas the nonmodified counterpart did not influence the dissociation. This mechanism was supported by the ability of the 6-oxocytosine-containing oligonucleotide to inhibit the strand transfer activity of HIV-1 preintegration complexes in vitro. Disruption of integrase-DNA complexes by 6-oxocytosine-containing oligonucleotides constitutes an original mechanism of integration inhibition, therefore suggesting a strategy for searching for inhibitors of the HIV-1 preintegration complexes.
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Affiliation(s)
- Priscille Brodin
- Institut Gustave Roussy, UMR 8532, 39 rue Camille Desmoulins, 94805 Villejuif, France
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Abstract
Human immunodeficiency virus Type 1 (HIV-1) integrase is an essential enzyme for the obligatory integration of the viral DNA into the infected cell chromosome. As no cellular homologue of HIV integrase has been identified, this unique HIV-1 enzyme is an attractive target for the development of new therapeutics. Treatment of HIV-1 infection and AIDS currently consists of the use of combinations of HIV-1 inhibitors directed against reverse transcriptase (RT) and protease. However, their numerous side effects and the rapid emergence of drug-resistant variants limit greatly their use in many AIDS patients. In principle, inhibitors of the HIV-1 integrase should be relatively non-toxic and provide additional benefits for AIDS chemotherapy. There have been many major advances in our understanding of the molecular mechanism of the integration reaction, although some critical aspects remain obscure. Several classes of compounds have been screened and further scrutinised for their inhibitory properties against the HIV integrase; however, there are currently no useful inhibitors available clinically for the treatment of AIDS patients. This review describes the current knowledge of the biological functions of the HIV-1 integrase and reports the major classes of integrase inhibitors identified to date.
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Affiliation(s)
- Khampoune Sayasith
- CRRA, Faculty of Veterinary Medicine, University of Montreal, PO Box 5000, St-Hyacinthe, Quebec, Canada J2S 7C6.
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Brodin P, Pinskaya M, Parsch U, Bischerour J, Leh H, Romanova E, Engels JW, Gottikh M, Mouscadet JF. 6-oxocytidine containing oligonucleotides inhibit the HIV-1 integrase in vitro. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2001; 20:481-6. [PMID: 11563063 DOI: 10.1081/ncn-100002322] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Integration of the proviral DNA into the genome of infected cells is a key step of HIV-1 replication. Integration is catalyzed by the viral enzyme integrase (IN). 6-oxocytidine-containing oligonucleotides were found to be efficient inhibitors of integrase in vitro. The inhibitory effect is sequence-specific and strictly requires the presence of the 6-oxocytidine base. It is due to the impairment of the integrase binding to its substrate and does not involve an auto-structure of the oligonucleotide.
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Affiliation(s)
- P Brodin
- UMR 8532, Institut Gustave Roussy, 39 rue Camille Desmoulins, 94805 Villejuif, France
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Snásel J, Rejman D, Liboska R, Tocík Z, Ruml T, Rosenberg I, Pichová I. Inhibition of HIV-1 integrase by modified oligonucleotides derived from U5' LTR. EUROPEAN JOURNAL OF BIOCHEMISTRY 2001; 268:980-6. [PMID: 11179964 DOI: 10.1046/j.1432-1327.2001.01956.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Retroviral integrase catalyzes integration of double-stranded viral DNA into the host chromosome by a process that has become an attractive target for drug design. In the 3' processing reaction, two nucleotides are specifically cleaved from both 3' ends of viral DNA yielding a 5' phosphorylated dimer (pGT). The resulting recessed 3' hydroxy groups of adenosine provide the attachment sites to the host DNA in the strand transfer reaction. Here, we studied the effect of modified double-stranded oligonucleotides mimicking both the unprocessed (21-mer oligonucleotides) and 3' processed (19-mer oligonucleotides) U5 termini of proviral DNA on activities of HIV-1 integrase in vitro. The inhibitions of 3' processing and strand transfer reactions were studied using 21-mer oligonucleotides containing isopolar, nonisosteric, both conformationally flexible and restricted phosphonate internucleotide linkages between the conservative AG of the sequence CAGT, and using a 21-mer oligonucleotide containing 2'-fluoroarabinofuranosyladenine. All modified 21-mer oligonucleotides competitively inhibited both reactions mediated by HIV-1 integrase with nanomolar IC50 values. Our studies with 19-mer oligonucleotides showed that modifications of the 3' hydroxyl significantly reduced the strand transfer reaction. The inhibition of integrase with 19-mer oligonucleotides terminated by (S)-9-(3-hydroxy-2-phosphonomethoxypropyl)adenine, 9-(2-phosphonomethoxyethyl)adenine, and adenosine showed that proper orientation of the 3' OH group and the presence of the furanose ring of adenosine significantly influence the strand transfer reaction.
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Affiliation(s)
- J Snásel
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Prague, Czech Republic
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Taktakishvili M, Neamati N, Pommier Y, Pal S, Nair V. Recognition and Inhibition of HIV Integrase by Novel Dinucleotides. J Am Chem Soc 2000. [DOI: 10.1021/ja992528d] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michael Taktakishvili
- Contribution from the Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242, and Laboratory of Pharmacology, National Cancer Institute, NIH, Bethesda, Maryland 20892
| | - Nouri Neamati
- Contribution from the Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242, and Laboratory of Pharmacology, National Cancer Institute, NIH, Bethesda, Maryland 20892
| | - Yves Pommier
- Contribution from the Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242, and Laboratory of Pharmacology, National Cancer Institute, NIH, Bethesda, Maryland 20892
| | - Suresh Pal
- Contribution from the Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242, and Laboratory of Pharmacology, National Cancer Institute, NIH, Bethesda, Maryland 20892
| | - Vasu Nair
- Contribution from the Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242, and Laboratory of Pharmacology, National Cancer Institute, NIH, Bethesda, Maryland 20892
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