Mechanisms of the inhibition of reverse transcription by unmodified and modified antisense oligonucleotides

Targeting a pre-mRNA structure with bipartite antisense molecules modulates tau alternative splicing

Approximately 15% of human genetic diseases are estimated to involve dysregulation of alternative pre-mRNA splicing. Antisense molecules designed to alter these and other splicing events typically target continuous linear sequences of the message. Here, we show that a structural feature in a pre-mRNA can be targeted by bipartite antisense molecules designed to hybridize with the discontinuous elements that flank the structure and thereby alter splicing. We targeted a hairpin structure at the boundary between exon 10 and intron 10 of the pre-mRNA of tau. Mutations in this region that are associated with certain forms of frontotemporal dementia, destabilize the hairpin to cause increased inclusion of exon 10. Via electrophoretic mobility shift and RNase protection assays, we demonstrate that bipartite antisense molecules designed to simultaneously interact with the available sequences that immediately flank the tau pre-mRNA hairpin do indeed bind to this structured region. Moreover, these agents inhibit exon 10 splicing and reverse the effect of destabilizing disease-causing mutations, in both in vitro splicing assays and cell culture. This general bipartite antisense strategy could be employed to modulate other splicing events that are regulated by RNA secondary structure.

Inhibitory effect of modified 5'-capped short RNA fragments on influenza virus RNA polymerase gene expression

We have shown previously that the 5'-capped short phosphodiester RNA fragments, Cap decoy, (Gm 12 nt) are potent inhibitors of influenza virus RNA polymerase gene expression. Here we investigate the modified capped RNA derivative containing phosphorothioate oligonucleotides (Cap decoy) as a potential influenza virus RNA polymerase inhibitor. The modified 5'-capped short phosphorothioate RNA fragments (Gms 12-15 nt) with the 5'-capped structure (m7GpppGm) were synthesized by T7 RNA polymerase. The 5'-capped short RNA fragments (Gms 12-15 nt) were encapsulated in liposome particulates and tested for their inhibitory effects on influenza virus RNA polymerase gene expression in the clone 76 cells. The 12-15 nt long Gms RNA fragments showed highly inhibitory effects. By contrast, the inhibitory effects of the 13 nt long short RNA fragments (Gm 13 nt) were considerably less in comparison with the 5'-capped short phosphorothioate RNA fragments (Gms 12-15 nt). In particular, the various Gms RNA chain lengths showed no significant differences in the inhibition of influenza virus RNA polymerase gene expression. Furthermore, the capped RNA with a phosphorothioate backbone was resistant to nuclease activity. These phosphorothioate RNA fragments exhibited higher inhibitory activity than the 5'-capped short RNA fragments (Gm 12 nt). These decoys may prove to be useful in anti-influenza virus therapeutics.

Anti-HIV-1 activity of an antisense phosphorothioate oligonucleotide bearing imidazole and primary amine groups

We have previously shown that RNA cleaving reagents with imidazole and primary amine groups on the 5'-end of antisense oligodeoxyribonucleotides could site-specifically cleave CpA as the target sequence of the substrate tRNA in vitro. In this study, a RNA cleaving reagent, composed of imidazole and primary amine groups on an antisense phosphorothioate oligonucleotide (Im-anti-s-ODN), was synthesized and evaluated for anti-HIV-1 activity in MT-4 cells. The sequence of the Im-anti-s-ODN was designed to be complementary to the HIV-1 gag-mRNA and to bind adjacent to the CpA cleavage site position. Im-anti-s-ODN encapsulated with the transfection reagent, DMRIE-C, had higher anti-HIV-1 activity than the unmodified antisense phosphorothioate oligonucleotide (anti-s-ODN) at a 2 microM concentration. Furthermore, the Im-anti-ODN encapsulated with DMRIE-C conferred sequence-specific inhibition.

Antisense therapy of influenza

The liposomally encapsulated and the free antisense phosphorothioate oligonucleotides (S-ODNs) with four target sites (PB1, PB2, PA, and NP) were tested for their abilities to inhibit virus-induced cytopathogenic effects by a MTT assay using MDCK cells. The liposomally encapsulated S-ODN complementary to the sites of the PB2-AUG initiation codon showed highly inhibitory effects. On the other hand, the inhibitory effect of the liposomally encapsulated S-ODN targeted to PB1 was considerably decreased in comparison with those directed to the PB2 target sites. The liposomally encapsulated antisense phosphorothioate oligonucleotides exhibited higher inhibitory activities than the free oligonucleotides, and showed sequence-specific inhibition, whereas the free antisense phosphorothioate oligonucleotides were observed to inhibit viral absorption to MDCK cells. Therefore, the antiviral effects of S-ODN-PB2-AUG and PA-AUG were examined in a mouse model of influenza virus A infection. Balb/c mice exposed to the influenza virus A (A/PR/8/34) strain at dose of 100 LD(50)s were treated i.v. with various doses (5-40 mg/kg) of liposomally (Tfx-10) encapsulated PB2-AUG or PA-AUG before virus infection and 1 and 3 days postinfection. PB2-AUG oligomer treated i.v. significantly prolonged the mean survival time in days (MDS) and increased the survival rates with a dose-dependent manner. We demonstrate the first successful in vivo antiviral activity of antisense administered i.v. in experimental respiratory tract infections induced with influenza virus A.

Specific inhibition of influenza virus RNA polymerase and nucleoprotein gene expression by liposomally encapsulated antisense phosphorothioate oligonucleotides in MDCK cells

We have demonstrated that antisense phosphorothioate oligonucleotides (S-ODNs) inhibit influenza A virus replication in MDCK cells. Liposomally encapsulated and free antisense S-ODNs with four target sites (PB1, PB2, PA and NP genes) were tested for their abilities to inhibit virus-induced cytopathogenic effects in a MTT assay using MDCK cells. The liposomally encapsulated S-ODN complementary to the site around the PB2 AUG initiation codon showed highly inhibitory effects. In contrast, the inhibitory effect of the liposomally encapsulated S-ODN targeted to PB1 was considerably decreased in comparison with that directed to the PB2 target site. The liposomally encapsulated antisense S-ODNs exhibited higher inhibitory activities than the free oligonucleotides, and showed sequence-specific inhibition, whereas free antisense S-ODNs were observed to inhibit viral adsorption to MDCK cells. Liposomal preparations of oligonucleotides facilitated their release from endocytic vesicles, and thus cytoplasmic and nuclear localization was observed. The activities of the antisense S-ODNs were effectively enhanced by using the liposomal carrier. Interestingly, the liposomally encapsulated FITC-S-ODN-PB2-as accumulated in the nuclear region of MDCK cells. However, weak fluorescence was observed within the endosomes and the cytoplasm of MDCK cells treated with the free antisense S-ODNs. The cationic lipid particles may thus be a potentially useful delivery vehicle for oligonucleotide-based therapeutics and transgenes, appropriate for use in vitro or in vivo.

Efficient in vitro inhibition of HIV-1 gag reverse transcription by peptide nucleic acid (PNA) at minimal ratios of PNA/RNA

We have tested the inhibitory potential of peptide nucleic acid (PNA) on in vitro reverse transcription of the HIV-1 gag gene. PNA was designed to target different regions of the HIV-1 gag gene and the effect on reverse transcription by HIV-1, MMLV and AMV reverse transcriptases (RTs) was investigated. We found that a bis-PNA (parallel antisense 10mer linked to antiparallel antisense 10mer) was superior to both the parallel antisense 10mer and antiparallel antisense 10mer in inhibiting reverse transcription of the gene, thus indicating triplex formation at the target sequence. A complete arrest of reverse transcription was obtained at approximately 6-fold molar excess of the bis-PNA with respect to the gag RNA. At this molar ratio we found no effect on in vitro translation of gag RNA. A 15mer duplex-forming PNA was also found to inhibit reverse transcription at very low molar ratios of PNA/ gag RNA. Specificity of the inhibition of reverse transcription by PNA was confirmed by RNA sequencing, which revealed that all tested RTs were stopped by the PNA/RNA complex at the predicted site. We propose that the effect of PNA is exclusively due to steric hindrance, as we found no signs of RNA degradation that would indicate PNA-mediated RNase H activation of the tested RTs. In conclusion, PNA appears to have a potential to become a specific and efficient inhibitor of reverse transcription in vivo , provided sufficient intracellular levels are achievable.

The multiple inhibitory mechanisms of GEM 91, a gag antisense phosphorothioate oligonucleotide, for human immunodeficiency virus type 1

GEM 91 (gene expression modulator) is a 25-mer oligonucleotide phosphorothioate complementary to the gag initiation site of HIV-1. GEM 91 has been studied in various in vitro cell culture models to examine inhibitory effects on different stages of HIV-1 replication. Experiments were focused on the binding of virions to the cell surface, inhibition of virus entry, reverse transcription (HIV DNA production), inhibition of steady state viral mRNA levels, inhibition of virus production from chronically infected cells, and inhibition of HIV genome packaging within virions. Experiments were also performed in vitro in an attempt to generate strains of HIV with reduced sensitivity to GEM 91. We observed sequence-dependent inhibition of virus entry/reverse transcription and a reduction in steady state viral RNA levels. We also observed sequence-independent inhibition of virion binding to cells and inhibition of virus production by chronically infected cells. Using in vitro methods that were successful in generating HIV strains with reduced sensitivity to AZT, we were unable to generate strains with reduced sensitivity to GEM 91.

Inhibition of HIV-1 replication by triple-helix-forming phosphorothioate oligonucleotides targeted to the polypurine tract

We show the effects of triple-helix formation by assays of primer extension inhibition in vitro using two systems (two-strand-system (FTFOs) or three-strand-system (TFOs) targeted to the polypurine tract (PPT) of HIV-1. The FTFOs were more effective than the TFOs. We found that the FTFOs containing phosphorothioate groups at the 3'- and 5'-ends, or inside the hairpin loop, exhibited higher inhibitory effects on cDNA synthesis and greater exonuclease resistance than the unmodified FTFOs and TFOs. The abilities of the FTFOs containing phosphorothioate groups at the antisense sequence sites to inhibit HIV-1 replications were examined. The FTFOs containing phosphorothioate groups at the antisense sequence sites inhibit the replication of HIV-1 more efficiently than the antisense oligonucleotides, indicating sequence-specific inhibition of HIV-1 replication.

Antisense inhibition of virus infections

This chapter summarizes the new approaches to identify novel antiviral drug targets and to develop novel antiviral strategies. The chapter also reviews genetic pharmacology as it relates to antiviral antisense research and drug development. Antisense oligonucleotides are selective compounds by virtue of their interaction with specific segments of RNA. For potential antivirals, identification of appropriate target RNA sequences for antisense oligonucleotides is performed at two levels: the optimal gene within the virus, and the optimal sequence within the RNA. The importance of these oligonucleotide modifications in designing effective drugs is just now being evaluated, both in animal model systems and in the clinic. The first generation of widely used antisense oligonucleotides has been the phosphorothioate (PS) compounds and a body of data on biodistribution, pharmacokinetics, and metabolism in animals and in humans is now available. Since the identification and sequencing of human immunodeficiency virus (HIV), there has been a strong interest in identifying a potent oligonucleotide inhibitor that would have the potential for development as a therapy for acquired immunodeficiency syndrome (AIDS). Numerous phosphorothioate oligonucleotides, with no apparent antisense sequence specificity, can have an anti-herpes simplex virus (HSV) effect. Oligonucleotides can be effective anti-influenza agents in cell culture assays. Hepatitis B virus (HBV) X protein that is a transactivator has been also reported to be targeted successfully by antisense oligonucleotides in vivo. Several of picornaviruses have been targets for antisense oligonucleotide inhibition, and the studies demonstrate the versatility of the antisense approach. However, the fact that oligonucleotides may contribute numerous mechanisms toward the antiviral activity, in addition to the antisense mechanism, may in some cases be an asset in the pursuit of clinically useful antiviral drugs.

5'-linked lipid-oligodeoxyridonucleotide derivatives as inhibitors of human immunodeficiency virus replication

The covalent attachment of a phospholipid moiety, bound to the 5'-ends of phosphodiester and phosphorothioate oligonucleotides (L-ODNs and LS-ODNs), was achieved using H-phosphonate chemistry, and the lipid-oligonucleotides were assayed for the inhibition of virus replication in HIV-1 infected MT-4 cells. In the anti-HIV activity test, lipid-phosphorothioate oligonucleotides showed higher anti-HIV activities than non-lipid-phosphorothioate oligonucleotides, at the low concentration of 0.04 microM. LS-ODNs can inhibit HIV-1 reverse transcriptase activity through interactions with the enzyme. We found that the covalent attachment of a phospholipid group to the 5'-end of the phosphorothioate oligonucleotide enhances its nonsequence specific anti-HIV activity.

Inhibition of neurotropic mouse retrovirus replication in glial cells by synthetic oligo(2'-O-methyl)ribonucleoside phosphorothioates

Synthetic oligo(2'-O-methyl)ribonucleoside phosphorothioate, FS-25, which is complementary to the splicing acceptor site of neurotropic mouse retrovirus (FrC6 virus), and non-complementary analogs including 2'-O-methylinosine homo oligomer (MIS-25), both inhibited viral infection in glial cells. In addition, FS-25 and MIS-25 partially suppressed viral production of glial cells persistently infected with FrC6 virus. Both FS-25 and MIS-25 potently inhibited reverse transcriptase activity of the FrC6 virus in a cell-free system. Addition of these compounds before or after second-round infection of the FrC6 virus inhibited the accumulation of unintegrated viral DNA. These results indicate that these compounds fundamentally inhibit retrovirus production in glial cells in the same manner in which they inhibit HIV production, by blocking several viral replication pathways including fresh infection, second-round infection, and reverse transcription of the viral genome. Our novel neurotropic retrovirus is a useful experimental model for the development of drugs against HIV infection.

Analysis of oligo(deoxynucleoside phosphorothioate)s and their diastereomeric composition

Short oligo(deoxynucleoside phosphorothioate)s were analyzed as a pool of individual diastereomeric species. The composition of such mixtures, determined by means of HPLC, indicates that consecutive couplings in commonly used phosphoramidite chemistry lead to increasing contents of the Rp isomer. Methods of analysis and mathematical basis for diastereomeric composition are discussed. Data presented include all 16 possible combinations of nucleosides in dinucleotide phosphorothioates, as well as examples of trimers and tetramers.

Antiviral effect of phosphorothioate oligodeoxyribonucleotides complementary to human immunodeficiency virus

Modifications of oligodeoxyribonucleotides include the replacement of the backbone phosphodiester groups with phosphorothioate (S-ODNs) groups and the substitution of phosphorothioate (SO-ODNs) groups at both the 3'- and 5'-ends. In assays for HIV, oligomers (S-ODNs) were more active at the micromolar range than were SO-ODNs of the same sequence. Furthermore, the abilities of antisense-, sense-, random-, and mismatched-oligomers, or homo-oligomers containing internucleotidic phosphorothioate linkages to inhibit HIV-1 replication were examined. Antisense oligonucleotides inhibit the replication and the expression of HIV-1 more efficiently than random-, sense-, mismatched-, and homo-oligomers of the same length or with the same internucleotide modification. Five different target sites (gag, pol, rev, tat, and tar) within the HIV genes were also studied with regard to the inhibition of HIV replication by antisense oligonucleotides. Antisense oligomers complementary to the sites of initiation sequences and to certain splice sites were most effective. The effect of antisense oligomer length on inhibiting viral replication was also investigated. Of particular interest was the S-ODNs-rev 15 mer, which possessed higher anti-HIV activity than the sense-, random-, mismatched-, and homo-20 mers.

Gene-targeted inhibition of transactivation of human immunodeficiency virus type-1 (HIV-1)-LTR by antisense oligonucleotides

We have used an in vitro approach to study the efficiency of antisense oligonucleotides in inhibiting LTR-(HIV-1)-directed CAT expression catalyzed by tat protein, the functional protein of the transactivator gene. We selected the target sequence localized near the 5' end of the tat mRNA. The following conclusions can be drawn from the data presented here: a) Antisense oligonucleotides modified by conjugation of cholesterol at the 3' end have a severalfold higher inhibitory response, b) inhibitory response is dependent on the mode of introducing oligonucleotides, and c) the inhibition by antisense oligonucleotides is sequence specific and directed towards the targeted region. This approach could be useful for targeting functional regions of regulatory gene products and designing gene-targeted inhibitors of virus replication.

Anti-human immunodeficiency virus type 1 activity of phosphorothioate analogs of oligodeoxynucleotides: penetration and localization of oligodeoxynucleotides in HIV-1-infected MOLT-4 cells

Phosphorothioate antisense oligodeoxynucleotide against HIV-1 rev (S-ODN-rev) inhibits virus-induced cytopathic effects (CPE) in acute infection and inhibits the expression of HIV-1 core protein, p24, in chronically infected cells in vitro. HIV-1 reverse transcriptase activity was not affected by S-ODN-rev at the high concentrations of 5-25 microM, which were 250-1250 times higher than the concentration required to achieve 100% HIV-1-induced CPE inhibition. [32P]-labeled S-ODN-rev was rapidly uptaken by MOLT-4 cells, whereas [32P]-SO-ODN-rev and [32P]-O-ODN-rev were not. In the observation of FITC-S-ODN-rev-treated MOLT-4 cells by a confocal laser scanning microscope, diffuse fluorescence was apparently observed in the cytoplasm. Interestingly, fluorescence signals were accumulated in the nuclear region of chronically infected MOLT-4/HIV-1 cells 60 min after incubation. FITC-labeled homooligomer, FITC-S-dC20 and FIT-C-S-dT20, also accumulated in the nucleus of MOLT-4/HIV-1 cells, but weak fluorescence was observed on the cell membrane and in the cytoplasm of the FITC-S-random treated MOLT-4/HIV-1 and MOLT-4 cells.

Gene therapy for human immunodeficiency virus infection: genetic antiviral strategies and targets for intervention

Gene therapeutic strategies for the treatment of human immunodeficiency virus type 1 (HIV-1) infection have received increased attention due to lack of chemotherapeutic drugs or vaccines that show long-term efficacy in vivo. An emerging group, referred to here as "genetic antivirals," is reviewed. Genetic antivirals are defined as DNA or RNA elements that are transferred into cells and affect their intracellular targets either directly, or after expression as RNA or proteins. They include antisense oligonucleotides, ribozymes, RNA decoys, transdominant mutants, toxins, and immunogens. They offer the possibility to target simultaneously multiple sites in the HIV genome, thereby minimizing the production of resistant viruses. We review the molecular mechanisms of genetic antivirals, their HIV molecular targets, and discuss issues concerning their application as anti-HIV agents.

A phosphorothioate oligonucleotide blocks reverse transcription via an antisense mechanism

We have studied the inhibition by a phosphorothioate oligodeoxynucleotide (17PScap) of cDNA synthesis performed by either avian or murine reverse transcriptase. Three different mechanisms of inhibition were identified: at low concentrations (< 100 nM), the cleavage of the RNA template by the retroviral RNase H at the level of the RNA/17PScap duplex accounted for most of the effect, whereas hybrid-arrested cDNA synthesis by an RNase H-independent mechanism marginally contributed to the inhibition. Both mechanisms were sequence-specific. Above 100 nM, the overall cDNA synthesis was reduced in a non-specific manner.