Mechanisms of inhibition of herpes simplex virus type 2 growth by 28-mer phosphorothioate oligodeoxycytidine

Inhibition of Human Cytomegalovirus DNA Replication with a Phosphorothioate Cholesteryl-Modified Oligonucleotide is Mediated by Rapid Cellular Association and Virus-Facilitated Nuclear Localization

We have previously shown that an antisense phosphorothioate (PS) oligodeoxynucleotide has potent anti-human cytomegalovirus (HCMV) activity (GS Pari, AK Field & JA Smith, Antimicrobial Agents and Chemotherapy 1995, 39: 1157–1161). We have now used a modified PS oligonucleotide having three 2′-O-methyl nucleotides at the 3′ end and four 2′-O-methyl nucleotides at the 5′ end, containing a cholesteryl moiety linked to the 3′ end by a novel thiono-triester linkage. This compound, UL36ANTI-M, is superior to the PS (UL36ANTI) version with respect to antiviral potency, melting temperature and nuclease resistance. Also, we show that cellular association for this oligonucleotide is rapid, occurring within 15 min after treatment and is about 12-fold higher when compared to UL36ANTI. This increased rate of cellular association also correlates with antiviral properties in that a 15 min incubation with UL36ANTI-M was sufficient to achieve 75% inhibition of viral DNA replication and complete inhibition was achieved after only a 1 h pretreatment. In addition confocal microscopic examination showed a change in subcellular distribution from perinuclear to nuclear for oligonucleotides in HCMV-infected human fibroblasts. However, the total amount of cell-associated oligonucleotide was unchanged in infected cells.

Inhibition of HSV-1 ocular infection with morpholino oligomers targeting ICP0 and ICP27

Alternative therapies are needed for HSV-1 infections in patients refractory to treatment with Acyclovir (ACV) and its derivatives. Peptide-conjugated phosphorodiamidate morpholino oligomers (PPMO) are single-stranded DNA analogues that enter cells readily and reduce target gene expression through steric blockage of complementary RNA. When applied before or soon after infection PPMO targeting the translation-start-site regions of HSV-1 ICP0 or ICP27 mRNA reduced HSV-1 plaque formation by 70-98% in vitro. The ICP0 PPMO also reduced ACV-resistant HSV-1 (strain 615.9) plaque formation by 70-90%, while an equivalent dose of ACV produced only 40-50% inhibition when the treatment was applied between 1 and 3hpi. Seven daily topical treatments of 100microg ICP0 PPMO caused no gross or microscopic damage to the corneas of uninfected mice. Topical application of 10microg ICP0 PPMO to the eyes of HSV-1 infected mice reduced the incidence of eye disease by 37.5-50% compared to controls. This study demonstrates that topically applied PPMO holds promise as an antiviral drug candidate against HSV-1 ocular infection.

A proviral role for CpG in cytomegalovirus infection

TLR9-dependent signaling in plasmacytoid dendritic cells is a key contributor to innate immune defense to mouse CMV infection. We aimed to study the expression and potential contribution of TLR9 signaling in human CMV (HCMV) infection of primary fibroblasts. HCMV infection strongly induced TLR9 expression in two of three fibroblast types tested. Furthermore, the TLR9 ligand CpG-B induced a strong proviral effect when added shortly after HCMV infection, enhancing virus production and cell viability. However, not all CpG classes displayed proviral activity, and this correlated with their IFN-beta-inducing ability. The proviral effect of CpG-B correlated completely with concurrent viral up-regulation of TLR9 in fibroblasts. Importantly, the timing of CpG addition was a critical parameter; in striking contrast to the proviral effect, CpG addition at the time of infection blocked viral uptake and nearly abolished HCMV production. The contrasting and time-dependent effects of CpG on HCMV infectivity reveal a complex interplay between CpG, TLR9, and HCMV infection. Additionally, the data suggest a potentially harmful role for CpG in the promotion of HCMV infection.

Amphipathic DNA polymers exhibit antiherpetic activity in vitro and in vivo

Phosphorothioated oligonucleotides have a sequence-independent antiviral activity as amphipathic polymers (APs). The activity of these agents against herpesvirus infections in vitro and in vivo was investigated. The previously established sequence-independent, phosphorothioation-dependent antiviral activity of APs was confirmed in vitro by showing that a variety of equivalently sized homo- and heteropolymeric AP sequences were similarly active against herpes simplex virus type 1 (HSV-1) infection in vitro compared to the 40mer degenerate parent compound (REP 9), while the absence of phosphorothioation resulted in the loss of antiviral activity. In addition, REP 9 demonstrated in vitro activity against a broad spectrum of other herpesviruses: HSV-2 (50% effective concentration [EC(50)], 0.02 to 0.06 microM), human cytomegalovirus (EC(50), 0.02 to 0.13 microM), varicella zoster virus (EC(50), <0.02 microM), Epstein-Barr virus (EC(50), 14.7 microM) and human herpesvirus types 6A/B (EC(50), 2.9 to 10.2 microM). The murine microbicide model of genital HSV-2 was then used to evaluate in vivo activity. REP 9 (275 mg/ml) protected 75% of animals from disease and infection when provided 5 or 30 min prior to vaginal challenge. When an acid-stable analog (REP 9C) was used, 75% of mice were protected when treated with 240 mg/ml 5 min prior to infection (P < 0.001), while a lower dose (100 mg/ml) protected 100% of the mice (P < 0.001). The acid stable REP 9C formulation also provided protection at 30 min (83%, P < 0.001) and 60 min (50%, P = 0.07) against disease. These observations suggest that APs may have microbicidal activity and potential as broad-spectrum antiherpetic agents and represent a novel class of agents that should be studied further.

Amphipathic DNA Polymers are Candidate Vaginal Microbicides and Block Herpes Simplex Virus Binding, Entry and Viral Gene Expression

Background

Amphipathic DNA polymers are promising therapies for the prevention of HIV and genital herpes infections. Recent studies on a panel of such compounds indicated potent activity against HIV binding and entry. This current study was conducted to explore the anti-herpes simplex virus (HSV) activity of the same panel of compounds and to determine their mechanism of activity.

Methods

The anti-HSV activity of a 40-nucleotide degenerate polymer (REP 9), a 40-nucleotide polycytidine amphipathic DNA polymer (REP 9C) and an analogue lacking amphipathic activity (Randomer 3) were compared in plaque reduction assays in the absence or presence of human genital tract secretions; the mechanisms of anti-HSV activity were explored.

Results

REP 9 inhibited HSV infection 10,000-fold, whereas Randomer 3 displayed no anti-HSV activity. The antiviral activity was independent of sequence but was dependent on size: the most potent activity was observed for analogues of 40 nucleotides in length. Mechanistic studies indicated that REP 9 and REP 9C blocked HSV-2 binding and entry, were active when added post-entry, inhibited viral gene expression and blocked HSV-induced apoptosis. Confocal microscopy studies showed rapid delivery of fluorescently tagged REP 9 and REP 9C into human epithelial cells, and delivery was significantly greater in infected cells as compared with uninfected cells. REP 9 exhibited no cytotoxicity and retained anti-HSV activity in the presence of cervicovaginal secretions and when virus was introduced in seminal plasma.

Conclusions

REP 9 and REP 9C represent a novel class of antiviral agents that act by multiple mechanisms. These compounds warrant further development for systemic or topical delivery for the prevention and treatment of HIV and HSV.

Binding features of BCL2-targeted oligodeoxynucleotides with K562 cells

Delivery of various oligodeoxynucleotides into cells is mediated by binding to certain surface proteins followed by receptor-mediated endocytosis. Moreover, oligonucleotides are able to provoke perturbation of cell surface proteins and growth factor receptors among them. Here we described binding sense BCL2 oligodeoxynucleotide targeted to translation start of BCL2 mRNA (ODN) with K562 cells. At low concentration ODN bound efficiently with K562 and penetrated into the cells via binding cell surface with rather high affinity and priming new binding sites. The loose binding constant at 4 degrees C was 1.8 x 10(9) M(-1) both for binding ODN in solution and ODN-associated liposome. The number of loose binding sites under both treatments was rather high: 4.6 to 6.6 pmoles per 10(6) cells. The extent of ODN penetration into the cells showed higher potential site numbers than initially seen and reached 8.6 pmoles per 10(6) cells for four hours incubation at 37 degrees C.

An oligonucleotide decoy for nuclear factor-kappa B inhibits tumor necrosis factor-alpha-induced human umbilical cord vein endothelial cell tissue factor expression in vitro

Abnormal tissue factor (TF) expression on vascular endothelial cells may account for thrombotic events associated with cardiovascular disease. The transcription factor nuclear factor-kappa B (NF-kappa B) activation plays a key role in endothelial cell injury and TF expression. Disruption of NF-kappa B activation in endothelial cells may inhibit TF expression and be protective in thrombosis. The purpose of the study was to determine whether NF-kappa B transcription factor decoy (TFD) could block TF expression. NF-kappa B TFD was transferred into cultured human umbilical cord vein endothelial cells (HUVEC) by liposomes, and the transfection efficiency was detected by flow cytometry. The effect of NF-kappa B TFD on TF mRNA levels was determined by reverse transcription-polymerase chain reaction. The expression of surface TF antigen was analyzed by flow cytometry. TF activity was studied by measuring enzymatic activation of factor X by the TF-activated factor VII complex. The results suggested that NF-kappa B decoy could be successfully transferred into HUVEC by liposome. The NF-kappa B TFD competed with the endogenous kappa B site sequence in the TF promoter for binding to transcription factor NF-kappa B in tumor necrosis factor-alpha-stimulated HUVEC, which could block the tumor necrosis factor-alpha-induced increase in TF mRNA levels, the upregulation of surface TF antigen and TF activity. This study demonstrated that NF-kappa B decoy could block HUVEC TF gene expression. Targeted genetic disruption of endothelial TF expression by NF-kappa B decoy may provide a possible therapeutic method for cardiovascular and thrombosis disease.

Optimization of functional efficacy of phosphorothioate-modified oligonucleotides in a human CD8+ T-cell ex vivo expansion model

Antisense oligodeoxyribonucleotides (ODNs) can specifically inhibit gene expression, but their application to fresh human CD8+ T cells is limited by poor spontaneous uptake (<2%). We have examined and optimized the uptake of phosphorothioate-modified oligodeoxyribonucleotides (PS-ODNs) into these cells in an ex vivo expansion model. Optimal antisense treatments were found to be, for fresh CD8+ T cells, 1 micro m PS-ODNs complexed with lipofectin (LF), which resulted in 35% uptake and 10 micro m PS-ODNs in the absence of LF, for cultured cells, which resulted in 95% uptake. The delivered antisenses were functional, as determined by the inhibition of protein expression. In this respect, partially phosphorothioate-modified ODNs (PS-ODNs-P) were twice as effective as completely modified (PS-ODNs-C), and the antisense specific for the cap site showed the highest protein suppression of those tested (68%). Uptake mechanisms were also investigated. To our knowledge, this is the first optimization of the delivery of antisense oligonucleotides into human CD8+ T cells. This protocol could be used to study the function of a particular gene in cytotoxic T lymphocytes and also by those looking for a method to deliver short interfering RNA into cell lines to specifically suppress a gene of interest.

Antisense oligonucleotides in cutaneous therapy

Antisense oligonucleotides have been the subject of intense interest as research tools to elucidate the functions of gene products and as therapeutic agents. Initially, their mode of action was poorly understood and the biological effects of oligonucleotides were often misinterpreted. However, research into these gene-based inhibitors of cellular action recently has succeeded in realising their exciting potential, particularly as novel therapeutic agents. An emerging application of this technology is in cutaneous therapy. The demand for more effective dermatological drugs will ensure further development of antisense strategies in skin, with key issues being drug delivery, therapeutic target selection, and clinical applicability.

Suppression of tumor necrosis factor secretion from white blood cells by synthetic antisense phosphorothioate oligodeoxynucleotides

In this ex vivo, rather than in vitro, experiment, a synthetic antisense oligodeoxynucleotide was tested to suppress tumor necrosis factor - alpha(TNF) secretion from lipopolysaccharide-stimulated white blood cells. Antisense oligomer showed significant and specific suppressive effect to the secretion of TNF at concentrations of 1.0 and 10 microM. At the concentration of 1 microM, there were 68.4 and 63.9% suppression of TNF secretion at 2 and 24 h after resuspension of blood cells. At the concentration of 10 microM, the suppressions were slightly higher than those at 1 microM, which were 71.8 and 76.2%, respectively. A 50%-matched scrambler showed suppressive effect only at 10 microM concentration, and the suppression only occurred at 2 and 24 h after incubation. Sense oligomer showed no suppressive effects at any of the concentrations. The specificity of this oligomer was documented by dose-effect phenomenon, sequence-dependent suppression and absence of effect on the synthesis of another cytokine (interleukin-6). A series of parallel studies was performed and showed that all three oligomers at any concentration tested had no effect on the interleukin-6 secretion after LPS stimulation.In conclusion, properly designed antisense oligodeoxynucleotide can significantly and specifically suppress the secretion of TNF by blood cells in an ex vivo system and it may be a good "information" drug to treat diseases that are caused by over production of TNF.

2-5A-DNA conjugate inhibition of respiratory syncytial virus replication: effects of oligonucleotide structure modifications and RNA target site selection

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.

Oligodeoxyribonucleotide Uptake in Primary Human Hematopoietic Cells Is Enhanced by Cationic Lipids and Depends on the Hematopoietic Cell Subset

The use of antisense oligodeoxyribonucleotides (ODN) is a potential method to switch off gene expression. The poor cellular uptake of ODN in primary cells still is a limiting factor that may contribute to the lack of functional efficacy. Various forms of cationic lipids have been developed for efficient delivery of nucleic acids into different cell types. We examined the two cationic lipids DOTAP and DOSPER to improve uptake of ODN into primary human hematopoietic cells. Using a radiolabeled 23-mer, ODN uptake into blood-derived mononuclear cells could be increased 42- to 93-fold by DOTAP and 440- to 1,025-fold by DOSPER compared with application of ODN alone. DOTAP was also effective for delivery of ODN into leukocytes within whole blood, which may resemble more closely the in vivo conditions. As assessed by fluorescein isothiocyanate–conjugated ODN both cationic lipids enhanced cytoplasmic accumulation of ODN in endosome/lysosome-like structures with a partial shift of fluorescence to the whole cytoplasm and the nucleus following an incubation of 24 hours. ODN uptake by cationic lipids into different hematopoietic cell subsets was examined by dual-color immunofluorescence analysis with subset-specific monoclonal antibodies. We found a cell type–dependent delivery of ODN with greatest uptake in monocytes and smallest uptake in T cells. CD34+ cells, B cells, and granulocytes took up ODN at an intermediate level. Uptake of ODN into isolated CD34+cells could be increased 100- to 240-fold using cationic lipids compared with application of ODN alone. Stimulation of CD34+ cells by interleukin-3 (IL-3), IL-6, and stem cell factor did not significantly improve cationic lipid-mediated ODN delivery. Sequence-specific antisense effects in clonogenic assays could be shown by transfection of bcr-abl oncogene-directed antisense ODN into primary cells of patients with chronic myelogenous leukemia using this established protocol. In conclusion, cationic lipids may be useful tools for delivery of antisense ODN into primary hematopoietic cells. These studies provide a basis for clinical protocols in the treatment of hematopoietic cells in patients with hematologic malignancies and viral diseases by antisense ODN.

Oligodeoxyribonucleotide Uptake in Primary Human Hematopoietic Cells Is Enhanced by Cationic Lipids and Depends on the Hematopoietic Cell Subset

The use of antisense oligodeoxyribonucleotides (ODN) is a potential method to switch off gene expression. The poor cellular uptake of ODN in primary cells still is a limiting factor that may contribute to the lack of functional efficacy. Various forms of cationic lipids have been developed for efficient delivery of nucleic acids into different cell types. We examined the two cationic lipids DOTAP and DOSPER to improve uptake of ODN into primary human hematopoietic cells. Using a radiolabeled 23-mer, ODN uptake into blood-derived mononuclear cells could be increased 42- to 93-fold by DOTAP and 440- to 1,025-fold by DOSPER compared with application of ODN alone. DOTAP was also effective for delivery of ODN into leukocytes within whole blood, which may resemble more closely the in vivo conditions. As assessed by fluorescein isothiocyanate–conjugated ODN both cationic lipids enhanced cytoplasmic accumulation of ODN in endosome/lysosome-like structures with a partial shift of fluorescence to the whole cytoplasm and the nucleus following an incubation of 24 hours. ODN uptake by cationic lipids into different hematopoietic cell subsets was examined by dual-color immunofluorescence analysis with subset-specific monoclonal antibodies. We found a cell type–dependent delivery of ODN with greatest uptake in monocytes and smallest uptake in T cells. CD34+ cells, B cells, and granulocytes took up ODN at an intermediate level. Uptake of ODN into isolated CD34+cells could be increased 100- to 240-fold using cationic lipids compared with application of ODN alone. Stimulation of CD34+ cells by interleukin-3 (IL-3), IL-6, and stem cell factor did not significantly improve cationic lipid-mediated ODN delivery. Sequence-specific antisense effects in clonogenic assays could be shown by transfection of bcr-abl oncogene-directed antisense ODN into primary cells of patients with chronic myelogenous leukemia using this established protocol. In conclusion, cationic lipids may be useful tools for delivery of antisense ODN into primary hematopoietic cells. These studies provide a basis for clinical protocols in the treatment of hematopoietic cells in patients with hematologic malignancies and viral diseases by antisense ODN.

Studies on the mechanism of stabilization of partially phosphorothioated oligonucleotides against nucleolytic degradation

The use of chimeric oligonucleotides (ODN), in which certain phosphodiester internucleoside linkages are replaced by phosphorothioate (PS) linkages to provide protection against degradation by nucleases, is gaining increasing attention because of their significantly decreased propensity for nonantisense effects as compared with uniformly PS-modified ODN. We have recently reported that partially PS-modified ODN, in which end- capping is used to prevent hydrolysis by exonucleases in combination with PS protection at internal pyrimidine residues which are the major sites of endonuclease degradation, are surprisingly stable in serum. The present study investigates an additional role of the backbone modification in the stabilization of ODN against nucleolytic degradation. We show that the stability of an unmodified ODN in fetal bovine serum is significantly enhanced in the presence of PS-modified ODN. The magnitude of stabilization is strongly dependent on the type and degree of backbone modification. The observed effect is stronger for PS-modified ODN than for methylphosphonate (MP)-modified ODN and increases as the number of PS linkages in the ODN increases. Thus, nuclease stability of partially PS-modified ODN is not only caused by direct prevention of nuclease attack at the phosphate center but is additionally supported by interference of the nucleases with the PS groups of ODN, resulting in decreased degradation. As the degree of many nonantisense effects caused by ODN, such as protein interactions and B cell stimulation, is dependent on the backbone modification, our results may have implications for the use of non-ODN nuclease inhibitors to reduce undesirable side effects.

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.

Liposomal targeting of bcl-2 antisense oligonucleotides with enhanced stability into human myeloma cell lines

Cationic liposomes improve the delivery of antisense oligonucleotides (ODNs) into cells. However, there is marked variability in the cellular uptake of ODNs into different cell lines. We used liposomes containing dimethyloctadecylammonium bromide (DDAB) and dioleoylphosphatidylethanolamine (DOPE) to increase the delivery of phosphodiester ODNs into four different myeloma cell lines. The delivery by cationic liposomes increased the delivery of bcl-2 antisense ODNs by a factor of 9 to 45 as compared to plain ODNs. The stability of ODNs was increased with liposomes both in the culture medium and within the cells. Intact liposomal ODNs were detected inside the cells up to 24 hours with gel electrophoresis and phosphor imager analysis. Antisense ODNs had no effect on bcl-2 mRNA levels. Also the proliferation of myeloma cells remained unchanged during the 3-day incubation period. Our study shows that liposomal antisense ODNs targeting bcl-2 of human myeloma cells result in increased stability of ODNs with minimal toxicity. However, further modifications are needed to gain biological effects of antisense ODNs on human myeloma cells.

Cellular uptake and biological effects of antisense oligodeoxynucleotide analogs targeted to herpes simplex virus

In this study, we synthesized antisense oligodeoxynucleotides (ODNs) with phosphodiester, phosphorothioate (S-ODNs), or methylphosphonate linkages complementary to the splicing acceptor site of immediate-early pre-mRNA 5 of herpes simplex virus type 1 (HSV-1). The antiviral activity of each analog on cytopathic effect in cells infected with HSV-1 or HSV-2 was assessed and compared with the cellular uptake of the analog. We found that antisense S-ODNs showed the most potent antiherpetic activity, with 50% inhibitory concentrations of 5 microM for HSV-1 and 0.25 microM for HSV-2. The antiviral effect of antisense S-ODNs was stronger and longer acting than that of acyclovir. Cell association of S-ODNs was the highest and paralleled antiviral activity. Furthermore, some fluorescein isothiocyanate (FITC)-labeled S-ODNs were recognized in the nuclei in HSV-1 infected cells by confocal laser scanning microscopy. S-ODNs located in the nucleus could access the targeted mRNA, which might be responsible for the antiviral activities. Although our study also showed non-sequence-specific activity, which implies that multiple mechanisms are involved, S-ODNs are a promising novel anti-herpetic agent.

Identification of two oligodeoxyribonucleotide binding proteins on plasma membranes of human cell lines

Two oligodeoxyribonucleotide (oligodN) binding proteins of approximately 100-110 kDa were identified in the plasma membranes of human HL-60, HepG2, H1, and KB cells by a photolabeling technique. Solubilization of cellular membranes with a nonionic detergent did not interfere with the binding of these two proteins to oligodNs, and both proteins were susceptible to serine protease action. The binding affinities of these two proteins to oligodNs were found to be similar; Scatchard plot analysis revealed the Kd for phosphodiester (PO) 21-mer oligodeoxycytidine to be 60 nM and binding sites numbered approximately 1.2 x 10(6)/cell for HepG2 cells. Both phosphorothioate (PS) and PO oligodNs could bind to these two proteins with the binding affinity for PS oligodNs being much stronger than that for PO oligodNs. The binding to oligodNs was affected by the ionic strength of the reaction. Dextran sulfate, tRNA, and double-stranded DNA inhibited the binding of oligodNs, whereas ATP, ADP, AMP, and TTP had no effect. Given their high affinity for oligodNs, these membranes proteins may play an important role in the action of oligodNs.

Herpes simplex virus-mediated activation of human immunodeficiency virus is inhibited by oligonucleoside methylphosphonates that target immediate-early mRNAs 1 and 3

IE1 and IE3 mRNAs and their protein products (IE110 and IE175, respectively) were detected in HSV-1-infected U937 cells at 4-15 hours postinfection. In transient expression assays with infectious HIV or an HIV-LTR-directed chloramphenicol acetyltransferase construction (HIV-LTRcat), HSV-1 caused HIV activation (86.7% +/- 6.4% conversion). Electrophoretic mobility shift assays with DNA sequences that encompass the LBP-1 binding site revealed increased levels of DNA-protein complex formation with nuclear extracts from HSV-1 infected as compared with uninfected U937 cells. Novel bands were not seen. HSV-1 mutants respectively deleted in IE110 (dl1403) or IE175 (d120) activated HIV as well as wild-type virus. However, HSV-1-mediated activation was inhibited (26% conversion) by simultaneous treatment with oligonucleoside methylphosphonates (ONMP) that specifically inhibit expression of IE110 (IE1TI) or IE175 (IE3TI). ONMP did not inhibit activation when used individually (83.8% and 67.8% conversion with IETI1 and IE3TI, respectively). Combinations of mutant ONMP that do not inhibit IE110 or IE175 expression did not reduce the levels of HSV-1-mediated activation. These findings suggest that HSV genes IE1 and IE3 can independently activate HIV in monocytic cells and ONMP that target HSV IE genes can be used to inhibit HIV activation.

The therapeutic potential of antisense oligonucleotides

Specific inhibition of gene expression by antisense agents provides the basis for rational drug discovery based on molecular targets. Due to the specificity of Watson-Crick base-pair hybridization, antisense oligodeoxynucleotides have been used extensively in attempts to inhibit gene expression in both in vitro and in vivo models. Analogues modified from normal phosphodiester oligodeoxynucleotides have entered clinical trials against diseases including AIDS and cancer. Although the precise mechanism of action of these drugs has not been clarified, these oligodeoxynucleotides offer considerable promise as novel molecular therapeutics. We review the recent attempts to harness the therapeutic potential of these oligodeoxynucleotides and appraise the near-term prospects for antisense technology.

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.

Inhibition of high affinity basic fibroblast growth factor binding by oligonucleotides

Oligonucleotides can be used to inhibit the binding of basic fibroblast growth factor to cells. Though standard phosphodiester oligonucleotides show a slight inhibition of binding, the oligonucleotides with phosphorothioate internucleoside linkages have inhibition levels equivalent to that of the polyanion heparin. Variations in sequence of the oligonucleotides does lead to differences in the inhibitory action of the oligonucleotides. This inhibition of basic fibroblast growth factor by phosphorothioate oligonucleotides may account for much of the published data on inhibition of various genes by proposed antisense oligonucleotides and needs to be taken into account when considering the mechanism of action of oligonucleotides in biological systems.

Inhibition of HIV-1 replication and activation of RNase L by phosphorothioate/phosphodiester 2',5'-oligoadenylate derivatives

2',5'-Oligoadenylate (2-5A) derivatives have been designed to act distal to the human immunodeficiency virus-1 (HIV-1)-induced blockade in the 2-5A synthetase/RNase L antiviral pathway. Stereochemical modification of individual internucleotide linkages of the 2-5A molecule was accomplished by phosphoramidite and phosphotriester chemical syntheses. Phosphorothioate/phosphodiester trimer and tetramer 2-5A derivatives revealed differences in the stereodynamics of activation of RNase L and inhibition of HIV-1 replication. The first and second internucleotide linkages are critical for activation of recombinant, human RNase L; A(Rp)ApA, A(Sp)ApA and ApA(Rp)A are agonists (IC50 = 2 x 10(-7), 2 x 10(-6) and 8 x 10(-6) M); ApA(Sp)A is an antagonist. The second and third internucleotide linkages are crucial for activation of murine RNase L; ApA(Rp)A, ApA(Rp)ApA, and ApApA(Rp)A are agonists (IC50 = 5 x 10(-7) M); ApA(Sp)A, ApA(Sp)ApA, and ApApA(Sp)A are antagonists. Inhibition of HIV-1-induced syncytia formation by the phosphorothioate/phosphodiester derivatives is specific for derivatives with substitution at the 2',3'-terminus. ApA(Rp)A, ApA(Sp)A, ApApA(Rp)A, and ApApA(Sp)A are potent inhibitors of HIV-1-induced syncytia formation (80-, 10-, 40-, and 15-fold more inhibitory, respectively, than solvent control). HIV-1 infection results in enhanced uptake and accumulation of ApA(Rp)A and ApA(Sp)A (7- and 10-fold, respectively). These stereochemically modified 2-5A derivatives are taken up preferentially by HIV-1-infected cells and show promise in anti-HIV-1 chemotherapy.

Inhibition of viral growth by antisense oligonucleotides directed against the IE110 and the UL30 mRNA of herpes simplex virus type-1

In the present work we elucidate that the identification of active sequences for a given target is one of the principle hurdles of antisense oligonucleotide therapeutics. A number of 100 oligonucleotides directed against different target genes of HSV-1 and different locations within those genes were screened for antiviral activity. To facilitate comparison, the same length and the same chemical modification were used for all oligonucleotides: 20mers with two phosphorothioate linkages at both the 5'- and the 3'-end. No sequence-independent effects were observed with this type of modification. Surprisingly, only six oligonucleotides did show significant antiviral activity, the most active one (#6) being directed against the translation initiation site of IE 110.

Suppression of human immunodeficiency virus type 1 activity in vitro by oligonucleotides which form intramolecular tetrads

An oligonucleotide (I100-15) composed of only deoxyguanosine and thymidine was able to inhibit human immunodeficiency virus type-1 (HIV-1) in culture assay systems. I100-15 did not block virus entry into cells but did reduce viral-specific transcripts. As assessed by NMR and polyacrylamide gel methods, I100-15 appears to form a structure in which two stacked guanosine tetrads are connected by three two-base long loops. Structure/activity experiments indicated that formation of intramolecular guanosine tetrads was necessary to achieve maximum antiviral activity. The single deoxyguanosine nucleotide present in each loop was found to be extremely important for the overall antiviral activity. The toxicity of I100-15 was determined to be well above the 50% effective dose (ED50) in culture which yielded a high therapeutic index (> 100). The addition of a cholesterol moiety to the 3' terminus of I100-15 (I100-23) reduced the ED50 value to less than 50 nM (from 0.12 microM for I100-15) and increased the duration of viral suppression to greater than 21 days (versus 7-10 days for I100-15) after removal of the drug from infected cell cultures. The favorable therapeutic index of such molecules coupled with the prolonged suppression of HIV-1, suggest that such compounds further warrant investigation as potential therapeutic agents.

Inhibition of herpes simplex virus in culture by oligonucleotides composed entirely of deoxyguanosine and thymidine

Oligodeoxynucleotides (ODNs) composed entirely of deoxyguanosine and thymidine, but not specifically designed to act as antisense agents, were able to significantly inhibit herpes simplex virus growth in acute infection assay systems. The guanosine/thymidine (GT) ODNs which demonstrated this antiviral activity contained either natural phosphodiester (PO) or phosphorothioate (PS) modified internucleoside linkages. In all experiments, the antiviral activity of the ODNs was enhanced when the backbone was modified to contain the PS linkages. When present during the time of virus addition, the ODNs were able to block the adsorption of virus to Vero cells. In this assay the PS-containing ODNs had ID50 values of approximately 0.020 microM for HSV-2 and of 0.3 microM for HSV-1. When these same PS-containing ODNs were used against HSV-2 in single-cycle viral yield assays, designed to minimize the effects due to external blockage of virus, the ID50 values rose to 0.2 microM. Analysis of viral DNA obtained 14 h post-HSV-2 infections in the single-cycle assay, revealed a decrease in replicated viral DNA in cells treated with PS-ODNs. Analysis of viral mRNA obtained 4 h post-HSV-2 infection revealed, in cells treated with the PS-ODNs, a decrease in measurable HSV-2 alpha- and beta-mRNAs. Although the mechanism of action of the antiviral activity (beyond adsorption blocking) is not fully understood, the toxicity of these compounds was low, giving high therapeutic indices for the GT-rich PS-ODNs. The good therapeutic index of GT-ODNs make this a class of compounds which warrant investigation as therapeutic agents to be used against herpes viruses.

Cationic liposomes improve stability and intracellular delivery of antisense oligonucleotides into CaSki cells

Antisense oligonucleotides (ODNs) are promising novel therapeutic agents against viral infections and cancer. However, problems with their inefficient delivery and inadequate stability have to be solved before they can be used in therapy. To circumvent these obstacles, a wide variety of improvements, including phosphorothioate ODNs and liposomes as a carrier system, have been developed. This study was designed to compare the effects of two cationic liposomes on the intracellular delivery and stability of ODNs in CaSki cell cultures. Also the stability of 3'-end phosphorothioate ODNs were investigated. The 3'-modification neither had any effect on the delivery, nor protected the ODNs against degradation. The cellular delivery and stability of ODNs was improved with both cationic liposomes, but a cationic liposomal preparations containing dimethyldioctadecylammonium bromide and dioleoylphosphatidylethanolamine (DDAB/DOPE) was more efficient than commercially available N-(1-(2,3-dioleoyloxy)propyl)-N,N,N-trimethylammoniummethylsulf ate (DOTAP). The improved cellular delivery was largely due to the stabilization of ODNs by cationic liposomes. The improved stability in the culture medium indicates that the cationic liposomes per se protect the ODNs from enzymatic degradation. Indeed, intact ODNs were found in the cytoplasm and nucleus only when delivered by cationic liposomes.

Stimulation of murine lymphocyte proliferation by a phosphorothioate oligonucleotide with antisense activity for herpes simplex virus

To investigate further the immunological properties of nucleic acids, the mitogenicity of a phosphorothioate oligonucleotide (S-oligo 1082) with antisense activity for herpes simplex virus was tested. This compound stimulated proliferation and antibody production by murine lymphocytes in in vitro cultures. Proliferation was dose-dependent and unaffected by T cell depletion. Furthermore, inclusion of a non-mitogenic DNA in the medium did not block stimulation. Since 1082 does not have homology to a known gene involved in lymphocyte activation, these observations suggest that S-oligo antisense compounds may display non-specific activating effects, at least on murine B cells.

Use of partially phosphorothioated "antisense" oligodeoxynucleotides for sequence-dependent modulation of hematopoiesis in culture

To distinguish between sequence-dependent effects and non-specific cytotoxicity of phosphorothioate antisense oligonucleotides (AS-oligos), we introduced AS-oligos blocking expression of 2Hs, the Homo sapiens cell division controller cdc2 kinase, its hematopoietically expressed homolog CHED, and the acetylcholine-hydrolyzing enzyme butyrylcholinesterase (BCHE) into primary murine bone marrow (BM) culture. Antisense oligonucleotides were fully phosphorothioated (Ts) or prepared with three phosphorothioate groups at their 3' termini (S3). Each of these oligos could cause reductions in colony counts either as a result of its sequence-dependent biological capacity or due to sequence-independent cytotoxicity. The Ts and S3 forms of the matching sense oligo, S-BCHE, served for comparison. The S3 forms of AS-2Hs, AS-BCHE, and S-BCHE caused more limited drops in colony counts than their Ts counterparts, reflecting lower cytotoxicity. When incubated with electroblotted BM proteins, Ts but not S3 oligos intensively labeled two protein bands. Moreover, 5'-end 32P-labeled (Ts) S-BCHE labeled nuclear proteins in situ in small, mitotic cells, suggesting correlation between oligo-protein interactions and the sequence-independent cytotoxicity of Ts AS-oligos. Extension of the apparently nontoxic AS-CHED by two adenosine residues at the 3' end, creating a potential for intramolecular hydrogen bond formation, resulted in increased toxicity. These findings recommend the use of nonlooped, partially phosphorothioated oligos for the modulation of hematopoiesis.

Antisense oligonucleotides as therapeutic agents--is the bullet really magical?

Because of the specificity of Watson-Crick base pairing, attempts are now being made to use oligodeoxynucleotides (oligos) in the therapy of human disease. However, for a successful outcome, the oligo must meet at least six criteria: (i) the oligos can be synthesized easily and in bulk; (ii) the oligos must be stable in vivo; (iii) the oligos must be able to enter the target cell; (iv) the oligos must be retained by the target cell; (v) the oligos must be able to interact with their cellular targets; and (vi) the oligos should not interact in a non-sequence-specific manner with other macromolecules. Phosphorothioate oligos are examples of oligos that are being considered for clinical therapeutic trials and meet some, but not all, of these criteria. The potential use of phosphorothioate oligos as inhibitors of viral replication is highlighted.

Antiviral effect of oligo(nucleoside methylphosphonates) complementary to the herpes simplex virus type 1 immediate early mRNAs 4 and 5

We have previously shown that an oligo(nucleoside methylphosphonate) (deoxynucleoside methylphosphonate residues in italics) complementary to the acceptor splice junction of herpes simplex virus type 1 (HSV-1) immediate-early (IE) pre-mRNAs 4,5 [d(TpTCCTCCTGCGG)], causes sequence-specific inhibition of virus growth in infected cell cultures (Smith et al., 1986; Kulka et al., 1989). Here we report a similar inhibition of HSV-1 growth by oligo(nucleoside methylphosphonates) complementary to the splice donor site of HSV-1 IE pre-mRNAs 4,5 [d(GpCTTACCCGTGC)] and to the translation initiation site of IE4 mRNA [d(ApATGTCGGCCAT)]. An oligomer complementary to the translation initiation site of IE5 mRNA [d(GpGCCCACGACAT)] or an unrelated oligomer [d(GpCGGGAAGGCAC)] did not inhibit virus growth. IC50 values were 20, 25 and 20 microM for d(TpTCCTCCTGCGG), d(GpCTTACCCGTGC) and d(ApATGTCGGCCAT) respectively. In infected BALB/c mice d(TpTCCTCCTGCGG) caused a significant decrease in HSV-1 growth (82% inhibition at 500 microM). A psoralen-derivative of d(TpTCCTCCTGCGG) that binds covalently to complementary sequences after exposure to 365 nm irradiation, inhibited HSV-1 growth (86-91%) at a 10-fold lower concentration than the non-derivatized oligomer. The inhibition was sequence-specific and significantly lower (27%) for HSV-2 that differs from HSV-1 in 7 of the 12 bases targeted by d(TpTCCTCCTGCGG). Virus growth was not inhibited by d(GpGCCCACGACAT). The data suggest that oligo(nucleoside methylphosphonates) may be effective antiviral agents.

Effects of sequence of thioated oligonucleotides on cultured human mammary epithelial cells

We have compared the effects of a number of different oligonucleotides on the growth and morphology of normal finite life span and immortally transformed human mammary epithelial cells. The oligonucleotide sequences chosen initially for study were based on that of the NB-1 gene, which encodes a calmodulin-like protein of unknown function. We found that certain thioated oligonucleotides 15-20 residues in length altered the morphology and decreased the growth rate of the normal cells in a concentration-dependent manner. These effects were rapid, occurring within 24-48 h of oligonucleotide addition. The effects, which occurred without an accompanying detectable decrease in the levels of NB-1 mRNA or protein, were most pronounced in the normal epithelial cells, less apparent in the immortalized epithelial cells, and unobserved in normal breast fibroblasts. Identical sequences having mixed phosphodiester and phosphorothioate backbones, or phosphodiester backbones alone, had little or no effect on normal epithelial cell morphology or growth. Two out of seven additional thioated oligonucleotides which were not complementary to NB-1 mRNA, also affected normal epithelial cell morphology and growth when used at similar concentrations (10 microM). Taken together, the observed effects on normal epithelial cells indicate that certain thioated oligonucleotides may have pharmacological consequences that do not depend on strict complementarity of their sequences to known mRNAs.

A sense phosphorothioate oligonucleotide directed to the initiation codon of transcription factor NF-kappa B p65 causes sequence-specific immune stimulation

Antisense oligonucleotides have proved effective in achieving targeted inhibition of gene expression. In such experiments, sense oligonucleotides have frequently been used as a control for nonspecific effects, but the results have been variable, raising questions about the reliability of sense oligomers as a control. It is possible that some of the effects of sense oligonucleotides may be specific. We have shown that phosphorothioate antisense oligonucleotides to the p65 subunit of NF-kappa B, a transcription factor, cause a block in cell adhesion. In our efforts to test the efficacy of NF-kappa B p65 oligonucleotides in vivo, we unexpectedly observed that the control p65-sense, but not the p65-antisense, oligonucleotides caused massive splenomegaly in mice. In the current study we demonstrate a sequence-specific stimulation of splenic cell proliferation, both in vivo and in vitro, by treatment with p65-sense oligonucleotides. Cells expanded by this treatment are primarily B-220+, sIg+ B cells. The secretion of immunoglobulins by the p65-sense oligonucleotide-treated splenocytes is also enhanced. In addition, the p65-sense-treated splenocytes, but not several other cell lines, showed an upregulation of NF-kappa B-like activity in the nuclear extracts, an effect not dependent on new protein or RNA synthesis. These results demonstrate that phosphorothioate oligonucleotides can exert sequence-specific effects in vivo, irrespective of sense or antisense orientation.

Oligonucleotides as therapeutic agents

Oligodeoxynucleotides can act as antisense complements to target sequences of mRNAs to selectively regulate gene expression. Chemically modified analogs that are nuclease-resistant enable this antisense strategy to be utilized in practice. Studies with oligodeoxynucleotide analogs in cell free systems, and their cellular uptake will be described. Certain analogs have been found to regulate viral and cellular gene expression. However, some also inhibit in a non-specific manner, that may be traced to their selective inhibition of viral and cellular polymerases. A chemically modified oligodeoxynucleotide analog can be regarded as an informational drug.

Antisense technology

During the past 12 months, significant advances have been reported in the medicinal chemistry, and the pharmacodynamic and pharmacokinetic characterization of oligonucleotides. Advances in medicinal chemistry suggest that the scope for additional modifications as a means of developing therapeutic agents is substantial. This is confirmed by our clearer understanding of the pharmacodynamic and pharmacokinetic properties of oligonucleotides and the increasing number of molecular targets against which they have been shown to be active.