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PubMed1984

Cleavage of phosphorothioate-substituted DNA by restriction endonucleases.

M13 RF DNA was synthesized in vitro in the presence of various single deoxynucleoside 5'-O-(1-thiotriphosphate) phosphorothioate analogues, and the three other appropriate deoxynucleoside triphosphates using a M13 (+)-single-stranded template, Escherichia coli DNA polymerase I and T4 DNA ligase. The resulting DNAs contained various restriction endonuclease recognition sequences which had been modified at their cleavage points in the (-)-strand by phosphorothioate substitution. The behavior of the restriction enzymes AvaI, BamHI, EcoRI, HindIII, and SalI towards these substituted DNAs was investigated. EcoRI, BamHI, and HindIII were found to cleave appropriate phosphorothioate-substituted DNA at a reduced rate compared to normal M13 RF DNA, and by a two-step process in which all of the DNA is converted to an isolable intermediate nicked molecule containing a specific discontinuity at the respective recognition site presumably in the (+)-strand. By contrast, SalI cleaved substituted DNA effectively without the intermediacy of a nicked form. AvaI, however, is only capable of cleaving the unsubstituted (+)-strand in appropriately modified DNA.

Bacteriophage phi X 174↗
PubMed1995

Phosphorothioate BCR-ABL antisense oligonucleotides induce cell death, but fail to reduce cellular bcr-abl protein levels.

The bcr-abl oncogene is a fusion gene resulting from a reciprocal translocation which forms the hallmark of chronic myeloid leukemia (CML). Antisense oligonucleotides complementary to the two possible mRNA breakpoints were found to inhibit cell growth of CML patient cells and cell lines, but doubt exists about their specificity. In order to test the specificity, phosphorothioate and 3' phosphorothioate capped antisense BCR-ABL oligonucleotides of different length were used. Stability, cellular uptake of oligonucleotides and effect on cell growth were studied in two CML cell lines, BV173 and LAMA-84. Phosphorothioate antisense BCR-ABL oligonucleotides were most stable, showed the highest uptake and induced cell death in BV173 but not in LAMA-84 cells. We selected the most effective antisense oligonucleotide for further analysis. The BV173 and LAMA-84 cell lines do not express the normal c-abl protein, we therefore used a c-abl specific monoclonal antibody for the detection of p210bcr-abl expression by flow cytometry. Dead cells found after treatment were gated out of analysis. Although BCR-ABL antisense oligonucleotides can induce apoptosis, no reduction of p210bcr-abl levels could be detected in living cells after treatment with antisense oligonucleotides. We conclude that antisense mediated inhibition of translation of mRNA into p210bcr-abl is not the mechanism responsible for the induction of apoptosis in cell line BV173.

Apoptosis↗
PubMed1993

Cellular pharmacology of phosphorothioate homooligodeoxynucleotides in human cells.

The uptake and distribution of phosphorothioate oligodeoxynucleotides by human cells were studied using 35S-labeled 28-mer phosphorothioate oligodeoxycytidine [S-(dC)28]. Accumulation of intracellular S-(dC)28 was found to be higher in the carcinoma cells (grown in monolayers) than in the leukemia cells (grown in suspension culture). A hepatoma cell line transfected with hepatitis B virus, 2215, was chosen for further studies. The uptake of S-(dC)28 was partially dependent on temperature and energy. The intracellular concentration was significantly higher than that in the medium and the amount accumulated was dependent on the extracellular concentration. It appears that the uptake of S-(dC)28 involves mechanisms of both fluid-phase pinocytosis and adsorptive endocytosis. Neither oligonucleotides nor 5'-phosphorylated nucleotides inhibited S-(dC)28 uptake. Unlike horseradish peroxidase, which was primarily associated with endosomes once it was taken into the cell, S-(dC)28 was found to be present in both nuclear and cytoplasmic fractions. Efflux of S-(dC)28 from the cell was multiphasic; a trapping mechanism that could be due to a potent interaction of S-(dC)28 with cellular proteins was implicated. This trapping mechanism could be responsible for the lack of biological activity such as cytotoxicity and antisense activity of phosphorothioate oligodeoxynucleotides in some human cells.

Carcinoma↗
PubMed1996

Pharmacokinetics and tissue disposition of a chimeric oligodeoxynucleoside phosphorothioate in rats after intravenous administration.

Antisense oligonucleotides represent a novel therapeutic principle for designing drugs against various diseases. Oligonucleotides can be chemically modified to improve their pharmacokinetics and in vivo stability, and it is important to understand the effect of these modifications. In the present study, the pharmacokinetics of a 25-mer phosphorothioate oligonucleotide containing four contiguous, internucleotide, methylphosphonate linkages at the 3'- and 5'-ends (chimeric oligonucleotide) were determined in rats after i.v. administration of the 35S-labeled oligonucleotide at a dose of 30 mg/kg. Plasma disappearance of the oligonucleotide could be described by a two-compartment model, with half-lives of 0.38 and 52.9 hr. The intact chimeric oligonucleotide was detected in plasma up to 6 hr after dosing. Urinary excretion represented the major elimination pathway, with approximately 21% of the administered dose being excreted within 24 hr and 35% being excreted over a 240-hr period after dosing. The majority of the radioactivity in urine was associated with the intact oligonucleotide within 6 hr after dosing and with increasing degradation products thereafter. Fecal excretion was a minor elimination pathway. The oligonucleotide was widely distributed in tissues, with the majority of the radioactivity in most tissues being intact up to 48 hr after dosing. Compared with oligodeoxynucleotide phosphorothioates, the chimeric oligonucleotide was significantly more stable in vivo. The presence of intact oligonucleotide in plasma and tissues even 12 hr after dosing is a significant advantage over an "all"-phosphorothioate analog. Thus, the chimeric oligonucleotide could provide a longer duration of action as an antisense agent after its administration.

Animals↗
PubMed1995

Synthesis of alpha-anomeric homopyrimidine oligo DNA phosphorothioates and their physicochemical and biochemical properties.

alpha-Anomeric 2'-deoxycytidine and thymidine were synthesized in a stereospecific manner. With these nucleosides, pyrimidine homooligomers having either exclusively phosphodiester or phosphorothioate linkages were prepared using phosphoramidite method. All tested alpha-DNA.RNA complex was found to be inert toward the action of RNase H, even when phosphorothioate analogs were used as the DNA component. Among the alpha-anomeric homooligomers, alpha-oligocytidilate phosphorothioate exhibited potent inhibitory effect towards the action of RNase H on a DNA.RNA complex.

Antiviral Agents↗
PubMed1997

[HPLC of oligodeoxyribonucleoside phosphorothioates ].

Conditions are described for the separation of synthetic oligodeoxyribonucleoside phosphorothioates by HPLC using a SCOUT WP PEI weak anion exchanger and for the separation of oligodeoxyribonucleotides with mixed phosphate and phosphorothioate internucleotide bonds on a Partisphere C18 support in ion-pair conditions. The influence of the nucleoside composition and the number of phosphorothioate bonds on the retention time was studied.

Chromatography, High Pressure Liquid↗
PubMed2003

Antisense phosphorothioate oligodeoxyribonucleotide targeted against ICAM-1: synthetic and biological characterization of a process-related impurity formed during oligonucleotide synthesis.

A phosphorothioate-linked oligonucleotide bearing a 3'-terminal phosphorothioate monoester has been synthesized and characterized. This oligonucleotide has been identified as a process-related impurity formed during synthesis of ISIS 2302. Biological properties of the compound have been determined. Based on these data, it can be concluded that this species (3'-TPT) has biological properties similar to parent drug.

Animals↗
PubMed1997

Inhibition of coagulation by a phosphorothioate oligonucleotide.

In the development of antisense therapeutics, there have been a number of hybridization-independent effects characterized for phosphorothioate oligodeoxynucleotides. One such effect is the transient prolongation of clotting times following intravenous infusion of high doses. In this study, inhibition of clotting times was characterized by determining the time course of both APTT and plasma oligonucleotide following intravenous infusion of ISIS 2302 in cynomolgus monkeys. Prolongation of APTT was also achieved by addition of ISIS 2302 to citrated blood from untreated monkeys, allowing the investigation of the mechanism of inhibition in vitro. Results from this study clearly indicate that the intrinsic pathway (APTT) was more sensitive to inhibition than the extrinsic pathway (PT). The prolongation of APTT was also shown to be transient and closely correlated with plasma oligonucleotide concentrations. The extent of APTT prolongation can be controlled by minimizing peak plasma oligonucleotide concentrations through lowering the dose or prolonging infusion duration. Direct addition of ISIS 2302 to blood produced quantitatively similar inhibition of clotting times. This effect was similar for a number of different phosphorothioate oligodeoxynucleotides, but oligonucleotides containing phosphodiester linkages and 2'-propoxy linkages were much less inhibitory. Additional in vitro studies indicated that the mechanism of inhibition was independent of that of heparin and possibly involved selective inhibition of the intrinsic pathway as well as the common clotting pathway. Investigation of selective clotting factors indicated that there was no direct inhibition of the enzymatic activity of factor Xa, XIa, or thrombin using chromogenic substrates. However, ISIS 2302 did produce a concentration-dependent increase in clotting time when fibrinogen was used as the substrate for thrombin.

Animals↗
PubMed2002

Assessment of the genotoxic potential of ISIS 2302: a phosphorothioate oligodeoxynucleotide.

ISIS 2302, a phosphorothioate oligodeoxynucleotide with antisense activity against human ICAM-1 mRNA, was evaluated in a battery of tests to assess genotoxic potential. There was no evidence of genotoxicity in three in vitro studies performed: (i) a bacterial reverse mutation test; (ii) a chromosomal aberration test in Chinese hamster ovary cells; (iii) a mammalian cell gene mutation assay in L5187Y cells. Additionally, there was no in vivo evidence of genetic toxicity in a bone marrow micronucleus study in male and female mice. For all tests, top concentrations or doses assessed met harmonized regulatory guidelines. The cellular uptake of ISIS 2302 into target cells was confirmed using capillary gel electrophoresis and immunohistochemistry. Intracellular uptake into CHO cells, L5187Y cells, Salmonella typhimurium TA98 and bone marrow was concentration- and time-dependent. Consistent with what is known about the physical and chemical properties of phosphorothioate oligodeoxynucleotides, there was no evidence of genotoxicity in any of the assessed end-points. Furthermore, the absence of genotoxicity could not be ascribed to test system insensitivity or to an absence of exposure of the test system to ISIS 2302.

Animals↗
PubMed2004

[Determination of antisense phosphorothioate oligonucleotide drug Cantide by capillary gel electrophoresis].

Cantide is a 20-mer antisense phosphorothioate oligonucleotide that inhibits telomerase catalytic subunit hTERT. A capillary gel electrophoresis (CGE) method with internal standard was used for the determination of Cantide. Cantide and the phosphorothioate internal standard were prepared on a solid-phase DNA synthesizer and purified by preparative strong anion-exchange chromatography and reversed-phase high performance liquid chromatography. Cantide and the internal standard had approximately equal percentage of base composition. Cantide was determined with capillary electrophoresis instrument and ssDNA kit. The size of the capillary column was 31 cm x 100 microm i.d. with an effective length of 20 cm. Samples were electrokinetically injected using -10 kV voltage for a duration of 1 s. The column temperature and sample storage temperature was 40 degrees C and 30 degrees C, respectively. The detection wavelength was 254 nm. The running buffer was a mixture of 7 mol/L urea-tris-boric acid (pH 8.5). The calibration curve was linear in the range of 12.5-800 mg/L with correlation coefficient of 0.99997. The limit of detection of Cantide was 0.220 mg/L. Intra-day and inter-day relative standard deviations (RSDs) for Cantide were 0.449%-1.89%, and 1.01%-1.48%, respectively. The average recovery was 96.95% with RSD of 6.88%. The assay validation study and the characterization of CGE revealed that the method can be used in quantitative analysis of Cantide for pharmacokinetic characterization, and the results are accurate and reproducible.

Chromatography, High Pressure Liquid↗
PubMed1997

Activation of the alternative pathway of complement by a phosphorothioate oligonucleotide: potential mechanism of action.

Intravenous infusion of high doses of phosphorothioate oligonucleotides in monkeys has been associated with transient alterations in hematologic and hemodynamic parameters, which appear to be secondary to complement activation. ISIS 2302, a phosphorothioate oligonucleotide specific for human intracellular adhesion molecule-1, was used to further characterize complement activation in monkeys. Complement activation occurred selectively through the alternative pathway resulting in increased plasma concentrations of the complement split products Bb, C3a and C5a. Marked fluctuations in circulating neutrophil counts and reductions in cardiac output were closely associated with peak production of anaphylatoxins C3a and C5a. Changing both dose and infusion duration revealed that complement activation is related to plasma levels of oligonucleotide, and that there is a minimum threshold concentration of approximately 50 micrograms/ml of ISIS 2302 that is required to activate complement. Dose regimens in which plasma concentrations do not exceed this threshold do not result in complement activation. Further investigation reveals that plasma concentrations of a key regulatory component of the alternative pathway, Factor H, were also decreased after administration of ISIS 2302. Decreases in Factor H levels are suggestive of a possible mechanism of complement activation. Direct interaction between ISIS 2302 and Factor H was demonstrated in a competition assay, where increasing concentrations of ISIS 2302 eluted Factor H from a heparin-sepharose column. These data demonstrate a clear correlation between plasma oligonucleotide concentrations and complement activation. Interactions between ISIS 2302 and Factor H may lead to activation of the alternative complement pathway.

Animals↗
PubMed1999

Inhibition of heparanase activity and tumor metastasis by laminarin sulfate and synthetic phosphorothioate oligodeoxynucleotides.

Heparanase activity correlates with the metastatic potential of tumor cells. Moreover, the anti-metastatic effect of non-anti-coagulant species of heparin and certain sulfated polysaccharides was attributed to their heparanase-inhibiting activity. We investigated the effect of a chemically sulfated polysaccharide (laminarin), consisting primarily of beta-1,3 glucan (sodium laminarin), and of synthetic phosphorothioate oligodeoxynucleotides, primarily phosphorothioate homopolymer of cytidine (SdC28), on heparanase activity and tumor metastasis. Investigation of the ability of tumor cells to degrade heparan sulfate in intact extracellular matrix revealed that heparanase activity expressed by B16-BL6 mouse melanoma cells and 13762 MAT rat mammary adenocarcinoma cells was effectively inhibited by LS (50% inhibition at 0.2-1 microgram/ml), but there was no inhibition by sodium laminarin up to a concentration of 50 microgram/ml. Complete inhibition of the melanoma heparanase was obtained in the presence of 0.1 microM SdC28. A single i.p. injection of laminarin sulfate, but not of sodium laminarin, before i.v. inoculation of the melanoma or breast-carcinoma cells inhibited the extent of lung colonization by the tumor cells by 80 to 90%. Similar inhibition was exerted by 0.1 microM SdC28. At the effective concentrations, both compounds had a small effect on proliferation of the tumor cells and on growth of the primary tumors in vivo. These results further emphasize the involvement of heparanase in tumor metastasis and the potential clinical application of diverse heparanase-inhibiting molecules such as sulfated polysaccharides and synthetic polyanionic molecules.

Animals↗
PubMed2006

The first automated synthesis of ferrocene-labelled phosphorothioate DNA probe: a new potential tool for the fabrication of DNA microarrays.

We report the synthesis and the characterisation of the first electroactive ferrocene-labelled oligonucleotide phosphorothioate (ODN-Fc-Ps) probe obtained by automated synthesis. The grafting of ODN-Fc-Ps probe on gold electrode resulted in the appearance of the ferrocene redox couple in cyclic voltammetry confirming the effectiveness of the ODN grafting. The electrochemical response of the modified electrode was analysed in aqueous media before and after hybridisation with ODN target. The hybridisation with ODN target induces a large conformational change in the surface-confined DNA structure monitored by cyclic voltammetry of the ferrocene marker which confirms the potential of ferrocene-labelled oligonucleotide phosphorothioate to develop electrochemical DNA chips.

DNA↗
PubMed2004

Effect of phosphorothioate chirality on the grooves of DNA double helices: a molecular dynamics study.

Phosphorothioate oligonucleotides (PS-ODNs) have gained considerable attention in drug therapy, primarily as potent antisense or antigene oligomers, which bind to specific DNA or mRNA sequences and lead to transcriptional or translational arrest. These are obtained by substituting one of the anionic oxygen of the phosphate group by a sulfur atom, which introduces chirality to the phosphorus atom of the DNA backbone. In this molecular dynamics simulation study, structural parameters like groove widths, environmental parameters like hydration or cation binding, and electrostatic energy surfaces of both the chiral forms of DNA/PS-DNA duplexes were assessed and compared with that of a normal DNA. Results indicate that, PS-S form with its sulfur atoms facing the minor groove has a widened minor groove, while the scenario is reverse for the PS-R form. Further analysis reveals the existence of several factors like large van der Waals radius of sulfur and the effect it has on its neighboring hydration pattern along with the net electrostatic environment, influencing such structural alterations. This also indicates, for the first time, the effect of absolute phosphorothioate chirality on the global structure of a DNA/PS-DNA hybrid that otherwise resembles a regular B-DNA structure.

Binding Sites↗
PubMed2006

Phosphorothioate analogues of alkyl lysophosphatidic acid as LPA3 receptor-selective agonists.

The metabolically stabilized LPA analogue 1-oleoyl-2-O-methyl-rac-glycerophosphorothioate (OMPT) was recently shown to be a potent subtype-selective agonist for LPA3, a G-protein-coupled receptor (GPCR) in the endothelial differentiation gene (EDG) family. Further stabilization was achieved by replacing the sn-1 O-acyl group with an O-alkyl ether. A new synthetic route for the enantiospecific synthesis of the resulting alkyl LPA phosphorothioate analogues is described. The pharmacological properties of the alkyl OMPT analogues were characterized for subtype-specific agonist activity using Ca2+-mobilization assays in RH7777 cells expressing the individual EDG family LPA receptors. Alkyl OMPT analogues induced cell migration in cancer cells mediated through LPA1. Alkyl OMPT analogues also activated Ca2+ release through LPA2 activation but with less potency than sn-1-oleoyl LPA. In contrast, alkyl OMPT analogues were potent LPA3 agonists. The alkyl OMPTs 1 and 3 induced cell proliferation at submicromolar concentrations in 10T 1/2 fibroblasts. Interestingly, the absolute configuration of the sn-2 methoxy group of the alkyl OMPT analogues was not recognized by any of the LPA receptors in the EDG family. By using a reporter gene assay for the LPA-activated nuclear transcription factor PPARgamma, we demonstrated that phosphorothioate diesters have agonist activity that is independent of their ligand properties at the LPA-activated GPCRs. The availability of new alkyl LPA analogues expands the scope of structure-activity studies and will further refine the molecular nature of ligand-receptor interactions for this class of GPCRs.

Animals↗
PubMed1998

Biodistribution, stability, and antiviral efficacy of liposome-entrapped phosphorothioate antisense oligodeoxynucleotides in ducks for the treatment of chronic duck hepatitis B virus infection.

This study investigated the feasibility of using liposomes to increase the hepatic delivery and antiviral efficacy of phosphorothioate antisense oligodeoxynucleotides (PS-ODN) for the in vivo treatment of hepatitis B virus (HBV) infection. Ducks infected with duck hepatitis B virus (DHBV) were used as the model. We studied the stability of an antisense PS-ODN in duck plasma, its integrity during the process of liposome entrapment, its in vivo biodistribution, plasma clearance, and excretion. In addition, the intrahepatic distribution of a labeled free and liposome-entrapped ODN was also investigated. The results of our studies show that: 1) phosphorothioate ODN remain stable during the process of liposome entrapment; 2) are stable in duck plasma for many hours; 3) are rapidly cleared from the plasma when injected intravenously; 4) intravenous injection of antisense ODNs entrapped within liposomes enhances delivery of the ODN to the liver; and 5) inhibit DHBV replication. Serum DHBV DNA levels fell rapidly, with a corresponding decrease in intrahepatic viral replicative intermediates at the end of the 5-day study period. Although inhibition of viral replication and a fall in the target protein was observed, a marked inhibition of viral replication was also observed with high doses of a random-sequence ODN. Thus, it is not certain that inhibition of viral replication was entirely through an antisense mechanism. Therefore, liposomes may be effective vehicles to improve the delivery of antisense oligonucleotides to the liver for the therapy of hepatotropic viruses.

Animals↗
PubMed2005

Peroxide-mediated desulfurization of phosphorothioate oligonucleotides and its prevention.

Desulfurization at the internucleotide phosphorothioate linkage of antisense oligonucleotides (ASOs) in dermatological formulations has been investigated using strong ion exchange chromatography and mass spectroscopy. The formation of phosphate diester linkages appeared to arise from a reaction between the phosphorothioate oligonucleotide and a potent oxidizing agent. Screening of excipients used in the formulation indicated that the cause of desulfurization was related to the presence of polyethylene glycol-derived nonionic surfactants MYRJ 52 or BRIJ 58. Autoxidation of the polyethylene glycol chain is suggested as the probable origin for the observed incompatibility. The ability of various antioxidants to prevent oxidative degradation of ASO-1 in simple test systems and in oil-in-water emulsions is described. It is found that in test systems both lipophilic and hydrophilic antioxidants are effective. However, in cream formulation (oil-in-water emulsions) of ASO-1 the addition of hydrophilic antioxidants L-cysteine or DL-alpha-lipoic acid has been shown to be superior in protecting the oligonucleotide from desulfurization upon storage.

Antioxidants↗
PubMed1994

Lipid membrane permeability of 2'-modified derivatives of phosphorothioate oligonucleotides.

Antisense oligonucleotides have the ability to inhibit gene expression in viral infections, malignancy, and other diseases. Even though much work has been accomplished with oligonucleotides demonstrating in vitro therapeutic effects, little work has been done to address how these molecules gain access to the cell. One of the plausible means of entrance could be through passive diffusion of the oligonucleotides through the cellular lipid bilayer. To enhance membrane permeability of oligonucleotides lipophilic moieties at the 2' position of the ribose ring have been added. To evaluate the effect of this modification, a liposome system was used. The oligonucleotides evaluated were a series composed of poly A 10mers phosphorothioates labeled at the 5' end with fluorescein and modified at the 2' position of the ribose ring with lipophilic alkyl chains ranging from methyl to nonyl. Efflux studies were accomplished by monitoring the appearance of the oligonucleotide in the incubation medium. There were modest but significant differences between the efflux half-life times of the 2'-modified compounds and the control compound. The values ranged from approximately 6 days for the control, unmodified compound to 4.6 days for the propyl modification. The nonyl derivative had a longer efflux half-life time (8.3 days) compared with the control, unmodified phosphorothioate oligonucleotide.

Chemical Phenomena↗