WO1994025037A1 - Anti-viral guanosine-rich oligonucleotides - Google Patents
Anti-viral guanosine-rich oligonucleotides Download PDFInfo
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- WO1994025037A1 WO1994025037A1 PCT/US1994/004529 US9404529W WO9425037A1 WO 1994025037 A1 WO1994025037 A1 WO 1994025037A1 US 9404529 W US9404529 W US 9404529W WO 9425037 A1 WO9425037 A1 WO 9425037A1
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Definitions
- the present invention relates generally to the field of oligonucleotide chemistry and anti-viral pharmacotherapy. More specifically, the present invention relates to novel guanosine-rich oligonucleotides and their use as novel anti- viral agents.
- a method of treating a pathophysiological state caused by a virus comprising the step of administering a pharmacological dose of an oligonucleotide, said dose being sufficient to inhibit production of said virus, wherein said oligonucleotide contains a high percentage of guanosine bases.
- the oligonucleotide has a three dimensional structure and this structure is stabilized by guanosine tetrads.
- the oligonucleotide has two or more runs of two contiguous deoxy guanosines.
- a method of treating a pathophysiological state caused by a herpes simplex virus comprising the step of administering a pharmacological dose of an oligonucleotide, said dose being sufficient to inhibit the replication of said virus, wherein said oligonucleotide contains a high percentage of guanosine bases.
- the oligonucleotide has a three dimensional structure and this structure is stabilized by guanosine tetrads.
- the oligonucleotide has two or more runs of two contiguous deoxyguanosines.
- a method of treating a pathophysiological state caused by human immunodeficiency viruses comprising the step of administering a pharmacological dose of an oligonucleotide, said dose being sufficient to inhibit the replication of said virus, wherein said oligonucleotide contains a high percentage of guanosine bases.
- the oligonucleotide has a three dimensional structure and this structure is stabilized by guanosine tetrads.
- the oligonucleotide has two or more runs of two contiguous deoxyguanosines.
- a method of treating a pathophysiological state caused by human papilloma virus comprising the step of administering a pharmacological dose of an oligonucleotide, said dose being sufficient to inhibit the replication of said virus, wherein said oligonucleotide contains a high percentage of guanosine bases.
- the oligonucleotide has a three dimensional structure and this structure is stabilized by guanosine tetrads.
- the oligonucleotide has two or more runs of two contiguous deoxyguanosines.
- a method of treating a pathophysiological state caused by human cytomegalovirus comprising the step of administering a pharmacological dose of an oligonucleotide, said dose being sufficient to inhibit the replication of said virus, wherein said oligonucleotide contains a high percentage of guanosine bases.
- the oligonucleotide has a three dimensional structure and this structure is stabilized by guanosine tetrads.
- the oligonucleotide has two or more runs of two contiguous deoxyguanosines.
- a method of treating a pathophysiological state caused by adenovirus comprising the step of administering a pharmacological dose of a oligonucleotide, said dose being sufficient to inhibit the replication of said virus, wherein said oligonucleotide contains a high percentage of guanosine bases.
- the oligonucleotide has a three dimensional structure and this structure is stabilized by guanosine tetrads.
- the oligonucleotide has two or more runs of two contiguous deoxyguanosines.
- a method of treating a pathophysiological state caused by hepatitis B virus comprising the step of administering a pharmacological dose of a oligonucleotide, said dose being sufficient to inhibit the replication of said virus, wherein said oligonucleotide contains a high percentage of guanosine bases.
- the oligonucleotide has a three dimensional structure and this structure is stabilized by guanosine tetrads.
- the oligonucleotide has two or more runs of two contiguous deoxyguanosines.
- a guanosine-rich oligonucleotide having a three dimensional structure, wherein the three dimensional structure is stabilized by guanosine tetrads or at least two runs of two contiguous deoxyguanosines and wherein these oligonucleotides exhibit anti-viral activity.
- the oligonucleotides of the present invention have partially or fully phosphorothioated internucleoside linkages (backbones) or other chemical modifications.
- the oligonucleotides of the present invention have chemically modified or unnatural (synthetic) bases.
- Figure 1A shows a 1973 base pair Hind III to Eco R1 sub fragment of the Friend Murine Leukemia Virus (FMLV) clone 57 genome.
- Figure 1B shows a 172 base pair (Hind III to Stu I) fragment which is an expanded portion of the 1973 base pair fragment. Within this fragment is the purine rich target to which triple helix forming oligonucleotides are directed.
- Figure 1C shows the entire Hind III/Eco R1 FMLV fragment cloned into the pT7-2 plasmid (United States Biochemical Corporation) yielding p275A. In this recombinant the Hind III site is 10 base pairs downstream of the T7 mRNA start site.
- the 5' portion of the triple helix target region is 63 base pairs downstream of the mRNA start and the Dde I site is 131 base pairs downstream of the mRNA start site.
- Figure 1D shows the Hind III/Eco R1 FMLV fragment was cloned into pBS (Stratagene) yielding pBSFMLV.
- the Hind III site, triple helix target site and Dde I site are respectively 50, 103 and 171 base pairs downstream from the mRNA start site.
- Figure 2 shows that G-Rich phosphorothioated-oligonucleotides induced reduction in HSV-2 viral titer.
- the filled square (B 106-62) represents a single concentration point (20 ⁇ M) for this oligonucleotide.
- B 106-96 is the fully phosphorothioated version of B106-62.
- B106-97 is the fully phosphorothioated version of B106-71.
- ACV (4a and 4b) is acyclovir tested against two different stock concentrations of HSV-2 strain HG52.
- the cells were rinsed with a pH 3 buffer in order to remove all virus not yet internalized (96p3 and 97p3).
- Figure 3 shows that the MT-2 cells infected with 0.01 m.o.i. of HIV-1 were treated with various concentrations of oligonucleotide or AZT or ddC.
- the data represents the number of viable cells remaining in the culture dish, i.e., not undergoing virus induced cytopathic effects (CPE).
- CPE virus induced cytopathic effects
- Figure 4 shows the culture media taken from NIH3T3 cells chronically infected with FMLV was mixed with various concentrations of I100-51 or I100-12 (fully phosphorothioate version of I100-00). The mixtures were then assayed for the presence of viral reverse transcriptase. The data is presented as a percent of measurable reverse transcriptase in culture medium not treated with oligonucleotide.
- Figures 5A, 5B and 5C show the radio-labelled ( 32 P) full-length or truncated mRNA transcripts were analyzed by polyacrylamide gel electrophoresis, and then quantitated by cutting out the specific transcript and measuring the radioactivity in a scintillation counter.
- Figure 5A shows that the reduction in full length transcripts directed by the T7 and T3 promoter when 1100-51 (anti-parallel triple helix forming oligonucleotide; FMLV2ap) was added. Samples in which no oligonucleotide was added were counted and used as 100% transcription reference points.
- Figure 6 shows inhibition of HIV-1 induced syncytia formation four days post-infection.
- SUP T1 cells were infected with HIV-1 DV for four hours and then treated with various concentrations of oligonucleotides.
- Four days post-infection cells were scored for syncytia formation. All assays were performed in quadruplicate and the average values used to plot this graph. The legend to the right of the graph indicates the symbol used for each oligonucleotide tested.
- Figure 7 shows continued suppression of HIV-1 p24 production seven days post removal of oligonucleotide.
- Four days post-infection with HIV-1 DV the media from infected cells treated with oligonucleotides (2.5 ⁇ M) was removed and replaced with fresh media without oligonucleotide.
- the presence of viral p24 antigen was then assayed 7 and 11-days post infection. All samples were assayed in quadruplicate and the average values used to plot this graph.
- the legend to the right of the graph indicates the symbol used for each oligonucleotide tested.
- Figure 8 shows a Dixon Plot of random oligonucleotide 1232 (SEQ. ID. NO.
- the inhibition constant K i was determined by simultaneously varying dNTP (without dATP) concentrations at the same time as inhibitor (oligonucleotide 1232). The K i determination was performed at 0.125 mM,
- HIV-RT 0.25 mM and 0.5 mM dNTP concentrations with constant Primer-Template concentration of 0.2 pM. HIV-RT was used at 1 unit in each reaction. The reported values are the result of simultaneous independent duplicates determinations.
- Figure 9A reveals PBMCs derived from HIV-1 positive patients were mixed with HIV-1 negative PBMCs in culture medium containing drug. On day 7 the cocultures were washed and resuspended in fresh medium containing drug. The p24 levels in medium collected on day 7 (before medium change) and day 10 were assayed for p24.
- Figure 5B HIV-1 negative PBMCs from two different donors were infected with HIV-1 DV and then incubated in the presence of drug for 10 days at which time the culture medium was assayed for the presence of p24 antigen.
- Figures 10A and 10B show inhibition of binding of V3 loop specific Mabs to HIV-1 gp120 by phosphorothioate containing oligonucleotides.
- Matched sequence oligonucleotides with either phosphodiester (PD) or phosphorothioate (PT) backbones were assayed for their ability to inhibit the interaction of V3 loop specific Mabs with the gp120 molecule: SEQ. ID. NOs. 31 (1173) and 32 (1174); SEQ ID. NOs. 24 (I100-07) and 39 (I100-21); or SEQ. ID. NOs. 42 (1229) and 43 (1230).
- immobilized gp120 was preincubated with oligonucleotides before washing and the addition of Mab
- Figure 11 shows a schematic diagram of the HIV-1 genome not drawn to scale.
- Figure 12 shows analysis of DNA (PCR) and RNA (RT-PCR) extracted from SUP Tl cells three days post-infection with HIV-1.
- PCR analysis of HIV-1 infected drug treated SUP Tl cell DNA used 0.1 ⁇ g of total extracted DNA for each reaction.
- either AZT, at 0.3 ⁇ M which is 10 fold over the ED 50 value (lane 1) or I100-15 at 5.0 (lane 2) or 0.3 ⁇ M (lane 3) were added to SUP Tl cells at the same time as HIV-1.
- Lanes 4 (AZT), 5 (5.0 ⁇ M I100-15) and 6(0.3 ⁇ M I100-15) are the results of DNA samples obtained from cells in which drug was added 8 hours post-infection.
- Lanes 8 to 10 contain 10, 100 or 1000 ng of DNA extracted from HIV-1 infected control SUP T1 cells.
- the band corresponding to 220 bp is the predicted size of the internal ⁇ -actin control and the 200 bp fragment is the predicted size for the amplified portion of the HIV-1 genome.
- the right panel contains RT-PCR analysis of extracted RNA (1 ⁇ g/reaction) obtained from cells treated in an identical fashion as those described in lanes 1-6 of the left panel.
- Lanes 7 and 8 are control HIV-1 infected cell mRNA and lanes 9 and
- Figure 13 shows the results of three oligonucleotides (10 -5 M) incubated with increasing concentrations (0,7.5,15,30,60 and 120 mM) of KCl (lanes 1-6 for I100-15, 7-12 for I100-18 and 13-18 for Z106-50).
- the nucleotide markers are poly dT.
- Figures 14A and 14B show a line model and space filling model for I100-15.
- a line model (14A) of I100-15 folded into an intramolecular tetrad of the Oxytricha class is depicted.
- the 5'-end of the molecule is in the bottom left hand side.
- the bases (Gs) are stacked on top of each other with the 4 bases in each plane stabilized through their hydrogen bonding with each other and their interaction with the K + ion complex in the center of the tetrad.
- the space filling model (14B) also has the 5' bases in the lower left hand corner.
- the lighter colored atoms are part of the G-tetrad and the darker shaded atoms are part of the loop structures.
- the K + ion is buried within the tetrad.
- Figure 15 displays a KCl titration.
- oligonucleotide as used herein is defined as a molecule comprised of two or more deoxyribonucleotides or ribonucleotides, preferably more than ten. Its exact size will depend on many factors including the specificity and anti- viral activity of the oligonucleotide for various viruses.
- bases can refer to unnatural (synthetic) bases used in place of an A, C, T or G.
- bases herein, the term includes both the deoxyribonucleic acids and ribonucleic acids.
- A refers to adenine as well as to its deoxyribose derivative
- T refers to thymine
- U refers to uridine
- G refers to guanine as well as its deoxyribose derivative
- C refers to cytosine as well as its deoxyribose derivative.
- bases can refer to unnatural (synthetic) bases used in place of an A, C, T, or G.
- inhibitory dose or therapeutic dose of the compounds in the present invention may be determined by assessing the effects of the oligonucleotide on viral replication in tissue culture or viral growth in an animal. The amount of oligonucleotide administered in a therapeutic dose is dependent upon the age, weight, kind of concurrent treatment and nature of the viral condition being treated.
- pharmacological dose refers to the dose of an oligonucleotide which causes a pharmacological effect when given to an animal or human.
- the pharmacological dose introduced into the animal or human to be treated will provide a sufficient quantity of oligonucleotide to provide a specific effect, e.g., (1) inhibition of viral protein or enzymes, (2) inhibition of viral-specific replication, (3) preventing the target site from functioning or (4) damaging the duplex DNA at the specific site or (5) ablating the DNA at the site or (6) inhibiting the transcription/translation of the gene under the regulation of the site being bound or (7) internal inhibition of transcription or translation of the gene containing the sequence.
- the dose will be dependent upon a variety of parameters, including the age, sex, height and weight of the human or animal to be treated, the organism or gene location which is to be attacked and the location of the target sequence within the organism. Given any set of parameters, one skilled in the art will be able to readily determine the appropriate dose.
- pathophysiological state refers to any abnormal, undesirable or life-threatening condition caused directly or indirectly by a virus.
- GTOs means an oligonucleotide in which there is a high percentage of deoxyguanosine, or contains two or more segments (runs) of two or more deoxyguanosine residues per segment.
- guanosine tetrads refers to the structure that is formed of eight hydrogen bonds by coordination of the four O 6 atoms of guanine with alkali cations believed to bind to the center of a quadruplex, and by strong stacking interactions.
- I100-15 class of GTO is the structure of the telomere sequence repeat T 4 G 4 , first detected in Oxytricha.
- the oxytricha repeat has been studied in oligonucleotides by NMR and by crystallographic methods. See Smith et al., Nature 1992, 356:164-68, and Kang et al., Nature 1992 356:126-31.
- the present invention provides a method of treating a pathophysiological state caused by a virus, comprising the step of administering a pharmacological dose of an oligonucleotide, said dose being sufficient to inhibit the replication of said virus, wherein said oligonucleotide contains sufficient contiguous guanosine so that a guanosine tetrad (inter- or intra- molecular) can form, and the three dimensional structure of the oligonucleotide is stabilized by guanosine tetrads formed at strategic locations.
- this method of treating a virus-induced pathophysiological state may be useful against any virus.
- the methods of the present invention may be useful in treating pathophysiological states caused by viruses such as herpes simplex virus, human papilloma virus, Epstein Barr virus, human immunodeficiency virus, adenovirus, respiratory syncytial virus, hepatitis B virus, human cytomegalovirus and HTLV I and II.
- viruses such as herpes simplex virus, human papilloma virus, Epstein Barr virus, human immunodeficiency virus, adenovirus, respiratory syncytial virus, hepatitis B virus, human cytomegalovirus and HTLV I and II.
- the oligonucleotides of the present invention contain a percentage of guanosine bases high enough to ensure anti- viral efficacy.
- the guanosine is important in forming tetrads which stabilize the three dimensional structure of the Oligonucleotides.
- the oligonucleotides of the present invention may have any percentage of guanosine bases which will allow for tetrad formation provided that the oligonucleotide exhibits anti- viral activity.
- the oligonucleotides of the present invention contain two or more segments of two or more guanosine bases, and an overall high percentage of G.
- the oligonucleotides of the present invention may be capped at either the 3' or the 5' terminus with a modifier.
- the modifier is selected from the group consisting of polyamine or similar compounds that confer a net positive charge to the end of the molecule, poly-L-lysine or other similar compounds that enhance uptake of the oligonucleotide, cholesterol or similar lipophilic compounds that enhance uptake of the oligonucleotide and propanolamine or similar amine groups that enhance stability of the molecule.
- the phosphodiester linkage of the oligonucleotides of the present invention may be modified to improve the stability or increase the anti-viral activity.
- the phosphodiester backbone of the oligonucleotide may be modified to a phosphorothioate linkage.
- Other such modifications to the oligonucleotide backbone will be obvious to those having ordinary skill in this art.
- the present invention also provides specific methods of treating viral states.
- the present invention provides a method of treating a pathophysiological state caused by a herpes simplex virus, comprising the step of administering a pharmacological dose of an oligonucleotide, said dose being sufficient to inhibit the replication of said virus, wherein the three dimensional structure of said oligonucleotide is stabilized by the formation of guanosine tetrads.
- Also provided in the instant application is a method of treating a pathophysiological state caused by human immunodeficiency virus, comprising the step of administering a pharmacological dose of an oligonucleotide, said dose being sufficient to inhibit the replication of said virus, wherein the three dimensional structure of said oligonucleotide is stabilized by the formation of guanosine tetrads.
- the present invention also provides a method of treating a pathophysiological state caused by human papilloma virus, comprising the step of administering a pharmacological dose of an oligonucleotide, said dose being sufficient to inhibit the replication of said virus, wherein the three dimensional structure of said oligonucleotide is stabilized by the formation of guanosine tetrads.
- the present invention provides a method of treating a pathophysiological state caused by human cytomegalovirus, comprising the step of administering a pharmacological dose of an oligonucleotide, said dose being sufficient to inhibit the replication of said virus, wherein the three dimensional structure of said oligonucleotide is stabilized by the formation of guanosine tetrads.
- the present invention also provides a method of treating a pathophysiological state caused by hepatitis B virus, comprising the step of administering a pharmacological dose of an oligonucleotide, said dose being sufficient to inhibit the replication of said virus, wherein the three dimensional structure of said oligonucleotide is stabilized by the formation of guanosine tetrads.
- This invention discloses a novel anti-viral technology.
- the total number of antiviral mechanisms by which oligonucleotides, and especially G-rich oligonucleotides, work is not completely known.
- G-rich oligonucleotides were able to significantly reduce virus production in each, and the present invention is drawn to oligonucleotides that have three dimensional structures stabilized by the formation of guanosine tetrads.
- Prior to this invention investigators tried to establish anti-viral mechanism based on anti-sense technology, and yet the present invention shows that oligonucleotide exhibition of anti-viral activity may not be via inhibition of translation events.
- the present invention demonstrates poly and/or oligonucleotides inhibit growth of HIV-1, HSV1, HSV2, FMLV and HCMV and other viruses if the molecule contains a high percentage of ribo- or deoxyriboguanosine.
- the rest of the molecule is composed of thymine, cytosine, xanthosine or adenine nucleotides (ribo- or deoxyribo-), their derivatives, or other natural or synthetic bases.
- the 5' and 3' termini of the oligonucleotide can have any attachment which may enhance stability, uptake into cells (and cell nuclei) or anti-viral activity.
- the backbone which connects the nucleotides can be the standard phosphodiester linkage or any modification of this linkage which may improve stability of the molecule or anti-viral activity of the molecule (such as a phosphorothioate linkage).
- the present invention also provides novel guanosine-rich oligonucleotides having anti-viral activity.
- Vero cells (4 ⁇ 10 4 cells/tissue culture well) were incubated with oligonucleotide (s) for 14 hours before the oligonucleotide was removed and virus (HSV-2 strain HG52) added to the cells at a multiplicity of infection (m.o.i.) of 0.1 to 1.0 (4 ⁇ 10 3 to 4 ⁇ 10 4 PFU). The infection was allowed to proceed for 10 minutes after which the cells are washed and fresh media, containing the same oligonucleotide is added for an additional 14 hours. Then the cells are subjected to a freeze/thaw lysis after which the released virus is titered.
- oligonucleotide s
- virus HBV-2 strain HG52
- the SUP Tl T lymphoma cell line was infected with HIV-1 strain DV at a multiplicity of infection (m.o.i.) of 0.1 for one hour at 37°C. After the infection, free virus was washed off and the newly infected cells were plated (5 ⁇ 10 4 cells) in quadruplicate in 96 well plates that had been prepared with various dilutions of oligonucleotide. The final concentration of drug varied between 0.1 and 20 uM. After 3 days of incubation at 37°C, the plates were scored for the presence of multinucleated giant cells (syncytia).
- oligonucleotides In assays designed to inhibit syncytia formation, a number of oligonucleotides exhibited anti-HIV-1 activity.
- I100-05 is the same as I100-01 with a cholesterol group attached to the 3' end via a triglycyl-linker.
- I100-08 is the same as I100-00 with a cholesterol group attached to the 3' end via a triglycyl-linker.
- I100-07 was designed as a sequence isomer to I100-01 and I100-06 is the cholesterol derivative of I100-07.
- A100-00 is the same sequence in the opposite orientation to HIB38p (A100-50).
- I100-07 originally designed as a control for I100-01 to be used in anti-FMLV experiments, was the most efficacious oligonucleotide tested against HIV-1.
- the HIV-1 strain LAV was used to infect MT-2 cells at an m.o.i of 0.01. After 7 days, these cells were scored for cytopathic effects (CPE).
- CPE cytopathic effects
- anti-HIV-1 assays in which MT-2 cells were infected at an m.o.i. of 0.01 several G-Rich oligonucleotides were able to inhibit viral-induced cytopathic effects with effective dose 50's (ED50s) in the 0.5-1.0 uM range (Figure 3).
- the oligonucleotides shown in Figure 3 were effective in the 0.5 to 1.0 uM range, including AlOO-00 (HIV38p) and A100-50 (HIV38ap),
- TE represents buffer alone, i.e., no drug, while AZT and ddC are control drugs.
- Friend Murine Leukemia Virus was grown in a chronically infected murine fibroblast cell line (pLRB215) or can be propagated in an acute assay system by infection of NIH3T3 cells.
- pLRB215 cells were split (1 ⁇ 10 5 ) into 24 well culture dishes and incubated 16 to 20 hours at 37°C. The media was then removed and replaced with media containing various concentrations of oligonucleotide. After 1, 3 or 5 days, culture media was assayed for the presence of the viral reverse transcriptase enzyme.
- NIH3T3 cells were split (1 ⁇ 10 4 ) into 96 well dishes and allowed to incubate for 16-20 hours. After incubation, culture media was removed and concentrated virus stock (10 ul) was added to each well in 100 ul of completed media containing 2 ug/ml polybrene. The virus infection was allowed to proceed for 18 hours at which time the virus containing media was removed and complete media containing various concentrations of oligonucleotide was added. After 4 to 7 days, the culture media was assayed for the presence of viral reverse transcriptase.
- Human cytomegalovirus was cultured in the human diploid lung fibroblast cell line MRC-5. These cells were split and placed into 24 well culture dishes and preincubated for 24 hours with various concentrations of oligonucleotide (0.5 to 20 uM) in complete media. The oligonucleotide was then washed off and virus was added to the cells (approximately 0.1 m.o.i.) for 2 hours at 37oC. The virus was then removed and complete media containing the same concentration of oligonucleotide was added. Cells were then placed at 37°C for 10-12 days at which time virus in the culture media was titered using a standard agar overlay procedure.
- reverse transcriptase (either MMLV which is commercially available or FMLV from pLRB215 culture media) was incubated with various concentrations of oligonucleotide and then assayed using the enzyme linked oligonucleotide sorbent assay (ELOSA), the ELOSA kit is commercially available from New England Nuclear.
- ELOSA enzyme linked oligonucleotide sorbent assay
- a recombinant plasmid containing the HSV-1 IE175 promoter fused to the bacterial chloramphenicol acetyltransferase gene (CAT) was linearized and used as a template for run off transcription studies.
- the commercially available HeLa cell nuclear extracts or prepared nuclear extracts of HSV-2 infected VERO cell were used.
- the oligonucleotide B106-62 was originally designed to form a triple helix structure with a portion of the promoter region of the major immediate early protein of HSV-2 (IE 175).
- the phosphorothioate derivatives of these two oligonucleotides were synthesized and tested for anti- viral activity against HSV-2.
- Figure 2 shows that the B 106-62 oligonucleotide at 20 ⁇ M was able to reduce viral titers by approximately 20% whereas the phosphorothioate version (B 106-96) reduced virus by 50% in the submicromolar concentration range.
- control oligonucleotide (B 106-97), the phosphorothioate backbone derivative of B106-71, was also able to inhibit virus at the same levels as B106-96. Even when an extensive washing procedure at a pH of 3 was employed to remove excess virus not internalized during the infection, incubation with both B106-96 and B106-97 were able to significantly reduce virus yield. Thus, the mechanism of anti-viral activity was not just blocking adsorption of HSV-2 virions to cells.
- Figure 2 also shows the results of acyclovir in the same molar range as the oligonucleotides. Acyclovir was tested against two different stocks of
- HSV-2 strain HG52 as illustrated in Figures 4a and 4b.
- the 47-mer DNA template oligonucleotide used was SEQ.ID. NO. 44 (1198) and the 15-mer primer sequence was SEQ.ID. NO. 45 (1200). All oligonucleotides used in these examples were synthesized on a DNA synthesizer (Applied Biosystems, Inc., model 380B or 394), using standard phosphoramidite methods. All oligonucleotides were synthesized with an amino modified 3'-terminal, which results in the covalent attachment of a propanolamine group to the 3'-hydroxyl group or with a cholesterol moiety attached to the 3'-terminal via a triglycyl-linker.
- Oligonucleotides used in this example were capped at their 3'-terminal with either a propanolamine or a cholesterol moiety to reduce degradation by cellular exonucleases.
- Phosphorothioate containing oligonucleotides were prepared using the sulfurizing agent TETD.
- the 3'-cholesteryl modified oligonucleotides were prepared and purified as described by Vu et al. (in Second International
- Oligonucleotides with either full length phosphodiester (PD) or full length phosphorothioate (PT) backbones were stable in the culture media for 4 days while oligonucleotides consisting of a more random composition of nucleotides were rapidly degraded. This indicates that the 3'-modified G-rich oligonucleotides with PD backbones were stable against both endonuclease and exonuclease digestion over a defined four day incubation in culture.
- the concentration of oligonucleotide needed to reduce cell proliferation by 50% (TC 50 ) of selected compounds, based on the dye metabolism assay was approximately 40 to 50 ⁇ M for oligonucleotides with PD backbones and 15 to 40 ⁇ M for those compounds containing a PT backbone.
- the TC 50 for selected oligonucleotides are presented in Table 3.
- I100-07 45 mer amine 5'-gtggtgggtgggtgggtggtggtggtggtggtggttgtgggtgggtggtg-3' >50 ⁇ M
- I100-06 45 mer cholesterol 5'-gtggtgggtgggtgggtggtgggtggtggtggtggtggttgtgggtgggtggtggtggtg-3'
- oligonucleotides listed were synthesized with phosphodiester backbones except 1100-12 which had phosphorothioate (PT) linkages.
- the capping group at the 3'-end of the oligonucleotide was either a propanolamine or cholesterol moiety.
- cytotoxicity of selected oligonucleotides was assayed using the CellTiter 96TM Aqueous Non-Radioactivity Cell Proliferation Assay (Promega).
- Dehydrogenase enzymes found in metabolically active cells convert MTS into a formazan product.
- the SUP T1 cells used in the cytotoxicity assays were in log phase growth at the time of the assay. Cytotoxicity profiles for GTOs with PD backbones such as I100-15 had TC 50 s (50% cytotoxic concentration) in the range of 30 to 50 ⁇ M while GTOs with PT backbones such as I100-15 had TC 50 S in the 10 to 30 ⁇ M range.
- the TC 50 for AZT in this assay format was approximately 10 ⁇ M .
- the aliquots at each time point were immediately extracted twice with 50:50 phenol-chloroform solution and then precipitated by the addition of ethanol.
- the recovered oligonucleotides were 5'-end-labeled using [ ⁇ - 32 P]ATP and polynucleotide kinase.
- the integrity of the oligonucleotides was then analyzed on a 20% polyacrylamide gel with 7 M urea. The results indicate that a portion of each GTO with a PD backbone was present in the culture medium of three to four days while oligonucleotides composed of a more random assortment of all four nucleotides were rapidly degraded.
- positions within PD GTOs where there exist two or more contiguous pyrimidines are more susceptible to endonuclease digestion than regions containing purines or alternating purines and pyrimidines.
- the anti-HIV-1 activity of a series of GTOs, with PD backbones, containing different sequences motifs was tested.
- One of the sequence motifs tested (oligonucleotide I100-07) was 10 fold more active at inhibiting HIV-1 induced syncytium formation than the other motifs tested (e.g. I100-00 shown in Table 1).
- I100-07 and its derivatives (length and chemical modification) were further tested for their ability to inhibit virus in a dose-dependent fashion by measurement of syncytium formation and viral p24 production.
- HIV-1 DV was used to infect the SUP Tl lymphoblastoid cell line at a multiplicity of infection (m.o.i.) of 0.1 TCID 50 for one hour at 37°C prior to washing and resuspension in increasing concentrations of GTOs.
- the cells (2 ⁇ 10 4 cells/well) were inoculated in triplicate in 200 ul of RPMI 1640 containing 10% fetal calf serum.
- the number of syncytia per well or the level of p24 in the medium was determined. The results of these assays are presented in Table 4.
- AZT 0.04 0.40 >200 a
- the internucleotide backbone linkages are denoted as PD for phosphodiester and PT for phosphorothioate.
- the duration of the viral suppression was assayed by changing the medium in HIV-1 infected cultures containing 2.5 uM of various oligonucleotides to complete media without added oligonucleotide on day 4 post- viral infection.
- the production of viral p24 antigen was then assayed on day 7 and day 11 post-infection.
- the results of this experiment indicated that the shorter variants of I100-07 (I100-15 and I100-16) as well as the PT version of this molecule (I100-21), were capable of totally suppressing HIV-1 p24 production for at least 7 days after removal of the drug from the culture medium (Table 6).
- d 1100-21 and 1100-12 contain phosphorothioate backbone linkages (PT).
- SUP T1 cells were counted for all treated samples 7 days after removal of the oligonucleotides from the infected cell cultures. The results indicated that for cells treated with 2.5 ⁇ M of drug there was no difference in the number of cells when compared with control cultures (uninfected, untreated) of SUP T1 cells.
- C Inhibition of HIV expression in patient derived peripheral blood mononuclear cells (PBMCs). I100-15 was assessed for activity in PBMC cultures derived from AIDS patients.
- PBMCs peripheral blood mononuclear cells
- PHA activated uninfected PBMCs were added to 4PBMC's derived from patients with HIV infection in the presence of varying concentrations of oligonucleotide. Anti-HIV activity was assessed by analyzing supernatants, collected every three days from these mixed cultures, for the presence of HIV p24.
- the PHA activated PBMCs were grown in the presence of 10 units/ml of IL-1 and medium was exchanged every three days for a period of three weeks. HIV p24 antigen production was assayed in drug-treated as compared to untreated control specimens. It is interesting to note that the results in these experiments ( Figure 9) observed for AZT were obtained when AZT was used at 12 uM which is roughly 300 fold greater than the ED 50 for this compound.
- Short oligonucleotides (18 mers) with PD or PT backbones were assayed to determine whether the nature of the nucleotide sequence contributed to inhibition of HIV-1 RT in this assay system.
- Comparison of the effects of the PD versions of a GTO (1173 or 1100-15), poly dC (1229) or a random nucleotide sequence (1231) suggested that at this length none of the sequence motifs inhibited RT (Table 7).
- Enzyme inhibition monitored by both K i and ID 50 was observed for the PT versions of these same 18 mer oligonucleotides (Table 7).
- the degree of enhancement of observed enzyme inhibition for all oligonucleotides tested when the sulfur group was present in the backbone was between one to three orders of magnitude (Table 7).
- oligonucleotides 1232 (GATC) 18 PT 0.56 0.045 a Each pair of oligonucleotides contain the same sequence and differ only in the nature of their backbone linkage. Oligonuc leotides 1229 and 1230 were poly dC while the 1231 and 1232 oligonucleotides were a random sequence of all four bases (GATC).
- the outer envelope glycoprotein gp120 of HIV-1 mediates viral attachment to the cell surface glycoprotein CD4 in the initial phase of HIV-1 infection.
- the effects of both PD and PT modified oligonucleotides on this interaction were examined using a gp120 capture ELISA kit.
- the concentration of the gp120 used in these studies (125 ng/ml) was determined to be within the linear range of the detection assay.
- the ability of oligonucleotides to inhibit gp120/CD4 interactions by binding to gp120 was determined by preincubation of the test compounds with soluble gp120 before addition to the immobilized
- a fixed length (18 mer) set of oligonucleotides with either PD or PT backbones were assayed to determine whether the nature of the nucleotide sequence contributed to inhibition of gp120/CD4 interactions.
- the PD versions of these molecules had little to no measurable effects on the binding of gp120 with CD4.
- the PT versions of these oligonucleotides did yield measurable inhibitory activity.
- the 18 mer GTO (1174) interrupted gp120/CD4 interactions at approximately 10 fold lower concentrations than poly (SdC) 18 (1230) while the random sequence 18 mer (1232) had no measurable activity (Table 7).
- RNA oligonucleotide interactions with the v3 loop was conducted using a v3 loop specific murine Mab, NEA-9284 (figure 10).
- PT oligonucleotides were able to inhibit binding of NEA-9284 to gp120.
- the presence of bound gp120 specific Mab was determined using a HRP-labeled goat- ⁇ -mouse antibody.
- the results of these experiments indicate that PT oligonucleotides were able to inhibit binding of NEA -9284 to gp120.
- the ID ⁇ for the most active oligonucleotide (1100-21) was approximately 4 to 7 ⁇ M.
- RNA and DNA were extracted from SUP Tl cells 36 hours after infection with 0.1 m.o.i of HIV-1 DV . In this assay the infected cells were treated with I100-15 or
- FIG. 11 A schematic diagram of the positions of the PCR primers used in the DNA and RNA analysis is shown in figure 11.
- Total extracted DNA was analyzed using a PCR primer set which would amplify a 200 bp portion of the viral genome spanning the repeat element (R) into the gag gene.
- the primer set detected full-length or nearly completely synthesized viral DNA. This is the last region of the minus strand of viral DNA that is synthesized. Thus, for DNA to be detected by this primer set, two template-switching events have occurred and contiguous 5'LTR to gag sequences must be present on either the minus or plus strand of DNA.
- a PCR primer set which would amplify a 220 bp region of the human b-actin gene was used.
- RNA extracted from HIV-1 infected cells was analyzed by RT-PCR.
- the antisense primer of the PCR primer pairs is used with MMLV RT and extracted mRNA to synthesize cDNA strand. This cDNA is then used as templates in PCR reactions.
- Two RNA primer sets were used to analyze unspliced (primers r1 and r2) and spliced (primers r1 and r3) HIV-1 transcripts. Predicted sizes of the amplified products were 101 bp and 214 bp for the unspliced and spliced species respectively.
- the same ⁇ -action primers used for the analysis of the DNA samples were used as controls in this experiment.
- I100-15 and I100-26 are composed entirely of deoxyguanosine (G) and deoxythymidine (T). These G-rich oligonucleotides were purified using anion exchange reverse phase HPLC. Using this procedure the oligonucleotide is purified in the presence of sodium ions. Monovalent cations are known to encourage self-associated structures for G-rich molecules, all of which involve formation of G-tetrads.
- the G-tetrad formation involves the formation of eight hydrogen bonds by coordination of the four O 6 atoms of guanine with alkali cations believed to bind to the center of a quadruplex, and by strong stacking interactions.
- the oligonucleotides purified using anion exchange chromatography then have an opportunity to form inter-or intramolecular tetrads.
- the tetrad structure can be strengthened by replacing the sodium ion with potassium.
- Intrabase H8-C1' and interbase H7-C2" NOE connectivity which demands a pattern of alternating syn-anti glycosidic bond angle throughout the "tetrad stem" of the folded structure.
- the structure is very compact, nearly spherical, with the three loop regions and the 5' "GT tail" comprising the surface of the tetrad core. Based upon this structure, it appears likely that interaction with cellular macromolecules will be heavily dominated by the structures of these surface loops. In that regard, it may be inappropriate to think of such interactions as "tetrad binding.”
- the inclusion of G-tetrads in such a structure may not be important as a recognition element per se, but instead provides a latticework upon which an orderly loop array is positioned.
- loop regions do not appear to be under mechanical stress, they are short enough so that they possess very configurational freedom. Because of those severe length constraints, we have found that all feasible loop models display a distinct "rabbit ears" structure, wherein the two base planes of the loop region are unstacked, and point outward from the center of the octet core. Such rigid, unstacked, single strand loop character is very distinctive as compared to other known folded nucleic acid structures. Therefore, varying the sequence or chemical structure of these loops, one at a time, is necessary to determine if bonding interactions between these loops and cellular macromolecules are important to the observed anti-HIV activity.
- the structures described above possess a single G-octet core, which is known to be the minimum structure required for nucleation of tetrad formation. Therefore, when paired with the observed short loop size, the intramolecular tetrad structure proposed for I100-15 is best described as meta-stable, relative to other more robust tetrads which have been described in the literature. An increase of the core from 2 to 3 stacked tetrads, or an increase in the length of flexibility of one or more loops would be expected to increase the thermodynamic and/or kinetic stability of this structure significantly. Thus, the observed anti-HIV activity can be improved by sequence modification which enhances the stability of the underlying tetrad latticework.
- I100-15 and homologues display profound resistance to cellular nucleases.
- One interesting aspect of the proposed structure is that, even in the loop domains, phosphodiester linkages (red) are generally buried from interaction with large solutes, such as a nuclease.
- the structure analysis proposed defines local phosphodiester backbone structure at low resolution. When paired with explicit biochemical analysis of phosphodiester cleavage rate, it is possible to define sites for selective introduction of backbone modification in I100-15 homologies, for the purpose of extending the biological half life in vivo.
- the gel electrophoresis data described above suggests that I100-15 spends every little time as a random coil at 25°C, under native salt conditions. Although the gel data rules out intermolecular associations, the data do not constrain the oligomer to any particular folded monomeric structure. Oligonucleotide folding in I100-15 has been studied employing a combination of high resolution NMR and methods.
- I100-15 has been synthesized at 15uM scale employing fast deblocking "Expedite” chemistry on a Milligen synthesizer. Subsequent to purification by denaturing anion-exchange chromatography in base (lOmM LiOH, 0.2 to 0.7M NaCl), oligomer purity was confirmed by denaturing gel electrophoresis (7M urea, 65°C). For NMR, the oligomer was desalted and transferred into 20mM LiC1 adjusted to pH 6.0, which minimizes folding to form tetrads. Oligonucleotide strand concentration was held constant at 2.7 mM. MMR was measured in H 20 , employing a Redfield pulse sequence to saturate the water resonance, as described previously, Dittrich et al., Biochemistry, 1994, in press.
- the imino proton spectrum undergoes an abrupt transition, which is likely to be representative of cooperative unfolding of the octet. Stability of this kind, accompanied by apparently high thermal cooperativity is very striking indeed, and is generally indicative of a single, well-defined folded oligonucleotide structure.
- oligonucleotides reduced HCMV titers in tissue culture. Each of the oligonucleotides contained a different percentage of guanosine residues and a different number of total nucleotides in the polymer.
- oligonucleotides (Figure 1) were capable of inhibiting virus production. However, oligonucleotides controls in this experiment were capable of inhibiting virus production in culture. EXAMPLE 12
- the I100-51 (FMLV2ap), attenuated full length transcription directed by either the T7 or T3 polymerases (Figure 5a).
- full length transcripts directed by the T7 promoter would be 131 bases long while full length transcripts directed by the T3 promoter would be 171 bases long (position of the Dde I site relative to the mRNA start site).
- both specific and control G-Rich oligonucleotides were capable of inhibiting eukaryotic transcription when a HeLa cell extract system was used.
- the oligonucleotides used were B133-54; B133-55 and B107-51 as specific inhibitors via potential triple helix mechanism of action and G101-50 and I100-11 as the low G-content control oligonucleotides.
- the present invention demonstrates anti-viral activity in tissue culture assays for several G-Rich oligonucleotides against HSV-2, HIV-1, HCMV and
- G-Rich oligonucleotides specifically inhibited the bacterial RNA polymerase enzymes T7 and T3, the FMLV and HIV-1 reverse transcriptase enzyme and eukaryotic RNA polymerase.
- MOLECULE TYPE DNA (genomic)
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- xi SEQUENCE DESCRIPTION: SEQ ID NO:14:
- MOLECULE TYPE DNA (genomic)
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- FEATURE FEATURE
- MOLECULE TYPE DNA (genomic)
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Abstract
Description
Claims
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AU69427/94A AU700196B2 (en) | 1993-04-23 | 1994-04-25 | Anti-viral guanosine-rich oligonucleotides |
JP6524457A JPH08509500A (en) | 1993-04-23 | 1994-04-25 | Antiviral guanosine rich oligonucleotide |
EP94917899A EP0699071A4 (en) | 1993-04-23 | 1994-04-25 | Anti-viral guanosine-rich oligonucleotides |
NO954217A NO954217L (en) | 1993-04-23 | 1995-10-20 | Guanosine-rich antivirus oligonucleotides |
US09/429,130 US6355785B1 (en) | 1993-04-23 | 1999-10-28 | Guanosine-rich oligonucleotide integrase inhibitors |
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US08/145,704 | 1993-10-28 |
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US08/682,255 Continuation-In-Part US6323185B1 (en) | 1993-04-23 | 1996-07-17 | Anti-viral guanosine-rich oligonucleotides and method of treating HIV |
US09/017,974 Continuation-In-Part US6288042B1 (en) | 1993-04-23 | 1998-02-03 | Anti-viral guanosine-rich tetrad forming oligonucleotides |
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US6020130A (en) * | 1995-06-07 | 2000-02-01 | Nexstar Pharmaceuticals, Inc. | Nucleic acid ligands that bind to and inhibit DNA polymerases |
US6183967B1 (en) | 1995-06-07 | 2001-02-06 | Nexstar Pharmaceuticals | Nucleic acid ligand inhibitors to DNA polymerases |
EP0871643A1 (en) * | 1995-07-19 | 1998-10-21 | Aronex Pharmaceuticals, Inc. | Anti-viral guanosine-rich oligonucleotides |
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US6489304B2 (en) * | 1997-05-01 | 2002-12-03 | Hybridon, Inc. | Hyperstructure-forming carriers |
WO2010133652A1 (en) * | 2009-05-19 | 2010-11-25 | Universite Victor Segalen Bordeaux 2 | Multimodal activity of g-quartet oligonucleotides and microbicide compositions |
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WO2011069487A3 (en) * | 2009-12-07 | 2011-10-13 | Universität Hamburg | Dna aptamers that specifically bind to the soluble interleukin-6 receptor |
WO2015177331A3 (en) * | 2014-05-23 | 2016-02-04 | INSERM (Institut National de la Santé et de la Recherche Médicale) | Nucleic acids acting as decoys for the treatment of lentivirus infection |
EP4108771A1 (en) * | 2021-06-24 | 2022-12-28 | Johann-Wolfgang-Goethe-Universität Frankfurt am Main | G- quadruplex- containing oligonucleotides for preventive and therapeutic treatment |
WO2022269013A1 (en) * | 2021-06-24 | 2022-12-29 | Johann Wolfgang Goethe-Universität Frankfurt | G- quadruplex- containing oligonucleotides for preventive and therapeutic treatment |
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Also Published As
Publication number | Publication date |
---|---|
AU700196B2 (en) | 1998-12-24 |
NO954217L (en) | 1995-12-18 |
JPH08509500A (en) | 1996-10-08 |
US6184369B1 (en) | 2001-02-06 |
EP0699071A4 (en) | 1998-12-23 |
EP0699071A1 (en) | 1996-03-06 |
CA2161243A1 (en) | 1994-11-10 |
US5567604A (en) | 1996-10-22 |
US6150339A (en) | 2000-11-21 |
AU6942794A (en) | 1994-11-21 |
NO954217D0 (en) | 1995-10-20 |
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