CA2211877A1

CA2211877A1 - Human immunodeficiency virus transcription inhibitors and methods of their use

Info

Publication number: CA2211877A1
Application number: CA 2211877
Authority: CA
Inventors: Jamal Temsamani; Valeri Metelev; Asya Levina; Sudhir Agrawal; Paul Zamecnik
Original assignee: Worcester Foundation for Biomedical Research; Hybridon Inc
Current assignee: Individual
Priority date: 1995-01-30
Filing date: 1996-01-24
Publication date: 1996-08-08
Also published as: EP0807172A1; AU4767896A; WO1996023878A1

Abstract

Disclosed are methods of inhibiting transcription using a synthetic oligonucleotide complementary to the Watson strand of a double-stranded DNA genome. Also disclosed are synthetic oligonucleotides which specifically inhibit transcription of the HIV-1 genome. Pharmaceutical compositions containing the synthetic oligonucleotides of the invention and methods of treating HIV infection using the oligonucleotides or pharmaceutical compositions of the invention are also provided.

Description

WQ96/23878 PCT~S96J01008 HUMAN IM~uN~ rl~l~N~Y VIRUS TRANSCRIPTION
INHIBITORS AND Mhl~S OF THEIR USE

FUNDING

This invention was made with Government support under Grant No. 2 UOL AI-24846-08 awarded by the Nat:ional Institutes of Health. The Government: therefore has certain rights in the invention.

BACKGROUND OF THE lNV~NlION
The present invention relates to the field of synthetic oligonucleotides which inhibit transcript:ion. This invention also relates to hllm~n 1mml~nodeficiency virus and its treatment using synt;hetic oligonucleotides which inhibit the transcript:ion of the viral genome.

Human immunodeficiency virus (HIV) is widely believed t:o be the causative agent of acquired immunodeficiency syndrome (AIDS). In recent years AIDS has become a major worldwide health problem, and enormous resources have been devoted to caring for AIDS patients and for HIV-infected individuals whose disease state has not yet progressed to AIDS. No cure for AIDS or HIV infection has been identified thus far. After a prolonged deteriorat:ion of health which includes numerous secondary infections by opportunistic organisms, virtually all AIDS patients die.
A few drugs have been developed which may slow the progression of HIV infection to AIDS.

CA 022ll877 l997-07-30 W O 96/23878 PCTrUS96/01008 These drugs generally inhibit the synthesis of HIV
DNA, for example, by incorporating nucleotide analogs which prevent further nucleotide addition such as azidothymidine, dideoxycytidine, dideoxyinosine, and the like into viral DNA.
However, these agents are not specific for viral DNA and thus the analogs are also randomly incorporated into the infected individual's DNA, causing significant damage to the infected individual as well as to the HIV. Recent studies have cast doubt on the long-term efficacy of azidothymidine therapy. Moreover, the nucleotide analogs also have severe side effects, and an analog may lose its efficacy against HIV in a particular individual, for unknown reasons. In these cases, the individuals may be switched to a new analog, or to a combination of analogs. Some individuals cannot tolerate a particular nucleotide analog, and some individuals cannot tolerate nucleotide analog therapy at all. At this time it is not possible to predict how an HIV-infected individual will respond to nucleotide analog therapy prior to actually administering the drugs.
In an effort to improve the specificity of anti-HIV therapy, therapeutic agents have been developed which specifically bind to HIV mRNA and thereby inhibit translation of viral proteins. A
number of such therapeutic agents, generally known as antisense agents, are described, ~or example, in U.S. Patent No. 4,806,463 and PCT publication No. WO 94/08004.

CA 022ll877 l997-07-30 W O 96123Mg PCTnUS96J~1008 Another anti-HIV strategy employs oligonucleotides which bind to double-stranded DN~
at regions of high homopyrimidine content, to form triple helical structures which are believed to block transcription and/or replication. This approach, ~;nown as the antigene strategy, is limited by its requirement for regions of high homopyrimidine content at a therapeutically relevant site within the viral DNA. Moreover, the nature of t:he hydrogen bonds which form the triple helical structures required for action of such agents is i.nherently weaker than that of the hydrogen bonds which form double helical structures. Thus antigene agents are expected to have less efficacy than antisense agents.

HIV is well-known to mutate extensively, resulting in a large number of strains which have been isolated from clinical specimens. New strains of HIV are likely to develop as the worldwide epidemic progresses. Moreover, infected individuals may respond idiosyncratically to known HIV therapeutic agents. Thus, there is a continued need for development of additional anti-HIV therapeutic agents.

SUMMARY OF THE INVENTION

It has been discovered that a synthetic oligonucleotide, preferably not bound to anintercalating agent, can be used to inhibit transcription. This discovery has been exploited to develop the present invention which includes a method of inhibiting the transcription of a gene.

W096/23878 PCT~S96/01008 In this method the transcription initiation region of the Watson strand of the gene from which transcription is to be inhibited is contacted with a synthetic oligonucleotide. As defined herein, the "Watson" strand of an HIV gene is the non-coding or antisense strand of the gene, while the "Crick" strand of an HIV gene is the coding or sense strand of the gene. The term "transcription initiation region" refers herein to the site at which the transcription of the genomic DNA into RNA begins. The oligonucleotide has a first nucleotide sequence complementary to and hybridizable with a second nucleotide sequence within the transcription initiation region, and in preferred embodiments, is not linked to an intercalating agent.

A number of short synthetic oligonucleotides have been identified which specifically inhibit transcription of the HIV genome, and thus which are useful as anti-HIV therapeutic agents. These oligonucleotides of the invention correspond to nucleotide sequences found within the transcription initiation region of the Crick strand of the HIV genome.

In one embodiment, the invention provides a synthetic oligonucleotide comprising a first nucleotide sequence complementary to and hybridizable with a second nucleotide sequence contained within the transcription initiation region of the Watson strand of the HIV genome.

WOg6/23878 PCT~S96101008 In some embodiments, the synthetic oligonucleotide is from about nine to about twenty-seven nucleotides in length. In other embodiments, the oligonucleotide is from about nine to about fifteen nucleotides in length.

In yet another embodiment, the invention provides a method o~ inhibiting the expression of HIV genes including gag, rev, tat, nef, or pol genes, comprising the step o~ contacting the Watson strand of the HIV genome with a synthetic oligonucleotide complementary to and hybridizable with a nucleotide sequence contained within the transcription initiation region of the Watson strand of the HIV genome.

The present invention also encompasses pharmaceutical compositions containing the synthetic oligonucleotides described herein, and methods of treatment or use which employ the synthetic oligonucleotides described herein.

BRIEF DESCRIPTION OF THE DRAWINGS

The foregoing and other objects of the present invention, the various features thereof, as well as the invention itself may be more fully understood from the following description, when read together with the accompanying drawings in which:

FIG. lA is a diagrammatic representation of the HIV-1 genome;

FIG. lB is a schematic representation of the transcription initiation region of the HIV-1 genome;

FIG. 2A is a schematic representation of the sequence of the T7 promoter in plasmid pDAB72 and the transcription initiation site, wherein the 20 arrow indicates the direction of transcription;

FIG. 2B is an autoradiogram of a gel demonstrating the inhibition of T7 RNA polymerase transcription of the HIV gag gene sequence 25 contained in plasmid pDAB72 by the synthetic oligonucleotide of SEQ ID NO :13 . The oligonucleotides were annealed to linearized plasmid prior to transcription. Lane 1, no oligonucleotide control; lane 2, sense 30 oligonucleotide having SEQ ID NO: 13; lane 3, antisense oligonucleotide having SEQ ID NO :14;
lane 4, random oligonucleotide having SEQ ID
NO:15;

W O 96123878 ~CTrUS96J~0~8 FIG. 3 is an autoradiogram of a gel demonstrating that the synthetic oligonucleotide with SEQ I:D NO:l inhibited T7 RNA polymerase . transcription of the HIV gag gene sequence contained in plasmid pDA~372 without a pre-annealing step. Lane 1, sense oligonucleotide having SEQ ID NO:13; lane 2, antisense oligonucleotide having SEQ ID NO:14; lane 3, random oligonucleotide having SEQ ID NO:15;
FIG. 4 is an autoradiogram of a gel demonstrating that inhibition of T7 RNA polymerase transcription by the oligonucleotide of SEQ ID
NO:13 is specific for HIV gag gene sequences.
Lane 1, no oligonucleotide control; lane 2, sense oligonucleotide having SEQ ID NO:13; lane 3, antisense oligonucleotide having SEQ ID NO:14;
lane 4, random oligonucleotide having SEQ ID
NO:15;
FIG. 5 is an autoradiogram of a gel showing that inhibition of T7 RNA polymerase transcription of the HIV gag gene sequences contained in p]asmid pDA~372 by an oligonucleotide of the invention is concentration dependent. Lane 1, no oligonucleotide control; lanes 2, S, 8, sense oligonucleotide having SEQ ID NO:13; lanes 3, 6, 9, antisen.se oligonucleotide having SEQ ID NO:14;
lanes 4, 7, 10, random oligonucleotide having SEQ
ID NO:15;

CA 022ll877 l997-07-30 W O 96/23878 PCTrUS96/01008 FIG. 6A is a schematic representation of the sequence of the transcription initiation site and the SP6 promoter in the pGEM-gag plasmid, wherein the arrow indicates the direction of transcription;

FIG. 6B is an autoradiogram of a gel showing the inhibition of SP6 RNA polymerase transcription of the HIV gag gene sequences contained in plasmid pGEM-gag by an oligonucleotide of the invention.
Lane 1, no oligonucleotide control; lane 2, sense oligonucleotide having SEQ ID NO:16; lane 3, antisense oligonucleotide having SEQ ID NO:17;
lane 4, random oligonucleotide having SEQ ID
NO:15; and FIG. 7 is an autoradiogram of a gel showing inhibition of T7 RNA polymerase transcription of the HIV gag gene sequences contained in plasmid pD~B72 by oligonucleotides of the invention. Lane 1, no oligonucleotide control; lane 2, sense oligonucleotide having SEQ ID NO:13; lane 3, antisense oligonucleotide having SEQ ID NO :14;
lane 4, sense oligonucleotide having SEQ ID NO:18;
lane 5, antisense oligonucleotide having SEQ ID
NO:19; and lane 6, random oligonucleotide having SEQ ID NO:15.

W096l23878 PCT~S96J01008 DETATr-~n Dl3SCRIPTION OF THE ~h:r~K~ED EMBODIMENTS

The patent and scienti~ic literature re~erred to herein establishes the knowledge that is available t:o those with skill in the art. The issued U.S. patents, allowed applications, and references cited herein are hereby incorporated by reference.

In accordance with the present invention, transcript:ion of a gene may be inhibited by contacting the transcription initiation region of the Watson strand of gene with a synthetic oligonucleotide including a first nucleotide sequence complementary to and hybridizable with a second nuc:Leotide sequence contained within the transcript:ion initiation region of the Watson strand of lhe gene.

As such, this method is useful for e~ml nlng the function of various genes, including those essential l_o animal development, for example, in an in vitro system. Presently, gene function can only be examined by the arduous task of making a "knock out" animal such as a mouse. This task is difficult, time-consuming and cannot be accomplished for genes essential to animal development since the "knock out" would produce a lethal phenotype. The present invention overcomes the shortcomings of this model.

The invention also provides synthetic ~ oligonucleotides which inhibit the transcription of any HIV gene. The oligonucleotides of the W O 96/23878 PCTrUS96/01008 invention comprise a first nucleotide se~lence complementary to and hybridizable with a second nucleotide sequence contained within the transcription initiation region of the Watson strand of the HIV genome. In the case of HIV-1, the transcription initiation region begins at nucleotide +1 of the long terminal repeat (LTR) region of the 5' end of the proviral DNA ( see FIG.
lA). FIG. lB shows the sequence of the transcription initiation site of HIV-1 in more detail. The region immediately preceding the transcription initiation region is the promoter region to which RNA polymerase initially and specifically binds. Oligonucleotides of the invention should include nucleotides which are complementary to at least one of the first 10 nucleotides (+1---+10) of the Watson strand of the transcription initiation region. Any one of, or any combination of, the oligonucleotides of the invention (examples of which are set forth in Table 1 below may be used to inhibit the transcription of the HIV gag, rev, tat, nef, pol, or any other HIV gene.

CA 02211877 1997~07~30 W ~ 96/23878 PCTnUs96l0laO8 H o ~ o U~

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'~ V
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V '~
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U ~ ~ r~ t ~ C
r _ ~ ~ ~ ~ ~ 3 ~, =
J ~ ~ ~ ~ c. ~ - ~ J -~ ~ r _ -r 3 - ~ ~ _ 3 ~ J ~ J _ V
a ~r I
~0 ~:: a ~ a~ ~ ~ ~ ~ o o o r r r r ~ t~ ~ ~ ~ O ~ ro~
+ + + + + ++ + + + + + +
~: o V o o ~ ~ l l l l l l l l l l l l J~ ~ O
~rl H ~d~ ~ ~ Ln ~ ~
+++++++++++++

U~ o Ln o ~ ~1 ~

W096/23878 PCT~S96/01008 Without being bound by any mechanistic theory, it is believed that the oligonucleotides of the present invention act as follows. After . HIV-l infection of a host cell, the viral RNA
genome, which contains the Crick or coding strands of the viral genes, is reverse transcribed into a double-stranded DNA provirus. The HIV-l provirus is integrated into the DNA of the host cell, and new viral RNA genomes are transcribed from the Watson or non-coding strand of the provirus by DNA-dependent RNA polymerase II of the host cell.
The DNA-dependent RNA polymerase II is believed to act by recognizing the promoter sequence upstream from the long terminal repeat (LTR) region (see FIGS. lA and lB) adjacent to the gag gene, and binding to the DNA helix in its "closed" or hydrogen bonded form. A short section (12-15 nucleotides) of the DNA helix is then unwound, forming an "open" complex or "transcription eye"
of non-hydrogen bonded DNA strands. The DNA-dependent RNA polymerase II then catalyzes polymerization of RNA into a single pre-mRNA
transcript encoding all of the HIV-l genes using the Watson or non-coding strand of the DNA as a template. This transcript is then spliced into multiple mRNAs encoding the HIV genes. The oligonucleotides of the invention are believed to act as an inhibitor of the DNA-dependent RNA
polymerase II within the open or unwound region of the promoter of the HIV-l genome. As such, a single oligonucleotide of the invention can inhibit transcription of all of the HIV-l genes normally transcribed during infection.

wa 96/23878 PCr~S96)~0~8 The o]igonucleotides of the invention are short synthetic oligonucleotides which, as used herein, encompass chemically synthesized polymers of about nine to about twenty-seven, preferably from about nine to about fifteen, and most preferably from about nine to fourteen nucleotide monomers (nucleotide bases) connected together or - linked by at least one 5~ to 3' internucleotide linkage.

The o].igonucleotides of the invention are composed o~. deoxyribonucleotides, ribonucleotides, or any combination thereof. Thus, the representat;ive oligodeoxyribonucleotides of the invention ~3et forth in Table 1 may also be oligoribonucleotide or ch,me~ic oligonucleotides.
The 5' end of one nucleotide and the 3' end of another nucleotide are covalently linked, in some cases, via a phosphodiester internucleotide linkage. ~'hese oligonucleotides can be prepared by art recognized methods such as phosphoramidate, H-phosphonate chemistry, or methylphosphoramidate chemistry l'see, e.g., Uhlmann et al. (1990) Chem. Rev.
90:543-584; Agrawal (ed.) Meth. Mol. Biol., Humana Press, Totowa, NJ (1993) Vol. 20; and U.S. Patent 5,149,798) which can be carried out manually or by an automated synthesizer and then processed (reviewed in Agrawal et al. (1992) Trends Biotechnol.
10:152-158).
The o]igonucleotides of the invention may also be modified in a number of ways without compromising their ability to hybridize to nucleotide sequences contained within the W O 96/23878 PCTrUS96/01008 transcription initiation region of the Watson strand of the HIV genome.

The term "modified oligonucleotide" as used herein describes an oligonucleotide in which at least two of its nucleotides are covalently linked via a synthetic linkage, i.e., a linkage other than a phosphodiester linkage between the 5' end of one nucleotide and the 3' end of another nucleotide in which the 5' nucleotide phosphate has been replaced with any number of chemical groups.

Preferable synthetic linkages include alkylphosphonates, phosphorothioates, phosphorodithioates, phosphate esters, alkylphosphonothioates, phosphoramidates, carbamates, carbonates, phosphate triesters, acetamidate, and carboxymethyl esters.
Oligonucleotides with these linkages or other modifications can be prepared according to known methods (see, e.g., Agrawal and Goodchild (Tetrahedron Lett. ( 19 87) 28:3539-3542); Agrawal et al.
(Proc. Natl. Acad. Sci. (USA) (1988) 85:7079-70~3);
Uhlmann et al. Chem. Rev. (1990) 90:534-583; Agrawal et al. (Trends Biotechnol. (1992) 10:152-158; Agrawal (ed.) Meth. Mol. Biol., Humana Press, Totowa, NJ
(1993) Vol. 20).

The term "modified oligonucleotide" also encompasses oligonucleotides with a modified base and/or sugar. For example, modified oligonucleotides, include a 3', 5'-substituted WO g6~23878 P~ g61~100 oligonucleotide having at both its most 3 and 5 positions ~3ugars which are attached to a chemical group other than a hydroxyl group (at its 3 position) cmd other than a phosphate group (at its 5' position). Such a modified oligonucleotide may also be referred to as a capped species. Other modified ribonucleotide-containing oligonucleotides include a 2 -O-alkylated ribose groups such as a 2 -O-methylated ribose, or oligonucleotides with arabinose instead of ribose.
In addition unoxidized or partially oxidized oligonucleotides having a substitution in one nonbridging oxygen per nucleotide in the molecule are also considered to be modified oligonucleotides.

Such modifications can be at some or all of the internucleoside linkages, as well as at either or both ends of the oligonucleotide and/or in the interior of the molecule (reviewed in Agrawal et al. (1992) TrendsBiotechnol. 10:152-158 and Agrawal (ed.) Meth. Mol. Biol. (Humana Press Totowa NJ
(1993) Vol. 20). Also considered as modified oligonucleotides are oligonucleotides having nuclease resistance-conferring bulky substituents at their 3' and/or 5 end(s) and/or various other structural modifications not found in vivo without human intervention. Other modifications include those which are internal or are at the end(s) of the oligonucleotide molecule and include additions to the molecule of the internucleoside phosphate linkages ;uch as cholesteryl or diamine compounds with varying numbers of carbon residues between the amino c~roups and terminal ribose deoxyribose CA 022ll877 l997-07-30 W 096123878 PCTnUS96/01008 and phosphate modifications which cleave, or crosslink to the opposite c~; n.q or to associated enzymes or other proteins which bind to the viral genome.

The synthetic oligonucleotides of the invention may be used to identify the presence of HIV nucleic acids in cells in vitro, for example, by labelling the oligonucleotide and screening for double-stranded, labelled DNA in the cells by in situ hybridization or some other art-recognized detection method.

The oligonucleotides of the invention may also be used to inhibit transcription of HIV genes within infected host cells and thus to inhibit production of HIV virions by those cells. The synthetic oligonucleotides of the invention are thus useful for treatment of HIV infection and AIDS in m~mm~l S, particularly the treatment of m~mm~31 S used as animal models to study HIV
infection and AIDS. The synthetic oligonucleotides of the invention are also useful for treatment of humans infected with HIV and those suffering from AIDS.

The synthetic oligonucleotides of the invention may be used as part of a pharmaceutical composition when combined with a physiologically and/or pharmaceutically acceptable carrier. The term "pharmaceutically acceptable" means a non-toxic material that does not interfere with the effectiveness of the biological activity of the active ingredient(s). The term "physiologically w~6/23878 PCT~S96J0~8 acceptable" refers to a non-toxic material that is compatible with a biological system such as a cell, cell culture, tissue, or organism. The characteristics of the carrier will depend on the route of administration. Such a composition may contain, in addition to the synthetic oligonucleotide and carrier, diluents, fillers, salts, bufEers, stabilizers, solubilizers, and other mate:rials well known in the art. The pharmaceut:ical composition of the invention may also conta:in other active factors and/or agents which enhance inhibition of HIV virion production by infected cells. For example, combinations of synthetic oligonucleotides, each of which inhibits transcription of a di~ferent HIV gene, may be used in the pha:rmaceutical compositions of the invention. The pharmaceutical composition of the invention may further contain nucleotide analogs such as azidothymidine, dideoxycytidine, dideosyinosine, and the like. Such additional factors and/or agents may be included in the pharmaceutical composition to produce a synergistic effect with the synthetic oligonucleotide of the invention, or to minimize side-effects caused by the synthetic oligonucleotide of the invention. Conversely, the synthetlc ollgonucleotlde of the invention may be included in formulations of a particular anti-HIV
factor and/or agent to minimize side effects of the anti-HIV factor and/or agent.

The pharmaceutical composition of the invention may be in the form of a liposome in which the synthetic oligonucleotides of the CA 022ll877 l997-07-30 W 096/23878 PCTrUS96/01008 invention is combined, in addition to other pharmaceutically acceptable carriers, with amphipathic agents such as lipids which exist in aggregated form as micelles, insoluble monolayers, liquid crystals, or lamellar layers which are in aqueous solution. Suitable lipids for liposomal formulation include, without limitation, monoglycerides, diglycerides, sulfatides, lysolecithin, phospholipids, saponin, bile acids, and the like. Preparation of such liposomal formulations is within the level of skill in the art, as disclosed, for example, in U.S. Patent No.
4,235,871; U.S. Patent No. 4,501,728; U.S. Patent No. 4,837,028; and U.S. Patent No. 4,737,323.
The pharmaceutical composition of the invention may further include compounds such as cyclodextrins and the.like which enhance delivery of oligonucleotides into cells, as described by Zhao et al. (in press).

As used herein, the term "therapeutically effective amount" means the total amount of each active component of the pharmaceutical composition or method that is sufficient to show a meaningful patient benefit, i.e., healing of chronic conditions characterized by HIV infection or increase in rate of healing of such conditions.
When applied to an individual active ingredient, administered alone, the term refers to that ingredient alone. When applied to a combi.nation, the term refers to combined amounts of the active ingredients that result in the therapeutic effect, ~Og6l2387g P~T~S96)~1008 ,-19-whether administered in combination, serially or simultaneously.

. In practicing the method of treatment or use of the present invention, a therapeutically ef~ective amount of one or more of the synthetic oligonucleotide of the invention is administered to a m~mm~ l infected with HIV. The synthetic oligonucleotide of the invention may be administered in accordance with the method of the invention either alone of in combination with other therapies such as treatments employing cytokines, lymphokines, other hematopoietic factors, other anti-viral agents, and the like.
When co-administered with one or more cytokines, lymphokine~~ or other hematopoietic factors, other anti-viral agents, the synthetic oligonucleotide of the invention may be administered either simultaneously with the cytokine(s), lymphokine(s), other hematopoietic factor(s), other antiviral agents, and the like, or sequentially. If administered sequentially, the attending physician will decide on the appropriate sequence of administering the synthetic oligonucleotide of the invention in combination with cytokine(s), lymphokine(s), other hematopoietic factor(s), anti-viral agents, and the like.

Administration of the synthetic - oligonucleotide of the invention used in the pharmaceutical composition or to practice the ~ method of the present invention can be carried out in a variety of conventional ways, such as oral W O 96/23878 PCTrUS96/01008 ingestion, inhalation, or cutaneous, subcutaneous, or intravenous injection.

When a therapeutically effective amount of synthetic oligonucleotide of the invention is administered orally, the synthetic oligonucleotide will be in the form of a tablet, capsule, powder, solution or elixir. When administered in tablet form, the pharmaceutical composition o~ the invention may additionally contain a solid carrier such as a gelatin or an adjuvant. The tablet, capsule, and powder contain from about 5 to 95 synthetic oligonucleotide and preferably from about 25 to 90~ synthetic oligonucleotide. When administered in liquid form, a liquid carrier such as water, petroleum, oils of animal or plant origin such as peanut oil, mineral oil, soybean oil, sesame oil, or synthetic oils may be added.
The liquid form of the pharmaceutical composition may further contain physiological saline solution, dextrose or other saccharide solution, or glycols such as ethylene glycol, propylene glycol or polyethylene glycol. When administered in liquid form, the pharmaceutical composition contains from about 0.5 to 90~ by weight of the synthetic oligonucleotide and preferably from about 1 to 50 synthetic oligonucleotide.

When a therapeutically effective amount of synthetic oligonucleotide of the invention is administered by intravenous, cutaneous or subcutaneous injection, the synthetic oligonucleotide will be in the form of a pyrogen-free, parenterally acceptable aqueous solution.

W096/23878 PCT~S9610100 The preparation of such parenterally acceptable solutions, having due regard to pH, isotonicity, stability, and the like, is within the skill in the art. A preferred pharmaceutical composition for intravenous, cutaneous, or subcutaneous injection should contain, in addition to the synthetic oligonucleotide, an isotonic vehicle such as Sodium Chloride Injection, Ringer's Injection, Dextrose In~ection, Dextrose and Sodium Chloride Injection, Lactated Ringer's Injection, or other vehicle as known in the art. The pharmaceutical composition of the present invention may also contain stabilizers, preservatives, buffers, antioxidants, or other additives known to those of skill in the art.

The amount of synthetic oligonucleotide in the pharmaceutical composition of the present invention will depend upon the nature and severity of the condition being treated, and on the nature of prior treatments which the patent has undergone. Ultimately, the attending physician will decide the amount of synthetic oligonucleotide with which to treat each individual patient. Initially, the attending physician will administer low doses of the synthetic oligonucleotide and observe the patient~s response. Larger doses of synthetic oligonucleo-tide may be administered until the optimal therapeutic effect is obtained for the ~ patient, an~ at that point the dosage is not increased further. It is contemplated that the ~ various pharmaceutical compositions used to practice the method of the present invention W 096/23878 PCTrUS96/01008 should contain about 1.0 ~g to about 100 mg of synthetic oligonucleotide per kg body weight.

The duration of intravenous therapy using the pharmaceutical composition of the present invention will vary, depending on the severity of the disease being treated and the condition and potential idiosyncratic response of each individual patient. It is contemplated that the duration of each application of the synthetic oligonucleotide will be in the range of 12 to 24 hours of continuous intravenous administration.
Ultimately the attending physician will decide on the appropriate duration of intravenous therapy using the pharmaceutical composition of the present invention.

The following examples illustrate the preferred modes of making and practicing the present invention, but are not meant to limit the scope of the invention since alternative methods may be used to obtain similar results.
. ~

Oliqonucleotide Synthesis Oligodeoxynucleotides were synthesized on an automated synthesizer (Biosearch 8700; Milligen) as described by Beaucage, (Protocolsfor Oligonucleotides 3o and Analogs: ~nthesis and Properties, (Agrawal, ed.) Humana Press, Totowa, N.J. (1993) Vol. 20 pp. 33-61).
After full deprotection, oligodeoxynucleo-tides were purified by ion-exchange HPLC on a Whatman PartiSphere SAX (Whatman, Clifton, NJ) cartridge W~96l23878 P~T~S96J01008 and finally desalted on Waters Sep-Pak C18 cartridges (Waters, Milford, MA).

Using these methods, the oligonucleotides of SEQ ID NO:1:3, SEQ ID NO:16, and SEQ NO:18 were prepared. The synthetic oligonucleotide of SEQ ID
NO:13 is a 14mer corresponding to nucleotides +4 to +17 of the plasmid pDA~372 containing the Watson strand of the HIV gag gene. The synthetic oligonucleotide of SEQ ID NO:16 is a 14mer corresponding to nucleotides +l to +14 of the pGEM-gag plasmid containing the watson strand of the HIV gag gene. The synthetic oligonucleotide of SEQ ID NO:18 is a 9mer corresponding to nucleotides 7 to 15 of the plasmid pDAB72 containing the Watson strand of the HIV gag gene.
Additional oligonucleotides were synthesized having SEQ :rD NOS:14, 17, and 19 which are complementa:ry to the oligonucleotides of SEQ ID
NO:13, SEQ ID NO:16, and SEQ ID NO:18, respectively, representing corresponding regions of the Crick or sense strand of the HIV gag gene in the plasmid. These oligonucleotides were used as oligonuc:Leotide controls in the transcription experiments set forth in Example 2.

Transcription Inhibition A. Plasmids The plasmid pDAB72 (Erikson-Viitanen et al.
(1989) AIDS ,Res. Hum. Retroviruses 5:577-591) represents W O 96/23878 PCTrUS96101008 the NcoI-BamHI insert, containing HIV sequences in the pTZ19R vector (Erikson-Viitanen et al., (ibid. ) ) . Linearization of this plasmid by PstI
and transcription by T7 RNA polymerase yields a gag RNA of about 640 nucleotides. The plasmid pGEM-gag was made by inserting the fragment SacI-ApaI (nucleotides 224-1551) of HIV in the SacI-ApaI sites of pGEM-llz(+) (Promega, Madison, WI).
Linearization of pGEM-gag by SacI and transcription by SP6 RNA polymerase yields a RNA
of about 1360 nucleotides. The plasmid pGU2Pre contains the sequence of U2 RNA (Kleinschmidt et al. (1989) Nucleic Acids Res. 17: 4817-4828; Temsamani et al. (1991) AntisenseRes. &Dev. 4: 35-42).
Linearization of pGU2PRE by BamHI and transcription by T7 RNA polymerase yields an RNA
of about 200 nucleotides.

B. In vitro Transcription Each transcription reaction (15 ~l) contained 100 ng of the linearized plasmid, 40 mM Tris-HCl pH 7.5, 6 mM MgCl2, 2 mM spermidine, 10 mM NaCl, 20 Units of RNasin, (Promega, Madison, WI), 2 mM
DTT, 0.5 mM of ATP, CTP, UTP and 0.05 mM GTP, and 10 ~Ci of 32P-GTP (specific activity 400 Ci/mmole, Amersham), the oligonucleotide (10 ~M) and 10 Units of DNA-dependent T7 RNA polymerase (Promega, Madison, WI). The reaction was carried out at 37~C for 20 minutes. The products were visualized by autoradiography after electrophoresis through a 4~ polyacrylamide gel containing 90 mM Tris-borate pH 8.3/8.3 M urea / 2.5 mM EDTA. The gel was WOg6/23878 PCT~S96J01008 exposed for. autoradiography and the results analyzed using the Molecular Imager GS-250 (Bio-Rad, Hercu]es, CA).

Initially, oligonucleotides were annealed to the linearized plasmid prior to addition of T7 RNA
polymerase. When the sythentic oligonucleotide of ~ SEQ ID NO::L3 was annealed to the linearized pDAB72 plasmid (see FIG. 2A), the plasmid was first added to the oli~onucleotide in 5 ~l of transcription buffer (40 mM Tris-HCl pH 7.5, 6 mM MgCl2, 2 mM
spermidine, 10 mM NaCl). The sample was heated at 90~C for 5 minutes then cooled down at room temperature for 30 minutes.
The t:ranscription reaction was then carried out for 20 minutes at 37~C, and the products were analyzed by gel electrophoresis. As judged by the migration on the gel, the expected HIV gag RNA of 640 nucleotides was transcribed in the absence of any added oligonucleotide (FIG. 2B, lane 1). An additional band was observed in all lanes which is believed to correspond to a transcription arrest of about 620 nucleotides. As measured by densitometry, the synthetic oligonucleotide of SEQ
ID NO:13 inhibited transcription by more than 80 (lane 2 of FIG. 2B), compared to the inhibition measured in the "no oligonucleotide" control (lane 1 of FIG. 2B). The oligonucleotide having SRQ ID
NO:14, which is the Watson complement of SEQ ID
NO:13 (lane 3 of FIG. 2B) inhibited transcription by about 15~, as did a random 14mer oligonucleotide having SEQ ID NO:16 (lane 4 of FIG. 2B) When the transcription reaction was W O 96123878 PCT~US96/01008 carried out for different time points (10 minutes and 45 minutes), similar results were obtained.
The inhibition observed with the random oligonucleotide may be a non-specific effect.

FIG. 3 shows that when the synthetic oligonucleotide of SEQ ID NO:13 was incubated with the plasmid DNA without pre-annealing, a similar level of inhibition was observed (lane 1).
Results similar to those of FIG. 2A and 2B were also obtained for the oligonucleotide having SEQ
ID NO:14, which is the Watson complement of the synthetic oligonucleotide of SEQ ID NO:13 (lane 2 of FIG. 2), and for the random 14mer oligonucleotide having SEQ ID NO:15 (lane 3 of FIG. 3). These results indicate that the synthetic oligonucleotide of SEQ ID NO:13 binds specifically to the DN,A open complex.

To confirm that the synthetic oligonucleotide of SEQ ID NO:13 specifically inhibits transcription of HIV gag RNA, transcription of U2 RNA from the pGU2Pre plasmid was measured in the absence of added oligonucleotide (lane 1 of FIG.
4) and in the presence of the synthetic oligonucleotide of SEQ ID NO:13 (lane 2 of FIG.
4), the Watson complement of the synthetic oligonucleotide of SEQ ID NO:13 having SEQ ID
NO:14 (lane 3 of FIG. 4), and the random 14mer oligonucleotide having SEQ ID NO:15 (lane 4 of FIG. 4). Some non-specific inhibition of U2 RNA
transcription was observed for all nucleotides added to the pGU2Pre plasmid. However, FIG. 4 shows that the synthetic oligonucleotide of SEQ ID

W O 96/23878 P~TnUS96)01008 NO:13, which was very efficient in inhibiting HIV
gag transcrlption, as indicated in FIGS. 2A, 2B, and 3, did not inhibit transcription of U2 RNA, further ind.icating the specificity of HIV gag transcription inhibition by the synthetic oligonucleotide of SEQ ID NO:13.

The ccncentration dependence of the inhibition of HIV gag transcription by the synthetic oligonucleotide of SEQ ID N0:13 is shown in FIG. 5. Plasmid pDAB72 was incubated with 2, S, and 10 ~M oligonucleotide of SEQ ID N0:13 (lanes 2, ~, and 8, respectively), 2, 5, and 10 ~M
of the Wat~,on complement of the synthetic oligonucleotide of SEQ ID N0:13 having SEQ ID
NO:14 (lanes 3, 6, and 9), and the random 14mer oligonuclec~tide having SEQ ID N0:15 (lanes 4, 7, and 10). P..t 2 ~M, almost no inhibition of transcripti.on was observed. At 5 ~M, the synthetic oligon~Lcleotide of SEQ ID NO:13 inhibited ~[IV gag transcription by about 40~ as compared wi.th the no oligonucleotide control (lane 1). At 10 ~M the synthetic oligonucleotide of SEQ
ID N0:13 demonstrated similar levels of HIV g~g transcripti.on inhibition as were observed in FIGS.
2A, 2B, ancl 3. No significant inhibition of HIV
gag transcription was observed with the Watson complement of the synthetic oligonucleotide of SEQ
ID N0:13 having SEQ ID N0:14, or with the random - 30 14mer oligonucleotide having SEQ ID N0:15. When 20 ~M of each oligonucleotide was added to plasmid ~ pDAB72, non-specific inhibition of transcription was observed.

W 096/23878 PCTnUS96/01008 Other Oliqonucleotides To confirm that inhibition of HIV gag transcription by synthetic oligonucleotides complementary to the transcription initiation region of the HIV genome is not limited to T7 RNA
polymerase, transcription experiments were performed using the SP6 RNA polymerase, the pGEM-gag plasmid, and the synthetic oligonucleotide of SEQ ID NO:16, which is complementary to nucleotides at positions +1 to +14 of the plasmid.
FIG. 6A shows the position of the transcription site starting at +1. The HIV gag transcription inhibiting activity of the synthetic oligonucleotide of SEQ ID NO:16 is demonstrated in FIG. 6B, lane 2, as compared to the "no oligonucleotide" control in lane 1. Using the synthetic oligonucleotide of SEQ ID NO:16, about 80~ inhibition is found. No significant inhibition of HIV gag transcription was observed with the Watson complement of the synthetic oligonucleotide of SEQ ID NO :14 having SEQ ID
NO:17 (lane 3) or with the random 14mer oligonucleotide having SEQ ID NO:15 (lane 4).

To determine whether the length of the oligonucleotide effected its ability to inhibit transcription, the 9mer synthetic oligonucleotide of SEQ ID NO: 18 was compared to the 14mer synthetic oligonucleotide of SEQ ID NO :13 in the T7 transcription system described above. FIG. 7 shows that the shorter (9mer) oligonucleotide CA 022ll877 l997-07-30 W O 96123878 P~T~US9fi)DlD~8 (lane 4) inhibited transcription o~ the HIV gag gene as efi-iciently as did the longer (14mer) oligonuclec~tide (lane 2). Inhibition of HIV gag transcriptLon by the synthetic oligonucleotide of SEQ ID N0: :L8 was specific, as indicated by the lack of inhibition by the Watson complement of the synthetic oligonucleotide of SEQ ID N0:18 having SEQ ID NO::L9 (lane 5) and by the random 14mer oligonucleotide of SEQ ID NO:15 (lane 6). FIG. 7 further shows the lack of inhibition with the Watson complement of the synthetic oligonucleotide of SEQ ID ~0:13 having SEQ ID NO: 14 ( lane 3).

EQUIV~iLENT'3 Those skilled in the art will recognize, or be able to ascertain, using no more than routine experimentation, numerous equivalents to the specific substances and procedures described herein. Such equivalents are considered to be within the scope of this invention, and are covered by the following claims.

W 096/23878 PCTrUS96/01008 SEQUENCE LISTING
(1) GENERAL INFORMATION:
(i) APPLICANT: Hybridon, Inc.
Worcester Foundation for Experimental Biology (ii) TITLE OF INVENTION: Human Immunodeficiency Virus . Transcription Inhibitors and Methods of Their Use (iii) NUMBER OF SEQUENCES: 20 (iv) CORRESPONDENCE ADDRESS:
(A) ADDRESSEE: Lappin & Kusmer (B) STREET: 200 State Street (C) CITY: Boston (D) STATE: Massachusetts (E) COUNTRY: USA
(F) ZIP: 02109 (v) COM~'l'~K READABLE FORM:
(A) MEDIUM TYPE: Floppy disk (B) COM~U~ ~: IBM PC compatible (C) OPERATING SYSTEM: PC-DOS/MS-DOS
(D) SOFTWARE:
(vi) CURRENT APPLICATION DATA:
(A) APPLICATION NUMBER:
(B) FILING DATE:
(C) CLASSIFICATION:
(viii) ATTORNEY/AGENT INFORMATION:
(A) NAME: Kerner, Ann-Louise (B) REGISTRATION NUMBER: 33,523 (C) REFERENCE/DOCKET NUMBER: HYZ-037PCT
(ix) TELECOMMUNICATION INFORMATION:
(A) TELEPHONE: 617-330-1300 (B) TELEFAX: 617-330-1311 (2) INFORMATION FOR SEQ ID NO:1:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 9 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear W096/23878 PCT~S96101008 (ii) MOLECULE TYPE: cDNA or cDNA/RNA
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
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(2) INFORMATION FOR SEQ ID NO:3:
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(2) INFORMATION FOR SEQ ID NO:4:

CA 022ll877 l997-07-30 W 096/23878 PCTrUS96/01008 (i) SEQUENCE CHARACTERISTICS:
(A) L~N~l~: 14 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: cDNA or cDNA/RNA
(iii) HYPOTHETICAL: NO
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(2) INFORMATION FOR SEQ ID NO:5:
(i) SEQUENCE CHARACTERISTICS:
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(2) INFORMATION FOR SEQ ID NO:6:
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(A) LENGTH: 14 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: cDNA or cDNA/RNA
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W O 96/23878 PC~nUS96JD~DD8 (2) INFORMATION FO:R SEQ ID NO:7:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 20 base pairs (B) TYPE: nucleic acid (C) STR~NDEDNESS: single (D) TOPO:LOGY: linear (ii) MOLECULE TYPE: cDNA or cDNA/RNA
(iii) HYPOTHETICAL: NO
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(2) INFORMATION FOR SEQ ID NO:8:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGrrH 20 base pairs (B) TYPE~ nucleic acid (C) STR~DEDNBSS: single (D) TOPOLOGY: linear (ii) MOLECULE l'YPE: cDNA or cDNA/RNA
(iii) HYPOTHETI(~L: NO
(iv) AWTI-SENSE: NO
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CTCTGGTTAG ACCAGATC'TG 20 (2) INFORMATION FOR SEQ ID NO:9:
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W O 96/23878 PCTrUS96/01008 (iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
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(2) INFORMATION FOR SEQ ID NO:ll:
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(2) INFORMATION FOR SEQ ID NO:14:
(i) SEQUENCE CHARACTERISTICS:
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(iv) ANTI-SENSE: YES
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W O 96/23878 PCTrUS96/01008 (2) INFORMATION FOR SEQ ID NO:15:
(i) SEQUENCE CHARACTERISTICS:
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(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: YES

W O 96/23878 PCTnUS96101008 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:17:

(2) INFORMATION FOR SEQ ID NO:18:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 9 base pairs (B) TYP:E: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: cDNA
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(2) INFORMATION FC)R SEQ ID NO:20:
(i) SEQUENCE CHARACTERISTICS:
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(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:20:

Claims

What is claimed is:

1. A synthetic oligonucleotide comprising a first nucleotide sequence complementary to and hybridizable with a second nucleotide sequence contained within the transcription initiation region of the Watson strand of the HIV genome, the second nucleotide sequence being a single-stranded nucleic acid.

2. The oligonucleotide of claim 1 wherein the oligonucleotide comprises from about nine to about twenty-seven nucleotides.

3. The oligonucleotide of claim 2, wherein the oligonucleotide comprises from about nine to about fifteen nucleotides.

4. The oligonucleotide of claim 1 which is modified.

5. A pharmaceutical composition comprising the synthetic oligonucleotide of claim 1.

6. A method of inhibiting the transcription of a gene comprising the step of contacting the transcription initiation region of the Watson strand of the gene with a synthetic oligonucleotide having a first nucleotide sequence complementary to and hybridizable with a second nucleotide sequence within the transcription initiation region, the second nucleotide sequence being a single-stranded nucleic acid, and the oligonucleotide not being linked to an intercalating agent.

7. A method of inhibiting the expression of the HIV gag gene comprising the step of contacting the HIV genome with a synthetic oligonucleotide complementary to and hybridizable with a nucleotide sequence contained within the transcription initiation region of the Watson strand of the HIV genome, the second nucleotide sequence being a single-stranded nucleic acid.

8. The method of claim 7 wherein the oligonucleotide comprises from about nine to about twenty-seven nucleotides.

9. The method of claim 8 wherein the oligonucleotide comprises from about nine to about fifteen oligonucleotides.

10. The method of claim 7 wherein the oligonucleotide is modified.

11. A method of inhibiting the expression of the HIV rev gene comprising the step of contacting the HIV genome with a synthetic oligonucleotide complementary to and hybridizable with a nucleotide sequence contained within the transcription initiation region of the Watson strand of the HIV genome, the second nucleotide sequence being a single-stranded nucleic acid.

12. The method of claim 11 wherein the oligonucleotide comprises from about nine to about twenty-seven nucleotides.

13. The method of claim 12 wherein the oligonucleotide comprises from about nine to about fifteen oligonucleotides.

14. The method of claim 11 wherein the oligonucleotide is modified.

15. A method of inhibiting the expression of the HIV tat gene comprising the step of contacting the HIV genome with a synthetic oligonucleotide complementary to and hybridizable with a nucleotide sequence contained within the transcription initiation region of the Watson strand of the HIV genome, the second nucleotide sequence being a single-stranded nucleic acid.

16. The method of claim 15 wherein the oligonucleotide comprises from about nine to about twenty-seven nucleotides.

17. The method of claim 16 wherein the oligonucleotide comprises from about nine to about fifteen oligonucleotides.

18. The method of claim 15 wherein the oligonucleotide is modified.

19. A method of inhibiting the expression of the HIV pol gene comprising the step of contacting the HIV genome with a synthetic oligonucleotide complementary to and hybridizable with a nucleotide sequence contained within the transcription initiation region of the Watson strand of the HIV genome, the second nucleotide sequence being a single-stranded nucleic acid.

20. The method of claim 19 wherein the oligonucleotide comprises from about nine to about twenty-seven nucleotides.

21. The method of claim 20 wherein the oligonucleotide comprises from about nine to about fifteen oligonucleotides.

22. The method of claim 19 wherein the oligonucleotide is modified.

23. A method of inhibiting the expression of the HIV nef gene comprising the step of contacting the HIV genome with a synthetic oligonucleotide complementary to and hybridizable with a nucleotide sequence contained within the transcription initiation region of the Watson strand of the HIV genome, the second nucleotide sequence being a single-stranded nucleic acid.

24. The method of claim 23 wherein the oligonucleotide comprises from about nine to about twenty-seven nucleotides.

25. The method of claim 24 wherein the oligonucleotide comprises from about nine to about fifteen oligonucleotides.

26. The method of claim 23 wherein the oligonucleotide is modified.