US20030216333A1

US20030216333A1 - Antisense modulation of glycogen synthase kinase3 alpha expression

Info

Publication number: US20030216333A1
Application number: US10/181,875
Authority: US
Inventors: Brett Monia; Robert McKay; Madeline Butler; Jacqueline Wyatt
Original assignee: Isis Pharmaceuticals Inc
Current assignee: Ionis Pharmaceuticals Inc
Priority date: 2000-01-21
Filing date: 2001-01-16
Publication date: 2003-11-20
Also published as: US6316259B1; CA2397202A1; WO2001052865A1; AU2001232814B2; EP1248635A4; EP1248635A1; JP2003520242A; AU3281401A

Abstract

Antisense compounds, compositions and methods are provided for modulating the expression of glycogen synthase kinase 3 alpha. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding glycogen synthase kinase 3 alpha. Methods of using these compounds for modulation of glycogen synthase kinase 3 alpha expression and for treatment of diseases associated with expression of glycogen synthase kinase 3 alpha are provided.

Description

FIELD OF THE INVENTION

The present invention provides compositions and methods for modulating the expression of glycogen synthase kinase 3 alpha. In particular, this invention relates to antisense compounds, particularly oligonucleotides, specifically hybridizable with nucleic acids encoding glycogen synthase kinase 3 alpha. Such oligonucleotides have been shown to modulate the expression of glycogen synthase kinase 3 alpha.

BACKGROUND OF THE INVENTION

One of the principal mechanisms by which cellular regulation is effected is through the transduction of extracellular signals across the membrane that in turn modulate biochemical pathways within the cell. Protein phosphorylation, orchestrated by enzymes known as kinases, represents one course by which intracellular signals are propagated from molecule to molecule resulting in a cellular response. These signal transduction cascades are highly regulated and often overlapping as evidenced by the existence of many protein kinases as well as phosphatases, which remove phosphate moieties. It is currently believed that a number of disease states and/or disorders are a result of either aberrant activation or functional mutations in the molecular components of kinase cascades. Consequently, considerable attention has been devoted to the characterization of kinases, especially those involved in energy metabolism. One such kinase is glycogen synthase kinase 3.

Two different mammalian isoforms of glycogen synthase kinase 3 have been identified and each is encoded by a separate gene (Shaw et al., Genome, 1998, 41, 720-727; Woodgett, Embo J., 1990, 9, 2431-2438). These isoforms, designated alpha and beta are expressed in different cell types and in different proportions. In some cells, the expression of these isoforms is under developmental control.

Glycogen synthase kinase 3 alpha (also known as Factor A (Woodgett, Embo J., 1990, 9, 2431-2438) and ACLK for ATP citrate lyase kinase (Hughes et al., Biochem. J., 1992, 288, 309-314)) is a serine/threonine protein kinase first described as a factor involved in glycogen synthesis. In this pathway, glycogen synthase kinase 3 phosphorylates select residues of glycogen synthase, the rate-limiting enzyme of glycogen deposition, thereby inactivating the enzyme. Therefore, glycogen synthase kinase 3 plays a predominant role in glycogen metabolism and has consequently been investigated as a potential therapeutic target in disease conditions such as diabetes and insulin regulation disorders (Cross et al., FEBS Lett., 1997, 406, 211-215; Eldar-Finkelman et al., Proc. Natl. Acad. Sci. U. S. A., 1996, 93, 10228-10233; Eldar-Finkelman and Krebs, Proc. Natl. Acad. Sci. U.S. A., 1997, 94, 9660-9664; Eldar-Finkelman et al., Diabetes, 1999, 48, 1662-1666).

Recently, it has been demonstrated that glycogen synthase kinase 3 alpha mediates signal transduction pathways by phosphorylating various cellular proteins (Plyte et al., Biochim. Biophys. Acta., 1992, 1114, 147-162). Included in this group are transcription factors such as Jun family members (Nikolakaki et al., Oncogene, 1993, 8, 833-840), NF-ATc (Beals et al., Science, 1997, 275, 1930-1934), and CREB (Bullock and Habener, Biochemistry, 1998, 37, 3795-3809) as well as proteins involved in apoptotic pathways (Pap and Cooper, J. Biol. Chem., 1998, 273, 19929-19932) and sperm motility (Smith et al., J. Androl., 1999, 20, 47-53; Vijayaraghavan et al., Biol. Reprod., 1996, 54, 709-718).

Currently, there are no known therapeutic agents which effectively inhibit the synthesis of glycogen synthase kinase 3 alpha and to date, investigative strategies aimed at modulating glycogen synthase kinase 3 alpha function have involved the use of antibodies and chemical inhibitors. A method for treating a biological condition mediated by glycogen synthase kinase 3 (GSK3) activity, said method comprising administering an effective amount of a pharmaceutical composition comprising a selective GSK3 inhibitor is disclosed in U.S. Pat. No. 6,057,117. The selective GSK3 inhibitors generally disclosed include peptides, peptoids, small organic molecules and polynucleotides. Disclosed in the PCT publication WO 97/41854 are methods to identify inhibitors of glycogen synthase kinase 3 and the use of these inhibitors for the treatment of bipolar disorders, mania, Alzheimer's disease, diabetes and leukopenia (Klein and Melton, 1997). Other inhibitory compounds are disclosed in WO 99/21859. These heterocyclic compounds are intended for the treatment of a disease mediated by a protein kinase, one of which is glycogen synthase kinase 3 (Cheung et al., 1999). There remains, however, a long felt need for additional agents capable of effectively inhibiting glycogen synthase kinase 3 alpha function. The pharmacological modulation of glycogen synthase kinase 3 alpha activity or expression may therefore be an appropriate point of therapeutic intervention in pathological conditions.

Antisense technology is emerging as an effective means for reducing the expression of specific gene products and may therefore prove to be uniquely useful in a number of therapeutic, diagnostic, and research applications for the modulation of glycogen synthase kinase 3 alpha expression.

The present invention provides compositions and methods for modulating glycogen synthase kinase 3 alpha expression.

SUMMARY OF THE INVENTION

The present invention is directed to antisense compounds, particularly oligonucleotides, which are targeted to a nucleic acid encoding glycogen synthase kinase 3 alpha, and which modulate the expression of glycogen synthase kinase 3 alpha. Pharmaceutical and other compositions comprising the antisense compounds of the invention are also provided. Further provided are methods of modulating the expression of glycogen synthase kinase 3 alpha in cells or tissues comprising contacting said cells or tissues with one or more of the antisense compounds or compositions of the invention. Further provided are methods of treating an animal, particularly a human, suspected of having or being prone to a disease or condition associated with expression of glycogen synthase kinase 3 alpha by administering a therapeutically or prophylactically effective amount of one or more of the antisense compounds or compositions of the invention.

DETAILED DESCRIPTION OF THE INVENTION

The present invention employs oligomeric antisense compounds, particularly oligonucleotides, for use in modulating the function of nucleic acid molecules encoding glycogen synthase kinase 3 alpha, ultimately modulating the amount of glycogen synthase kinase 3 alpha produced. This is accomplished by providing antisense compounds which specifically hybridize with one or more nucleic acids encoding glycogen synthase kinase 3 alpha. As used herein, the terms “target nucleic acid” and “nucleic acid encoding glycogen synthase kinase 3 alpha” encompass DNA encoding glycogen synthase kinase 3 alpha, RNA (including pre-mRNA and mRNA) transcribed from such DNA, and also cDNA derived from such RNA. The specific hybridization of an oligomeric compound with its target nucleic acid interferes with the normal function of the nucleic acid. This modulation of function of a target nucleic acid by compounds which specifically hybridize to it is generally referred to as “antisense”. The functions of DNA to be interfered with include replication and transcription. The functions of RNA to be interfered with include all vital functions such as, for example, translocation of the RNA to the site of protein translation, translation of protein from the RNA, splicing of the RNA to yield one or more mRNA species, and catalytic activity which may be engaged in or facilitated by the RNA. The overall effect of such interference with target nucleic acid function is modulation of the expression of glycogen synthase kinase 3 alpha. In the context of the present invention, “modulation” means either an increase (stimulation) or a decrease (inhibition) in the expression of a gene. In the context of the present invention, inhibition is the preferred form of modulation of gene expression and mRNA is a preferred target.

It is preferred to target specific nucleic acids for antisense. “Targeting” an antisense compound to a particular nucleic acid, in the context of this invention, is a multistep process. The process usually begins with the identification of a nucleic acid sequence whose function is to be modulated. This may be, for example, a cellular gene (or mRNA transcribed from the gene) whose expression is associated with a particular disorder or disease state, or a nucleic acid molecule from an infectious agent. In the present invention, the target is a nucleic acid molecule encoding glycogen synthase kinase 3 alpha. The targeting process also includes determination of a site or sites within this gene for the antisense interaction to occur such that the desired effect, e.g., detection or modulation of expression of the protein, will result. Within the context of the present invention, a preferred intragenic site is the region encompassing the translation initiation or termination codon of the open reading frame (ORF) of the gene. Since, as is known in the art, the translation initiation codon is typically 5′-AUG (in transcribed mRNA molecules; 5′-ATG in the corresponding DNA molecule), the translation initiation codon is also referred to as the “AUG codon,” the “start codon” or the “AUG start codon”. A minority of genes have a translation initiation codon having the RNA sequence 5′-GUG, 5′-UUG or 5′-CUG, and 5′-AUA, 5′-ACG and 5′-CUG have been shown to function in vivo. Thus, the terms “translation initiation codon” and “start codon” can encompass many codon sequences, even though the initiator amino acid in each instance is typically methionine (in eukaryotes) or formylmethionine (in prokaryotes). It is also known in the art that eukaryotic and prokaryotic genes may have two or more alternative start codons, any one of which may be preferentially utilized for translation initiation in a particular cell type or tissue, or under a particular set of conditions. In the context of the invention, “start codon” and “translation initiation codon” refer to the codon or codons that are used in vivo to initiate translation of an mRNA molecule transcribed from a gene encoding glycogen synthase kinase 3 alpha, regardless of the sequence(s) of such codons.

It is also known in the art that a translation termination codon (or “stop codon”) of a gene may have one of three sequences, i.e., 5′-UAA, 5′-UAG and 5′-UGA (the corresponding DNA sequences are 5′-TAA, 5′-TAG and 5′-TGA, respectively). The terms “start codon region” and “translation initiation codon region” refer to a portion of such an mRNA or gene that encompasses from about 25 to about 50 contiguous nucleotides in either direction (i.e., 5′ or 3′) from a translation initiation codon. Similarly, the terms “stop codon region” and “translation termination codon region” refer to a portion of such an mRNA or gene that encompasses from about 25 to about 50 contiguous nucleotides in either direction (i.e., 5′ or 3′) from a translation termination codon.

The open reading frame (ORF) or “coding region,” which is known in the art to refer to the region between the translation initiation codon and the translation termination codon, is also a region which may be targeted effectively. Other target regions include the 5′ untranslated region (5′UTR), known in the art to refer to the portion of an mRNA in the 5′ direction from the translation initiation codon, and thus including nucleotides between the 5′ cap site and the translation initiation codon of an mRNA or corresponding nucleotides on the gene, and the 3′ untranslated region (3′UTR), known in the art to refer to the portion of an mRNA in the 3′ direction from the translation termination codon, and thus including nucleotides between the translation termination codon and 3′ end of an mRNA or corresponding nucleotides on the gene. The 5′ cap of an mRNA comprises an N7-methylated guanosine residue joined to the 5′-most residue of the mRNA via a 5′-5′ triphosphate linkage. The 5′ cap region of an mRNA is considered to include the 5′ cap structure itself as well as the first 50 nucleotides adjacent to the cap. The 5′ cap region may also be a preferred target region.

Although some eukaryotic mRNA transcripts are directly translated, many contain one or more regions, known as “introns,” which are excised from a transcript before it is translated. The remaining (and therefore translated) regions are known as “exons” and are spliced together to form a continuous mRNA sequence. mRNA splice sites, i.e., intron-exon junctions, may also be preferred target regions, and are particularly useful in situations where aberrant splicing is implicated in disease, or where an overproduction of a particular mRNA splice product is implicated in disease. Aberrant fusion junctions due to rearrangements or deletions are also preferred targets. It has also been found that introns can also be effective, and therefore preferred, target regions for antisense compounds targeted, for example, to DNA or pre-mRNA.

Once one or more target sites have been identified, oligonucleotides are chosen which are sufficiently complementary to the target, i.e., hybridize sufficiently well and with sufficient specificity, to give the desired effect.

In the context of this invention, “hybridization” means hydrogen bonding, which may be Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding, between complementary nucleoside or nucleotide bases. For example, adenine and thymine are complementary nucleobases which pair through the formation of hydrogen bonds. “Complementary,” as used herein, refers to the capacity for precise pairing between two nucleotides. For example, if a nucleotide at a certain position of an oligonucleotide is capable of hydrogen bonding with a nucleotide at the same position of a DNA or RNA molecule, then the oligonucleotide and the DNA or RNA are considered to be complementary to each other at that position. The oligonucleotide and the DNA or RNA are complementary to each other when a sufficient number of corresponding positions in each molecule are occupied by nucleotides which can hydrogen bond with each other. Thus, “specifically hybridizable” and “complementary” are terms which are used to indicate a sufficient degree of complementarity or precise pairing such that stable and specific binding occurs between the oligonucleotide and the DNA or RNA target. It is understood in the art that the sequence of an antisense compound need not be 100% complementary to that of its target nucleic acid to be specifically hybridizable. An antisense compound is specifically hybridizable when binding of the compound to the target DNA or RNA molecule interferes with the normal function of the target DNA or RNA to cause a loss of utility, and there is a sufficient degree of complementarity to avoid non-specific binding of the antisense compound to non-target sequences under conditions in which specific binding is desired, i.e., under physiological conditions in the case of in vivo assays or therapeutic treatment, and in the case of in vitro assays, under conditions in which the assays are performed.

Antisense compounds are commonly used as research reagents and diagnostics. For example, antisense oligonucleotides, which are able to inhibit gene expression with exquisite specificity, are often used by those of ordinary skill to elucidate the function of particular genes. Antisense compounds are also used, for example, to distinguish between functions of various members of a biological pathway. Antisense modulation has, therefore, been harnessed for research use.

The specificity and sensitivity of antisense is also harnessed by those of skill in the art for therapeutic uses. Antisense oligonucleotides have been employed as therapeutic moieties in the treatment of disease states in animals and man. Antisense oligonucleotides have been safely and effectively administered to humans and numerous clinical trials are presently underway. It is thus established that oligonucleotides can be useful therapeutic modalities that can be configured to be useful in treatment regimes for treatment of cells, tissues and animals, especially humans.

In the context of this invention, the term “oligonucleotide” refers to an oligomer or polymer of ribonucleic acid (RNA) or deoxyribonucleic acid (DNA) or mimetics thereof. This term includes oligonucleotides composed of naturally-occurring nucleobases, sugars and covalent internucleoside (backbone) linkages as well as oligonucleotides having non-naturally-occurring portions which function similarly. Such modified or substituted oligonucleotides are often preferred over native forms because of desirable properties such as, for example, enhanced cellular uptake, enhanced affinity for nucleic acid target and increased stability in the presence of nucleases.

While antisense oligonucleotides are a preferred form of antisense compound, the present invention comprehends other oligomeric antisense compounds, including but not limited to oligonucleotide mimetics such as are described below. The antisense compounds in accordance with this invention preferably comprise from about 8 to about 30 nucleobases (i.e. from about 8 to about 30 linked nucleosides). Particularly preferred antisense compounds are antisense oligonucleotides, even more preferably those comprising from about 12 to about 25 nucleobases. As is known in the art, a nucleoside is a base-sugar combination. The base portion of the nucleoside is normally a heterocyclic base. The two most common classes of such heterocyclic bases are the purines and the pyrimidines. Nucleotides are nucleosides that further include a phosphate group covalently linked to the sugar portion of the nucleoside. For those nucleosides that include a pentofuranosyl sugar, the phosphate group can be linked to either the 2′, 3′ or 5′ hydroxyl moiety of the sugar. In forming oligonucleotides, the phosphate groups covalently link adjacent nucleosides to one another to form a linear polymeric compound. In turn the respective ends of this linear polymeric structure can be further joined to form a circular structure, however, open linear structures are generally preferred. Within the oligonucleotide structure, the phosphate groups are commonly referred to as forming the internucleoside backbone of the oligonucleotide. The normal linkage or backbone of RNA and DNA is a 3′ to 5′ phosphodiester linkage.

Specific examples of preferred antisense compounds useful in this invention include oligonucleotides containing modified backbones or non-natural internucleoside linkages. As defined in this specification, oligonucleotides having modified backbones include those that retain a phosphorus atom in the backbone and those that do not have a phosphorus atom in the backbone. For the purposes of this specification, and as sometimes referenced in the art, modified oligonucleotides that do not have a phosphorus atom in their internucleoside backbone can also be considered to be oligonucleosides.

Preferred modified oligonucleotide backbones include, for example, phosphorothioates, chiral phosphorothioates, phosphorodithioates, phosphotriesters, aminoalkyl-phosphotriesters, methyl and other alkyl phosphonates including 3′-alkylene phosphonates and chiral phosphonates, phosphinates, phosphoramidates including 3′-amino phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, and boranophosphates having normal 3′-5′ linkages, 2′-5′ linked analogs of these, and those having inverted polarity wherein the adjacent pairs of nucleoside units are linked 3′-5′ to 5′-3′ or 2′-5′ to 5′-2′. Various salts, mixed salts and free acid forms are also included.

Representative United States patents that teach the preparation of the above phosphorus-containing linkages include, but are not limited to, U.S. Pat. Nos. 3,687,808; 4,469,863; 4,476,301; 5,023,243; 5,177,196; 5,188,897; 5,264,423; 5,276,019; 5,278,302; 5,286,717; 5,321,131; 5,399,676; 5,405,939; 5,453,496; 5,455,233; 5,466,677; 5,476,925; 5,519,126; 5,536,821; 5,541,306; 5,550,111; 5,563,253; 5,571,799; 5,587,361; and 5,625,050, certain of which are commonly owned with this application, and each of which is herein incorporated by reference.

Preferred modified oligonucleotide backbones that do not include a phosphorus atom therein have backbones that are formed by short chain alkyl or cycloalkyl internucleoside linkages, mixed heteroatom and alkyl or cycloalkyl internucleoside linkages, or one or more short chain heteroatomic or heterocyclic internucleoside linkages. These include those having morpholino linkages (formed in part from the sugar portion of a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfone backbones; formacetyl and thioformacetyl backbones; methylene formacetyl and thioformacetyl backbones; alkene containing backbones; sulfamate backbones; methyleneimino and methylenehydrazino backbones; sulfonate and sulfonamide backbones; amide backbones; and others having mixed N, O, S and CH ₂component parts.

Representative United States patents that teach the preparation of the above oligonucleosides include, but are not limited to, U.S. Pat. Nos. 5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141; 5,235,033; 5,264,562; 5,264,564; 5,405,938; 5,434,257; 5,466,677; 5,470,967; 5,489,677; 5,541,307; 5,561,225; 5,596,086; 5,602,240; 5,610,289; 5,602,240; 5,608,046; 5,610,289; 5,618,704; 5,623,070; 5,663,312; 5,633,360; 5,677,437; and 5,677,439, certain of which are commonly owned with this application, and each of which is herein incorporated by reference.

In other preferred oligonucleotide mimetics, both the sugar and the internucleoside linkage, i.e., the backbone, of the nucleotide units are replaced with novel groups. The base units are maintained for hybridization with an appropriate nucleic acid target compound. One such oligomeric compound, an oligonucleotide mimetic that has been shown to have excellent hybridization properties, is referred to as a peptide nucleic acid (PNA). In PNA compounds, the sugar-backbone of an oligonucleotide is replaced with an amide containing backbone, in particular an aminoethylglycine backbone. The nucleobases are retained and are bound directly or indirectly to aza nitrogen atoms of the amide portion of the backbone. Representative United States patents that teach the preparation of PNA compounds include, but are not limited to, U.S. Pat. Nos. 5,539,082; 5,714,331; and 5,719,262, each of which is herein incorporated by reference. Further teaching of PNA compounds can be found in Nielsen et al., Science, 1991, 254, 1497-1500.

Most preferred embodiments of the invention are oligonucleotides with phosphorothioate backbones and oligonucleosides with heteroatom backbones, and in particular —CH ₂—NH—O—CH₂—, —CH₂—N(CH₃)—O—CH₂— [known as a methylene (methylimino) or MMI backbone], —CH₂—O—N(CH₃) —CH₂—, —CH₂—N(CH₃)—N(CH₃)—CH₂— and —O—N(CH₃)—CH₂—CH₂— [wherein the native phosphodiester backbone is represented as —O—P—O—CH₂—] of the above referenced U.S. Pat. No. 5,489,677, and the amide backbones of the above referenced U.S. Pat. No. 5,602,240. Also preferred are oligonucleotides having morpholino backbone structures of the above-referenced U.S. Pat. No. 5,034,506.

Modified oligonucleotides may also contain one or more substituted sugar moieties. Preferred oligonucleotides comprise one of the following at the 2′ position: OH; F; O—S—, or N-alkyl; O—, S—, or N-alkenyl; O—, S— or N-alkynyl; or O-alkyl-O-alkyl, wherein the alkyl, alkenyl and alkynyl may be substituted or unsubstituted C ₁to C₁₀alkyl or C₂to C10 alkenyl and alkynyl. Particularly preferred are O[(CH₂)_nO]_mCH₃, O(CH₂)_nOCH₃, O(CH₂)_nNH₂, O(CH₂)_nCH₃, O(CH₂)_nONH₂, and O(CH₂)_nON[(CH₂)_nCH₃)]₂, where n and m are from 1 to about 10. Other preferred oligonucleotides comprise one of the following at the 2′ position: C₁to C₁₀lower alkyl, substituted lower alkyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH₃, OCN, Cl, Br, CN, CF₃, OCF₃, SOCH₃, SO₂CH₃, ONO₂, NO₂, N₃, NH₂, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl, an RNA cleaving group, a reporter group, an intercalator, a group for improving the pharmacokinetic properties of an oligonucleotide, or a group for improving the pharmacodynamic properties of an oligonucleotide, and other substituents having similar properties. A preferred modification includes 2′-methoxyethoxy (2′-O—CH₂CH₂OCH₃, also known as 2′-O-(2-methoxyethyl) or 2′-MOE) (Martin et al., Helv. Chim. Acta, 1995, 78, 486-504) i.e., an alkoxyalkoxy group. A further preferred modification includes 2′-dimethylaminooxyethoxy, i.e., a O(CH₂)₂ON(CH₃)₂group, also known as 2′-DMAOE, as described in examples hereinbelow, and 2′-dimethylaminoethoxyethoxy (also known in the art as 2′-O-dimethylaminoethoxyethyl or 2′-DMAEOE), i.e., 2′-O—CH₂—O—CH₂—N(CH₂)₂, also described in examples hereinbelow.

Other preferred modifications include 2′-methoxy (2′-O—CH ₃), 2′-aminopropoxy (2′-OCH₂CH₂CH₂NH₂) and 2′-fluoro (2′-F). Similar modifications may also be made at other positions on the oligonucleotide, particularly the 3′ position of the sugar on the 3′ terminal nucleotide or in 2′-5′ linked oligonucleotides and the 5′ position of 5′ terminal nucleotide. Oligonucleotides may also have sugar mimetics such as cyclobutyl moieties in place of the pentofuranosyl sugar. Representative United States patents that teach the preparation of such modified sugar structures include, but are not limited to, U.S. Pat. Nos. 4,981,957; 5,118,800; 5,319,080; 5,359,044; 5,393,878; 5,446,137; 5,466,786; 5,514,785; 5,519,134; 5,567,811; 5,576,427; 5,591,722; 5,597,909; 5,610,300; 5,627,053; 5,639,873; 5,646,265; 5,658,873; 5,670,633; and 5,700,920, certain of which are commonly owned with the instant application, and each of which is herein incorporated by reference in its entirety.

Oligonucleotides may also include nucleobase (often referred to in the art simply as “base”) modifications or substitutions. As used herein, “unmodified” or “natural” nucleobases include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) and uracil (U). Modified nucleobases include other synthetic and natural nucleobases such as 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine, 5-propynyl uracil and cytosine, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines and guanines, 5-halo particularly 5-bromo, 5-trifluoromethyl and other 5-substituted uracils and cytosines, 7-methylguanine and 7-methyladenine, 8-azaguanine and 8-azaadenine, 7-deazaguanine and 7-deazaadenine and 3-deazaguanine and 3-deazaadenine. Further nucleobases include those disclosed in U.S. Pat. No. 3,687,808, those disclosed in The Concise Encyclopedia Of Polymer Science And Engineering, pages 858-859, Kroschwitz, J. I., ed. John Wiley & Sons, 1990, those disclosed by Englisch et al., Angewandte Chemie, International Edition, 1991, 30, 613, and those disclosed by Sanghvi, Y. S., Chapter 15, Antisense Research and Applications, pages 289-302, Crooke, S. T. and Lebleu, B., ed., CRC Press, 1993. Certain of these nucleobases are particularly useful for increasing the binding affinity of the oligomeric compounds of the invention. These include 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and 0-6 substituted purines, including 2-aminopropyladenine, 5-propynyluracil and 5-propynylcytosine. 5-methylcytosine substitutions have been shown to increase nucleic acid duplex stability by 0.6-1.2° C. (Sanghvi, Y. S., Crooke, S. T. and Lebleu, B., eds., Antisense Research and Applications, CRC Press, Boca Raton, 1993, pp. 276-278) and are presently preferred base substitutions, even more particularly when combined with 2′-O-methoxyethyl sugar modifications.

Representative United States patents that teach the preparation of certain of the above noted modified nucleobases as well as other modified nucleobases include, but are not limited to, the above noted U.S. Pat. No. 3,687,808, as well as U.S. Pat. Nos. 4,845,205; 5,130,302; 5,134,066; 5,175,273; 5,367,066; 5,432,272; 5,457,187; 5,459,255; 5,484,908; 5,502,177; 5,525,711; 5,552,540; 5,587,469; 5,594,121, 5,596,091; 5,614,617; and 5,681,941, certain of which are commonly owned with the instant application, and each of which is herein incorporated by reference, and U.S. Pat. No. 5,750,692, which is commonly owned with the instant application and also herein incorporated by reference.

Another modification of the oligonucleotides of the invention involves chemically linking to the oligonucleotide one or more moieties or conjugates which enhance the activity, cellular distribution or cellular uptake of the oligonucleotide. Such moieties include but are not limited to lipid moieties such as a cholesterol moiety (Letsinger et al., Proc. Natl. Acad. Sci. USA, 1989, 86, 6553-6556), cholic acid (Manoharan et al., Bioorg. Med. Chem. Let., 1994, 4, 1053-1060), a thioether, e.g., hexyl-S-tritylthiol (Manoharan et al., Ann. N.Y. Acad. Sci., 1992, 660, 306-309; Manoharan et al., Bioorg. Med. Chem. Let., 1993, 3, 2765-2770), a thiocholesterol (Oberhauser et al., Nucl. Acids Res., 1992, 20, 533-538), an aliphatic chain, e.g., dodecandiol or undecyl residues (Saison-Behmoaras et al., EMBO J., 1991, 10, 1111-1118; Kabanov et al., FEBS Lett., 1990, 259, 327-330; Svinarchuk et al., Biochimie, 1993, 75, 49-54), a phospholipid, e.g., di-hexadecyl-rac-glycerol or triethylammonium 1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate (Manoharan et al., Tetrahedron Lett., 1995, 36, 3651-3654; Shea et al., Nucl. Acids Res., 1990, 18, 3777-3783), a polyamine or a polyethylene glycol chain (Manoharan et al., Nucleosides & Nucleotides, 1995, 14, 969-973), or adamantane acetic acid (Manoharan et al., Tetrahedron Lett., 1995, 36, 3651-3654), a palmityl moiety (Mishra et al., Biochim. Biophys. Acta, 1995, 1264, 229-237), or an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety (Crooke et al., J. Pharmacol. Exp. Ther., 1996, 277, 923-937.

Representative United States patents that teach the preparation of such oligonucleotide conjugates include, but are not limited to, U.S. Pat. Nos. 4,828,979; 4,948,882; 5,218,105; 5,525,465; 5,541,313; 5,545,730; 5,552,538; 5,578,717, 5,580,731; 5,580,731; 5,591,584; 5,109,124; 5,118,802; 5,138,045; 5,414,077; 5,486,603; 5,512,439; 5,578,718; 5,608,046; 4,587,044; 4,605,735; 4,667,025; 4,762,779; 4,789,737; 4,824,941; 4,835,263; 4,876,335; 4,904,582; 4,958,013; 5,082,830; 5,112,963; 5,214,136; 5,082,830; 5,112,963; 5,214,136; 5,245,022; 5,254,469; 5,258,506; 5,262,536; 5,272,250; 5,292,873; 5,317,098; 5,371,241, 5,391,723; 5,416,203, 5,451,463; 5,510,475; 5,512,667; 5,514,785; 5,565,552; 5,567,810; 5,574,142; 5,585,481; 5,587,371; 5,595,726; 5,597,696; 5,599,923; 5,599,928 and 5,688,941, certain of which are commonly owned with the instant application, and each of which is herein incorporated by reference.

It is not necessary for all positions in a given compound to be uniformly modified, and in fact more than one of the aforementioned modifications may be incorporated in a single compound or even at a single nucleoside within an oligonucleotide. The present invention also includes antisense compounds which are chimeric compounds. “Chimeric” antisense compounds or “chimeras,” in the context of this invention, are antisense compounds, particularly oligonucleotides, which contain two or more chemically distinct regions, each made up of at least one monomer unit, i.e., a nucleotide in the case of an oligonucleotide compound. These oligonucleotides typically contain at least one region wherein the oligonucleotide is modified so as to confer upon the oligonucleotide increased resistance to nuclease degradation, increased cellular uptake, and/or increased binding affinity for the target nucleic acid. An additional region of the oligonucleotide may serve as a substrate for enzymes capable of cleaving RNA:DNA or RNA:RNA hybrids. By way of example, RNase H is a cellular endonuclease which cleaves the RNA strand of an RNA:DNA duplex. Activation of RNase H, therefore, results in cleavage of the RNA target, thereby greatly enhancing the efficiency of oligonucleotide inhibition of gene expression. Consequently, comparable results can often be obtained with shorter oligonucleotides when chimeric oligonucleotides are used, compared to phosphorothioate deoxyoligonucleotides hybridizing to the same target region. Cleavage of the RNA target can be routinely detected by gel electrophoresis and, if necessary, associated nucleic acid hybridization techniques known in the art.

Chimeric antisense compounds of the invention may be formed as composite structures of two or more oligonucleotides, modified oligonucleotides, oligonucleosides and/or oligonucleotide mimetics as described above. Such compounds have also been referred to in the art as hybrids or gapmers. Representative United States patents that teach the preparation of such hybrid structures include, but are not limited to, U.S. Pat. Nos. 5,013,830; 5,149,797; 5,220,007; 5,256,775; 5,366,878; 5,403,711; 5,491,133; 5,565,350; 5,623,065; 5,652,355; 5,652,356; and 5,700,922, certain of which are commonly owned with the instant application, and each of which is herein incorporated by reference in its entirety.

The antisense compounds used in accordance with this invention may be conveniently and routinely made through the well-known technique of solid phase synthesis. Equipment for such synthesis is sold by several vendors including, for example, Applied Biosystems (Foster City, Calif.). Any other means for such synthesis known in the art may additionally or alternatively be employed. It is well known to use similar techniques to prepare oligonucleotides such as the phosphorothioates and alkylated derivatives.

The antisense compounds of the invention are synthesized in vitro and do not include antisense compositions of biological origin, or genetic vector constructs designed to direct the in vivo synthesis of antisense molecules.

The compounds of the invention may also be admixed, encapsulated, conjugated or otherwise associated with other molecules, molecule structures or mixtures of compounds, as for example, liposomes, receptor targeted molecules, oral, rectal, topical or other formulations, for assisting in uptake, distribution and/or absorption. Representative United States patents that teach the preparation of such uptake, distribution and/or absorption assisting formulations include, but are not limited to, U.S. Pat. Nos. 5,108,921; 5,354,844; 5,416,016; 5,459,127; 5,521,291; 5,543,158; 5,547,932; 5,583,020; 5,591,721; 4,426,330; 4,534,899; 5,013,556; 5,108,921; 5,213,804; 5,227,170; 5,264,221; 5,356,633; 5,395,619; 5,416,016; 5,417,978; 5,462,854; 5,469,854; 5,512,295; 5,527,528; 5,534,259; 5,543,152; 5,556,948; 5,580,575; and 5,595,756, each of which is herein incorporated by reference.

The antisense compounds of the invention encompass any pharmaceutically acceptable salts, esters, or salts of such esters, or any other compound which, upon administration to an animal including a human, is capable of providing (directly or indirectly) the biologically active metabolite or residue thereof. Accordingly, for example, the disclosure is also drawn to prodrugs and pharmaceutically acceptable salts of the compounds of the invention, pharmaceutically acceptable salts of such prodrugs, and other bioequivalents.

The term “prodrug” indicates a therapeutic agent that is prepared in an inactive form that is converted to an active form (i.e., drug) within the body or cells thereof by the action of endogenous enzymes or other chemicals and/or conditions. In particular, prodrug versions of the oligonucleotides of the invention are prepared as SATE [(S-acetyl-2-thioethyl) phosphate] derivatives according to the methods disclosed in WO 93/24510 to Gosselin et al., published Dec. 9, 1993 or in WO 94/26764 to Imbach et al.

The term “pharmaceutically acceptable salts” refers to physiologically and pharmaceutically acceptable salts of the compounds of the invention: i.e., salts that retain the desired biological activity of the parent compound and do not impart undesired toxicological effects thereto.

Pharmaceutically acceptable base addition salts are formed with metals or amines, such as alkali and alkaline earth metals or organic amines. Examples of metals used as cations are sodium, potassium, magnesium, calcium, and the like. Examples of suitable amines are N,N′-dibenzylethylenediamine, chloroprocaine, choline, diethanolamine, dicyclohexylamine, ethylenediamine, N-methylglucamine, and procaine (see, for example, Berge et al., “Pharmaceutical Salts,” J. of Pharma Sci., 1977, 66, 1-19). The base addition salts of said acidic compounds are prepared by contacting the free acid form with a sufficient amount of the desired base to produce the salt in the conventional manner. The free acid form may be regenerated by contacting the salt form with an acid and isolating the free acid in the conventional manner. The free acid forms differ from their respective salt forms somewhat in certain physical properties such as solubility in polar solvents, but otherwise the salts are equivalent to their respective free acid for purposes of the present invention. As used herein, a “pharmaceutical addition salt” includes a pharmaceutically acceptable salt of an acid form of one of the components of the compositions of the invention. These include organic or inorganic acid salts of the amines. Preferred acid salts are the hydrochlorides, acetates, salicylates, nitrates and phosphates. Other suitable pharmaceutically acceptable salts are well known to those skilled in the art and include basic salts of a variety of inorganic and organic acids, such as, for example, with inorganic acids, such as for example hydrochloric acid, hydrobromic acid, sulfuric acid or phosphoric acid; with organic carboxylic, sulfonic, sulfo or phospho acids or N-substituted sulfamic acids, for example acetic acid, propionic acid, glycolic acid, succinic acid, maleic acid, hydroxymaleic acid, methylmaleic acid, fumaric acid, malic acid, tartaric acid, lactic acid, oxalic acid, gluconic acid, glucaric acid, glucuronic acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, salicylic acid, 4-aminosalicylic acid, 2-phenoxybenzoic acid, 2-acetoxybenzoic acid, embonic acid, nicotinic acid or isonicotinic acid; and with amino acids, such as the 20 alpha-amino acids involved in the synthesis of proteins in nature, for example glutamic acid or aspartic acid, and also with phenylacetic acid, methanesulfonic acid, ethanesulfonic acid, 2-hydroxyethanesulfonic acid, ethane-1,2-disulfonic acid, benzenesulfonic acid, 4-methylbenzenesulfoic acid, naphthalene-2-sulfonic acid, naphthalene-1,5-disulfonic acid, 2- or 3-phosphoglycerate, glucose-6-phosphate, N-cyclohexylsulfamic acid (with the formation of cyclamates), or with other acid organic compounds, such as ascorbic acid. Pharmaceutically acceptable salts of compounds may also be prepared with a pharmaceutically acceptable cation. Suitable pharmaceutically acceptable cations are well known to those skilled in the art and include alkaline, alkaline earth, ammonium and quaternary ammonium cations. Carbonates or hydrogen carbonates are also possible.

For oligonucleotides, preferred examples of pharmaceutically acceptable salts include but are not limited to (a) salts formed with cations such as sodium, potassium, ammonium, magnesium, calcium, polyamines such as spermine and spermidine, etc.; (b) acid addition salts formed with inorganic acids, for example hydrochloric acid, hydrobromic acid, sulfuric acid, phosphoric acid, nitric acid and the like; (c) salts formed with organic acids such as, for example, acetic acid, oxalic acid, tartaric acid, succinic acid, maleic acid, fumaric acid, gluconic acid, citric acid, malic acid, ascorbic acid, benzoic acid, tannic acid, palmitic acid, alginic acid, polyglutamic acid, naphthalenesulfonic acid, methanesulfonic acid, p-toluenesulfonic acid, naphthalenedisulfonic acid, polygalacturonic acid, and the like; and (d) salts formed from elemental anions such as chlorine, bromine, and iodine.

The antisense compounds of the present invention can be utilized for diagnostics, therapeutics, prophylaxis and as research reagents and kits. For therapeutics, an animal, preferably a human, suspected of having a disease or disorder which can be treated by modulating the expression of glycogen synthase kinase 3 alpha is treated by administering antisense compounds in accordance with this invention. The compounds of the invention can be utilized in pharmaceutical compositions by adding an effective amount of an antisense compound to a suitable pharmaceutically acceptable diluent or carrier. Use of the antisense compounds and methods of the invention may also be useful prophylactically, e.g., to prevent or delay infection, inflammation or tumor formation, for example.

The antisense compounds of the invention are useful for research and diagnostics, because these compounds hybridize to nucleic acids encoding glycogen synthase kinase 3 alpha, enabling sandwich and other assays to easily be constructed to exploit this fact. Hybridization of the antisense oligonucleotides of the invention with a nucleic acid encoding glycogen synthase kinase 3 alpha can be detected by means known in the art. Such means may include conjugation of an enzyme to the oligonucleotide, radiolabelling of the oligonucleotide or any other suitable detection means. Kits using such detection means for detecting the level of glycogen synthase kinase 3 alpha in a sample may also be prepared.

The present invention also includes pharmaceutical compositions and formulations which include the antisense compounds of the invention. The pharmaceutical compositions of the present invention may be administered in a number of ways depending upon whether local or systemic treatment is desired and upon the area to be treated. Administration may be topical (including ophthalmic and to mucous membranes including vaginal and rectal delivery), pulmonary, e.g., by inhalation or insufflation of powders or aerosols, including by nebulizer; intratracheal, intranasal, epidermal and transdermal), oral or parenteral. Parenteral administration includes intravenous, intraarterial, subcutaneous, intraperitoneal or intramuscular injection or infusion; or intracranial, e.g., intrathecal or intraventricular, administration. Oligonucleotides with at least one 2′-O-methoxyethyl modification are believed to be particularly useful for oral administration.

Pharmaceutical compositions and formulations for topical administration may include transdermal patches, ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders. Conventional pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the like may be necessary or desirable. Coated condoms, gloves and the like may also be useful.

Compositions and formulations for oral administration include powders or granules, suspensions or solutions in water or non-aqueous media, capsules, sachets or tablets. Thickeners, flavoring agents, diluents, emulsifiers, dispersing aids or binders may be desirable.

Compositions and formulations for parenteral, intrathecal or intraventricular administration may include sterile aqueous solutions which may also contain buffers, diluents and other suitable additives such as, but not limited to, penetration enhancers, carrier compounds and other pharmaceutically acceptable carriers or excipients.

Pharmaceutical compositions of the present invention include, but are not limited to, solutions, emulsions, and liposome-containing formulations. These compositions may be generated from a variety of components that include, but are not limited to, preformed liquids, self-emulsifying solids and self-emulsifying semisolids.

The pharmaceutical formulations of the present invention, which may conveniently be presented in unit dosage form, may be prepared according to conventional techniques well known in the pharmaceutical industry. Such techniques include the step of bringing into association the active ingredients with the pharmaceutical carrier(s) or excipient(s). In general the formulations are prepared by uniformly and intimately bringing into association the active ingredients with liquid carriers or finely divided solid carriers or both, and then, if necessary, shaping the product.

The compositions of the present invention may be formulated into any of many possible dosage forms such as, but not limited to, tablets, capsules, liquid syrups, soft gels, suppositories, and enemas. The compositions of the present invention may also be formulated as suspensions in aqueous, non-aqueous or mixed media. Aqueous suspensions may further contain substances which increase the viscosity of the suspension including, for example, sodium carboxymethylcellulose, sorbitol and/or dextran. The suspension may also contain stabilizers.

In one embodiment of the present invention the pharmaceutical compositions may be formulated and used as foams. Pharmaceutical foams include formulations such as, but not limited to, emulsions, microemulsions, creams, jellies and liposomes. While basically similar in nature these formulations vary in the components and the consistency of the final product. The preparation of such compositions and formulations is generally known to those skilled in the pharmaceutical and formulation arts and may be applied to the formulation of the compositions of the present invention.

Emulsions

The compositions of the present invention may be prepared and formulated as emulsions. Emulsions are typically heterogenous systems of one liquid dispersed in another in the form of droplets usually exceeding 0.1 μm in diameter. (Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199; Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., Volume 1, p. 245; Block in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 2, p. 335; Higuchi et al., in Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa., 1985, p. 301). Emulsions are often biphasic systems comprising of two immiscible liquid phases intimately mixed and dispersed with each other. In general, emulsions may be either water-in-oil (w/o) or of the oil-in-water (o/w) variety. When an aqueous phase is finely divided into and dispersed as minute droplets into a bulk oily phase the resulting composition is called a water-in-oil (w/o) emulsion. Alternatively, when an oily phase is finely divided into and dispersed as minute droplets into a bulk aqueous phase the resulting composition is called an oil-in-water (o/w) emulsion. Emulsions may contain additional components in addition to the dispersed phases and the active drug which may be present as a solution in either the aqueous phase, oily phase or itself as a separate phase. Pharmaceutical excipients such as emulsifiers, stabilizers, dyes, and anti-oxidants may also be present in emulsions as needed. Pharmaceutical emulsions may also be multiple emulsions that are comprised of more than two phases such as, for example, in the case of oil-in-water-in-oil (o/w/o) and water-in-oil-in-water (w/o/w) emulsions. Such complex formulations often provide certain advantages that simple binary emulsions do not. Multiple emulsions in which individual oil droplets of an o/w emulsion enclose small water droplets constitute a w/o/w emulsion. Likewise a system of oil droplets enclosed in globules of water stabilized in an oily continuous provides an o/w/o emulsion.

Emulsions are characterized by little or no thermodynamic stability. Often, the dispersed or discontinuous phase of the emulsion is well dispersed into the external or continuous phase and maintained in this form through the means of emulsifiers or the viscosity of the formulation. Either of the phases of the emulsion may be a semisolid or a solid, as is the case of emulsion-style ointment bases and creams. Other means of stabilizing emulsions entail the use of emulsifiers that may be incorporated into either phase of the emulsion. Emulsifiers may broadly be classified into four categories: synthetic surfactants, naturally occurring emulsifiers, absorption bases, and finely dispersed solids (Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199).

Synthetic surfactants, also known as surface active agents, have found wide applicability in the formulation of emulsions and have been reviewed in the literature (Rieger, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 285; Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), Marcel Dekker, Inc., New York, N.Y., 1988, volume 1, p. 199). Surfactants are typically amphiphilic and comprise a hydrophilic and a hydrophobic portion. The ratio of the hydrophilic to the hydrophobic nature of the surfactant has been termed the hydrophile/lipophile balance (HLB) and is a valuable tool in categorizing and selecting surfactants in the preparation of formulations. Surfactants may be classified into different classes based on the nature of the hydrophilic group: nonionic, anionic, cationic and amphoteric (Rieger, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 285).

Naturally occurring emulsifiers used in emulsion formulations include lanolin, beeswax, phosphatides, lecithin and acacia. Absorption bases possess hydrophilic properties such that they can soak up water to form w/o emulsions yet retain their semisolid consistencies, such as anhydrous lanolin and hydrophilic petrolatum. Finely divided solids have also been used as good emulsifiers especially in combination with surfactants and in viscous preparations. These include polar inorganic solids, such as heavy metal hydroxides, nonswelling clays such as bentonite, attapulgite, hectorite, kaolin, montmorillonite, colloidal aluminum silicate and colloidal magnesium aluminum silicate, pigments and nonpolar solids such as carbon or glyceryl tristearate.

A large variety of non-emulsifying materials are also included in emulsion formulations and contribute to the properties of emulsions. These include fats, oils, waxes, fatty acids, fatty alcohols, fatty esters, humectants, hydrophilic colloids, preservatives and antioxidants (Block, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 335; Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199).

Hydrophilic colloids or hydrocolloids include naturally occurring gums and synthetic polymers such as polysaccharides (for example, acacia, agar, alginic acid, carrageenan, guar gum, karaya gum, and tragacanth), cellulose derivatives (for example, carboxymethylcellulose and carboxypropylcellulose), and synthetic polymers (for example, carbomers, cellulose ethers, and carboxyvinyl polymers). These disperse or swell in water to form colloidal solutions that stabilize emulsions by forming strong interfacial films around the dispersed-phase droplets and by increasing the viscosity of the external phase.

Since emulsions often contain a number of ingredients such as carbohydrates, proteins, sterols and phosphatides that may readily support the growth of microbes, these formulations often incorporate preservatives. Commonly used preservatives included in emulsion formulations include methyl paraben, propyl paraben, quaternary ammonium salts, benzalkonium chloride, esters of p-hydroxybenzoic acid, and boric acid. Antioxidants are also commonly added to emulsion formulations to prevent deterioration of the formulation. Antioxidants used may be free radical scavengers such as tocopherols, alkyl gallates, butylated hydroxyanisole, butylated hydroxytoluene, or reducing agents such as ascorbic acid and sodium metabisulfite, and antioxidant synergists such as citric acid, tartaric acid, and lecithin.

The application of emulsion formulations via dermatological, oral and parenteral routes and methods for their manufacture have been reviewed in the literature (Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199). Emulsion formulations for oral delivery have been very widely used because of reasons of ease of formulation, efficacy from an absorption and bioavailability standpoint. (Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 245; Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199). Mineral-oil base laxatives, oil-soluble vitamins and high fat nutritive preparations are among the materials that have commonly been administered orally as o/w emulsions.

In one embodiment of the present invention, the compositions of oligonucleotides and nucleic acids are formulated as microemulsions. A microemulsion may be defined as a system of water, oil and amphiphile which is a single optically isotropic and thermodynamically stable liquid solution (Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 245). Typically microemulsions are systems that are prepared by first dispersing an oil in an aqueous surfactant solution and then adding a sufficient amount of a fourth component, generally an intermediate chain-length alcohol to form a transparent system. Therefore, microemulsions have also been described as thermodynamically stable, isotropically clear dispersions of two immiscible liquids that are stabilized by interfacial films of surface-active molecules (Leung and Shah, in: Controlled Release of Drugs: Polymers and Aggregate Systems, Rosoff, M., Ed., 1989, VCH Publishers, New York, pages 185-215). Microemulsions commonly are prepared via a combination of three to five components that include oil, water, surfactant, cosurfactant and electrolyte. Whether the microemulsion is of the water-in-oil (w/o) or an oil-in-water (o/w) type is dependent on the properties of the oil and surfactant used and on the structure and geometric packing of the polar heads and hydrocarbon tails of the surfactant molecules (Schott, in Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa., 1985, p. 271).

The phenomenological approach utilizing phase diagrams has been extensively studied and has yielded a comprehensive knowledge, to one skilled in the art, of how to formulate microemulsions (Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 245; Block, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 335). Compared to conventional emulsions, microemulsions offer the advantage of solubilizing water-insoluble drugs in a formulation of thermodynamically stable droplets that are formed spontaneously.

Surfactants used in the preparation of microemulsions include, but are not limited to, ionic surfactants, non-ionic surfactants, Brij 96, polyoxyethylene oleyl ethers, polyglycerol fatty acid esters, tetraglycerol monolaurate (ML310), tetraglycerol monooleate (MO310), hexaglycerol monooleate (PO310), hexaglycerol pentaoleate (P0500), decaglycerol monocaprate (MCA750), decaglycerol monooleate (MO750), decaglycerol sequioleate (S0750), decaglycerol decaoleate (DA0750), alone or in combination with cosurfactants. The cosurfactant, usually a short-chain alcohol such as ethanol, 1-propanol, and 1-butanol, serves to increase the interfacial fluidity by penetrating into the surfactant film and consequently creating a disordered film because of the void space generated among surfactant molecules. Microemulsions may, however, be prepared without the use of cosurfactants and alcohol-free self-emulsifying microemulsion systems are known in the art. The aqueous phase may typically be, but is not limited to, water, an aqueous solution of the drug, glycerol, PEG300, PEG400, polyglycerols, propylene glycols, and derivatives of ethylene glycol. The oil phase may include, but is not limited to, materials such as Captex 300, Captex 355, Capmul MCM, fatty acid esters, medium chain (C8-C12) mono, di, and tri-glycerides, polyoxyethylated glyceryl fatty acid esters, fatty alcohols, polyglycolized glycerides, saturated polyglycolized C8-C10 glycerides, vegetable oils and silicone oil.

Microemulsions are particularly of interest from the standpoint of drug solubilization and-the enhanced absorption of drugs. Lipid based microemulsions (both o/w and w/o) have been proposed to enhance the oral bioavailability of drugs, including peptides (Constantinides et al., Pharmaceutical Research, 1994, 11, 1385-1390; Ritschel, Meth. Find. Exp. Clin. Pharmacol., 1993, 13, 205). Microemulsions afford advantages of improved drug solubilization, protection of drug from enzymatic hydrolysis, possible enhancement of drug absorption due to surfactant-induced alterations in membrane fluidity and permeability, ease of preparation, ease of oral administration over solid dosage forms, improved clinical potency, and decreased toxicity (Constantinides et al., Pharmaceutical Research, 1994, 11, 1385; Ho et al., J. Pharm. Sci., 1996, 85, 138-143). Often microemulsions may form spontaneously when their components are brought together at ambient temperature. This may be particularly advantageous when formulating thermolabile drugs, peptides or oligonucleotides. Microemulsions have also been effective in the transdermal delivery of active components in both cosmetic and pharmaceutical applications. It is expected that the microemulsion compositions and formulations of the present invention will facilitate the increased systemic absorption of oligonucleotides and nucleic acids from the gastrointestinal tract, as well as improve the local cellular uptake of oligonucleotides and nucleic acids within the gastrointestinal tract, vagina, buccal cavity and other areas of administration.

Microemulsions of the present invention may also contain additional components and additives such as sorbitan monostearate (Grill 3), Labrasol, and penetration enhancers to improve the properties of the formulation and to enhance the absorption of the oligonucleotides and nucleic acids of the present invention. Penetration enhancers used in the microemulsions of the present invention may be classified as belonging to one of five broad categories—surfactants, fatty acids, bile salts, chelating agents, and non-chelating non-surfactants (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p. 92). Each of these classes has been discussed above.

Liposomes

There are many organized surfactant structures besides microemulsions that have been studied and used for the formulation of drugs. These include monolayers, micelles, bilayers and vesicles. Vesicles, such as liposomes, have attracted great interest because of their specificity and the duration of action they offer from the standpoint of drug delivery. As used in the present invention, the term “liposome” means a vesicle composed of amphiphilic lipids arranged in a spherical bilayer or bilayers.

Liposomes are unilamellar or multilamellar vesicles which have a membrane formed from a lipophilic material and an aqueous interior. The aqueous portion contains the composition to be delivered. Cationic liposomes possess the advantage of being able to fuse to the cell wall. Non-cationic liposomes, although not able to fuse as efficiently with the cell wall, are taken up by macrophages in vivo.

In order to cross intact mammalian skin, lipid vesicles must pass through a series of fine pores, each with a diameter less than 50 nm, under the influence of a suitable transdermal gradient. Therefore, it is desirable to use a liposome which is highly deformable and able to pass through such fine pores.

Further advantages of liposomes include; liposomes obtained from natural phospholipids are biocompatible and biodegradable; liposomes can incorporate a wide range of water and lipid soluble drugs; liposomes can protect Encapsulated drugs in their internal compartments from metabolism and degradation (Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 245). Important considerations in the preparation of liposome formulations are the lipid surface charge, vesicle size and the aqueous volume of the liposomes.

Liposomes are useful for the transfer and delivery of active ingredients to the site of action. Because the liposomal membrane is structurally similar to biological membranes, when liposomes are applied to a tissue, the liposomes start to merge with the cellular membranes. As the merging of the liposome and cell progresses, the liposomal contents are emptied into the cell where the active agent may act.

Liposomal formulations have been the focus of extensive investigation as the mode of delivery for many drugs. There is growing evidence that for topical administration, liposomes present several advantages over other formulations. Such advantages include reduced side-effects related to high systemic absorption of the administered drug, increased accumulation of the administered drug at the desired target, and the ability to administer a wide variety of drugs, both hydrophilic and hydrophobic, into the skin.

Several reports have detailed the ability of liposomes to deliver agents including high-molecular weight DNA into the skin. Compounds including analgesics, antibodies, hormones and high-molecular weight DNAs have been administered to the skin. The majority of applications resulted in the targeting of the upper epidermis.

Liposomes fall into two broad classes. Cationic liposomes are positively charged liposomes which interact with the negatively charged DNA molecules to form a stable complex. The positively charged DNA/liposome complex binds to the negatively charged cell surface and is internalized in an endosome. Due to the acidic pH within the endosome, the liposomes are ruptured, releasing their contents into the cell cytoplasm (Wang et al., Biochem. Biophys. Res. Commun., 1987, 147, 980-985).

Liposomes which are pH-sensitive or negatively-charged, entrap DNA rather than complex with it. Since both the DNA and the lipid are similarly charged, repulsion rather than complex formation occurs. Nevertheless, some DNA is entrapped within the aqueous interior of these liposomes. pH-sensitive liposomes have been used to deliver DNA encoding the thymidine kinase gene to cell monolayers in culture. Expression of the exogenous gene was detected in the target cells (Zhou et al., Journal of Controlled Release, 1992, 19, 269-274).

One major type of liposomal composition includes phospholipids other than naturally-derived phosphatidylcholine. Neutral liposome compositions, for example, can be formed from dimyristoyl phosphatidylcholine (DMPC) or dipalmitoyl phosphatidylcholine (DPPC). Anionic liposome compositions generally are formed from dimyristoyl phosphatidylglycerol, while anionic fusogenic liposomes are formed primarily from dioleoyl phosphatidylethanolamine (DOPE). Another type of liposomal composition is formed from phosphatidylcholine (PC) such as, for example, soybean PC, and egg PC. Another type is formed from mixtures of phospholipid and/or phosphatidylcholine and/or cholesterol.

Several studies have assessed the topical delivery of liposomal drug formulations to the skin. Application of liposomes containing interferon to guinea pig skin resulted in a reduction of skin herpes sores while delivery of interferon via other means (e.g. as a solution or as an emulsion) were ineffective (Weiner et al., Journal of Drug Targeting, 1992, 2, 405-410). Further, an additional study tested the efficacy of interferon administered as part of a liposomal formulation to the administration of interferon using an aqueous system, and concluded that the liposomal formulation was superior to aqueous administration (du Plessis et al., Antiviral Research, 1992, 18, 259-265).

Non-ionic liposomal systems have also been examined to determine their utility in the delivery of drugs to the skin, in particular systems comprising non-ionic surfactant and cholesterol. Non-ionic liposomal formulations comprising Novasome™ I (glyceryl dilaurate/cholesterol/polyoxyethylene-10-stearyl ether) and Novasome™ II (glyceryl distearate/cholesterol/polyoxyethylene-10-stearyl ether) were used to deliver cyclosporin-A into the dermis of mouse skin. Results indicated that such non-ionic liposomal systems were effective in facilitating the deposition of cyclosporin-A into different layers of the skin (Hu et al. S.T.P.Pharma. Sci., 1994, 4, 6, 466).

Liposomes also include “sterically stabilized” liposomes, a term which, as used herein, refers to liposomes comprising one or more specialized lipids that, when incorporated into liposomes, result in enhanced circulation lifetimes relative to liposomes lacking such specialized lipids. Examples of sterically stabilized liposomes are those in which part of the vesicle-forming lipid portion of the liposome (A) comprises one or more glycolipids, such as monosialoganglioside G _Ml, or (B) is derivatized with one or more hydrophilic polymers, such as a polyethylene glycol (PEG) moiety. While not wishing to be bound by any particular theory, it is thought in the art that, at least for sterically stabilized liposomes containing gangliosides, sphingomyelin, or PEG-derivatized lipids, the enhanced circulation half-life of these sterically stabilized liposomes derives from a reduced uptake into cells of the reticuloendothelial system (RES) (Allen et al., FEBS Letters, 1987, 223, 42; Wu et al., Cancer Research, 1993, 53, 3765). Various liposomes comprising one or more glycolipids are known in the art. Papahadjopoulos et al. (Ann. N.Y. Acad. Sci., 1987, 507, 64) reported the ability of monosialoganglioside G_Ml, galactocerebroside sulfate and phosphatidylinositol to improve blood half-lives of liposomes. These findings were expounded upon by Gabizon et al. (Proc. Natl. Acad. Sci. U.S.A., 1988, 85, 6949). U.S. Pat. No. 4,837,028 and WO 88/04924, both to Allen et al., disclose liposomes comprising (1) sphingomyelin and (2) the ganglioside G_Mlor a galactocerebroside sulfate ester. U.S. Pat. No. 5,543,152 (Webb et al.) discloses liposomes comprising sphingomyelin. Liposomes comprising 1,2-sn-dimyristoylphosphatidylcholine are disclosed in WO 97/13499 (Lim et al.).

Many liposomes comprising lipids derivatized with one or more hydrophilic polymers, and methods of preparation thereof, are known in the art. Sunamoto et al. ( Bull. Chem. Soc. Jpn., 1980, 53, 2778) described liposomes comprising a nonionic detergent, 2C₁₂15G, that contains a PEG moiety. Illum et al. (FEBS Lett., 1984, 167, 79) noted that hydrophilic coating of polystyrene particles with polymeric glycols results in significantly enhanced blood half-lives. Synthetic phospholipids modified by the attachment of carboxylic groups of polyalkylene glycols (e.g., PEG) are described by Sears (U.S. Pat. Nos. 4,426,330 and 4,534,899). Klibanov et al. (FEBS Lett., 1990, 268, 235) described experiments demonstrating that liposomes comprising phosphatidylethanolamine (PE) derivatized with PEG or PEG stearate have significant increases in blood circulation half-lives. Blume et al. (Biochimica et Biophysica Acta, 1990, 1029, 91) extended such observations to other PEG-derivatized phospholipids, e.g., DSPE-PEG, formed from the combination of distearoylphosphatidylethanolamine (DSPE) and PEG. Liposomes having covalently bound PEG moieties on their external surface are described in European Patent No. EP 0 445 131 B1 and WO 90/04384 to Fisher. Liposome compositions containing 1-20 mole percent of PE derivatized with PEG, and methods of use thereof, are described by Woodle et al. (U.S. Pat. Nos. 5,013,556 and 5,356,633) and Martin et al. (U.S. Pat. No. 5,213,804 and European Patent No. EP 0 496 813 B1). Liposomes comprising a number of other lipid-polymer conjugates are disclosed in WO 91/05545 and U.S. Pat. No. 5,225,212 (both to Martin et al.) and in WO 94/20073 (Zalipsky et al.) Liposomes comprising PEG-modified ceramide lipids are described in WO 96/10391 (Choi et al.). U.S. Pat. Nos. 5,540,935 (Miyazaki et al.) and 5,556,948 (Tagawa et al.) describe PEG-containing liposomes that can be further derivatized with functional moieties on their surfaces.

A limited number of liposomes comprising nucleic acids are known in the art. WO 96/40062 to Thierry et al. discloses methods for encapsulating high molecular weight nucleic acids in liposomes. U.S. Pat. No. 5,264,221 to Tagawa et al. discloses protein-bonded liposomes and asserts that the contents of such liposomes may include an antisense RNA. U.S. Pat. No. 5,665,710 to Rahman et al. describes certain methods of encapsulating oligodeoxynucleotides in liposomes. WO 97/04787 to Love et al. discloses liposomes comprising antisense oligonucleotides targeted to the raf gene.

Transfersomes are yet another type of liposomes, and are highly deformable lipid aggregates which are attractive candidates for drug delivery vehicles. Transfersomes may be described as lipid droplets which are so highly deformable that they are easily able to penetrate through pores which are smaller than the droplet. Transfersomes are adaptable to the environment in which they are used, e.g. they are self-optimizing (adaptive to the shape of pores in the skin), self-repairing, frequently reach their targets without fragmenting, and often self-loading. To make transfersomes it is possible to add surface edge-activators, usually surfactants, to a standard liposomal composition. Transfersomes have been used to deliver serum albumin to the skin. The transfersome-mediated delivery of serum albumin has been shown to be as effective as subcutaneous injection of a solution containing serum albumin.

Surfactants find wide application in formulations such as emulsions (including microemulsions) and liposomes. The most common way of classifying and ranking the properties of the many different types of surfactants, both natural and synthetic, is by the use of the hydrophile/lipophile balance (HLB). The nature of the hydrophilic group (also known as the “head”) provides the most useful means for categorizing the different surfactants used in formulations (Rieger, in Pharmaceutical Dosage Forms, Marcel Dekker, Inc., New York, N.Y., 1988, p. 285).

If the surfactant molecule is not ionized, it is classified as a nonionic surfactant. Nonionic surfactants find wide application in pharmaceutical and cosmetic products and are usable over a wide range of pH values. In general their HLB values range from 2 to about 18 depending on their structure. Nonionic surfactants include nonionic esters such as ethylene glycol esters, propylene glycol esters, glyceryl esters, polyglyceryl esters, sorbitan esters, sucrose esters, and ethoxylated esters. Nonionic alkanolamides and ethers such as fatty alcohol ethoxylates, propoxylated alcohols, and ethoxylated/propoxylated block polymers are also included in this class. The polyoxyethylene surfactants are the most popular members of the nonionic surfactant class.

If the surfactant molecule carries a negative charge when it is dissolved or dispersed in water, the surfactant is classified as anionic. Anionic surfactants include carboxylates such as soaps, acyl lactylates, acyl amides of amino acids, esters of sulfuric acid such as alkyl sulfates and ethoxylated alkyl sulfates, sulfonates such as alkyl benzene sulfonates, acyl isethionates, acyl taurates and sulfosuccinates, and phosphates. The most important members of the anionic surfactant class are the alkyl sulfates and the soaps.

If the surfactant molecule carries a positive charge when it is dissolved or dispersed in water, the surfactant is classified as cationic. Cationic surfactants include quaternary ammonium salts and ethoxylated amines. The quaternary ammonium salts are the most used members of this class.

If the surfactant molecule has the ability to carry either a positive or negative charge, the surfactant is classified as amphoteric. Amphoteric surfactants include acrylic acid derivatives, substituted alkylamides, N-alkylbetaines and phosphatides.

The use of surfactants in drug products, formulations and in emulsions has been reviewed (Rieger, in Pharmaceutical Dosage Forms, Marcel Dekker, Inc., New York, N.Y., 1988, p. 285).

Penetration Enhancers

In one embodiment, the present invention employs various penetration enhancers to effect the efficient delivery of nucleic acids, particularly oligonucleotides, to the skin of animals. Most drugs are present in solution in both ionized and nonionized forms. However, usually only lipid soluble or lipophilic drugs readily cross cell membranes. It has been discovered that even non-lipophilic drugs may cross cell membranes if the membrane to be crossed is treated with a penetration enhancer. In addition to aiding the diffusion of non-lipophilic drugs across cell membranes, penetration enhancers also enhance the permeability of lipophilic drugs.

Penetration enhancers may be classified as belonging to one of five broad categories, i.e., surfactants, fatty acids, bile salts, chelating agents, and non-chelating non-surfactants (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p.92). Each of the above mentioned classes of penetration enhancers are described below in greater detail.

Surfactants: In connection with the present invention, surfactants (or “surface-active agents”) are chemical entities which, when dissolved in an aqueous solution, reduce the surface tension of the solution or the interfacial tension between the aqueous solution and another liquid, with the result that absorption of oligonucleotides through the mucosa is enhanced. In addition to bile salts and fatty acids, these penetration enhancers include, for example, sodium lauryl sulfate, polyoxyethylene-9-lauryl ether and polyoxyethylene-20-cetyl ether) (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p.92); and perfluorochemical emulsions, such as FC-43. Takahashi et al., J. Pharm. Pharmacol., 1988, 40, 252).

Fatty acids: Various fatty acids and their derivatives which act as penetration enhancers include, for example, oleic acid, lauric acid, capric acid (n-decanoic acid), myristic acid, palmitic acid, stearic acid, linoleic acid, linolenic acid, dicaprate, tricaprate, monoolein (1-monooleoyl-rac-glycerol), dilaurin, caprylic acid, arachidonic acid, glycerol 1-monocaprate, 1-dodecylazacycloheptan-2-one, acylcarnitines, acylcholines, C _1-10alkyl esters thereof (e.g., methyl, isopropyl and t-butyl), and mono- and di-glycerides thereof (i.e., oleate, laurate, caprate, myristate, palmitate, stearate, linoleate, etc.) (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p.92; Muranishi, Critical Reviews in Therapeutic Drug Carrier Systems, 1990, 7, 1-33; El Hariri et al., J. Pharm. Pharmacol., 1992, 44, 651-654).

Bile salts: The physiological role of bile includes the facilitation of dispersion and absorption of lipids and fat-soluble vitamins (Brunton, Chapter 38 in: Goodman & Gilman's The Pharmacological Basis of Therapeutics, 9th Ed., Hardman et al. Eds., McGraw-Hill, New York, 1996, pp. 934-935). Various natural bile salts, and their synthetic derivatives, act as penetration enhancers. Thus the term “bile salts” includes any of the naturally occurring components of bile as well as any of their synthetic derivatives. The bile salts of the invention include, for example, cholic acid (or its pharmaceutically acceptable sodium salt, sodium cholate), dehydrocholic acid (sodium dehydrocholate), deoxycholic acid (sodium deoxycholate), glucholic acid (sodium glucholate), glycholic acid (sodium glycocholate), glycodeoxycholic acid (sodium glycodeoxycholate), taurocholic acid (sodium taurocholate), taurodeoxycholic acid (sodium taurodeoxycholate), chenodeoxycholic acid (sodium chenodeoxycholate), ursodeoxycholic acid (UDCA), sodium tauro-24,25-dihydro-fusidate (STDHF), sodium glycodihydrofusidate and polyoxyethylene-9-lauryl ether (POE) (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, page 92; Swinyard, Chapter 39 In: Remington's Pharmaceutical Sciences, 18th Ed., Gennaro, ed., Mack Publishing Co., Easton, Pa., 1990, pages 782-783; Muranishi, Critical Reviews in Therapeutic Drug Carrier Systems, 1990, 7, 1-33; Yamamoto et al., J. Pharm. Exp. Ther., 1992, 263, 25; Yamashita et al., J. Pharm. Sci., 1990, 79, 579-583).

Chelating Agents: Chelating agents, as used in connection with the present invention, can be defined as compounds that remove metallic ions from solution by forming complexes therewith, with the result that absorption of oligonucleotides through the mucosa is enhanced. With regards to their use as penetration enhancers in the present invention, chelating agents have the added advantage of also serving as DNase inhibitors, as most characterized DNA nucleases require a divalent metal ion for catalysis and are thus inhibited by chelating agents (Jarrett, J. Chromatogr., 1993, 618, 315-339). Chelating agents of the invention include but are not limited to disodium ethylenediaminetetraacetate (EDTA), citric acid, salicylates (e.g., sodium salicylate, 5-methoxysalicylate and homovanilate), N-acyl derivatives of collagen, laureth-9 and N-amino acyl derivatives of beta-diketones (enamines)(Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, page 92; Muranishi, Critical Reviews in Therapeutic Drug Carrier Systems, 1990, 7, 1-33; Buur et al., J. Control Rel., 1990, 14, 43-51).

Non-chelating non-surfactants: As used herein, non-chelating non-surfactant penetration enhancing compounds can be defined as compounds that demonstrate insignificant activity as chelating agents or as surfactants but that nonetheless enhance absorption of oligonucleotides through the alimentary mucosa (Muranishi, Critical Reviews in Therapeutic Drug Carrier Systems, 1990, 7, 1-33). This class of penetration enhancers include, for example, unsaturated cyclic ureas, 1-alkyl- and 1-alkenylazacyclo-alkanone derivatives (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, page 92); and non-steroidal anti-inflammatory agents such as diclofenac sodium, indomethacin and phenylbutazone (Yamashita et al., J. Pharm. Pharmacol., 1987, 39, 621-626).

Agents that enhance uptake of oligonucleotides at the cellular level may also be added to the pharmaceutical and other compositions of the present invention. For example, cationic lipids, such as lipofectin (Junichi et al, U.S. Pat. No. 5,705,188), cationic glycerol derivatives, and polycationic molecules, such as polylysine (Lollo et al., PCT Application WO 97/30731), are also known to enhance the cellular uptake of oligonucleotides.

Other agents may be utilized to enhance the penetration of the administered nucleic acids, including glycols such as ethylene glycol and propylene glycol, pyrrols such as 2-pyrrol, azones, and terpenes such as limonene and menthone.

Carriers

Certain compositions of the present invention also incorporate carrier compounds in the formulation. As used herein, “carrier compound” or “carrier” can refer to a nucleic acid, or analog thereof, which is inert (i.e., does not possess biological activity per se) but is recognized as a nucleic acid by in vivo processes that reduce the bioavailability of a nucleic acid having biological activity by, for example, degrading the biologically active nucleic acid or promoting its removal from circulation. The coadministration of a nucleic acid and a carrier compound, typically with an excess of the latter substance, can result in a substantial reduction of the amount of nucleic acid recovered in the liver, kidney or other extracirculatory reservoirs, presumably due to competition between the carrier compound and the nucleic acid for a common receptor. For example, the recovery of a partially phosphorothioate oligonucleotide in hepatic tissue can be reduced when it is coadministered with polyinosinic acid, dextran sulfate, polycytidic acid or 4-acetamido-4′isothiocyano-stilbene-2,2′-disulfonic acid (Miyao et al., Antisense Res. Dev., 1995, 5, 115-121; Takakura et al., Antisense & Nucl. Acid Drug Dev., 1996, 6, 177-183).

Excipients

In contrast to a carrier compound, a “pharmaceutical carrier” or “excipient” is a pharmaceutically acceptable solvent, suspending agent or any other pharmacologically inert vehicle for delivering one or more nucleic acids to an animal. The excipient may be liquid or solid and is selected, with the planned manner of administration in mind, so as to provide for the desired bulk, consistency, etc., when combined with a nucleic acid and the other components of a given pharmaceutical composition. Typical pharmaceutical carriers include, but are not limited to, binding agents (e.g., pregelatinized maize starch, polyvinylpyrrolidone or hydroxypropyl methylcellulose, etc.); fillers (e.g., lactose and other sugars, microcrystalline cellulose, pectin, gelatin, calcium sulfate, ethyl cellulose, polyacrylates or calcium hydrogen phosphate, etc.); lubricants (e.g., magnesium stearate, talc, silica, colloidal silicon dioxide, stearic acid, metallic stearates, hydrogenated vegetable oils, corn starch, polyethylene glycols, sodium benzoate, sodium acetate, etc.); disintegrants (e.g., starch, sodium starch glycolate, etc.); and wetting agents (e.g., sodium lauryl sulphate, etc.).

Pharmaceutically acceptable organic or inorganic excipient suitable for non-parenteral administration which do not deleteriously react with nucleic acids can also be used to formulate the compositions of the present invention. Suitable pharmaceutically acceptable carriers include, but are not limited to, water, salt solutions, alcohols, polyethylene glycols, gelatin, lactose, amylose, magnesium stearate, talc, silicic acid, viscous paraffin, hydroxymethylcellulose, polyvinylpyrrolidone and the like.

Formulations for topical administration of nucleic acids may include sterile and non-sterile aqueous solutions, non-aqueous solutions in common solvents such as alcohols, or solutions of the nucleic acids in liquid or solid oil bases. The solutions may also contain buffers, diluents and other suitable additives. Pharmaceutically acceptable organic or inorganic excipients suitable for non-parenteral administration which do not deleteriously react with nucleic acids can be used.

Suitable pharmaceutically acceptable excipients include, but are not limited to, water, salt solutions, alcohol, polyethylene glycols, gelatin, lactose, amylose, magnesium stearate, talc, silicic acid, viscous paraffin, hydroxymethylcellulose, polyvinylpyrrolidone and the like.

Other Components

The compositions of the present invention may additionally contain other adjunct components conventionally found in pharmaceutical compositions, at their art-established usage levels. Thus, for example, the compositions may contain additional, compatible, pharmaceutically-active materials such as, for example, antipruritics, astringents, local anesthetics or anti-inflammatory agents, or may contain additional materials useful in physically formulating various dosage forms of the compositions of the present invention, such as dyes, flavoring agents, preservatives, antioxidants, opacifiers, thickening agents and stabilizers. However, such materials, when added, should not unduly interfere with the biological activities of the components of the compositions of the present invention. The formulations can be sterilized and, if desired, mixed with auxiliary agents, e.g., lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, colorings, flavorings and/or aromatic substances and the like which do not deleteriously interact with the nucleic acid(s) of the formulation.

Aqueous suspensions may contain substances which increase the viscosity of the suspension including, for example, sodium carboxymethylcellulose, sorbitol and/or dextran. The suspension may also contain stabilizers.

Certain embodiments of the invention provide pharmaceutical compositions containing (a) one or more antisense compounds and (b) one or more other chemotherapeutic agents which function by a non-antisense mechanism. Examples of such chemotherapeutic agents include, but are not limited to, anticancer drugs such as daunorubicin, dactinomycin, doxorubicin, bleomycin, mitomycin, nitrogen mustard, chlorambucil, melphalan, cyclophosphamide, 6-mercaptopurine, 6-thioguanine, cytarabine (CA), 5-fluorouracil (5-FU), floxuridine (5-FUdR), methotrexate (MTX), colchicine, vincristine, vinblastine, etoposide, teniposide, cisplatin and diethylstilbestrol (DES). See, generally, The Merck Manual of Diagnosis and Therapy, 15th Ed., Berkow et al., eds., 1987, Rahway, N.J., pages 1206-1228). Anti-inflammatory drugs, including but not limited to nonsteroidal anti-inflammatory drugs and corticosteroids, and antiviral drugs, including but not limited to ribivirin, vidarabine, acyclovir and ganciclovir, may also be combined in compositions of the invention. See, generally, The Merck Manual of Diagnosis and Therapy, 15th Ed., Berkow et al., eds., 1987, Rahway, N.J., pages 2499-2506 and 46-49, respectively). Other non-antisense chemotherapeutic agents are also within the scope of this invention. Two or more combined compounds may be used together or sequentially.

In another related embodiment, compositions of the invention may contain one or more antisense compounds, particularly oligonucleotides, targeted to a first nucleic acid and one or more additional antisense compounds targeted to a second nucleic acid target. Numerous examples of antisense compounds are known in the art. Two or more combined compounds may be used together or sequentially.

The formulation of therapeutic compositions and their subsequent administration is believed to be within the skill of those in the art. Dosing is dependent on severity and responsiveness of the disease state to be treated, with the course of treatment lasting from several days to several months, or until a cure is effected or a diminution of the disease state is achieved. Optimal dosing schedules can be calculated from measurements of drug accumulation in the body of the patient. Persons of ordinary skill can easily determine optimum dosages, dosing methodologies and repetition rates. Optimum dosages may vary depending on the relative potency of individual oligonucleotides, and can generally be estimated based on EC ₅₀s found to be effective in in vitro and in vivo animal models. In general, dosage is from 0.01 ug to 100 g per kg of body weight, and may be given once or more daily, weekly, monthly or yearly, or even once every 2 to 20 years. Persons of ordinary skill in the art can easily estimate repetition rates for dosing based on measured residence times and concentrations of the drug in bodily fluids or tissues. Following successful treatment, it may be desirable to have the patient undergo maintenance therapy to prevent the recurrence of the disease state, wherein the oligonucleotide is administered in maintenance doses, ranging from 0.01 ug to 100 g per kg of body weight, once or more daily, to once every 20 years.

While the present invention has been described with specificity in accordance with certain of its preferred embodiments, the following examples serve only to illustrate the invention and are not intended to limit the same.

EXAMPLES

Example 1

Nucleoside Phosphoramidites for Oligonucleotide Synthesis Deoxy and 2′-alkoxy Amidites [0115]
2′-Deoxy and 2′-methoxy beta-cyanoethyldiisopropyl phosphoramidites were purchased from commercial sources (e.g. Chemgenes, Needham Mass. or Glen Research, Inc. Sterling Va.). Other 2′-O-alkoxy substituted nucleoside amidites are prepared as described in U.S. Pat. No. 5,506,351, herein incorporated by reference. For oligonucleotides synthesized using 2′-alkoxy amidites, the standard cycle for unmodified oligonucleotides was utilized, except the wait step after pulse delivery of tetrazole and base was increased to 360 seconds. [0116]
Oligonucleotides containing 5-methyl-2′-deoxycytidine (5-Me-C) nucleotides were synthesized according to published methods [Sanghvi, et. al., [0117] Nucleic Acids Research, 1993, 21, 3197-3203] using commercially available phosphoramidites (Glen Research, Sterling Va. or ChemGenes, Needham Mass.).
2′-Fluoro Amidites [0118]
2′-Fluorodeoxyadenosine Amidites [0119]
2′-fluoro oligonucleotides were synthesized as described previously [Kawasaki, et. al., [0120] J. Med. Chem., 1993, 36, 831-841] and U.S. Pat. No. 5,670,633, herein incorporated by reference. Briefly, the protected nucleoside N6-benzoyl-2′-deoxy-2′-fluoroadenosine was synthesized utilizing commercially available 9-beta-D-arabinofuranosyladenine as starting material and by modifying literature procedures whereby the 2′-alpha-fluoro atom is introduced by a S_N2-displacement of a 2′-beta-trityl group. Thus N6-benzoyl-9-beta-D-arabinofuranosyladenine was selectively protected in moderate yield as the 3′,5′-ditetrahydropyranyl (THP) intermediate. Deprotection of the THP and N6-benzoyl groups was accomplished using standard methodologies and standard methods were used to obtain the 5′-dimethoxytrityl-(DMT) and 5′-DMT-3′-phosphoramidite intermediates.
2′-Fluorodeoxyguanosine [0121]
The synthesis of 2′-deoxy-2′-fluoroguanosine was accomplished using tetraisopropyldisiloxanyl (TPDS) protected 9-beta-D-arabinofuranosylguanine as starting material, and conversion to the intermediate diisobutyryl-arabinofuranosylguanosine. Deprotection of the TPDS group was followed by protection of the hydroxyl group with THP to give diisobutyryl di-THP protected arabinofuranosylguanine. Selective O-deacylation and triflation was followed by treatment of the crude product with fluoride, then deprotection of the THP groups. Standard methodologies were used to obtain the 5′-DMT- and 5′-DMT-3′-phosphoramidites. [0122]
2′-Fluorouridine [0123]
Synthesis of 2′-deoxy-2′-fluorouridine was accomplished by the modification of a literature procedure in which 2,2′-anhydro-1-beta-D-arabinofuranosyluracil was treated with 70% hydrogen fluoride-pyridine. Standard procedures were used to obtain the 5′-DMT and 5′-DMT-3′phosphoramidites. [0124]
2′-Fluorodeoxycytidine [0125]
2′-deoxy-2′-fluorocytidine was synthesized via amination of 2′-deoxy-2′-fluorouridine, followed by selective protection to give N4-benzoyl-2′-deoxy-2′-fluorocytidine. Standard procedures were used to obtain the 5′-DMT and 5′-DMT-3′phosphoramidites. [0126]
2′-O-(2-Methoxyethyl) Modified Amidites [0127]
2′-O-Methoxyethyl-substituted nucleoside amidites are prepared as follows, or alternatively, as per the methods of Martin, P., [0128] Helvetica Chimica Acta, 1995, 78, 486-504.
2,2′-Anhydro[1-(beta-D-arabinofuranosyl)-5-methyluridine][0129]
5-Methyluridine (ribosylthymine, commercially available through Yamasa, Choshi, Japan) (72.0 g, 0.279 M), diphenylcarbonate (90.0 g, 0.420 M) and sodium bicarbonate (2.0 g, 0.024 M) were added to DMF (300 mL). The mixture was heated to reflux, with stirring, allowing the evolved carbon dioxide gas to be released in a controlled manner. After 1 hour, the slightly darkened solution was concentrated under reduced pressure. The resulting syrup was poured into diethylether (2.5 L), with stirring. The product formed a gum. The ether was decanted and the residue was dissolved in a minimum amount of methanol (ca. 400 mL). The solution was poured into fresh ether (2.5 L) to yield a stiff gum. The ether was decanted and the gum was dried in a vacuum oven (60° C. at 1 mm Hg for 24 h) to give a solid that was crushed to a light tan powder (57 g, 85% crude yield). The NMR spectrum was consistent with the structure, contaminated with phenol as its sodium salt (ca. 5%). The material was used as is for further reactions (or it can be purified further by column chromatography using a gradient of methanol in ethyl acetate (10-25%) to give a white solid, mp 222-4° C.). [0130]
2′-O-Methoxyethyl-5-methyluridine [0131]
2,2′-Anhydro-5-methyluridine (195 g, 0.81 M), tris(2-methoxyethyl)borate (231 g, 0.98 M) and 2-methoxyethanol (1.2 L) were added to a 2 L stainless steel pressure vessel and placed in a pre-heated oil bath at 160° C. After heating for 48 hours at 155-160° C., the vessel was opened and the solution evaporated to dryness and triturated with MeOH (200 mL). The residue was suspended in hot acetone (1 L). The insoluble salts were filtered, washed with acetone (150 mL) and the filtrate evaporated. The residue (280 g) was dissolved in CH[0132] ₃CN (600 mL) and evaporated. A silica gel column (3 kg) was packed in CH₂Cl₂/acetone/MeOH (20:5:3) containing 0.5% Et₃NH. The residue was dissolved in CH₂Cl₂(250 mL) and adsorbed onto silica (150 g) prior to loading onto the column. The product was eluted with the packing solvent to give 160 g (63%) of product. Additional material was obtained by reworking impure fractions.
2′-O-Methoxyethyl-5′-O-dimethoxytrityl-5-methyluridine [0133]
2′-o-Methoxyethyl-5-methyluridine (160 g, 0.506 M) was co-evaporated with pyridine (250 mL) and the dried residue dissolved in pyridine (1.3 L). A first aliquot of dimethoxytrityl chloride (94.3 g, 0.278 M) was added and the mixture stirred at room temperature for one hour. A second aliquot of dimethoxytrityl chloride (94.3 g, 0.278 M) was added and the reaction stirred for an additional one hour. Methanol (170 mL) was then added to stop the reaction. HPLC showed the presence of approximately 70% product. The solvent was evaporated and triturated with CH[0134] ₃CN (200 mL). The residue was dissolved in CHCl3 (1.5 L) and extracted with 2×500 mL of saturated NaHCO₃and 2×500 mL of saturated NaCl. The organic phase was dried over Na₂SO₄, filtered and evaporated. 275 g of residue was obtained. The residue was purified on a 3.5 kg silica gel column, packed and eluted with EtOAc/hexane/acetone (5:5:1) containing 0.5% Et₃NH. The pure fractions were evaporated to give 164 g of product. Approximately 20 g additional was obtained from the impure fractions to give a total yield of 183 g (57%).
3′-O-Acetyl-2′-O-methoxyethyl-5′-O-dimethoxytrityl-5-methyluridine [0135]
2′-O-Methoxyethyl-5′-O-dimethoxytrityl-5-methyluridine (106 g, 0.167 M), DMF/pyridine (750 mL of a 3:1 mixture prepared from 562 mL of DMF and 188 mL of pyridine) and acetic anhydride (24.38 mL, 0.258 M) were combined and stirred at room temperature for 24 hours. The reaction was monitored by TLC by first quenching the TLC sample with the addition of MeOH. Upon completion of the reaction, as judged by TLC, MeOH (50 mL) was added and the mixture evaporated at 35° C. The residue was dissolved in CHCl[0136] ₃(800 mL) and extracted with 2×200 mL of saturated sodium bicarbonate and 2×200 mL of saturated NaCl. The water layers were back extracted with 200 mL of CHCl₃. The combined organics were dried with sodium sulfate and evaporated to give 122 g of residue (approx. 90% product). The residue was purified on a 3.5 kg silica gel column and eluted using EtOAc/hexane (4:1). Pure product fractions were evaporated to yield 96 g (84%). An additional 1.5 g was recovered from later fractions.
3′-O-Acetyl-2′-O-methoxyethyl-5′-O-dimethoxytrityl-5-methyl-4-triazoleuridine [0137]
A first solution was prepared by dissolving 3′-O-acetyl-2′-O-methoxyethyl-5′-O-dimethoxytrityl-5-methyluridine (96 g, 0.144 M) in CH[0138] ₃CN (700 mL) and set aside. Triethylamine (189 mL, 1.44 M) was added to a solution of triazole (90 g, 1.3 M) in CH₃CN (1 L), cooled to −5° C. and stirred for 0.5 h using an overhead stirrer. POCl₃was added dropwise, over a 30 minute period, to the stirred solution maintained at −0-10° C., and the resulting mixture stirred for an additional 2 hours. The first solution was added dropwise, over a 45 minute period, to the latter solution. The resulting reaction mixture was stored overnight in a cold room. Salts were filtered from the reaction mixture and the solution was evaporated. The residue was dissolved in EtOAc (1 L) and the insoluble solids were removed by filtration. The filtrate was washed with 1×300 mL of NaHCO₃and 2×300 mL of saturated NaCl, dried over sodium sulfate and evaporated. The residue was triturated with EtOAc to give the title compound.
2′-O-Methoxyethyl-5′-O-dimethoxytrityl-5-methylcytidine [0139]
A solution of 31-O-acetyl-2′-O-methoxyethyl-5′-O-dimethoxytrityl-5-methyl-4-triazoleuridine (103 g, 0.141 M) in dioxane (500 mL) and NH[0140] ₄OH (30 mL) was stirred at room temperature for 2 hours. The dioxane solution was evaporated and the residue azeotroped with MeOH (2×200 mL). The residue was dissolved in MeOH (300 mL) and transferred to a 2 liter stainless steel pressure vessel. MeOH (400 mL) saturated with NH₃gas was added and the vessel heated to 100° C. for 2 hours (TLC showed complete conversion). The vessel contents were evaporated to dryness and the residue was dissolved in EtOAc (500 mL) and washed once with saturated NaCl (200 mL). The organics were dried over sodium sulfate and the solvent was evaporated to give 85 g (95%) of the title compound.
N4-Benzoyl-2′-O-methoxyethyl-5′-O-dimethoxytrityl-5-methylcytidine [0141]
2′-O-Methoxyethyl-5′-O-dimethoxytrityl-5-methyl-cytidine (85 g, 0.134 M) was dissolved in DMF (800 mL) and benzoic anhydride (37.2 g, 0.165 M) was added with stirring. After stirring for 3 hours, TLC showed the reaction to be approximately 95% complete. The solvent was evaporated and the residue azeotroped with MeOH (200 mL). The residue was dissolved in CHCl[0142] ₃(700 mL) and extracted with saturated NaHCO₃(2×300 mL) and saturated NaCl (2×300 mL), dried over MgSO₄and evaporated to give a residue (96 g). The residue was chromatographed on a 1.5 kg silica column using EtOAc/hexane (1:1) containing 0.5% Et₃NH as the eluting solvent. The pure product fractions were evaporated to give 90 g (90%) of the title compound.
N4-Benzoyl-2′-O-methoxyethyl-5′-O-dimethoxytrityl-5-methylcytidine-3′-amidite [0143]
N4-Benzoyl-2′-O-methoxyethyl-5′-O-dimethoxytrityl-5-methylcytidine (74 g, 0.10 M) was dissolved in CH[0144] ₂Cl₂(1 L). Tetrazole diisopropylamine (7.1 g) and 2-cyanoethoxy-tetra-(isopropyl)phosphite (40.5 mL, 0.123 M) were added with stirring, under a nitrogen atmosphere. The resulting mixture was stirred for 20 hours at room temperature (TLC showed the reaction to be 95% complete). The reaction mixture was extracted with saturated NaHCO₃(1×300 mL) and saturated NaCl (3×300 mL). The aqueous washes were back-extracted with CH₂Cl₂(300 mL), and the extracts were combined, dried over MgSO₄and concentrated. The residue obtained was chromatographed on a 1.5 kg silica column using EtOAc/hexane (3:1) as the eluting solvent. The pure fractions were combined to give 90.6 g (87%) of the title compound.
2′-O-(Aminooxyethyl) nucleoside amidites and 2′-O--(dimethylaminooxyethyl) Nucleoside Amidites [0145]
2′-(Dimethylaminooxyethoxy) nucleoside amidites 2′-(Dimethylaminooxyethoxy) nucleoside amidites [also known in the art as 2′-O-(dimethylaminooxyethyl) nucleoside amidites] are prepared as described in the following paragraphs. Adenosine, cytidine and guanosine nucleoside amidites are prepared similarly to the thymidine (5-methyluridine) except the exocyclic amines are protected with a benzoyl moiety in the case of adenosine and cytidine and with isobutyryl in the case of guanosine. [0146]
5′-O-tert-Butyldiphenylsilyl-O[0147] ²-2′-anhydro-5-methyluridine
O[0148] ²-2′-anhydro-5-methyluridine (Pro. Bio. Sint., Varese, Italy, 100.0 g, 0.416 mmol), dimethylaminopyridine (0.66 g, 0.013 eq, 0.0054 mmol) were dissolved in dry pyridine (500 ml) at ambient temperature under an argon atmosphere and with mechanical stirring tert-Butyldiphenylchlorosilane (125.8 g, 119.0 mL, 1.1 eq, 0.458 mmol) was added in one portion. The reaction was stirred for 16 h at ambient temperature. TLC (Rf 0.22, ethyl acetate) indicated a complete reaction. The solution was concentrated under reduced pressure to a thick oil. This was partitioned between dichloromethane (1 L) and saturated sodium bicarbonate (2×1 L) and brine (1 L). The organic layer was dried over sodium sulfate and concentrated under reduced pressure to a thick oil. The oil was dissolved in a 1:1 mixture of ethyl acetate and ethyl ether (600 mL) and the solution was cooled to
−10° C. The resulting crystalline product was collected by filtration, washed with ethyl ether (3×200 mL) and dried (40° C., 1 mm Hg, 24 h) to 149 g (74.8%) of white solid. TLC and NMR were consistent with pure product. [0149]
5′-O-tert-Butyldiphenylsilyl-2′-O-(2-hydroxyethyl)-5-methyluridine [0150]
In a 2 L stainless steel, unstirred pressure reactor was added borane in tetrahydrofuran (1.0 M, 2.0 eq, 622 mL). In the fume hood and with manual stirring, ethylene glycol (350 mL, excess) was added cautiously at first until the evolution of hydrogen gas subsided. 5′-O-tert-Butyldiphenylsilyl-O[0151] ²-2′-anhydro-5-methyluridine (149 g, 0.311 mol) and sodium bicarbonate (0.074 g, 0.003 eq) were added with manual stirring. The reactor was sealed and heated in an oil bath until an internal temperature of 160° C. was reached and then maintained for 16 h (pressure <100 psig). The reaction vessel was cooled to ambient and opened. TLC (Rf 0.67 for desired product and Rf 0.82 for ara-T side product, ethyl acetate) indicated about 70% conversion to the product. In order to avoid additional side product formation, the reaction was stopped, concentrated under reduced pressure (10 to 1 mm Hg) in a warm water bath (40-100° C.) with the more extreme conditions used to remove the ethylene glycol. [Alternatively, once the low boiling solvent is gone, the remaining solution can be partitioned between ethyl acetate and water. The product will be in the organic phase.] The residue was purified by column chromatography (2 kg silica gel, ethyl acetate-hexanes gradient 1:1 to 4:1). The appropriate fractions were combined, stripped and dried to product as a white crisp foam (84 g, 50%), contaminated starting material (17.4 g) and pure reusable starting material 20 g. The yield based on starting material less pure recovered starting material was 58%. TLC and NMR were consistent with 99% pure product.
2′-O-([2-phthalimidoxy)ethyl]-5′-t-butyldiphenylsilyl-5-methyluridine [0152]
5′-O-tert-Butyldiphenylsilyl-2′-O-(2-hydroxyethyl)-5-methyluridine (20 g, 36.98 mmol) was mixed with triphenylphosphine (11.63 g, 44.36 mmol) and N-hydroxyphthalimide (7.24 g, 44.36 mmol). It was then dried over P[0153] ₂O₅under high vacuum for two days at 40° C. The reaction mixture was flushed with argon and dry THF (369.8 mL, Aldrich, sure seal bottle) was added to get a clear solution. Diethyl-azodicarboxylate (6.98 mL, 44.36 mmol) was added dropwise to the reaction mixture. The rate of addition is maintained such that resulting deep red coloration is just discharged before adding the next drop. After the addition was complete, the reaction was stirred for 4 hrs. By that time TLC showed the completion of the reaction (ethylacetate:hexane, 60:40). The solvent was evaporated in vacuum. Residue obtained was placed on a flash column and eluted with ethyl acetate:hexane (60:40), to get 2′-O-([2-phthalimidoxy)ethyl]-5′-t-butyldiphenylsilyl-5-methyluridine as white foam (21.819 g, 86%).
5′-O-tert-butyldiphenylsilyl-2′-O-[(2-formadoximinooxy)ethyl]-5-methyluridine [0154]
2′-O-([2-phthalimidoxy)ethyl]-5′-t-butyldiphenylsilyl-5-methyluridine (3.1 g, 4.5 mmol) was dissolved in dry CH[0155] ₂Cl₂(4.5 mL) and methylhydrazine (300 mL, 4.64 mmol) was added dropwise at −10° C. to 0° C. After 1 h the mixture was filtered, the filtrate was washed with ice cold CH₂Cl₂and the combined organic phase was washed with water, brine and dried over anhydrous Na₂SO₄. The solution was concentrated to get 2′-O-(aminooxyethyl) thymidine, which was then dissolved in MeOH (67.5 mL). To this formaldehyde (20% aqueous solution, w/w, 1.1 eq.) was added and the resulting mixture was strirred for 1 h. Solvent was removed under vacuum; residue chromatographed to get 5′-O-tert-butyldiphenylsilyl-2′-O-[(2-formadoximinooxy) ethyl]-5-methyluridine as white foam (1.95 g, 78%).
5′-O-tert-Butyldiphenylsilyl-2′-O-[N,N-dimethylaminooxyethyl]-5-methyluridine [0156]
5′-O-tert-butyldiphenylsilyl-2′-O-[(2-formadoximinooxy)ethyl]-5-methyluridine (1.77g, 3.12 mmol) was dissolved in a solution of 1M pyridinium p-toluenesulfonate (PPTS) in dry MeOH (30.6 mL). Sodium cyanoborohydride (0.39 g, 6.13 mmol) was added to this solution at 10° C. under inert atmosphere. The reaction mixture was stirred for 10 minutes at 10° C. After that the reaction vessel was removed from the ice bath and stirred at room temperature for 2 h, the reaction monitored by TLC (5% MeOH in CH[0157] ₂Cl₂). Aqueous NaHCO₃solution (5%, 10 mL) was added and extracted with ethyl acetate (2×20 mL). Ethyl acetate phase was dried over anhydrous Na₂SO₄, evaporated to dryness. Residue was dissolved in a solution of 1M PPTS in MeOH (30.6 mL). Formaldehyde (20% w/w, 30 mL, 3.37 mmol) was added and the reaction mixture was stirred at room temperature for 10 minutes. Reaction mixture cooled to 10° C. in an ice bath, sodium cyanoborohydride (0.39 g, 6.13 mmol) was added and reaction mixture stirred at 10° C. for 10 minutes. After 10 minutes, the reaction mixture was removed from the ice bath and stirred at room temperature for 2 hrs. To the reaction mixture 5% NaHCO₃(25 mL) solution was added and extracted with ethyl acetate (2×25 mL). Ethyl acetate layer was dried over anhydrous Na₂SO₄and evaporated to dryness. The residue obtained was purified by flash column chromatography and eluted with 5% MeOH in CH₂Cl₂to get 5′-O-tert-butyldiphenylsilyl-2′-O-[N,N-dimethylaminooxyethyl]-5-methyluridine as a white foam (14.6g, 80%).
2′-O-(dimethylaminooxyethyl)-5-methyluridine [0158]
Triethylamine trihydrofluoride (3.91 mL, 24.0 mmol) was dissolved in dry THF and triethylamine (1.67 mL, 12 mmol, dry, kept over KOH). This mixture of triethylamine-2HF was then added to 5′-O-tert-butyldiphenylsilyl-2′-O-[N,N-dimethylaminooxyethyl]-5-methyluridine (1.40 g, 2.4 mmol) and stirred at room temperature for 24 hrs. Reaction was monitored by TLC (5% MeOH in CH[0159] ₂Cl₂). Solvent was removed under vacuum and the residue placed on a flash column and eluted with 10% MeOH in CH₂Cl₂to get 2′-O-(dimethylaminooxyethyl)-5-methyluridine (766 mg, 92.5%).
5′-O-DMT-2′-O-(dimethylaminooxyethyl)-5-methyluridine [0160]
2′-O-(dimethylaminooxyethyl)-5-methyluridine (750 mg, 2.17 mmol) was dried over P[0161] ₂O₅under high vacuum overnight at 40° C. It was then co-evaporated with anhydrous pyridine (20 mL). The residue obtained was dissolved in pyridine (11 mL) under argon atmosphere. 4-dimethylaminopyridine (26.5 mg, 2.60 mmol), 4,4′-dimethoxytrityl chloride (880 mg, 2.60 mmol) was added to the mixture and the reaction mixture was stirred at room temperature until all of the starting material disappeared. Pyridine was removed under vacuum and the residue chromatographed and eluted with 10% MeOH in CH₂Cl₂(containing a few drops of pyridine) to get 5′-O-DMT-2′-O-(dimethylamino-oxyethyl)-5-methyluridine (1.13 g, 80%).
5′-O-DMT-2′-O-(2-N,N-dimethylaminooxyethyl)-5-methyluridine-3′-[(2-cyanoethyl)-N,N-diisopropylphosphoramidite][0162]
5′-O-DMT-2′-O-(dimethylaminooxyethyl)-5-methyluridine (1.08 g, 1.67 mmol) was co-evaporated with toluene (20 mL). To the residue N,N-diisopropylamine tetrazonide (0.29 g, 1.67 mmol) was added and dried over P[0163] ₂O, under high vacuum overnight at 40° C. Then the reaction mixture was dissolved in anhydrous acetonitrile (8.4 mL) and 2-cyanoethyl-N,N,N¹,N¹-tetraisopropylphosphoramidite (2.12 mL, 6.08 mmol) was added. The reaction mixture was stirred at ambient temperature for 4 hrs under inert atmosphere. The progress of the reaction was monitored by TLC (hexane:ethyl acetate 1:1). The solvent was evaporated, then the residue was dissolved in ethyl acetate (70 mL) and washed with 5% aqueous NaHCO₃(40 mL). Ethyl acetate layer was dried over anhydrous Na₂SO₄and concentrated. Residue obtained was chromatographed (ethyl acetate as eluent) to get 5′-O-DMT-2′-O-(2-N,N-dimethylaminooxyethyl)-5-methyluridine-3′-[(2-cyanoethyl)-N,N-diisopropylphosphoramidite] as a foam (1.04g, 74.9%).
2′-(Aminooxyethoxy) Nucleoside Amidites [0164]
2′-(Aminooxyethoxy) nucleoside amidites [also known in the art as 2′-O-(aminooxyethyl) nucleoside amidites] are prepared as described in the following paragraphs. Adenosine, cytidine and thymidine nucleoside amidites are prepared similarly. [0165]
N2-isobutyryl-6-O-diphenylcarbamoyl-2′-O-(2-ethylacetyl)-5′-O-(4,4′-dimethoxytrityl)guanosine-3′-[(2-cyanoethyl)-N,N-diisopropylphosphoramidite][0166]
The 2′-O-aminooxyethyl guanosine analog may be obtained by selective 2′-O-alkylation of diaminopurine riboside. Multigram quantities of diaminopurine riboside may be purchased from Schering A G (Berlin) to provide 2′-O-(2-ethylacetyl) diaminopurine riboside along with a minor amount of the 3′-O-isomer. 2′-O-(2-ethylacetyl) diaminopurine riboside may be resolved and converted to 2′-O-(2-ethylacetyl)guanosine by treatment with adenosine deaminase. (McGee, D. P. C., Cook, P. D., Guinosso, C. J., WO 94/02501 Al 940203.) Standard protection procedures should afford 2′-O-(2-ethylacetyl)-5′-O-(4,4′dimethoxytrityl)guanosine and 2-N-isobutyryl-6-O-diphenylcarbamoyl-2′-O-(2-ethylacetyl)-5′-O-(4,4′-dimethoxytrityl)guanosine which may be reduced to provide 2-N-isobutyryl-6-O-diphenylcarbamoyl-2′-O-(2-ethylacetyl)-5′-O-(4,4′-dimethoxytrityl)guanosine. As before the hydroxyl group may be displaced by N-hydroxyphthalimide via a Mitsunobu reaction, and the protected nucleoside may phosphitylated as usual to yield 2-N-isobutyryl-6-O-diphenylcarbamoyl-2′-O-(2-ethylacetyl)-5′-O-(4,4′-dimethoxytrityl)guanosine-3′-[(2-cyanoethyl)-N,N-diisopropylphosphoramidite]. [0167]
2′-dimethylaminoethoxyethoxy (2′-DMAEOE) Nucleoside Amidites [0168]
2′-dimethylaminoethoxyethoxy nucleoside amidites (also known in the art as 2′-O-dimethylaminoethoxyethyl, i.e., 2′-O—CH[0169] ₂-O—CH₂—N(CH₂)₂₁or 2′-DMAEOE nucleoside amidites) are prepared as follows. Other nucleoside amidites are prepared similarly.
2′-O-[2(2-N,N-dimethylaminoethoxy)ethyl]-5-methyl Uridine [0170]
2[2-(Dimethylamino)ethoxy]ethanol (Aldrich, 6.66 g, 50 mmol) is slowly added to a solution of borane in tetra-hydrofuran (1 M, 10 mL, 10 mmol) with stirring in a 100 mL bomb. Hydrogen gas evolves as the solid dissolves. O[0171] ²-,2′-anhydro-5-methyluridine (1.2 g, 5 mmol), and sodium bicarbonate (2.5 mg) are added and the bomb is sealed, placed in an oil bath and heated to 155° C. for 26 hours. The bomb is cooled to room temperature and opened-. The crude solution is concentrated and the residue partitioned between water (200 mL) and hexanes (200 mL). The excess phenol is extracted into the hexane layer. The aqueous layer is extracted with ethyl acetate (3×200 mL) and the combined organic layers are washed once with water, dried over anhydrous sodium sulfate and concentrated. The residue is columned on silica gel using methanol/methylene chloride 1:20 (which has 2% triethylamine) as the eluent. As the column fractions are concentrated a colorless solid forms which is collected to give the title compound as a white solid.
5′-O-dimethoxytrityl-2′-O-[2(2-N,N-dimethylaminoethoxy) ethyl)]-5-methyl Uridine [0172]
To 0.5 g (1.3 mmol) of 2′-O-[2(2-N,N-dimethylamino-ethoxy)ethyl)]-5-methyl uridine in anhydrous pyridine (8 mL), triethylamine (0.36 mL) and dimethoxytrityl chloride (DMT-Cl, 0.87 g, 2 eq.) are added and stirred for 1 hour. The reaction mixture is poured into water (200 mL) and extracted with CH[0173] ₂Cl₂(2×200 mL). The combined CH₂Cl₂layers are washed with saturated NaHCO₃solution, followed by saturated NaCl solution and dried over anhydrous sodium sulfate. Evaporation of the solvent followed by silica gel chromatography using MeOH:CH₂Cl₂:Et₃N (20:1, v/v, with 1% triethylamine) gives the title compound.
5′-O-Dimethoxytrityl-2′-O-[2(2-N,N-dimethylaminoethoxy)ethyl)]-5-methyl uridine-3′-O-(cyanoethyl-N,N-diisopropyl)phosphoramidite [0174]
Diisopropylaminotetrazolide (0.6 g) and 2-cyanoethoxy-N,N-diisopropyl phosphoramidite (1.1 mL, 2 eq.) are added to a solution of 5′-O-dimethoxytrityl-2′-O-[2(2-N,N-dimethylaminoethoxy)ethyl)]-5-methyluridine (2.17 g, 3 mmol) dissolved in CH[0175] ₂Cl₂(20 mL) under an atmosphere of argon. The reaction mixture is stirred overnight and the solvent evaporated. The resulting residue is purified by silica gel flash column chromatography with ethyl acetate as the eluent to give the title compound.

Example 2

Oligonucleotide Synthesis [0176]
Unsubstituted and substituted phosphodiester (P=O) oligonucleotides are synthesized on an automated DNA synthesizer (Applied Biosystems model 380B) using standard phosphoramidite chemistry with oxidation by iodine. [0177]
Phosphorothioates (P=S) are synthesized as for the phosphodiester oligonucleotides except the standard oxidation bottle was replaced by 0.2 M solution of 3H-1,2-benzodithiole-3-one 1,1-dioxide in acetonitrile for the stepwise thiation of the phosphite linkages. The thiation wait step was increased to 68 sec and was followed by the capping step. After cleavage from the CPG column and deblocking in concentrated ammonium hydroxide at 55° C. (18 h), the oligonucleotides were purified by precipitating twice with 2.5 volumes of ethanol from a 0.5 M NaCl solution. Phosphinate oligonucleotides are prepared as described in U.S. Pat. No. 5,508,270, herein incorporated by reference. [0178]
Alkyl phosphonate oligonucleotides are prepared as described in U.S. Pat. No. 4,469,863, herein incorporated by reference. [0179]
3′,-Deoxy-3′-methylene phosphonate oligonucleotides are prepared as described in U.S. Pat. Nos. 5,610,289 or 5,625,050, herein incorporated by reference. [0180]
Phosphoramidite oligonucleotides are prepared as described in U.S. Patent, 5,256,775 or U.S. Pat. No. 5,366,878, herein incorporated by reference. [0181]
Alkylphosphonothioate oligonucleotides are prepared as described in published PCT applications PCT/US94/00902 and PCT/US93/06976 (published as WO 94/17093 and WO 94/02499, respectively), herein incorporated by reference. 3′-Deoxy-3′-amino phosphoramidate oligonucleotides are prepared as described in U.S. Pat. No. 5,476,925, herein incorporated by reference. [0182]
Phosphotriester oligonucleotides are prepared as described in U.S. Pat. No. 5,023,243, herein incorporated by reference. [0183]
Borano phosphate oligonucleotides are prepared as described in U.S. Pat. Nos. 5,130,302 and 5,177,198, both herein incorporated by reference. [0184]

Example 3

Oligonucleoside Synthesis [0185]
Methylenemethylimino linked oligonucleosides, also identified as MMI linked oligonucleosides, methylenedi-methylhydrazo linked oligonucleosides, also identified as MDH linked oligonucleosides, and methylenecarbonylamino linked oligonucleosides, also identified as amide-3 linked oligonucleosides, and methyleneaminocarbonyl linked oligo-nucleosides, also identified as amide-4 linked oligonucleo-sides, as well as mixed backbone compounds having, for instance, alternating MMI and P=O or P=S linkages are prepared as described in U.S. Pat. Nos. 5,378,825, 5,386,023, 5,489,677, 5,602,240 and 5,610,289, all of which are herein incorporated by reference. [0186]
Formacetal and thioformacetal linked oligonucleosides are prepared as described in U.S. Pat. Nos. 5,264,562 and 5,264,564, herein incorporated by reference. [0187]
Ethylene oxide linked oligonucleosides are prepared as described in U.S. Pat. No. 5,223,618, herein incorporated by reference. [0188]

Example 4

PNA Synthesis [0189]
Peptide nucleic acids (PNAs) are prepared in accordance with any of the various procedures referred to in Peptide Nucleic Acids (PNA): Synthesis, Properties and Potential Applications, [0190] Bioorganic & Medicinal Chemistry, 1996, 4, 5-23. They may also be prepared in accordance with U.S. Pat. Nos. 5,539,082, 5,700,922, and 5,719,262, herein incorporated by reference.

Example 5

Synthesis of Chimeric Oligonucleotides [0191]
Chimeric oligonucleotides, oligonucleosides or mixed oligonucleotides/oligonucleosides of the invention can be of several different types. These include a first type wherein the “gap” segment of linked nucleosides is positioned between 5′ and 3′ “wing” segments of linked nucleosides and a second “open end” type wherein the “gap” segment is located at either the 3′ or the 5′ terminus of the oligomeric compound. Oligonucleotides of the first type are also known in the art as “gapmers” or gapped oligonucleotides. Oligonucleotides of the second type are also known in the art as “hemimers” or “wingmers”. [0192]
[2′-O-Me]—[2′-deoxy]—[2′-O-Me] Chimeric Phosphorothioate Oligonucleotides [0193]
Chimeric oligonucleotides having 2′-O-alkyl phosphorothioate and 2′-deoxy phosphorothioate oligo-nucleotide segments are synthesized using an Applied Biosystems automated DNA synthesizer Model 380B, as above. Oligonucleotides are synthesized using the automated synthesizer and 2′-deoxy-5′-dimethoxytrityl-3′-O-phosphor-amidite for the DNA portion and 5′-dimethoxytrityl-2′-O-methyl-3′-O-phosphoramidite for 5′ and 3′ wings. The standard synthesis cycle is modified by increasing the wait step after the delivery of tetrazole and base to 600 s repeated four times for RNA and twice for -2′-O-methyl. The fully protected oligonucleotide is cleaved from the support and the phosphate group is deprotected in 3:1 ammonia/ethanol at room temperature overnight then lyophilized to dryness. Treatment in methanolic ammonia for 24 hrs at room temperature is then done to deprotect all bases and sample was again lyophilized to dryness. The pellet is resuspended in 1M TBAF in THF for 24 hrs at room temperature to deprotect the 2′ positions. The reaction is then quenched with 1M TEAA and the sample is then reduced to ½ volume by rotovac before being desalted on a G25 size exclusion column. The oligo recovered is then analyzed spectrophotometrically for yield and for purity by capillary electrophoresis and by mass spectrometry. [0194]
[2′-O-(2-Methoxyethyl)]—[2′-deoxy]—[2′-O-(Methoxyethyl)] Chimeric Phosphorothioate Oligonucleotides [0195]
[2′-O-(2-methoxyethyl)]—[2′-deoxy)]—[-2′-O-(methoxy-ethyl)] chimeric phosphorothioate oligonucleotides were prepared as per the procedure above for the 2′-O-methyl chimeric oligonucleotide, with the substitution of 2′-O-(methoxyethyl) amidites for the 2′-O-methyl amidites. [0196]
[2′-O-(2-Methoxyethyl)Phosphodiester]—[2′-deoxy Phosphorothioate]—[2′-O-(2-Methoxyethyl) Phosphodiester] Chimeric Oligonucleotides [0197]
[2′-O-(2-methoxyethyl phosphodiester]—[2′-deoxy phosphorothioate]—[2′-O-(methoxyethyl) phosphodiester] chimeric oligonucleotides are prepared as per the above procedure for the 2′-O-methyl chimeric oligonucleotide with the substitution of 2′-O-(methoxyethyl) amidites for the 2′-O-methyl amidites, oxidization with iodine to generate the phosphodiester internucleotide linkages within the wing portions of the chimeric structures and sulfurization utilizing 3,H-1,2 benzodithiole-3-one 1,1 dioxide (Beaucage Reagent) to generate the phosphorothioate internucleotide linkages for the center gap. [0198]
Other chimeric oligonucleotides, chimeric oligonucleosides and mixed chimeric oligonucleotides/oligonucleosides are synthesized according to U.S. Pat. No. 5,623,065, herein incorporated by reference. [0199]

Example 6

Oligonucleotide Isolation [0200]
After cleavage from the controlled pore glass column (Applied Biosystems) and deblocking in concentrated ammonium hydroxide at 55° C. for 18 hours, the oligonucleotides or oligonucleosides are purified by precipitation twice out of 0.5 M NaCl with 2.5 volumes ethanol. Synthesized oligonucleotides were analyzed by polyacrylamide gel electrophoresis on denaturing gels and judged to be at least 85% full length material. The relative amounts of phosphorothioate and phosphodiester linkages obtained in synthesis were periodically checked by [0201] ³¹P nuclear magnetic resonance spectroscopy, and for some studies oligonucleotides were purified by HPLC, as described by Chiang et al., J. Biol. Chem. 1991, 266, 18162-18171. Results obtained with HPLC-purified material were similar to those obtained with non-HPLC purified material.

Example 7

Oligonucleotide Synthesis—96 Well Plate Format [0202]
Oligonucleotides were synthesized via solid phase P(III) phosphoramidite chemistry on an automated synthesizer capable of assembling 96 sequences simultaneously in a standard 96 well format. Phosphodiester internucleotide linkages were afforded by oxidation with aqueous iodine. Phosphorothioate internucleotide linkages were generated by sulfurization utilizing 3,H-1,2 benzodithiole-3-one 1,1 dioxide (Beaucage Reagent) in anhydrous acetonitrile. Standard base-protected beta-cyanoethyldiisopropyl phosphoramidites were purchased from commercial vendors (e.g. PE-Applied Biosystems, Foster City, Calif., or Pharmacia, Piscataway, N.J.). Non-standard nucleosides are synthesized as per known literature or patented methods. They are utilized as base protected beta-cyanoethyldiisopropyl phosphoramidites. [0203]
Oligonucleotides were cleaved from support and deprotected with concentrated NH[0204] ₄OH at elevated temperature (55-60° C.) for 12-16 hours and the released product then dried in vacuo. The dried product was then re-suspended in sterile water to afford a master plate from which all analytical and test plate samples are then diluted utilizing robotic pipettors.

Example 8

Oligonucleotide Analysis—96 Well Plate Format [0205]
The concentration of oligonucleotide in each well was assessed by dilution of samples and UV absorption spectroscopy. The full-length integrity of the individual products was evaluated by capillary electrophoresis (CE) in either the 96 well format (Beckman P/ACE™ MDQ) or, for individually prepared samples, on a commercial CE apparatus (e.g., Beckman P/ACE™ 5000, ABI 270). Base and backbone composition was confirmed by mass analysis of the compounds utilizing electrospray-mass spectroscopy. All assay test plates were diluted from the master plate using single and multi-channel robotic pipettors. Plates were judged to be acceptable if at least 85% of the compounds on the plate were at least 85% full length. [0206]

Example 9

Cell Culture and Oligonucleotide Treatment [0207]
The effect of antisense compounds on target nucleic acid expression can be tested in any of a variety of cell types provided that the target nucleic acid is present at measurable levels. This can be routinely determined using, for example, PCR or Northern blot analysis. The following 4 cell types are provided for illustrative purposes, but other cell types can be routinely used, provided that the target is expressed in the cell type chosen. This can be readily determined by methods routine in the art, for example Northern blot analysis, Ribonuclease protection assays, or RT-PCR. [0208]
T-24 Cells: [0209]
The transitional cell bladder carcinoma cell line T-24 was obtained from the American Type Culture Collection (ATCC) (Manassas, Va.). T-24 cells were routinely cultured in complete McCoy's 5A basal media (Gibco/Life Technologies, Gaithersburg, Md.) supplemented with 10% fetal calf serum (Gibco/Life Technologies, Gaithersburg, Md.), penicillin 100 units per mL, and streptomycin 100 micrograms per mL (Gibco/Life Technologies, Gaithersburg, Md.). Cells were routinely passaged by trypsinization and dilution when they reached 90% confluence. Cells were seeded into 96-well plates (Falcon-Primaria #3872) at a density of 7000 cells/well for use in RT-PCR analysis. [0210]
For Northern blotting or other analysis, cells may be seeded onto 100 mm or other standard tissue culture plates and treated similarly, using appropriate volumes of medium and oligonucleotide. A549 cells: [0211]
The human lung carcinoma cell line A549 was obtained from the American Type Culture Collection (ATCC) (Manassas, Va.). A549 cells were routinely cultured in DMEM basal media (Gibco/Life Technologies, Gaithersburg, Md.) supplemented with 10% fetal calf serum (Gibco/Life Technologies, Gaithersburg, Md.), penicillin 100 units per mL, and streptomycin 100 micrograms per mL (Gibco/Life Technologies, Gaithersburg, Md.). Cells were routinely passaged by trypsinization and dilution when they reached 90% confluence. [0212]
NHDF cells: [0213]
Human neonatal dermal fibroblast (NHDF) were obtained from the Clonetics Corporation (Walkersville Md.). NHDFs were routinely maintained in Fibroblast Growth Medium (Clonetics Corporation, Walkersville Md.) supplemented as recommended by the supplier. Cells were maintained for up to 10 passages as recommended by the supplier. HEK cells: [0214]
Human embryonic keratinocytes (HEK) were obtained from the Clonetics Corporation (Walkersville Md.). HEKs were routinely maintained in Keratinocyte Growth Medium (Clonetics Corporation, Walkersville Md.) formulated as recommended by the supplier. Cells were routinely maintained for up to 10 passages as recommended by the supplier. [0215]
Treatment with Antisense Compounds: [0216]
When cells reached 80% confluency, they were treated with oligonucleotide. For cells grown in 96-well plates, wells were washed once with 200 μL OPTI-MEM™-l reduced-serum medium (Gibco BRL) and then treated with 130 AL of OPTI-MEM™-1 containing 3.75 μg/mL LIPOFECTIN™ (Gibco BRL) sand the desired concentration of oligonucleotide. After 4-7 hours of treatment, the medium was replaced with fresh medium. Cells were harvested 16-24 hours after oligonucleotide treatment. [0217]
The concentration of oligonucleotide used varies from cell line to cell line. To determine the optimal oligonucleotide concentration for a particular cell line, the cells are treated with a positive control oligonucleotide at a range of concentrations. For human cells the positive control oligonucleotide is ISIS 13920, TCCGTCATCGCTCCTCAGGG, SEQ ID NO: 1, a 2′-O-methoxyethyl gapmer (2′-O-methoxyethyls shown in bold) with a phosphorothioate backbone which is targeted to human H-ras. For mouse or rat cells the positive control oligonucleotide is ISIS 15770, ATGCATTCTGCCCCCAAGGA, SEQ ID NO: 2, a 2′-O-methoxyethyl gapmer (2′-O-methoxyethyls shown in bold) with a phosphorothioate backbone which is targeted to both mouse and rat c-raf. The concentration of positive control oligonucleotide that results in 80% inhibition of c-Ha-ras (for ISIS 13920) or c-raf (for ISIS 15770) mRNA is then utilized as the screening concentration for new oligonucleotides in subsequent experiments for that cell line. If 80% inhibition is not achieved, the lowest concentration of positive control oligonucleotide that results in 60% inhibition of H-ras or c-raf mRNA is then utilized as the oligonucleotide screening concentration in subsequent experiments for that cell line. If 60% inhibition is not achieved, that particular cell line is deemed as unsuitable for oligonucleotide transfection experiments. [0218]

Example 10

Analysis of Oligonucleotide Inhibition of Glycogen Synthase Kinase 3 Alpha Expression [0219]
Antisense modulation of glycogen synthase kinase 3 alpha expression can be assayed in a variety of ways known in the art. For example, glycogen synthase kinase 3 alpha mRNA levels can be quantitated by, e.g., Northern blot analysis, competitive polymerase chain reaction (PCR), or real-time PCR (RT-PCR). Real-time quantitative PCR is presently preferred. RNA analysis can be performed on total cellular RNA or poly(A)+ mRNA. Methods of RNA isolation are taught in, for example, Ausubel, F. M. et al., [0220] Current Protocols in Molecular Biology, Volume 1, pp. 4.1.1-4.2.9 and 4.5.1-4.5.3, John Wiley & Sons, Inc., 1993. Northern blot analysis is routine in the art and is taught in, for example, Ausubel, F. M. et al., Current Protocols in Molecular Biology, Volume 1, pp. 4.2.1-4.2.9, John Wiley. & Sons, Inc., 1996. Real-time quantitative (PCR) can be conveniently accomplished using the commercially available ABI PRISM™ 7700 Sequence Detection System, available from PE-Applied Biosystems, Foster City, Calif. and used according to manufacturer's instructions. Prior to quantitative PCR analysis, primer-probe sets specific to the target gene being measured are evaluated for their ability to be “multiplexed” with a GAPDH amplification reaction. In multiplexing, both the target gene and the internal standard gene GAPDH are amplified concurrently in a single sample. In this analysis, mRNA isolated from untreated cells is serially diluted. Each dilution is amplified in the presence of primer-probe sets specific for GAPDH only, target gene only (“single-plexing”), or both (multiplexing). Following PCR amplification, standard curves of GAPDH and target mRNA signal as a function of dilution are generated from both the single-plexed and multiplexed samples. If both the slope and correlation coefficient of the GAPDH and target signals generated from the multiplexed samples fall within 10% of their corresponding values generated from the single-plexed samples, the primer-probe set specific for that target is deemed as multiplexable. Other methods of PCR are also known in the art.
Protein levels of glycogen synthase kinase 3 alpha can be quantitated in a variety of ways well known in the art, such as immunoprecipitation, Western blot analysis (immunoblotting), ELISA or fluorescence-activated cell sorting (FACS). Antibodies directed to glycogen synthase kinase 3 alpha can be identified and obtained from a variety of sources, such as the MSRS catalog of antibodies (Aerie Corporation, Birmingham, Mich.), or can be prepared via conventional antibody generation methods. Methods for preparation of polyclonal antisera are taught in, for example, Ausubel, F. M. et al., [0221] Current Protocols in Molecular Biology, Volume 2, pp. 11.12.1-11.12.9, John Wiley & Sons, Inc., 1997. Preparation of monoclonal antibodies is taught in, for example, Ausubel, F. M. et al., Current Protocols in Molecular Biology, Volume 2, pp. 11.4.1-11.11.5, John Wiley & Sons, Inc., 1997.
Immunoprecipitation methods are standard in the art and can be found at, for example, Ausubel, F. M. et al., [0222] Current Protocols in Molecular Biology, Volume 2, pp. 10.16.1-10.16.11, John Wiley & Sons, Inc., 1998. Western blot (immunoblot) analysis is standard in the art and can be found at, for example, Ausubel, F. M. et al., Current Protocols in Molecular Biology, Volume 2, pp. 10.8.1-10.8.21, John Wiley & Sons, Inc., 1997. Enzyme-linked immunosorbent assays (ELISA) are standard in the art and can be found at, for example, Ausubel, F. M. et al., Current Protocols in Molecular Biology, Volume 2, pp. 11.2.1-11.2.22, John Wiley & Sons, Inc., 1991.

Example 11

Poly(A)+ mRNA Isolation [0223]
Poly(A)+ mRNA was isolated according to Miura et al., [0224] Clin. Chem., 1996, 42, 1758-1764. Other methods for poly(A)+ mRNA isolation are taught in, for example, Ausubel, F. M. et al., Current Protocols in Molecular Biology, Volume 1, pp. 4.5.1-4.5.3, John Wiley & Sons, Inc., 1993. Briefly, for cells grown on 96-well plates, growth medium was removed from the cells and each well was washed with 200 μcold PBS. 60 μL lysis buffer (10 mM Tris-HCl, pH 7.6, 1 mM EDTA, 0.5 M NaCl, 0.5w NP-40, 20 mM vanadyl-ribonucleoside complex) was added to each well, the plate was gently agitated and then incubated at room temperature for five minutes. 55 AL of lysate was transferred to Oligo d(T) coated 96-well plates (AGCT Inc., Irvine Calif.). Plates were incubated for 60 minutes at room temperature, washed 3 times with 200 μL of wash buffer (10 mM Tris-HCl pH 7.6, 1 mM EDTA, 0.3 M NaCl). After the final wash, the plate was blotted on paper towels to remove excess wash buffer and then air-dried for 5 minutes. 60 AL of elution buffer (5 mM Tris-HCl pH 7.6), preheated to 70° C. was added to each well, the plate was incubated on a 90° C. hot plate for 5 minutes, and the eluate was then transferred to a fresh 96-well plate.
Cells grown on 100 mm or other standard plates may be treated similarly, using appropriate volumes of all solutions. [0225]

Example 12

Total RNA Isolation [0226]
Total mRNA was isolated using an RNEASY 96™ kit and buffers purchased from Qiagen Inc. (Valencia Calif.) following the manufacturer's recommended procedures. Briefly, for cells grown on 96-well plates, growth medium was removed from the cells and each well was washed with 200 AL cold PBS. 100 AL Buffer RLT was added to each well and the plate vigorously agitated for 20 seconds. 100 μL of 70% ethanol was then added to each well and the contents mixed by pipetting three times up and down. The samples were then transferred to the RNEASY 96™ well plate attached to a QIAVAC™ manifold fitted with a waste collection tray and attached to a vacuum source. Vacuum was applied for 15 seconds. 1 mL of Buffer RW1 was added to each well of the RNEASY 96™ plate and the vacuum again applied for 15 seconds. 1 mL of Buffer RPE was then added to each well of the RNEASY 96™ plate and the vacuum applied for a period of 15 seconds. The Buffer RPE wash was then repeated and the vacuum was applied for an additional 10 minutes. The plate was then removed from the QIAVAC™ manifold and blotted dry on paper towels. The plate was then re-attached to the QIAVAC™ manifold fitted with a collection tube rack containing 1.2 mL collection tubes. RNA was then eluted by pipetting 60 μL water into each well, incubating 1 minute, and then applying the vacuum for 30 seconds. The elution step was repeated with an additional 60 μL water. [0227]
The repetitive pipetting and elution steps may be automated using a QIAGEN Bio-Robot 9604 (Qiagen, Inc., Valencia Calif.). Essentially, after lysing of the cells on the culture plate, the plate is transferred to the robot deck where the pipetting, DNase treatment and elution steps are carried out. [0228]

Example 13

Real-Time Quantitative PCR Analysis of Glycogen Synthase Kinase 3 Alpha mRNA Levels [0229]
Quantitation of glycogen synthase kinase 3 alpha mRNA levels was determined by real-time quantitative PCR using the ABI PRISM™ 7700 Sequence Detection System (PE-Applied Biosystems, Foster City, Calif.) according to manufacturer's instructions. This is a closed-tube, non-gel-based, fluorescence detection system which allows high-throughput quantitation of polymerase chain reaction (PCR) products in real-time. As opposed to standard PCR, in which amplification products are quantitated after the PCR is completed, products in real-time quantitative PCR are quantitated as they accumulate. This is accomplished by including in the PCR reaction an oligonucleotide probe that anneals specifically between the forward and reverse PCR primers, and contains two fluorescent dyes. A reporter dye (e.g., JOE, FAM, or VIC, obtained from either Operon Technologies Inc., Alameda, Calif. or PE-Applied Biosystems, Foster City, Calif.) is attached to the 5′ end of the probe and a quencher dye (e.g., TAMRA, obtained from either Operon Technologies Inc., Alameda, Calif. or PE-Applied Biosystems, Foster City, Calif.) is attached to the 3′ end of the probe. When the probe and dyes are intact, reporter dye emission is quenched by the proximity of the 3′ quencher dye. During amplification, annealing of the probe to the target sequence creates a substrate that can be cleaved by the 5′-exonuclease activity of Taq polymerase. During the extension phase of the PCR amplification cycle, cleavage of the probe by Taq polymerase releases the reporter dye from the remainder of the probe (and hence from the quencher moiety) and a sequence-specific fluorescent signal is generated. With each cycle, additional reporter dye molecules are cleaved from their respective probes, and the fluorescence intensity is monitored at regular intervals by laser optics built into the ABI PRISM™ 7700 Sequence Detection System. In each assay, a series of parallel reactions containing serial dilutions of mRNA from untreated control samples generates a standard curve that is used to quantitate the percent inhibition after antisense oligonucleotide treatment of test samples. [0230]
PCR reagents were obtained from PE-Applied Biosystems, Foster City, Calif. RT-PCR reactions were carried out by adding 25 AL PCR cocktail (1x TAQMAN™ buffer A, 5.5 mM MgCl[0231] ₂, 300 μM each of DATP, dCTP and dGTP, 600 μM of dUTP, 100 nM each of forward primer, reverse primer, and probe, 20 Units RNAse inhibitor, 1.25 Units AMPLITAQ GOLD™, and 12.5 Units MULV reverse transcriptase) to 96 well plates containing 25 μL poly(A) mRNA solution. The RT reaction was carried out by incubation for 30 minutes at 48° C. Following a 10 minute incubation at 95° C. to activate the AMPLITAQ GOLD™, 40 cycles of a two-step PCR protocol were carried out: 95° C. for 15 seconds (denaturation) followed by 60° C. for 1.5 minutes (annealing/extension).
Probes and primers to human glycogen synthase kinase 3 alpha were designed to hybridize to a human glycogen synthase kinase 3 alpha sequence, using published sequence information (GenBank accession number D63424, incorporated herein as SEQ ID NO:3). For human glycogen synthase kinase 3 alpha the PCR primers were: forward primer: CAAGAAGTGGCTTACACGGACAT (SEQ ID NO: 4) reverse primer: GGCGACTAGTTCCCTGGTCTCT (SEQ ID NO: 5) and the PCR probe was: FAM-AAAGTGATTGGCAATGGCTCATTTGGG-TAMRA (SEQ ID NO: 6) where FAM (PE-Applied Biosystems, Foster City, Calif.) is the fluorescent reporter dye) and TAMRA (PE-Applied Biosystems, Foster City, Calif.) is the quencher dye. For human GAPDH the PCR primers were: forward primer: GAAGGTGAAGGTCGGAGTC (SEQ ID NO: 7) reverse primer: GAAGATGGTGATGGGATTTC (SEQ ID NO: 8) and the PCR probe was: 5′ JOE-CAAGCTTCCCGTTCTCAGCC-TAMRA 3′ (SEQ ID NO: 9) where JOE (PE-Applied Biosystems, Foster City, Calif.) is the fluorescent reporter dye) and TAMRA (PE-Applied Biosystems, Foster City, Calif.) is the quencher dye. [0232]

Example 14

Northern Blot Analysis of Glycogen Synthase Kinase 3 Alpha mRNA Levels [0233]
Eighteen hours after antisense treatment, cell monolayers were washed twice with cold PBS and lysed in 1 mL RNAZOL™ (TEL-TEST “B” Inc., Friendswood, Tex.). Total RNA was prepared following manufacturer's recommended protocols. Twenty micrograms of total RNA was fractionated by electrophoresis through 1.2% agarose gels containing 1.1 formaldehyde using a MOPS buffer system (AMRESCO, Inc. Solon, Ohio). RNA was transferred from the gel to HYBOND™-N+ nylon membranes (Amersham Pharmacia Biotech, Piscataway, N.J.) by overnight capillary transfer using a Northern/Southern Transfer buffer system (TEL-TEST “B” Inc., Friendswood, Tex.). RNA transfer was confirmed by UV visualization. Membranes were fixed by UV cross-linking using a STRATALINKER™ UV Crosslinker 2400 (Stratagene, Inc, La Jolla, Calif.) and then robed using QUICKHYB™ hybridization solution (Stratagene, La Jolla, Calif.) using manufacturer's recommendations for stringent conditions. [0234]
To detect human glycogen synthase kinase 3 alpha, a human glycogen synthase kinase 3 alpha specific probe was prepared by PCR using the forward primer CAAGAAGTGGCTTACACGGACAT (SEQ ID NO: 4) and the reverse primer GGCGACTAGTTCCCTGGTCTCT (SEQ ID NO: 5). To normalize for variations in loading and transfer efficiency membranes were stripped and probed for human glyceraldehyde-3-phosphate dehydrogenase (GAPDH) RNA (Clontech, Palo Alto, Calif.). [0235]
Hybridized membranes were visualized and quantitated using a PHOSPHORIMAGER™ and IMAGEQUANT™ Software V3.3 (Molecular Dynamics, Sunnyvale, Calif.). Data was normalized to GAPDH levels in untreated controls. [0236]

Example 15

Antisense Inhibition of Human Glycogen Synthase Kinase 3 Alpha Expression by Chimeric Phosphorothioate Oligonucleotides Having 2′-MOE Wings and a Deoxy Gap [0237]

In accordance with the present invention, a series of oligonucleotides were designed to target different regions of the human glycogen synthase kinase 3 alpha RNA, using published sequences (GenBank accession number D63424, incorporated herein as SEQ ID NO: 3, and GenBank accession number AC006486, of which the complement of nucleotides 22041 to 34434 are incorporated herein as SEQ ID NO: 10). The oligonucleotides are shown in Table 1. “Target site” indicates the the first (5′-most) nucleotide number on the particular target sequence to which the oligonucleotide All compounds in Table 1 are chimeric oligonucleotides (“gapmers”) 20 nucleotides in length, composed of a central “gap” region consisting of ten 2′-deoxynucleotides, which is flanked on both sides (5′ and 3′ directions) by five-nucleotide “wings”. The wings are composed of 2′-methoxyethyl (2′-MOE)nucleotides. The internucleoside (backbone) linkages are phosphorothioate (P═S) throughout the oligonucleotide. All cytidine residues are 5-methylcytidines. The compounds were analyzed for their effect on human glycogen synthase kinase 3 alpha mRNA levels by quantitative real-time PCR as described in other examples herein. Data are averages from two experiments. If present, “N.D.” indicates “no data”.

TABLE 1


Inhibition of human glycogen synthase kinase 3 alpha mRNA
levels by chimeric phosphorothioate oligonucleotides having
2′-MOE wings and a deoxy gap

		TARGET	TARGET			SEQ ID
ISIS #	REGION	SEQ ID NO	SITE	SEQUENCE	% INHIB	NO

116598	5′ UTR	3	3	cgcctcccccggagcccaag	0	11
116599	Start	3	84	gccgccgctcatggcgccga	23	12
	Codon
116600	Start	3	91	aaggcccgccgccgctcatg	12	13
	Codon
116601	Coding	3	230	acagatgcctttccgccgcc	31	14
116602	Coding	3	307	ctccgctgcctcctccgccg	88	15
116603	Coding	3	353	cccagcttcaccccgggcgg	90	16
116604	Coding	3	370	ccttcccgctgtcacggccc	32	17
116605	Coding	3	371	accttcccgctgtcacggcc	14	18
116606	Coding	3	375	ggtcaccttcccgctgtcac	68	19
116607	Coding	3	410	cgctctgggccttggcctag	0	20
116608	Coding	3	431	gtgtaagccacttcttggga	16	21
116609	Coding	3	442	ctttgatgtccgtgtaagcc	19	22
116610	Coding	3	445	tcactttgatgtccgtgtaa	28	23
116611	Coding	3	491	tctgccagccgtgcctggta	23	24
116612	Coding	3	518	ttcttgatggcgactagttc	14	25
116613	Coding	3	535	tcttgtcctggagaaccttc	0	26
116614	Coding	3	565	gcatgatctgcagctctcgg	79	27
116615	Coding	3	573	cagcttacgcatgatctgca	39	28
116616	Coding	3	617	ctggagtagaaaaagtatct	0	29
116617	Coding	3	626	ttctcgccactggagtagaa	35	30
116618	Coding	3	629	ttcttctcgccactggagta	38	31
116619	Coding	3	632	tctttcttctcgccactgga	46	32
116620	Coding	3	665	acatattccagcaccagatt	24	33
116621	Coding	3	706	ccttggtgaagtggcgggcc	3	34
116622	Coding	3	782	gagtggatgtaggccaagct	36	35
116623	Coding	3	840	agtgtcagggtccaccagca	49	36
116624	Coding	3	859	cgcagagcttgaggacagca	0	37
116625	Coding	3	887	cggaccaactgctttgcact	79	38
116626	Coding	3	890	cctcggaccaactgctttgc	31	39
116627	Coding	3	914	cagatgtaggagacattggg	0	40
116628	Coding	3	960	atcagtggctccaaagatga	12	41
116629	Coding	3	963	gtaatcagtggctccaaaga	19	42
116630	Coding	3	966	ggtgtaatcagtggctccaa	17	43
116631	Coding	3	1058	agctggtccaccccactgtc	74	44
116632	Coding	3	1309	gctgggttcccagacatcgc	63	45
116633	Coding	3	1354	cagcactgaagttgaagaga	0	46
116634	Coding	3	1491	ggtcgactgccagtctgagc	24	47
116635	Coding	3	1514	ttagtgagggtaggtgtggc	0	48
116636	Stop	3	1530	gggccctcaggaggagttag	0	49
	Codon
116637	3′ UTR	3	1708	ttaaaaagcccaccacaggg	9	50
116638	3′ UTR	3	1710	tcttaaaaagcccaccacag	10	51
116639	3′ UTR	3	1747	tgtccttctcttccctcccc	24	52
116640	3′ UTR	3	1755	caacaccctgtccttctctt	34	53
116641	3′ UTR	3	1936	tcgacgttttctttaagaaa	22	54
116642	3′ UTR	3	1943	gtgcgaatcgacgttttctt	37	55
116643	3′ UTR	3	1954	caggttggacggtgcgaatc	22	56
116644	3′ UTR	3	2064	gacatcaggagctctctcca	26	57
116645	3′ UTR	3	2116	taatttattgaacggaggtc	23	58
116646	Intron	10	516	gaagagggctcggatccccg	0	59
116647	Intron	10	686	ttataatgaatagcaacatc	1	60
116648	Intron	10	1191	agccaatgacaccatacctt	89	61
116649	Intron	10	1309	tcccaaagtgctgggattac	13	62
116650	Intron	10	1476	tgctgggttcaagcgattct	0	63
116651	Intron	10	1735	ccaaattatgataatgatga	0	64
116652	Intron	10	1906	tggttcttggtgacagaaat	0	65
116653	Intron	10	2646	cagtccccaaacctccctgt	47	66
116654	Intron	10	2938	caggcaatcctcttacctga	78	67
116655	Intron	10	3066	cttcagaaccacccgcgcta	1	68
116656	Intron	10	3241	aggctcagttctcctacatc	54	69
116657	Intron	10	3504	tctggtcccgtggaagcatc	19	70
116658	Intron	10	4021	gaggttgcagtgacccgaga	5	71
116659	Intron	10	4446	gccaaggcagggaaatcact	0	72
116660	Intron	10	4475	tcacccctgtaatcccagca	0	73
116661	Coding	10	5633	tgcagctctcggttcttgag	27	74
116662	Intron	10	5788	gaaggtatgcagggagcagt	26	75
116663	Intron	10	6647	agagcccacgtcggctcacc	31	76
116664	Intron	10	7056	gggcctagacagaccaggtc	46	77
116665	Intron	10	7190	aatccgacaatcaaaaccac	31	78
116666	Intron	10	7296	aacccttggcagaagcctga	0	79
116667	Intron	10	7312	ccactgctttaatcacaacc	19	80
116668	Intron	10	7823	cccaccagcttggcctgaag	18	81
116669	Intron	10	8748	taccttgacccccacagcac	63	82
116670	Intron	10	8967	ctcagttcctctctctgcta	63	83
116671	Intron	10	9681	actatatgagccctgctgac	0	84
116672	Intron	10	9827	tactcctgttatctcactgc	13	85
116673	Intron	10	10612	atgtcgatgatttaaaaata	8	86
116674	Intron	10	10669	ataccctctaaaggtggtca	21	87
116675	Intron	10	11332	atgagcgtgtaatcccaggt	7	88

As shown in Table 1, SEQ ID NOs 12, 14, 15, 16, 17, 19, 23, 24, 27, 28, 30, 31, 32, 33, 35, 36, 38, 39, 44, 45, 47, 52, 53, 54, 55, 56, 57, 58, 61, 66, 67, 69, 74, 75, 76, 77, 78, 82, 83 and 87 demonstrated at least 20% inhibition of human glycogen synthase kinase 3 alpha expression in say and are therefore preferred. [0239]

Example 16

Western Blot Analysis of Glycogen Synthase Kinase 3 Alpha Protein Levels [0240]
Western blot analysis (immunoblot analysis) is carried out using standard methods. Cells are harvested 16-20 h after oligonucleotide treatment, washed once with PBS, suspended in Laemmli buffer (100 ul/well), boiled for 5 minutes and loaded on a 16% SDS-PAGE gel. Gels are run for 1.5 hours at 150 V, and transferred to membrane for western blotting. Appropriate primary antibody directed to glycogen synthase kinase 3 alpha is used, with a radiolabelled or fluorescently labeled secondary antibody directed against the primary antibody species. Bands are visualized using a PHOSPHORIMAGER™ (Molecular Dynamics, Sunnyvale Calif.). [0241]
1 88 1 20 DNA Artificial Sequence Antisense Oligonucleotide 1 tccgtcatcg ctcctcaggg 20 2 20 DNA Artificial Sequence Antisense Oligonucleotide 2 atgcattctg cccccaagga 20 3 2154 DNA Homo sapiens CDS (92)...(1543) 3 ggcttgggct ccgggggagg cggcggccgc ggcggcggct ggggcagccc gggcagcccg 60 agccccgcag cctgggcctg tgctcggcgc c atg agc ggc ggc ggg cct tcg 112 Met Ser Gly Gly Gly Pro Ser 1 5 gga ggc ggc cct ggg ggc tcg ggc agg gcg cgg act agc tcg ttc gcg 160 Gly Gly Gly Pro Gly Gly Ser Gly Arg Ala Arg Thr Ser Ser Phe Ala 10 15 20 gag ccc ggc ggc gga ggc gga gga ggc ggc ggc ggc ccc gga ggc tcg 208 Glu Pro Gly Gly Gly Gly Gly Gly Gly Gly Gly Gly Pro Gly Gly Ser 25 30 35 gcc tcc ggc cca ggc ggc acc ggc ggc gga aag gca tct gtc ggg gcc 256 Ala Ser Gly Pro Gly Gly Thr Gly Gly Gly Lys Ala Ser Val Gly Ala 40 45 50 55 atg ggt ggg ggc gtc ggg gcc tcg agc tcc ggg ggt gga ccc ggc ggc 304 Met Gly Gly Gly Val Gly Ala Ser Ser Ser Gly Gly Gly Pro Gly Gly 60 65 70 agc ggc gga gga ggc agc gga ggc ccc ggc gca ggc act agc ttc ccg 352 Ser Gly Gly Gly Gly Ser Gly Gly Pro Gly Ala Gly Thr Ser Phe Pro 75 80 85 ccg ccc ggg gtg aag ctg ggc cgt gac agc ggg aag gtg acc aca gtc 400 Pro Pro Gly Val Lys Leu Gly Arg Asp Ser Gly Lys Val Thr Thr Val 90 95 100 gta gcc act cta ggc caa ggc cca gag cgc tcc caa gaa gtg gct tac 448 Val Ala Thr Leu Gly Gln Gly Pro Glu Arg Ser Gln Glu Val Ala Tyr 105 110 115 acg gac atc aaa gtg att ggc aat ggc tca ttt ggg gtc gtg tac cag 496 Thr Asp Ile Lys Val Ile Gly Asn Gly Ser Phe Gly Val Val Tyr Gln 120 125 130 135 gca cgg ctg gca gag acc agg gaa cta gtc gcc atc aag aag gtt ctc 544 Ala Arg Leu Ala Glu Thr Arg Glu Leu Val Ala Ile Lys Lys Val Leu 140 145 150 cag gac aag agg ttc aag aac cga gag ctg cag atc atg cgt aag ctg 592 Gln Asp Lys Arg Phe Lys Asn Arg Glu Leu Gln Ile Met Arg Lys Leu 155 160 165 gac cac tgc aat att gtg agg ctg aga tac ttt ttc tac tcc agt ggc 640 Asp His Cys Asn Ile Val Arg Leu Arg Tyr Phe Phe Tyr Ser Ser Gly 170 175 180 gag aag aaa gac gag ctt tac cta aat ctg gtg ctg gaa tat gtg ccc 688 Glu Lys Lys Asp Glu Leu Tyr Leu Asn Leu Val Leu Glu Tyr Val Pro 185 190 195 gag aca gtg tac cgg gtg gcc cgc cac ttc acc aag gcc aag ttg acc 736 Glu Thr Val Tyr Arg Val Ala Arg His Phe Thr Lys Ala Lys Leu Thr 200 205 210 215 atc cct atc ctc tat gtc aag gtg tac atg tac cag ctc ttc cgc agc 784 Ile Pro Ile Leu Tyr Val Lys Val Tyr Met Tyr Gln Leu Phe Arg Ser 220 225 230 ttg gcc tac atc cac tcc cag ggc gtg tgt cac cgc gac atc aag ccc 832 Leu Ala Tyr Ile His Ser Gln Gly Val Cys His Arg Asp Ile Lys Pro 235 240 245 cag aac ctg ctg gtg gac cct gac act gct gtc ctc aag ctc tgc gat 880 Gln Asn Leu Leu Val Asp Pro Asp Thr Ala Val Leu Lys Leu Cys Asp 250 255 260 ttt ggc agt gca aag cag ttg gtc cga ggg gag ccc aat gtc tcc tac 928 Phe Gly Ser Ala Lys Gln Leu Val Arg Gly Glu Pro Asn Val Ser Tyr 265 270 275 atc tgt tct cgc tac tac cgg gcc cca gag ctc atc ttt gga gcc act 976 Ile Cys Ser Arg Tyr Tyr Arg Ala Pro Glu Leu Ile Phe Gly Ala Thr 280 285 290 295 gat tac acc tca tcc atc gat gtt tgg tca gct ggc tgt gta ctg gca 1024 Asp Tyr Thr Ser Ser Ile Asp Val Trp Ser Ala Gly Cys Val Leu Ala 300 305 310 gag ctc ctc ttg ggc cag ccc atc ttc cct ggg gac agt ggg gtg gac 1072 Glu Leu Leu Leu Gly Gln Pro Ile Phe Pro Gly Asp Ser Gly Val Asp 315 320 325 cag ctg gtg gag atc atc aag gtg ctg gga aca cca acc cgg gaa caa 1120 Gln Leu Val Glu Ile Ile Lys Val Leu Gly Thr Pro Thr Arg Glu Gln 330 335 340 atc cga gag atg aac ccc aac tac acg gag ttc aag ttc cct cag att 1168 Ile Arg Glu Met Asn Pro Asn Tyr Thr Glu Phe Lys Phe Pro Gln Ile 345 350 355 aaa gct cac ccc tgg aca aag gtg ttc aaa tct cga acg ccg cca gag 1216 Lys Ala His Pro Trp Thr Lys Val Phe Lys Ser Arg Thr Pro Pro Glu 360 365 370 375 gcc atc gcg ctc tgc tct agc ctg ctg gag tac acc cca tcc tca agg 1264 Ala Ile Ala Leu Cys Ser Ser Leu Leu Glu Tyr Thr Pro Ser Ser Arg 380 385 390 ctc tcc cca cta gag gcc tgt gcg cac agc ttc ttt gat gaa ctg cga 1312 Leu Ser Pro Leu Glu Ala Cys Ala His Ser Phe Phe Asp Glu Leu Arg 395 400 405 tgt ctg gga acc cag ctg cct aac aac cgc cca ctt ccc cct ctc ttc 1360 Cys Leu Gly Thr Gln Leu Pro Asn Asn Arg Pro Leu Pro Pro Leu Phe 410 415 420 aac ttc agt gct ggt gaa ctc tcc atc caa ccg tct ctc aac gcc att 1408 Asn Phe Ser Ala Gly Glu Leu Ser Ile Gln Pro Ser Leu Asn Ala Ile 425 430 435 ctc atc cct cct cac ttg agg tcc cca gcg ggc act acc acc ctc acc 1456 Leu Ile Pro Pro His Leu Arg Ser Pro Ala Gly Thr Thr Thr Leu Thr 440 445 450 455 ccg tcc tca caa gct tta act gag act ccg acc agc tca gac tgg cag 1504 Pro Ser Ser Gln Ala Leu Thr Glu Thr Pro Thr Ser Ser Asp Trp Gln 460 465 470 tcg acc gat gcc aca cct acc ctc act aac tcc tcc tga gggccccacc 1553 Ser Thr Asp Ala Thr Pro Thr Leu Thr Asn Ser Ser 475 480 aagcaccctt ccacttccat ctgggagccc caagaggggc tgggaagggg ggccatagcc 1613 catcaagctc ctgccctggc tgggccccta gactagaggg cagaggtaaa tgagtccctg 1673 tccccacctc cagtccctcc ctcaccagcc tcacccctgt ggtgggcttt ttaagaggat 1733 tttaactggt tgtggggagg gaagagaagg acagggtgtt ggggggatga ggacctccta 1793 cccccttggc cccctcccct cccccagacc tccacctcct ccagaccccc tcccctcctg 1853 tgtcccttgt aaatagaacc agcccagccc gtctcctctt cccttccctg gcccccgggt 1913 gtaaatagat tgttataatt tttttcttaa agaaaacgtc gattcgcacc gtccaacctg 1973 gccccgcccc tcctacagct gtaactcccc tcctgtcctc tgcccccaag gtctactccc 2033 tcctcacccc accctggagg gccaggggag tggagagagc tcctgatgtc ttagtttcca 2093 cagtaaggtt tgcctgtgta cagacctccg ttcaataaat tattggcatg aaaacctgaa 2153 a 2154 4 23 DNA Artificial Sequence PCR Primer 4 caagaagtgg cttacacgga cat 23 5 22 DNA Artificial Sequence PCR Primer 5 ggcgactagt tccctggtct ct 22 6 27 DNA Artificial Sequence PCR Probe 6 aaagtgattg gcaatggctc atttggg 27 7 19 DNA Artificial Sequence PCR Primer 7 gaaggtgaag gtcggagtc 19 8 20 DNA Artificial Sequence PCR Primer 8 gaagatggtg atgggatttc 20 9 20 DNA Artificial Sequence PCR Probe 9 caagcttccc gttctcagcc 20 10 12394 DNA Homo sapiens CDS (115)...(397) CDS (2438)...(2625) CDS (5639)...(5722) CDS (5864)...(5974) CDS (7902)...(8032) CDS (8121)...(8227) CDS (9197)...(9294) CDS (9375)...(9470) CDS (9898)...(10084) CDS (10431)...(10523) CDS (11713)...(11786) 10 gccagagcgg cgcggcctgg aagaggccag ggcccggggg aggcggcggc agcggcggcg 60 gctggggcag cccgggcagc ccgagccccg cagcctgggc ctgtgctcgg cgcc atg 117 Met 1 agc ggc ggc ggg cct tcg gga ggc ggc cct ggg ggc tcg ggc agg gcg 165 Ser Gly Gly Gly Pro Ser Gly Gly Gly Pro Gly Gly Ser Gly Arg Ala 5 10 15 cgg act agc tcg ttc gcg gag ccc ggc ggc gga ggc gga gga ggc ggc 213 Arg Thr Ser Ser Phe Ala Glu Pro Gly Gly Gly Gly Gly Gly Gly Gly 20 25 30 ggc ggc ccc gga ggc tcg gcc tcc ggc cca ggc ggc acc ggc ggc gga 261 Gly Gly Pro Gly Gly Ser Ala Ser Gly Pro Gly Gly Thr Gly Gly Gly 35 40 45 aag gca tct gtc ggg gcc atg ggt ggg ggc gtc ggg gcc tcg agc tcc 309 Lys Ala Ser Val Gly Ala Met Gly Gly Gly Val Gly Ala Ser Ser Ser 50 55 60 65 ggg ggt gga ccc ggc ggc agc ggc gga gga ggc agc gga ggc ccc ggc 357 Gly Gly Gly Pro Gly Gly Ser Gly Gly Gly Gly Ser Gly Gly Pro Gly 70 75 80 gca ggc act agc ttc ccg ccg ccc ggg gtg aag ctg ggc c gtgagtacta 407 Ala Gly Thr Ser Phe Pro Pro Pro Gly Val Lys Leu Gly 85 90 gtggcgcccg tgtagggtgg tgattagggt tcccaaagct cctcagacat ccatcagatt 467 ctttcatgtg cttagatagg agctcgaggt cactgtgcct ccccataccg gggatccgag 527 ccctcttcct cccaggaaaa ggagtcttgg ggttaccatc tcttggagat cagaattact 587 cgtggatcag aattactaac acttaaagaa acgggttaca agtctctgtt cttccattat 647 tgaggtcttg ggtccttgag ccttaagaac aggtatctga tgttgctatt cattataata 707 ttggatcaga ggtcacagtc gcttgcaaat ggggatctag ggttattgtc tcctaagaga 767 acaagaataa gaccaacccc gaaaaagagg gatctgcatt ccctgtcctt cagaagatgg 827 ggatttggag cgaatatcac ttagaagcag ggctttgagg ttactgtgtt ttgtccccaa 887 agaatagggc caggctttcc aaacctggta ctcagatcat cttccctatt aaaaccaaga 947 cctggcatca ttacccaccc taaatcttgt tgagctgtac tgccaatggt gagaattaat 1007 agttactgcc ttttagatat aaagacattg ggagtcagca tatccttcaa accaagtcca 1067 tagtccatgt tttaaaatac atggcttggt gtgtctcctt taacaaaaat ggaatggagc 1127 agggtaggtc acagtttcct acagaatatg gatctaaggt tatacttttt taataattgt 1187 tctaaggtat ggtgtcattg gctctgaaaa aaaaaagtga tgtagggtta tctccctctg 1247 aaagaacttg tcactggccc ctcaaaatgg atttggtggc cgggcgcggt ggctcacgcc 1307 tgtaatccca gcactttggg aggctgaggt gggcggatca cctgcggtca ggagttcgag 1367 accagcctgg ccaactggtg gaaccctgtc tctactaaaa atataaaaaa ttagctgggc 1427 gtggtggcgg gcgcctgtaa tcccagcttc tcgggaggct gaggcaggag aatcgcttga 1487 acccagcagg cggaggttgc agtgagtcga gatcgtgcca ctgcactcca gctgggcaac 1547 gagagcgaaa ctgtgtctca aaaaaaaaaa caaaaaaatg gatttggttc atcagttact 1607 caaaggggtc actatcctct aagaatggca ccaaggtttg ccaccatttg aataatggga 1667 attgggaatt atagctttcc ttcaaaggac tgaggctgga atagctcctt gataataaag 1727 gtcaggttca tcattatcat aatttggtgc ttgtccatta gggaccaccc acatatagtg 1787 aggggtctgg gtctctggac cactcagatg aagaggtcag gtcagtgttt ttttctaacc 1847 tcaaagtacc aaaaagtgag ggtcagggca ctggcactta tagcaggaga ggacattcat 1907 ttctgtcacc aagaaccagt aaagttacca gctctacagg ggaggactta gaggtcagta 1967 tcctctaggc tgtgagagag gttagtgctt tcctaaagta ggagtacctc agggttactg 2027 ctccctgaag tggaagaggc tcggtcaagc tttctccaaa taggaggggc cagagggcag 2087 tagatccaga gtagatggag tcaacatctg atgtctccca gtaccaagat ggaccagtga 2147 tctgttgctt cctagaagta gaaatttggg gttgccaacc cttgaagcag agagatttag 2207 gtatcaatat cctcctatgt ggaggggagc aggacttaag attcccagaa aggaagaggg 2267 gaaaagtcac tgggaaggtc ccagcatcca cctttcctca aagaggagga ggggacaaag 2327 aggtccccaa cgagcttcct gcagagattt cccttcctcc cacagcccca ggatagggtg 2387 atgcgcaggc aggatgggtc agtggatcgt gtatcccctt tgttccccag gt gac 2442 Arg Asp 95 agc ggg aag gtg acc aca gtc gta gcc act cta ggc caa ggc cca gag 2490 Ser Gly Lys Val Thr Thr Val Val Ala Thr Leu Gly Gln Gly Pro Glu 100 105 110 cgc tcc caa gaa gtg gct tac acg gac atc aaa gtg att ggc aat ggc 2538 Arg Ser Gln Glu Val Ala Tyr Thr Asp Ile Lys Val Ile Gly Asn Gly 115 120 125 tca ttt ggg gtc gtg tac cag gca cgg ctg gca gag acc agg gaa cta 2586 Ser Phe Gly Val Val Tyr Gln Ala Arg Leu Ala Glu Thr Arg Glu Leu 130 135 140 gtc gcc atc aag aag gtt ctc cag gac aag agg ttc aag gtagcttggg 2635 Val Ala Ile Lys Lys Val Leu Gln Asp Lys Arg Phe Lys 145 150 155 cgggatgggg acagggaggt ttggggactg ggtgtgactg gtgggagaac ctgagccaga 2695 gagctggagg cttgggtttc agagccatgg gccagaagag aagggggaaa agaggaaatg 2755 agacctgtga aagatgggaa atgtggatcc caggagagcc cagagctttt actgggcatt 2815 tgctcaatgt aagtgcttaa taagcaaatt cttgtttaat ttacataaag attctctgag 2875 ggtaggtact gtggttatac ccattctaag tgtaagctaa gtttaaaagc agggaaacaa 2935 actcaggtaa gaggattgcc tgaggtcata gagcaagtgc cccagtcaag gctggaatct 2995 gattcccaaa ccctctacct taaccatttg gttacacttc ttcccaggag agaaagggac 3055 ctggcagggc tagcgcgggt ggttctgaag gtcgcgctct tcccaggtgt ttggccagcg 3115 cagaatggaa tggaggtgcc ctgtgagcta ggagaggctc agggaactag aaggagatgg 3175 aggaagtgga agttgaggaa taattggtgt ttaagggcct ggcatttgga gcttagacta 3235 gtctggatgt aggagaactg agcctagact ggaaaggaac cagaccaggg cctcggtctt 3295 ggcagggagg gcccttgggc aggaggagct ccagggtgtc agaatttgat tggagttgag 3355 ttccagaagt aagagggatg taggggcagg gagttcctag gcctcactga ggaatagaga 3415 atggggaaga atgctgagac cgcattctgg gaaaagtcca atgcctggag tctgggactc 3475 aggatcctag atagagttcg aggacccaga tgcttccacg ggaccagagt gagctggatg 3535 gccactacct gtctgttgtt gcttgtgcca ggtagggggg caagcctcat gtgcccatgc 3595 ctgatttttt ttttttgaga tggagtctta ctctgtcacc caggctggag tgcagtggca 3655 cgatcttggc ccgctacaac ctctgcctcc caggttcaag cgattcttgt gcctcaacca 3715 cctgagtagc tgggattgca ggcatgggcc actatgcctg gctaattttt tttttttgta 3775 tttttagtag agacagggtt ttgccatgtt ggccaggctg gtctcgaact cctgacctca 3835 agtaatccgc ccccacctcg acctcccaaa gtgctggtat tacaggcatg agccagcata 3895 cctagccctg atttttcaag acaaactgaa aactggattt agatgtgaaa tctttttttt 3955 tttttttttt ttttttttga gacggagtct catgctgtca cccaggctgg agtgtggtgg 4015 cgtgatctcg ggtcactgca acctccgcct gccgggttca agcgattctt ctgcctcagc 4075 ctccctagta gctgggacta caggcgtgtg ccaccactct cggctaattt tttgtatttc 4135 tagtagggac ggggtttcac cgagttagcc aggatggtct ctattttttt tttttttttt 4195 ttaagacaga atctcgttct gtcactaagg ctggagtgca gtggtgtgat gtcggctcac 4255 tgcaacctct gcctcctggg ttcaagcgct gcaacctctg cctcctgggt tcaagcaatt 4315 cttgtacctc atccacctga gtagttggaa tcacaggcgt gcgccaccat gcccagctaa 4375 tttttttgta tttttagtag agatggggtt ttgccacgtt ggccaggctg gtctcgaact 4435 cctggcctca agtgatttcc ctgccttggc ctcccaaagt gctgggatta caggggtgag 4495 ccaccatgcc cagctgtttt ttattttatt tttattttaa ggctgggtat ggtagctcat 4555 gcctgtaatc cttgaacttg gagagcccga ggcaggagga ttgcctgaga ctaggagttc 4615 aaaaccaacc tggccaacat agccaggttc ttttaaaaat aataataata ataaatttta 4675 tcttatttat ttatttatta ttattatttt ttgagacaga gtctgtcgcc caggctggag 4735 tgcagtggcg cgatctcagc tcactgcaag ctccgcctcc tgggttcacg ccattctcct 4795 gcctcagcct cccgagtagc tgggactaca ggtgcctgcc accatgcttg gctaattttt 4855 tttgtatttt tagtagagac agggtttcac cgtgttaacc aggatggtct caatctcctg 4915 acttcgtgat ccacccacct cagcctccca aagtgctggg attacaggcg tgagccacca 4975 cgcctggccc tggcctatcc tttttaaaac tttattttgg agaaaaaaat cagaaggtgc 5035 catttggctt ttacatgtca gcaataagtt gaaaaaaaat ttttttttaa gtggggtggc 5095 tgggcgcggt gcctcacgcc tgtaatccca gcactttggg aggctgaggc ctgtggatca 5155 tgaggtcagg gaggctgagg caggtggatc acaaggtcag gagatcgaga ccatcctggc 5215 taacgtggtg aaaccccatc tctactaaaa atacaaaaat tagctgggcg tggtggtgca 5275 tgcctgtaat cccagctact tggaaggctg aggcaggaga attgcttgac ccagggaggc 5335 agaggttgca gtgagccgat attgagccac tgcatgccag cctggcaaca gagcaagact 5395 ctgtctcaaa aaaaaaaaaa aatggggtga agaaaacaca tctgtggcct gggtttaacc 5455 tgtgggcttc cagctcctgt gggaggggaa tagtctggag acaaggaatt gggggatact 5515 ccaggggacc ttggagctgg gacacaggga gtagctgcct ggctgttgtt gggagtgagt 5575 gtgagtaggg aggagcagcc gagagagttg gttgtattct gagactctcc ctttgccctc 5635 aag aac cga gag ctg cag atc atg cgt aag ctg gac cac tgc aat att 5683 Asn Arg Glu Leu Gln Ile Met Arg Lys Leu Asp His Cys Asn Ile 160 165 170 gtg agg ctg aga tac ttt ttc tac tcc agt ggc gag aag gtgagatctc 5732 Val Arg Leu Arg Tyr Phe Phe Tyr Ser Ser Gly Glu Lys 175 180 185 gaggtggtgg tggtgggttg ctccagccat tttcctgcct gcctgccttt cccccactgc 5792 tccctgcata ccttccttcc ccctcctcac tcttctcaca gtgcctcaca cctctccttt 5852 gctccctgca g aaa gac gag ctt tac cta aat ctg gtg ctg gaa tat gtg 5902 Lys Asp Glu Leu Tyr Leu Asn Leu Val Leu Glu Tyr Val 190 195 ccc gag aca gtg tac cgg gtg gcc cgc cac ttc acc aag gcc aag ttg 5950 Pro Glu Thr Val Tyr Arg Val Ala Arg His Phe Thr Lys Ala Lys Leu 200 205 210 acc atc cct atc ctc tat gtc aag gtaggccagc aggtgggctg ctgggaccca 6004 Thr Ile Pro Ile Leu Tyr Val Lys 215 220 ggcccacaaa gccaggggct ctggagcctc ctgcctttta tgggatccct catccgccaa 6064 gtttatgttg gtttttggag gccccatgtc ccctgctgtt gttcccataa ccccccgaga 6124 tggagctcgc ctaacacagg ggagggccaa ggcaggcaag gcctgactga atcaggaagg 6184 cagcctgaca cctggggttg cagaagctgc caggtagttg ctcaggtcca tacagggagt 6244 ccagtggcac cagagatgtt ggagttagct caggataagg gggtggtggg gaccaggact 6304 gcacagagac agctgctgag gccagagttc gggcctttag agccttggct gggggtaggt 6364 gggaaggagt tagggctgga ggaaggttag catccacaga gccaggaatg catctccgtc 6424 catcatctgt gcaggctcat tccccagtgc ctggcatcgt gccctgggtg ttacagacct 6484 tcaggaggtg tttgaatgaa tgaatgaatg attgcagccc agggatgatg tggcgaacag 6544 gctggagcag cctactgcat tggaaggagg tgggtgggtt tgtttgctga aggtcacttg 6604 gggcccagct gctgctcctg ctggctttac gtaccaagca cgggtgagcc gacgtgggct 6664 ctaccagtgg ttgtggctgt tggacctcac ttcccaggag gggagctctc tggtttggcg 6724 aatctgtcct gtggctgcct gcatacgggt cccagggctg aggaattcca gaggcaccac 6784 tgactgcgac ccaggccttg gccttgaaga gctctcagtt tggtagggta gaaaggcgtc 6844 atcacagaaa actattaaat gaactagctg ctgccatacc agaaggagca cagggaattc 6904 tggaaatgga ggaagcaccc agcctggttt gtgggtgaga aggatcaagg aaggcttcct 6964 ggaggagacc aagcacaggg caaggaagtg gcatctttgg ccgaggggaa ctggaataaa 7024 aggaaggggg cctaggaagc agccgtgtca ggacctggtc tgtctaggcc ctgggggatg 7084 cagcagtaac tgaaactcaa aatcctgctc tcacggtact tctgttctag tcagtgggag 7144 ggagagtggc aggaaaatgg agctggagag ggggcaggct caggggtggt tttgattgtc 7204 ggattaagga gccagtggtt ttggtgaggg ggaagctgag tgcctggctc cctagcctgt 7264 tttatgacaa cctcccgatg taccttactc atcaggcttc tgccaagggt tgtgattaaa 7324 gcagtggttc tcagagtgtg gtccggggac cagcatcagt gctggagagc ttgttgcaaa 7384 tgcctcattc agaactcact gatcagaaac tctaagagtg gggcccagca gtcccttttt 7444 ttttgttttt tttgagacag ggtctctgtc acccacgctg gagtgcagtg gtgcgatctc 7504 ggctcactgc aacctccgcc tcctgagttc aagtgattct tctgcctcag cctcccgagt 7564 agctgggatt acaggtgtgc accaccacgc ccggctaatt tttgtatttt tagtagagac 7624 gggatctcaa catgttggcg aggctggtct tggcctccca aaataccggg attacaggcg 7684 tgacccgcca cgcccagcca gtagtccctg ttttaacaag tccttcaagt gattgtggtg 7744 cacattaaga gaaccaaggt ttcaaatggg tttccccaaa gctgtggggg cagcagggag 7804 agtgggcctg gaagggctct tcaggccaag ctggtggggt agtggtgctg tatggggaaa 7864 gctgggctaa agttctgcta tcctgtgccc gccgcag gtg tac atg tac cag ctc 7919 Val Tyr Met Tyr Gln Leu 225 ttc cgc agc ttg gcc tac atc cac tcc cag ggc gtg tgt cac cgc gac 7967 Phe Arg Ser Leu Ala Tyr Ile His Ser Gln Gly Val Cys His Arg Asp 230 235 240 atc aag ccc cag aac ctg ctg gtg gac cct gac act gct gtc ctc aag 8015 Ile Lys Pro Gln Asn Leu Leu Val Asp Pro Asp Thr Ala Val Leu Lys 245 250 255 260 ctc tgc gat ttt ggc ag gtgggcctgg ggcatgttgg gtggctgaag aggcaggggg 8072 Leu Cys Asp Phe Gly Ser 265 gaccccaacc cttgcctcac gtgtacccct gcccatctct tcccacag t gca aag 8127 Ala Lys cag ttg gtc cga ggg gag ccc aat gtc tcc tac atc tgt tct cgc tac 8175 Gln Leu Val Arg Gly Glu Pro Asn Val Ser Tyr Ile Cys Ser Arg Tyr 270 275 280 tac cgg gcc cca gag ctc atc ttt gga gcc act gat tac acc tca tcc 8223 Tyr Arg Ala Pro Glu Leu Ile Phe Gly Ala Thr Asp Tyr Thr Ser Ser 285 290 295 300 atc g gtcagagtta tgggagggtg gcggggggag tggcaatctg ggaagttttg 8277 Ile gagttttctg tgtgctgtat gccaagcttg gtgatgaaag cttaacttct gttcttgtat 8337 ccagtcctca caaacttagg aggctgatgc tgttgaatgc taattttaca gatgagctta 8397 gagctgtgag gccgcctgcc cgcactggca ccactaggac tgggcaggac tgggatttga 8457 aagctgacct gactccagag tccataccag ctctggaacc tccctgtcag ccctctgttc 8517 tcagctaggg ggaagggctg ctggagacct tgggggaacc gggaagcaag gctttgccac 8577 catgaaggtg caacttgctc ccagggcctc tgtgtccttc cctgtttgtg gggacaactg 8637 ccattttcca ggcatgaggg gaagtctgaa ttgagggaat gggcatgaga gtttgaaagg 8697 gcaccttcca cagcagcatg acgaactgtg gagtccttag gtatgaactc gtgctgtggg 8757 ggtcaaggta caaagcaggg aggggtgaga ctgccacgct gcagctcttc tcatgggcag 8817 gagagaggct ggaacaagag gaaggcagtc caggatttaa ggctgtacct tcctgtggcc 8877 caaagaacat gggtgcctgt tggcaggttt gggcctaatt tggtctgtcg tccaaggcta 8937 gcgggagaga aggagctcat tggggtcctt agcagagaga ggaactgagg gctggaaaca 8997 cacctagact agagagtaca gcaaaggcag ggtcaaggtc gggcccatgt ttctaagctg 9057 catgtgacct tgggccaggt gctttgtctt tgagaaaacg gggctcctga cactcttagg 9117 atggccatga ggaataaaag cattgggagg ttggtggccc tactcgccta gccctgacgc 9177 tccctccatt tcccctcag at gtt tgg tca gct ggc tgt gta ctg gca gag 9228 Asp Val Trp Ser Ala Gly Cys Val Leu Ala Glu 305 310 ctc ctc ttg ggc cag ccc atc ttc cct ggg gac agt ggg gtg gac cag 9276 Leu Leu Leu Gly Gln Pro Ile Phe Pro Gly Asp Ser Gly Val Asp Gln 315 320 325 ctg gtg gag atc atc aag gtgaggggcg gggctgggct gggcaggggg tggggctgag 9334 Leu Val Glu Ile Ile Lys 330 ggatggggcc cttgtctcag acccctccct ctctttacag gtg ctg gga aca cca 9389 Val Leu Gly Thr Pro 335 acc cgg gaa caa atc cga gag atg aac ccc aac tac acg gag ttc aag 9437 Thr Arg Glu Gln Ile Arg Glu Met Asn Pro Asn Tyr Thr Glu Phe Lys 340 345 350 355 ttc cct cag att aaa gct cac ccc tgg aca aag gtggggcagg gctaggggct 9490 Phe Pro Gln Ile Lys Ala His Pro Trp Thr Lys 360 365 cagggcagta tggctgagag ctggtccccc ttggaggtca actgttctgt ggacctagcc 9550 tcagaatcac ggcttgggag gatttgaaga gttatccagg gatcaataac atccatccgc 9610 tttcaaagtt tatggcattt taaaagttga gaacccacaa gtaaattcaa gattccaatt 9670 tttatggagg gtcagcaggg ctcatatagt cccagacctg ggctgcctgc ttacccgata 9730 caaactgacc tctccttagt ggttgggcct tagtttcttc atttggaagg tgggggtgtg 9790 ggaagcaacc agtcataact tgccgcaggc actgtggcag tgagataaca ggagtatgcc 9850 agtgtccagg gcatctcacc ctcatgagcc ctgcacccat ccctcag gtg ttc aaa 9906 Val Phe Lys tct cga acg ccg cca gag gcc atc gcg ctc tgc tct agc ctg ctg gag 9954 Ser Arg Thr Pro Pro Glu Ala Ile Ala Leu Cys Ser Ser Leu Leu Glu 370 375 380 385 tac acc cca tcc tca agg ctc tcc cca cta gag gcc tgt gcg cac agc 10002 Tyr Thr Pro Ser Ser Arg Leu Ser Pro Leu Glu Ala Cys Ala His Ser 390 395 400 ttc ttt gat gaa ctg cga tgt ctg gga acc cag ctg cct aac aac cgc 10050 Phe Phe Asp Glu Leu Arg Cys Leu Gly Thr Gln Leu Pro Asn Asn Arg 405 410 415 cca ctt ccc cct ctc ttc aac ttc agt gct ggt g gtgagggcat 10094 Pro Leu Pro Pro Leu Phe Asn Phe Ser Ala Gly 420 425 agcctgggat ctggggagtg gggcggggta ggggggcagc caaagattgt gaggagcttg 10154 gtgttgaagc aggagtgggg agctaagggc agggtacaag gcaggcctgg ggctcaggaa 10214 agatgactcc cagattcagg gggaatcgaa cctgcttcag ttgtgcttta ctgtgatctg 10274 ccttgtgcta agctttttct ggtttttcat tgagagaggt ctgtggctga aggtgtccac 10334 aaacaactgg ccttcccaat agctgggttc ccatttggtg cccatcataa ccctgctgta 10394 gtctaccctg actagcatgt caattcctgt ttctag aa ctc tcc atc caa ccg 10447 Glu Leu Ser Ile Gln Pro 430 tct ctc aac gcc att ctt atc cct cct cac ttg agg tcc cca gcg ggc 10495 Ser Leu Asn Ala Ile Leu Ile Pro Pro His Leu Arg Ser Pro Ala Gly 435 440 445 450 act acc acc ctc acc ccg tcc tca caa g gtaagtgggg accatctgct 10543 Thr Thr Thr Leu Thr Pro Ser Ser Gln 455 gggggttaaa gtatctctca gcctggagag ggtggggctg ttcgctcagt gactgggttt 10603 cctgaatgta tttttaaatc atcgacattt tgatggcata ggaaacacat cttacaacat 10663 gtgaatgacc acctttagag ggtattcttg cgtacaaatg tttaaatgtg tttaatgcca 10723 atgggaaagc cagagaaata acgtctggcc tgaacacaaa caaaaagttg aattcgttgc 10783 ccaagtttgt tttttttttt tttgtgcaat agagtttcac tcgccaccca ggctgcagtg 10843 cagtggctcg atctcggctc actgcaatct ccgcctcctg ggctcaggca attctcctgc 10903 ctcagcctcc gagtagctgg gattacagac acacaccact acgcctggct aatttttgta 10963 tttttactag agatgaggtt tcaccatgtt ggccagactg gtcttgaact tcaggtgatt 11023 ttcccgcttg gcctcctaaa gtgttgggat tacaggcgtg aaccgctgtg cctggccatg 11083 gtgtccacgt ttaaaaatgg ggctatttta tgtaaaaatt cagatttcct gtttctcttg 11143 gggaagaaaa tcagattggg cagcaatggg cccgcccatc ctactgacag tagacagtgg 11203 gcgcccttta tattttttag acggagtctt tttctgtcac ccaggctgga gtgcagtggc 11263 acaatcccgg ctcactccaa cttctgcctc ctgggttcaa gtgattctcc tgcctcagcc 11323 tcctaagtac ctgggattac acgctcatac caccatgcct ggcttatttt tgtattttga 11383 gtagacatgg agtttcacca tgttggccag gctggtctcg aactgctgac cttgtgatct 11443 gcccacctca gcctcccaaa gtgctgggat tacaggcgtg agccactgtg cccagcccag 11503 ccaccgcctt atatggagcc tggcactctg gtgtgtcact cagttactat cgtggccctt 11563 tagcacttga gtttgcaacc cttcacctaa agtaacagct tgtaactttt aatgtagcat 11623 ctatgacaag agaattccta cttttgggtt gggcgaaggg gtgtctgaaa ggcaaaggct 11683 aactctgctc cttccctgcc tccctccag ct tta act gag act ccg acc agc 11735 Ala Leu Thr Glu Thr Pro Thr Ser 460 465 tca gac tgg cag tcg acc gat gcc aca cct acc ctc act aac tcc tcc 11783 Ser Asp Trp Gln Ser Thr Asp Ala Thr Pro Thr Leu Thr Asn Ser Ser 470 475 480 tga gggccccacc aagcaccctt ccacttccat ctgggagccc caagaggggc 11836 tgggaagggg ggccatagcc catcaagctc ctgccctggc tgggccccta gactagaggg 11896 cagaggtaaa tgagtccctg tccccacctc cagtccctcc ctcaccagcc tcacccctgt 11956 ggtgggcttt ttaagaggat tttaactggt tgtggggagg gaagagaagg acagggtgtt 12016 ggggggatga ggacctccta cccccttggc cccctcccct cccccagacc tccacctcct 12076 ccagaccccc tcccctcctg tgtcccttgt aaatagaacc agcccagccc gtctcctctt 12136 cccttccctg gcccccgggt gtaaatagat tgttataatt tttttcttaa agaaaacgtc 12196 gattcgcacc gtccaacctg gccccgcccc tcctacagct gtaactcccc tcctgtcctc 12256 tgcccccaag gtctactccc tcctcacccc accctggagg gccaggggag tggagagagc 12316 tcctgatgtc ttagtttcca cagtaaggtt tgcctgtgta cagacctccg ttcaataaat 12376 tattggcatg aaaacctg 12394 11 20 DNA Artificial Sequence Antisense Oligonucleotide 11 cgcctccccc ggagcccaag 20 12 20 DNA Artificial Sequence Antisense Oligonucleotide 12 gccgccgctc atggcgccga 20 13 20 DNA Artificial Sequence Antisense Oligonucleotide 13 aaggcccgcc gccgctcatg 20 14 20 DNA Artificial Sequence Antisense Oligonucleotide 14 acagatgcct ttccgccgcc 20 15 20 DNA Artificial Sequence Antisense Oligonucleotide 15 ctccgctgcc tcctccgccg 20 16 20 DNA Artificial Sequence Antisense Oligonucleotide 16 cccagcttca ccccgggcgg 20 17 20 DNA Artificial Sequence Antisense Oligonucleotide 17 ccttcccgct gtcacggccc 20 18 20 DNA Artificial Sequence Antisense Oligonucleotide 18 accttcccgc tgtcacggcc 20 19 20 DNA Artificial Sequence Antisense Oligonucleotide 19 ggtcaccttc ccgctgtcac 20 20 20 DNA Artificial Sequence Antisense Oligonucleotide 20 cgctctgggc cttggcctag 20 21 20 DNA Artificial Sequence Antisense Oligonucleotide 21 gtgtaagcca cttcttggga 20 22 20 DNA Artificial Sequence Antisense Oligonucleotide 22 ctttgatgtc cgtgtaagcc 20 23 20 DNA Artificial Sequence Antisense Oligonucleotide 23 tcactttgat gtccgtgtaa 20 24 20 DNA Artificial Sequence Antisense Oligonucleotide 24 tctgccagcc gtgcctggta 20 25 20 DNA Artificial Sequence Antisense Oligonucleotide 25 ttcttgatgg cgactagttc 20 26 20 DNA Artificial Sequence Antisense Oligonucleotide 26 tcttgtcctg gagaaccttc 20 27 20 DNA Artificial Sequence Antisense Oligonucleotide 27 gcatgatctg cagctctcgg 20 28 20 DNA Artificial Sequence Antisense Oligonucleotide 28 cagcttacgc atgatctgca 20 29 20 DNA Artificial Sequence Antisense Oligonucleotide 29 ctggagtaga aaaagtatct 20 30 20 DNA Artificial Sequence Antisense Oligonucleotide 30 ttctcgccac tggagtagaa 20 31 20 DNA Artificial Sequence Antisense Oligonucleotide 31 ttcttctcgc cactggagta 20 32 20 DNA Artificial Sequence Antisense Oligonucleotide 32 tctttcttct cgccactgga 20 33 20 DNA Artificial Sequence Antisense Oligonucleotide 33 acatattcca gcaccagatt 20 34 20 DNA Artificial Sequence Antisense Oligonucleotide 34 ccttggtgaa gtggcgggcc 20 35 20 DNA Artificial Sequence Antisense Oligonucleotide 35 gagtggatgt aggccaagct 20 36 20 DNA Artificial Sequence Antisense Oligonucleotide 36 agtgtcaggg tccaccagca 20 37 20 DNA Artificial Sequence Antisense Oligonucleotide 37 cgcagagctt gaggacagca 20 38 20 DNA Artificial Sequence Antisense Oligonucleotide 38 cggaccaact gctttgcact 20 39 20 DNA Artificial Sequence Antisense Oligonucleotide 39 cctcggacca actgctttgc 20 40 20 DNA Artificial Sequence Antisense Oligonucleotide 40 cagatgtagg agacattggg 20 41 20 DNA Artificial Sequence Antisense Oligonucleotide 41 atcagtggct ccaaagatga 20 42 20 DNA Artificial Sequence Antisense Oligonucleotide 42 gtaatcagtg gctccaaaga 20 43 20 DNA Artificial Sequence Antisense Oligonucleotide 43 ggtgtaatca gtggctccaa 20 44 20 DNA Artificial Sequence Antisense Oligonucleotide 44 agctggtcca ccccactgtc 20 45 20 DNA Artificial Sequence Antisense Oligonucleotide 45 gctgggttcc cagacatcgc 20 46 20 DNA Artificial Sequence Antisense Oligonucleotide 46 cagcactgaa gttgaagaga 20 47 20 DNA Artificial Sequence Antisense Oligonucleotide 47 ggtcgactgc cagtctgagc 20 48 20 DNA Artificial Sequence Antisense Oligonucleotide 48 ttagtgaggg taggtgtggc 20 49 20 DNA Artificial Sequence Antisense Oligonucleotide 49 gggccctcag gaggagttag 20 50 20 DNA Artificial Sequence Antisense Oligonucleotide 50 ttaaaaagcc caccacaggg 20 51 20 DNA Artificial Sequence Antisense Oligonucleotide 51 tcttaaaaag cccaccacag 20 52 20 DNA Artificial Sequence Antisense Oligonucleotide 52 tgtccttctc ttccctcccc 20 53 20 DNA Artificial Sequence Antisense Oligonucleotide 53 caacaccctg tccttctctt 20 54 20 DNA Artificial Sequence Antisense Oligonucleotide 54 tcgacgtttt ctttaagaaa 20 55 20 DNA Artificial Sequence Antisense Oligonucleotide 55 gtgcgaatcg acgttttctt 20 56 20 DNA Artificial Sequence Antisense Oligonucleotide 56 caggttggac ggtgcgaatc 20 57 20 DNA Artificial Sequence Antisense Oligonucleotide 57 gacatcagga gctctctcca 20 58 20 DNA Artificial Sequence Antisense Oligonucleotide 58 taatttattg aacggaggtc 20 59 20 DNA Artificial Sequence Antisense Oligonucleotide 59 gaagagggct cggatccccg 20 60 20 DNA Artificial Sequence Antisense Oligonucleotide 60 ttataatgaa tagcaacatc 20 61 20 DNA Artificial Sequence Antisense Oligonucleotide 61 agccaatgac accatacctt 20 62 20 DNA Artificial Sequence Antisense Oligonucleotide 62 tcccaaagtg ctgggattac 20 63 20 DNA Artificial Sequence Antisense Oligonucleotide 63 tgctgggttc aagcgattct 20 64 20 DNA Artificial Sequence Antisense Oligonucleotide 64 ccaaattatg ataatgatga 20 65 20 DNA Artificial Sequence Antisense Oligonucleotide 65 tggttcttgg tgacagaaat 20 66 20 DNA Artificial Sequence Antisense Oligonucleotide 66 cagtccccaa acctccctgt 20 67 20 DNA Artificial Sequence Antisense Oligonucleotide 67 caggcaatcc tcttacctga 20 68 20 DNA Artificial Sequence Antisense Oligonucleotide 68 cttcagaacc acccgcgcta 20 69 20 DNA Artificial Sequence Antisense Oligonucleotide 69 aggctcagtt ctcctacatc 20 70 20 DNA Artificial Sequence Antisense Oligonucleotide 70 tctggtcccg tggaagcatc 20 71 20 DNA Artificial Sequence Antisense Oligonucleotide 71 gaggttgcag tgacccgaga 20 72 20 DNA Artificial Sequence Antisense Oligonucleotide 72 gccaaggcag ggaaatcact 20 73 20 DNA Artificial Sequence Antisense Oligonucleotide 73 tcacccctgt aatcccagca 20 74 20 DNA Artificial Sequence Antisense Oligonucleotide 74 tgcagctctc ggttcttgag 20 75 20 DNA Artificial Sequence Antisense Oligonucleotide 75 gaaggtatgc agggagcagt 20 76 20 DNA Artificial Sequence Antisense Oligonucleotide 76 agagcccacg tcggctcacc 20 77 20 DNA Artificial Sequence Antisense Oligonucleotide 77 gggcctagac agaccaggtc 20 78 20 DNA Artificial Sequence Antisense Oligonucleotide 78 aatccgacaa tcaaaaccac 20 79 20 DNA Artificial Sequence Antisense Oligonucleotide 79 aacccttggc agaagcctga 20 80 20 DNA Artificial Sequence Antisense Oligonucleotide 80 ccactgcttt aatcacaacc 20 81 20 DNA Artificial Sequence Antisense Oligonucleotide 81 cccaccagct tggcctgaag 20 82 20 DNA Artificial Sequence Antisense Oligonucleotide 82 taccttgacc cccacagcac 20 83 20 DNA Artificial Sequence Antisense Oligonucleotide 83 ctcagttcct ctctctgcta 20 84 20 DNA Artificial Sequence Antisense Oligonucleotide 84 actatatgag ccctgctgac 20 85 20 DNA Artificial Sequence Antisense Oligonucleotide 85 tactcctgtt atctcactgc 20 86 20 DNA Artificial Sequence Antisense Oligonucleotide 86 atgtcgatga tttaaaaata 20 87 20 DNA Artificial Sequence Antisense Oligonucleotide 87 ataccctcta aaggtggtca 20 88 20 DNA Artificial Sequence Antisense Oligonucleotide 88 atgagcgtgt aatcccaggt 20

Claims

What is claimed is:

1. An antisense compound 8 to 30 nucleobases in length targeted to a nucleic acid molecule encoding glycogen synthase kinase 3 alpha, wherein said antisense compound specifically hybridizes with and inhibits the expression of glycogen synthase kinase 3 alpha.

2. The antisense compound of claim 1 which is an antisense oligonucleotide.

3. The antisense compound of claim 2 wherein the antisense oligonucleotide has a sequence comprising SEQ ID NO: 12, 14, 15, 16, 17, 19, 23, 24, 27, 28, 30, 31, 32, 33, 35, 36, 38, 39, 44, 45, 47, 52, 53, 54, 55, 56, 57, 58, 61, 66, 67, 69, 74, 75, 76, 77, 78, 82, 83 or 87.

4. The antisense compound of claim 2 wherein the antisense oligonucleotide comprises at least one modified internucleoside linkage.

5. The antisense compound of claim 4 wherein the modified internucleoside linkage is a phosphorothioate linkage.

6. The antisense compound of claim 2 wherein the antisense oligonucleotide comprises at least one modified sugar moiety.

7. The antisense compound of claim 6 wherein the modified sugar moiety is a 2′-O-methoxyethyl sugar moiety.

8. The antisense compound of claim 2 wherein the antisense oligonucleotide comprises at least one modified nucleobase.

9. The antisense compound of claim 8 wherein the modified nucleobase is a 5-methylcytosine.

10. The antisense compound of claim 2 wherein the antisense oligonucleotide is a chimeric oligonucleotide.

11. A composition comprising the antisense compound of claim 1 and a pharmaceutically acceptable carrier or diluent.

12. The composition of claim 11 further comprising a colloidal dispersion system.

13. The composition of claim 11 wherein the antisense compound is an antisense oligonucleotide.

14. A method of inhibiting the expression of glycogen synthase kinase 3 alpha in cells or tissues comprising contacting said cells or tissues with the antisense compound of claim 1 so that expression of glycogen synthase kinase 3 alpha is inhibited.

15. A method of treating a human having a disease or condition associated with glycogen synthase kinase 3 alpha comprising administering to said animal a therapeutically or prophylactically effective amount of the antisense compound of claim 1 so that expression of glycogen synthase kinase 3 alpha is inhibited.

16. The method of claim 15 wherein the disease or condition is diabetes.

17. The method of claim 15 wherein the disease or condition is a neurological disorder.

18. The method of claim 15 wherein the disease or condition is a haematopoetic disorder.

19. The method of claim 15 wherein the disease or condition is a hyperproliferative disorder.

20. The method of claim 15 wherein the disease or condition is a developmental disorder.