Enhanced antisense oligonucleotides

This application claims the priority to U.S. Application No. 60/611,100 filed on Sep. 17, 2004 and to U.S. Application No. 60/663,442 filed on Mar. 18, 2005, each of which is herein incorporated by reference in its entirety. The instant application is also related to U.S. Application 60/718,685, and U.S. Application 60/718,684, each of which was filed on the same day as the instant application and is herein incorporated by reference in its entirety.

A paper copy of the sequence listing and a computer-readable form of the sequence listing, on diskette, containing the file named CORE0051USSEQ.txt, which was created on Sep. 19, 2005, are herein incorporated by reference.

The present invention provides chimeric antisense compounds having enhanced in vivo potency and thus an improved therapeutic index. The compounds described herein have widened deoxy gaps and enhanced in vivo potency which is unexpected based on their in vitro activity.

Antisense oligonucleotides are accepted therapeutic modalities and many thousands of patients have been treated with antisense compounds. The original “first generation” antisense compounds employed in the first antisense clinical trials were oligodeoxynucleotides having 2′-deoxy ribonucleotides and phosphorothioate internucleoside linkages. Subsequently, chimeric “second generation” antisense oligonucleotides exhibited a marked improvement in potency over first generation antisense oligonucleotides. Second generation antisense oligonucleotides are chimeric oligonucleotides typically having a 2′-deoxy “gap” region flanked by “wings” having nucleotides with 2′-modified ribonucleotides, referred to as “gapmers.” The most widely used of the “second generation” antisense motifs is often referred to as a “MOE gapmer” in which the 2′-modified ribonucleotide is a 2′-O-methoxyethyl (2′-MOE or simply MOE) modification, and each of the internucleotide linkages is a phosphorothioate. Predominantly, second generation oligonucleotides have a length of 20 nucleotides of which the 5 nucleotides at each terminus are 2′-MOE nucleotides and the center ten nucleotides are 2′-deoxyribonucleotides. These second generation oligonucleotides are referred to as “5-10-5 MOE gapmers” have a 5-10-5 wing-gap-wing motif. Chimeric antisense compounds with other arrangements of modifications have also been made. “Hemimers,” are chimeric compounds in which there is a single 2′-modified “wing” adjacent to (on either the 5′, or the 3′ side of) a 2′-deoxy gap have been described (Geary et al., 2001, J. Pharm. Exp. Therap., 296, 898-904).

The present invention is directed to “gap-widened” antisense oligonucleotides having a gap region of greater than 11 2′deoxyribonucleotides flanked by two “wing” regions having from one to eight nucleotides which do not support RNase H activity. The gap-widened antisense oligonucleotide of the present invention have been shown to have an improved therapeutic index as compared to a corresponding antisense oligonucleotide having a 5-10-5 MOE gamer antisense oligonucletide with the same sequence. The gap-widened antisense oligonucleotides of the present invention exhibit increased in vivo potency or improved tissue exposure as compared with the corresponding 5-10-5 MOE gapmer antisense oligonucleotide with the same sequence. Most interestingly, there is a lack of correlation between the in vitro potency and the in vivo potency of the gap-widened antisense oligonucleotides described herein. The gap-widened antisense oligonucleotides of the present invention are 18 to 24 nucleotides in length. In particular, the gap-widened antisense oligonucleotides of the present invention have wing regions having 2′-O-(2-methoxyethyl) ribonucleotides.

In an additional embodiment of the present invention is a method of reducing expression of a target RNA in an animal in need of reducing expression of said target RNA, comprising administering to said animal a gap-widened antisense oligonucleotide 18 to 24 nucleotides in length comprising: a gap region having greater than 11 contiguous 2′-deoxyribonucleotides; and a first wing region and a second wing region flanking the gap region, wherein each of said first and second wing regions independently have 1 to 8 2′-O-(2-methoxyethyl) ribonucleotides, having an improved therapeutic index as compared to a corresponding 5-10-5 MOE gapmer antisense oligonucleotide having a gap region of 10 contiguous 2′-deoxyribonucleotides and a first wing region and a second wing region flanking the gap region of 5 2′-O-(2-methoxyethyl) ribonucleotides. The improvement in therapeutic index is characterized by equal or increased potency coupled with a reduction in tissue concentration, or increased potency coupled with equal tissue exposures as compared to a corresponding 5-10-5 MOE gapmer antisense oligonucleotide of the same sequence. In addition, the improvement in therapeutic index may be characterized by an increased liver to kidney concentration ratio as compared to a corresponding 5-10-5 MOE gapmer antisense oligonucleotide of the same sequence. In particular, the method of the present invention is useful in reducing the expression of RNA targets expressed in the kidney, liver, or adipose tissues. The method of the present invention is also useful in reducing the expression of target RNA associated with a metabolic or cardiovascular disease or condition. The method of the present invention is useful wherein the metabolic disease or condition is selected from diabetes, hepatic steatosis, fatty liver disease, non-alcoholic steatohepatitis, metabolic syndrome, obesity, or the like. In addition, the method of the present invention is useful wherein the cardiovascular disease or condition is selected from hypercholesterolemia, atherosclerosis, hyperlipidemia, familial hypercholesterolemia, or the like.

An additional method of the present invention is a method of selecting a gap-widened antisense oligonucleotide with an improved therapeutic index, the method comprising:

screening in vitro a plurality of antisense oligonucleotides targeting a human RNA and having a single wing-gap-wing motif;

identifying a parent antisense oligonucleotide from the plurality of antisense oligonucleotides having a potent in vitro activity;

synthesizing a plurality of gap-widened antisense oligonucleotides having the same sequence as the parent antisense oligonucleotide, wherein said gap-widened antisense oligonucleotide is 18 to 24 nucleotides in length comprising a gap region having greater than 11 contiguous 2′-deoxyribonucleotides; and a first wing region and a second wing region flanking the gap region, wherein each of said first and second wing regions independently has 1 to 8 2′-O-(2-methoxyethyl) ribonucleotides;

testing said plurality of gap-widened antisense oligonucleotides in a plurality of animals;

obtaining potency and tissue concentration data from said testing step; and

determining an optimized gap-widened oligonucleotide wing-gap-wing motif with an improved therapeutic index, improved potency, reduced tissue exposure, or reduced toxicity, or a combination thereof as compared to the parent antisense oligonucleotide.

In one embodiment, the method of selecting a gap-widened antisense oligonucleotide further comprises the step of designing a rodent sequence analogous or a non-human primate sequence to said parent antisense oligonucleotide. In one embodiment, the step of determining the optimized gap-widened antisense oligonucleotide wing-gap-wing motif with an improved therapeutic index includes identifying a gap-widened antisense oligonucleotide which has equal or increased potency as compared to the parent antisense oligonucleotide.

In the step of screening, each of said antisense oligonucleotides has the same wing-gap-wing motif selected from 2-16-2, 3-14-3, 4-12-4, or 5-10-5. In a further embodiment, the wing portions of the gap-widened antisense oligonucleotides are 2′-O-(2-methoxyethyl) ribonucleotides. In particular, the step of screening is performed in primary hepatocytes, HepG2, bEND, or HeLa cells. In the step of identifying, the potent in vitro activity is greater than 50% reduction in the target mRNA expression as compared to a saline control. In alternate embodiments, in the step of identifying, the potent in vitro activity is greater than 30%, greater than 40%, greater than 50%, greater than 60%, greater than 70%, greater than 80%, or greater than 90%

In the step of synthesizing, the gap-widened antisense oligonucleotides each have different wing-gap-wing motifs. In particular, the gap-widened antisense oligonucleotides have gaps of 12, 13, 14, 15, 16, 17, or 18 2′-deoxyribonucleotides in length. In the step of testing, the animals are selected from rodents such as mice and rats, and non-human primates, such as cynomolgous monkeys.

In the step of obtaining, the tissue concentration data are concentrations of full-length gap-widened antisense oligonucleotides particularly measured in the liver, kidney, or adipose tissue. In one embodiment, each optimized gap-widened antisense oligonucleotide is selected because of equal or improved potency data. In another embodiment, each optimized gap-widened antisense oligonucleotide is selected because of reduced tissue exposure. In another embodiment, each optimized gap-widened antisense oligonucleotide is selected because of reduced toxicity. In another embodiment, each optimized gap-widened antisense oligonucleotide is selected because of improved therapeutic index. In another embodiment, each optimized gap-widened antisense oligonucleotide is selected because of reduced tissue exposure, reduced toxicity, improved potency, or a combination thereof.

The gap-widened antisense oligonucleotides described herein may have various wing-gap-wing motifs selected from: 1-16-1, 2-15-1, 1-15-2, 1-14-3, 3-14-1, 2-14-2, 1-13-4, 4-13-1, 2-13-3, 3-13-2, 1-12-5, 5-12-1, 2-12-4, 4-12-2, 3-12-3, 1-11-6, 6-11-1, 2-11-5, 5-11-2, 3-11-4, 4-11-3, 1-17-1, 2-16-1, 1-16-2, 1-15-3, 3-15-1, 2-15-2, 1-14-4, 4-14-1, 2-14-3, 3-14-2, 1-13-5, 5-13-1, 2-13-4, 4-13-2, 3-13-3, 1-12-6, 6-12-1, 2-12-5, 5-12-2, 3-12-4, 4-12-3, 1-11-7, 7-11-1, 2-11-6, 6-11-2, 3-11-5, 5-11-3, 4-11-4, 1-18-1, 1-17-2, 2-17-1, 1-16-3, 1-16-3, 2-16-2, 1-15-4, 4-15-1, 2-15-3, 3-15-2, 1-14-5, 5-14-1, 2-14-4, 4-14-2, 3-14-3, 1-13-6, 6-13-1, 2-13-5, 5-13-2, 3-13-4, 4-13-3, 1-12-7, 7-12-1, 2-12-6, 6-12-2, 3-12-5, 5-12-3, 4-12-4, 1-11-8, 8-11-1, 2-11-7, 7-11-2, 3-11-6, 6-11-3, 4-11-5, 5-11-4, 1-18-1, 1-17-2, 2-17-1, 1-16-3, 3-16-1, 2-16-2, 1-15-4, 4-15-1, 2-15-3, 3-15-2, 1-14-5, 2-14-4, 4-14-2, 3-14-3, 1-13-6, 6-13-1, 2-13-5, 5-13-2, 3-13-4, 4-13-3, 1-12-7, 7-12-1, 2-12-6, 6-12-2, 3-12-5, 5-12-3, 4-12-4, 1-11-8, 8-11-1, 2-11-7, 7-11-2, 3-11-6, 6-11-3, 4-11-5, 5-11-4, 1-19-1, 1-18-2, 2-18-1, 1-17-3, 3-17-1, 2-17-2, 1-16-4, 4-16-1, 2-16-3, 3-16-2, 1-15-5, 2-15-4, 4-15-2, 3-15-3, 1-14-6, 6-14-1, 2-14-5, 5-14-2, 3-14-4, 4-14-3, 1-13-7, 7-13-1, 2-13-6, 6-13-2, 3-13-5, 5-13-3, 4-13-4, 1-12-8, 8-12-1, 2-12-7, 7-12-2, 3-12-6, 6-12-3, 4-12-5, 5-12-4, 2-11-8, 8-11-2, 3-11-7, 7-11-3, 4-11-6, 6-11-4, 5-11-5, 1-20-1, 1-19-2, 2-19-1, 1-18-3, 3-18-1, 2-18-2, 1-17-4, 4-17-1, 2-17-3, 3-17-2, 1-16-5, 2-16-4, 4-16-2, 3-16-3, 1-15-6, 6-15-1, 2-15-5, 5-15-2, 3-15-4, 4-15-3, 1-14-7, 7-14-1, 2-14-6, 6-14-2, 3-14-5, 5-14-3, 4-14-4, 1-13-8, 8-13-1, 2-13-7, 7-13-2, 3-13-6, 6-13-3, 4-13-5, 5-13-4, 2-12-8, 8-12-2, 3-12-7, 7-12-3, 4-12-6, 6-12-4, 5-12-5, 3-11-8, 8-11-3, 4-11-7, 7-11-4, 5-11-6, 6-11-5, 1-21-1, 1-20-2, 2-20-1, 1-20-3, 3-19-1, 2-19-2, 1-18-4, 4-18-1, 2-18-3, 3-18-2, 1-17-5, 2-17-4, 4-17-2, 3-17-3, 1-16-6, 6-16-1, 2-16-5, 5-16-2, 3-16-4, 4-16-3, 1-15-7, 7-15-1, 2-15-6, 6-15-2, 3-15-5, 5-15-3, 4-15-4, 1-14-8, 8-14-1, 2-14-7, 7-14-2, 3-14-6, 6-14-3, 4-14-5, 5-14-4, 2-13-8, 8-13-2, 3-13-7, 7-13-3, 4-13-6, 6-13-4, 5-13-5, 1-12-10, 10-12-1, 2-12-9, 9-12-2, 3-12-8, 8-12-3, 4-12-7, 7-12-4, 5-12-6, 6-12-5, 4-11-8, 8-11-4, 5-11-7, 7-11-5, 6-11-6, 1-22-1, 1-21-2, 2-21-1, 1-21-3, 3-20-1, 2-20-2, 1-19-4, 4-19-1, 2-19-3, 3-19-2, 1-18-5, 2-18-4, 4-18-2, 3-18-3, 1-17-6, 6-17-1, 2-17-5, 5-17-2, 3-17-4, 4-17-3, 1-16-7, 7-16-1, 2-16-6, 6-16-2, 3-16-5, 5-16-3, 4-16-4, 1-15-8, 8-15-1, 2-15-7, 7-15-2, 3-15-6, 6-15-3, 4-15-5, 5-15-4, 2-14-8, 8-14-2, 3-14-7, 7-14-3, 4-14-6, 6-14-4, 5-14-5, 3-13-8, 8-13-3, 4-13-7, 7-13-4, 5-13-6, 6-13-5, 4-12-8, 8-12-4, 5-12-7, 7-12-5, 6-12-6, 5-11-8, 8-11-5, 6-11-7, or 7-11-6. In a particular embodiment, the gap-widened antisense oligonucleotides of the present invention have a 2-16-2, 3-14-3, or 4-12-4 wing-gap-wing motif.

Another aspect of the present invention is the use of a gap-widened antisense oligonucleotide 18-24 nucleotides in length comprising: a gap region having greater than 11 contiguous 2′-deoxyribonucleotides; and a first wing region and a second wing region flanking the gap region, wherein each of said first and second wing regions independently have 1 to 8 2′-O-(2-methoxyethyl) ribonucleotides, having an improved therapeutic index as compared to a corresponding 5-10-5 antisense oligonucleotide having a gap region of 10 contiguous 2′-deoxyribonucleotides and a first wing region and a second wing region flanking the gap region of 5 2′-O-(2-methoxyethyl) ribonucleotides in the manufacture of a medicament for the treatment of disorders and diseases related to target RNA levels. Another embodiment of the present invention is a pharmaceutical composition comprising a gap-widened antisense oligonucleotide 18-24 nucleotides in length comprising: a gap region having greater than 11 contiguous 2′-deoxyribonucleotides; and a first wing region and a second wing region flanking the gap region, wherein each of said first and second wing regions independently have 1 to 8 2′-O-(2-methoxyethyl) ribonucleotides, having an improved therapeutic index as compared to a corresponding 5-10-5 antisense oligonucleotide having a gap region of 10 contiguous 2′-deoxyribonucleotides and a first wing region and a second wing region flanking the gap region of 5 2′-O-(2-methoxyethyl) ribonucleotides and optionally a pharmaceutically acceptable carrier, diluent, enhancer or excipient. Another embodiment of the present invention is a gap-widened antisense oligonucleotide 18-24 nucleotides in length comprising: a gap region having greater than 11 contiguous 2′-deoxyribonucleotides; and a first wing region and a second wing region flanking the gap region, wherein each of said first and second wing regions independently have 1 to 8 2′-O-(2methoxyethyl) ribonucleotides, having lower kidney accumulation as compared to a corresponding 5-10-5 antisense oligonucleotide having a gap region of 10 contiguous 2′-deoxyribonucleotides and a first wing region and a second wing region flanking the gap region of 5 2′-O-(2-methoxyethyl) ribonucleotides as measured by plasma protein binding capacity of said gap-widened antisense oligonucleotide. Also provided is a method of modulating gene expression in an animal comprising the step of contacting said animal with the pharmaceutical composition. Another embodiment is a method of modulating gene expression in an animal comprising the step of contacting said animal with a gap-widened antisense oligonucleotide of the invention wherein the accumulation of the gap-widened antisense oligonucleotide in the kidney is less compared to a corresponding 5-10-5 antisense oligonucleotide having a gap region of 10 contiguous 2′-deoxyribonucleotides and a first wing region and a second wing region flanking the gap region of 5 2′-O-(2-methoxyethyl) ribonucleotides. In one embodiment, the kidney accumulation is measured by plasma protein binding capacity of said gap-widened antisense oligonucleotide.

Another embodiment of the present invention is a method of reducing levels of a preselected RNA target in the liver of an animal comprising administering to said animal a chimeric antisense compound 11 to 80 nucleobases in length which is targeted to said preselected RNA target wherein said chimeric antisense compound comprises a first gap region consisting of at least 10 contiguous 2′-deoxynucleotides and a wing region which consists of from 1 to 4 contiguous nucleosides or nucleoside analogs which are not substrates for RNaseH. In particular embodiments, said first gap region consists of at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, or at least 18 contiguous 2′-deoxynucleotides. In one embodiment, the chimeric antisense compound comprises second wing region which consists of from 1 to 7 contiguous nucleosides or nucleoside analogs which are not substrates for RNase H, and wherein said gap region is located between said first wing region and said second wing region. In another embodiment, the chimeric antisense compound is a chimeric antisense oligonucleotide, and the nucleosides or nucleoside analog which is not a substrate for RNase H is a nucleotide having a 2′ modification of the sugar moiety. In one embodiment, the nucleotide having a 2′ modification of the sugar moiety is a 2′-O-methoxyethyl nucleotide. In some embodiments the compound is a 2-16-2 MOE gapmer, a 3-12-3 MOE gapmer, a 3-10-7 MOE gapmer or a 7-10-3 MOE gapmer. In one embodiment, the chimeric antisense oligonucleotide has at least one phosphorothioate backbone linkage.

Another embodiment of the present invention is a pharmaceutical composition for use in reducing levels of a preselected RNA target in the liver of an animal comprising a chimeric antisense compound targeted to said preselected RNA target, wherein said chimeric antisense compound comprises a first gap region consisting of at least 10 contiguous 2′-deoxynucleotides and a wing region which consists of from 1 to 4 contiguous nucleosides or nucleoside analogs which are not substrates for RNase H.

FIG. 1 . Depicts a comparison of in vivo effects of a 5-10-5 MOE gapmer (SEQ ID NO:1) and the corresponding gap-widened 2-16-2 MOE gapmer (SEQ ID NO:1).

FIG. 2 . Depicts a comparison the persistence of target mRNA modulation of a 5-10-5 MOE gapmer (SEQ ID NO:1) and the corresponding gap-widened 2-16-2 MOE gapmer (SEQ ID NO:1).

FIG. 3 . Depicts a comparison of in vitro effects of a 5-10-5 MOE gapmer and the corresponding gap-widened 2-16-2 MOE gapmer.

FIG. 4 . Depicts a comparison of the concentrations of a 5-10-5 MOE gapmer and the corresponding gap-widened 2-16-2 MOE gapmer in liver and kidney tissues.

FIG. 5 . Depicts a comparison of the in vitro effects of oligonucleotides having the same sequence (SEQ ID NO:3) but varied wing-gap-wing motifs.

FIG. 6 . Depicts a comparison of the in vivo effects of oligonucleotides having the same sequence (SEQ ID NO:3) but varied wing-gap-wing motifs.

Certain gap sizes are optimal for in vivo efficacy of antisense compounds. Surprisingly, improved potency (3-10× improvement) in mouse or rat liver has been demonstrated for gap-widened antisense oligonucleotides compared to standard 5-10-5 MOE gapmer (for example, 2-16-2, 2-14-2, 3-12-3 gapmers) antisense oligonucleotides. This has been shown for several distinct antisense targets and this improved potency is not observed in cultured cells transfected with the same gap-widened antisense oligonucleotides. Thus the “gap-widened” motifs appear to convey some benefit to in vivo potency, particularly in the liver. It is demonstrated herein that chimeric antisense compounds having a gap of greater than eleven contiguous deoxynucleotides flanked by wing regions consisting of from 1 to 4 nucleotides which are not substrates for RNase H are particularly effective at reducing target RNA levels in vivo, particularly in the liver.

Therapeutic Index

Therapeutic index is a measure which relates the dose of a drug required to produce a specified effect to that which produces an undesired effect. In one embodiment, improved therapeutic index of a gap-widened antisense oligonucleotide is characterized by equal or increased potency and a reduction in tissue concentration. In another embodiment, improved therapeutic index of a gap-widened antisense oligonucleotide is characterized by increased potency and equal tissue concentrations as compared to a corresponding 5-10-5 antisense oligonucleotide. In another embodiment, improved therapeutic index of a gap-widened antisense oligonucleotide is characterized by increased potency and decreased toxicity as compared to a corresponding 5-10-5 antisense oligonucleotide. In another embodiment, improved therapeutic index of a gap-widened antisense oligonucleotide is characterized by comparable potency and decreased toxicity as compared to a corresponding 5-10-5 antisense oligonucleotide. In some embodiments, the toxicity is renal toxicity. In some embodiments, the toxicity is hepatic toxicity.

Indications

An embodiment of the present invention is a method of treating a disease or condition wherein a target RNA is associated with said disease or condition by administering a compound of the invention. Another embodiment of the present invention is a method of preventing or delaying the onset of a disease or condition wherein a target RNA is associated with said disease or condition by administering a compound of the invention. Diseases or conditions include metabolic and cardiovascular diseases or conditions. In some embodiments, the disease or condition is metabolic syndrome, diabetes, obesity, hyperlipidemia, hypercholesterolemia, hypertriglyceridemia, Type 2 diabetes, diet-induced obesity, hyperglycemia, or insulin resistance. In one embodiment, the disease or condition is hepatic steatosis. In some embodiments, the steatosis is steatohepatitis or NASH. In some embodiments, the disease or condition is familial hypercholesterolemia, nonfamilial hypercholesterolemia, mixed dyslipidemia, dysbetalipoproteinemia, atherosclerosis, coronary artery disease, myocardial infarction, hypertension, carotid artery diseases, stroke, cerebrovascular disease, carotid artery disease, stroke, cerebrovascular disease, peripheral vascular disease, thrombosis, or arterial aneurism.

NAFLD and Metabolic Syndrome

The term “nonalcoholic fatty liver disease” (NAFLD) encompasses a disease spectrum ranging from simple triglyceride accumulation in hepatocytes (hepatic steatosis) to hepatic steatosis with inflammation (steatohepatitis), fibrosis, and cirrhosis. Nonalcoholic steatohepatitis (NASH) occurs from progression of NAFLD beyond deposition of triglycerides. A second-hit capable of inducing necrosis, inflammation, and fibrosis is required for development of NASH. Candidates for the second-hit can be grouped into broad categories: factors causing an increase in oxidative stress and factors promoting expression of proinflammatory cytokines. It has been suggested that increased liver triglycerides lead to increased oxidative stress in hepatocytes of animals and humans, indicating a potential cause-and-effect relationship between hepatic triglyceride accumulation, oxidative stress, and the progression of hepatic steatosis to NASH (Browning and Horton, J. Clin. Invest., 2004, 114, 147-152). Hypertriglyceridemia and hyperfattyacidemia can cause triglyceride accumulation in peripheral tissues (Shimamura et al., Biochem. Biophys. Res. Commun., 2004, 322, 1080-1085).

“Metabolic syndrome” is defined as a clustering of lipid and non-lipid cardiovascular risk factors of metabolic origin. It is closely linked to the generalized metabolic disorder known as insulin resistance. The National Cholesterol Education Program (NCEP) Adult Treatment Panel III (ATPIII) established criteria for diagnosis of metaolic syndrome when three or more of five risk determinants are present. The five risk determinants are abdominal obesity defined as waist circumference of greater than 102 cm for men or greater than 88 cm for women, triglyceride levels greater than or equal to 150 mg/dL, HDL cholesterol levels of less than 40 mg/dL for men and less than 50 mg/dL for women, blood pressure greater than or equal to 130/85 mm Hg and fasting glucose levels greater than or equal to 110 mg/dL. These determinants can be readily measured in clinical practice ( JAMA, 2001, 285, 2486-2497).

HbA1c

HbA1c is a stable minor hemoglobin variant formed in vivo via posttranslational modification by glucose, and it contains predominantly glycated NH2-terminal β-chains. There is a strong correlation between levels of HbA1c and the average blood glucose levels over the previous 3 months. Thus HbA1c is often viewed as the “gold standard” for measuring sustained blood glucose control (Bunn, H. F. et al., 1978, Science. 200, 21-7). HbA1c can be measured by ion-exchange HPLC or immunoassay; home blood collection and mailing kits for HbA1c measurement are now widely available. Serum fructosamine is another measure of stable glucose control and can be measured by a colorimetric method (Cobas Integra, Roche Diagnostics).

Cardiovascular Risk Profile

Conditions associated with risk of developing a cardiovascular disease include, but are not limited to, history of myocardial infarction, unstable angina, stable angina, coronary artery procedures (angioplasty or bypass surgery), evidence of clinically significant myocardial ischemia, noncoronary forms of atherosclerotic disease (peripheral arterial disease, abdominal aortic aneurysm, carotid artery disease), diabetes, cigarette smoking, hypertension, low HDL cholesterol, family history of premature CHD, obesity, physical inactivity, elevated triglyceride, or metabolic syndrome (Jama, 2001, 285, 2486-2497; Grundy et al., Circulation, 2004, 110, 227-239).

When cells reach 65-75% confluency, they are treated with oligonucleotide. Oligonucleotide is mixed with LIPOFECTIN™ Invitrogen Life Technologies, Carlsbad, Calif.) in Opti-MEM™-1 reduced serum medium (Invitrogen Life Technologies, Carlsbad, Calif.) to achieve the desired concentration of oligonucleotide and a LIPOFECTIN™ concentration of 2.5 or 3 μg/mL per 100 nM oligonucleotide. This transfection mixture iss incubated at room temperature for approximately 0.5 hours. For cells grown in 96-well plates, wells are washed once with 100 μL OPTI-MEM™-1 and then treated with 130 μL of the transfection mixture. Cells grown in 24-well plates or other standard tissue culture plates are treated similarly, using appropriate volumes of medium and oligonucleotide. Cells are treated and data are obtained in duplicate or triplicate. After approximately 4-7 hours of treatment at 37° C., the medium containing the transfection mixture is replaced with fresh culture medium. Cells are harvested 16-24 hours after oligonucleotide treatment.

Non-limiting examples of 2′-modified nucleosides useful in the compounds of the present invention, include but are not limited to 2′-O-alkyl, 2′-O-alkyl-O-alkyl wherein alkyl is a C 1 to C 6 alkyl or C 1 to C 6 alkylene when alkyl is not a terminal substituent. These include 2′-O-methyl, 2′-O-propyl and 2′-O-methoxyethyl nucleosides.

Details

The present invention uses 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. 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, increased stability 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-mediated inhibition of gene expression. The cleavage of RNA:RNA hybrids can, in like fashion, be accomplished through the actions of endoribonucleases, such as RNAseL which cleaves both cellular and viral RNA. 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, each of which is herein incorporated by reference in its entirety.

Synthesis of Nucleoside Phosphoramidites

The following compounds, including amidites and their intermediates were prepared as described in U.S. Pat. No. 6,426,220 and published PCT WO 02/36743; 5′-ODimethoxytrityl-thymidine intermediate for 5-methyl dC amidite, 5′-O-Dimethoxytrityl2′-deoxy-5-methylcytidine intermediate for 5-methyl-dC amidite, 5′-O-Dimethoxytrityl2′-deoxy-N-4-benzoyl-5-methylcytidine penultimate intermediate for 5-methyl dC amidite, [5′-O-(4,4′-Dimethoxytriphenylmethyl)-2′-deoxy-N-4-benzoyl-5-methylcytidin-3′O-yl]-2-cyanoethyl-N,N-diisopropylphosphoramidite (5-methyl dC amidite), 2′-Fluorodeoxyadenosine, 2′-Fluorodeoxyguanosine, 2′-Fluorouridine, 2′Fluorodeoxycytidine, 2′-O-(2-Methoxyethyl) modified amidites, 2′-O-(2-methoxyethyl)5-methyluridine intermediate, 5′-O-DMT-2′-O-(2-methoxyethyl)-5-methyluridine penultimate intermediate, [5′-O-(4,4′-Dimethoxytriphenylmethyl)-2′-O-(2-methoxyethyl)5-methyluridin-3′-O-yl]-2-cyanoethyl-N,N-diisopropylphosphoramidite (MOE T amidite), 5′-O-Dimethoxytrityl-2′-O-(2-methoxyethyl)-5-methylcytidine intermediate, 5′O-dimethoxytrityl-2′-O-(2-methoxyethyl)-N-4-benzoyl-5-methyl-cytidine penultimate intermediate, [5′-O-(4,4′-Dimethoxytriphenylmethyl)-2′-O-(2-methoxyethyl)-N-4-benzoyl5-methylcytidin-3′-O-yl]-2-cyanoethyl-N,N-diisopropylphosphoramidite (MOE 5-Me-C amidite), [5′-O-(4,4′-Dimethoxytriphenylmethyl)-2′-O-(2-methoxyethyl)-N6benzoyladenosin-3′-O-yl]-2-cyanoethyl-N,N-diisopropylphosphoramidite (MOE A amdite), [5′-O-(4,4′-Dimethoxytriphenylmethyl)-2′-O-(2-methoxyethyl)-N4isobutyrylguanosin-3′-O-yl]-2-cyanoethyl-N,N-diisopropylphosphoramidite (MOE G amidite), 2′-O-(Aminooxyethyl) nucleoside amidites and 2′-O-(dimethylaminooxyethyl) nucleoside amidites, 2′-(Dimethylaminooxyethoxy) nucleoside amidites, 5′-O-tertButyldiphenylsilyl-O2-2′-anhydro-5-methyluridine, 5′-O-tert-Butyldiphenylsilyl-2′-O-(2hydroxyethyl)-5-methyluridine, 2′-O-([2-phthalimidoxy)ethyl]-5′-t-butyldiphenylsilyl-5-methyluridine, 5′-O-tert-butyldiphenylsilyl-2′-O-[(2-formadoximinooxy)ethyl]-5methyluridine, 5′-O-tert-Butyldiphenylsilyl-2′-O-[N,N dimethylaminooxyethyl]-5methyluridine, 2′-O-(dimethylaminooxyethyl)-5-methyluridine, 5′-O-DMT-2′-O(dimethylaminooxyethyl)-5-methyluridine, 5′-O-DMT-2′-O-(2-N,Ndimethylaminooxyethyl)-5-methyluridine-3′-[(2-cyanoethyl)-N,N-diisopropylphosphoramidite], 2′-(Aminooxyethoxy) nucleoside amidites, N2-isobutyryl6-O-diphenylcarbamoyl-2′-O-(2-ethylacetyl)-5′-O-(4,4′-dimethoxytrityl)guanosine-3′-[(2cyanoethyl)-N,N-diisopropylphosphoramidite], 2′-dimethylaminoethoxyethoxy (2′DMAEOE) nucleoside amidites, 2′-O-[2(2-N,N-dimethylaminoethoxy)ethyl]-5-methyl uridine, 5′-O-dimethoxytrityl-2′-O-[2(2-N,N-dimethylaminoethoxy)-ethyl)]-5-methyl uridine and 5′-O-Dimethoxytrityl-2′-O-[2(2-N,N-dimethylaminoethoxy)-ethyl)]-5-methyl uridine-3′-O-(cyanoethyl-N,N-diisopropyl)phosphoramidite.

Oligonucleotide and Oligonucleoside Synthesis

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.Oligonucleotides: Unsubstituted and substituted phosphodiester (P═O) oligonucleotides are synthesized on an automated DNA synthesizer (Applied Biosystems model 394) using standard phosphoramidite chemistry with oxidation by iodine. Phosphorothioates (P═S) are synthesized similar to phosphodiester oligonucleotides with the following exceptions: thiation was effected by utilizing a 10% w/v solution of 3,H-1,2-benzodithiole-3-one 1,1-dioxide in acetonitrile for the oxidation of the phosphite linkages. The thiation reaction step time was increased to 180 sec and preceded by the normal capping step. After cleavage from the CPG column and deblocking in concentrated ammonium hydroxide at 55° C. (12-16 hr), the oligonucleotides were recovered by precipitating with >3 volumes of ethanol from a 1 M NH4OAc solution. Phosphinate oligonucleotides are prepared as described in U.S. Pat. No. 5,508,270, herein incorporated by reference. Alkyl phosphonate oligonucleotides are prepared as described in U.S. Pat. No. 4,469,863, herein incorporated by reference.3′-Deoxy-3′-methylene phosphonate oligonucleotides are prepared as described in U.S. Pat. No. 5,610,289 or 5,625,050, herein incorporated by reference. Phosphoramidite oligonucleotides are prepared as described in U.S. Pat. No. 5,256,775 or U.S. Pat. No. 5,366,878, herein incorporated by reference. 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. Phosphotriester oligonucleotides are prepared as described in U.S. Pat. No. 5,023,243, herein incorporated by reference. Borano phosphate oligonucleotides are prepared as described in U.S. Pat. Nos. 5,130,302 and 5,177,198, both herein incorporated by reference. Oligonucleosides: Methylenemethylimino linked oligonucleosides, also identified as MMI linked oligonucleosides, methylenedimethylhydrazo linked oligonucleosides, also identified as MDH linked oligonucleosides, and methylenecarbonyl amino linked oligonucleosides, also identified as amide-3 linked oligonucleosides, and methyleneaminocarbonyl linked oligonucleosides, also identified as amide-4 linked oligonucleosides, 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. 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. Ethylene oxide linked oligonucleosides are prepared as described in U.S. Pat. No. 5,223,618, herein incorporated by reference.

RNA Synthesis

In general, RNA synthesis chemistry is based on the selective incorporation of various protecting groups at strategic intermediary reactions. Although one of ordinary skill in the art will understand the use of protecting groups in organic synthesis, a useful class of protecting groups includes silyl ethers. In particular bulky silyl ethers are used to protect the 5′-hydroxyl in combination with an acid-labile orthoester protecting group on the 2′hydroxyl. This set of protecting groups is then used with standard solid-phase synthesis technology. It is important to lastly remove the acid labile orthoester protecting group after all other synthetic steps. Moreover, the early use of the silyl protecting groups during synthesis ensures facile removal when desired, without undesired deprotection of 2′ hydroxyl. Following this procedure for the sequential protection of the 5′-hydroxyl in combination with protection of the 2′-hydroxyl by protecting groups that are differentially removed and are differentially chemically labile, RNA oligonucleotides were synthesized. RNA oligonucleotides are synthesized in a stepwise fashion. Each nucleotide is added sequentially (3′- to 5′-direction) to a solid support-bound oligonucleotide. The first nucleoside at the 3′-end of the chain is covalently attached to a solid support. The nucleotide precursor, a ribonucleoside phosphoramidite, and activator are added, coupling the second base onto the 5′-end of the first nucleoside. The support is washed and any unreacted 5′-hydroxyl groups are capped with acetic anhydride to yield 5′-acetyl moieties. The linkage is then oxidized to the more stable and ultimately desired P(V) linkage. At the end of the nucleotide addition cycle, the 5′-silyl group is cleaved with fluoride. The cycle is repeated for each subsequent nucleotide. Following synthesis, the methyl protecting groups on the phosphates are cleaved in 30 minutes utilizing 1 M disodium-2-carbamoyl-2-cyanoethylene-1,1-dithiolate trihydrate (S2Na2) in DMF. The deprotection solution is washed from the solid supportbound oligonucleotide using water. The support is then treated with 40% methylamine in water for 10 minutes at 55° C. This releases the RNA oligonucleotides into solution, deprotects the exocyclic amines, and modifies the 2′-groups. The oligonucleotides can be analyzed by anion exchange HPLC at this stage.

The 2′-orthoester groups are the last protecting groups to be removed. The ethylene glycol monoacetate orthoester protecting group developed by Dharmacon Research, Inc. (Lafayette, Colo.), is one example of a useful orthoester protecting group which, has the following important properties. It is stable to the conditions of nucleoside phosphoramidite synthesis and oligonucleotide synthesis. However, after oligonucleotide synthesis the oligonucleotide is treated with methylamine which not only cleaves the oligonucleotide from the solid support but also removes the acetyl groups from the orthoesters. The resulting 2-ethyl-hydroxyl substituents on the orthoester are less electron withdrawing than the acetylated precursor. As a result, the modified orthoester becomes more labile to acid-catalyzed hydrolysis. Specifically, the rate of cleavage is approximately 10 times faster after the acetyl groups are removed, Therefore, this orthoester possesses sufficient stability in order to be compatible with oligonucleotide synthesis and yet, when subsequently modified, permits deprotection to be carried out under relatively mild aqueous conditions compatible with the final RNA oligonucleotide product. Additionally, methods of RNA synthesis are well known in the art (Scaringe, S. A. Ph.D. Thesis, University of Colorado, 1996; Scaringe, S. A., et al., J. Am. Chem. Soc., 1″8, 120, 11820-11821; Matteucci, M. D. and Caruthers, M. H. J. Am. Chem. Soc., 1981, 103, 3185-3191; Beaucage, S. L. and Caruthers, M. H. Tetrahedron Lett., 1981, 22, 1859-1862; Dahl, B. J., et al., Acta Chem. Scand, 1990, 44, 639-641; Reddy, M. P., et al., Tetrahedron Lett., 1994, 25, 4311-4314; Wincott, F. et al., Nucleic Acids Res., 1995, 23, 2677-2684; Griffin, B. E., et al., Tetrahedron, 1967, 23, 2301-2313; Griffin, B. E., et al., Tetrahedron, 1967, 23, 2315-2331).

RNA antisense compounds (RNA oligonucleotides) of the present invention can be synthesized by the methods herein or purchased from Dharmacon Research, Inc (Lafayette, Colo.). Once synthesized, complementary RNA antisense compounds can then be annealed by methods known in the art to form double stranded (duplexed) antisense compounds. For example, duplexes can be formed by combining 30 μl of each of the complementary strands of RNA oligonucleotides (50 uM RNA oligonucleotide solution) and 15 μl of 5× annealing buffer (100 mM potassium acetate, 30 mM HEPES-KOH pH 7.4, 2 mM magnesium acetate) followed by heating for 1 minute at 90° C., then 1 hour at 37° C. The resulting duplexed antisense compounds can be used in kits, assays, screens, or other methods to investigate the role of a target nucleic acid.

Synthesis of Chimeric Oligonucleotides

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”.

[2′-O-Me]-[2′-deoxy]-[2′-O-Me] Chimeric Phosphorothioate Oligonucleotides

Chimeric oligonucleotides having 2′-O-alkyl phosphorothioate and 2′-deoxy phosphorothioate oligonucleotide segments are synthesized using an Applied Biosystems automated DNA synthesizer Model 394, as above. Oligonucleotides are synthesized using the automated synthesizer and 2′-deoxy-5′-dimethoxytrityl-3′-O-phosphoramidite 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 incorporating coupling steps with increased reaction times for the 5′-dimethoxytrityl-2′-O-methyl-3′-O-phosphoramidite. The fully protected oligonucleotide is cleaved from the support and deprotected in concentrated ammonia (NH4OH) for 12-16 hr at 55° C. The deprotected oligo is then recovered by an appropriate method (precipitation, column chromatography, volume reduced in vacuo and analyzed spetrophotometrically for yield and for purity by capillary electrophoresis and by mass spectrometry.

[2′-O-(2-Methoxyethyl)]-[2′-deoxy]; -[2′-O-(Methoxyethyl)] Chimeric Phosphorothioate Oligonucleotides

[2′-O-(2-methoxyethyl)]-[2′-deoxy]-[-2′-O-(methoxyethyl)] 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.

[2′-O-(2-Methoxyethyl)Phosphodiester]-[2′-deoxy Phosphorothioate]-[2′-O-(2Methoxyethyl) Phosphodiester] Chimeric Oligonucleotides

[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, oxidation 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.

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.

The methods of the present invention are particularly useful in antisense therapeutics. It is not necessary that the antisense target be associated with liver disease per se, since many current antisense targets are expressed to high levels in liver and other organs. In particular, targets associated with metabolic and cardiovascular diseases and conditions are particularly amenable to knockdown in the liver and have been shown in animals and in clinical studies to have therapeutic effects).

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. 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.