# Patent

## Title
Compositions and methods

## Abstract

Provided herein are oligomeric compounds with conjugate groups. In certain embodiments, the oligomeric compounds are conjugated to N-Acetylgalactosamine.

## Background
SEQUENCE LISTING
The present application is being filed along with a Sequence Listing in electronic format. The Sequence Listing is provided as a file entitled BIOL0255USASEQ_ST25.txt created Oct. 30, 2015, which is 504 Kb in size. The information in the electronic format of the sequence listing is incorporated herein by reference in its entirety.
BACKGROUND OF THE INVENTION
The principle behind antisense technology is that an antisense compound hybridizes to a target nucleic acid and modulates the amount, activity, and/or function of the target nucleic acid. For example in certain instances, antisense compounds result in altered transcription or translation of a target. Such modulation of expression can be achieved by, for example, target mRNA degradation or occupancy-based inhibition. An example of modulation of RNA target function by degradation is RNase H-based degradation of the target RNA upon hybridization with a DNA-like antisense compound. Another example of modulation of gene expression by target degradation is RNA interference (RNAi). RNAi refers to antisense-mediated gene silencing through a mechanism that utilizes the RNA-induced siliencing complex (RISC). An additional example of modulation of RNA target function is by an occupancy-based mechanism such as is employed naturally by microRNA. MicroRNAs are small non-coding RNAs that regulate the expression of protein-coding RNAs. The binding of an antisense compound to a microRNA prevents that microRNA from binding to its messenger RNA targets, and thus interferes with the function of the microRNA. MicroRNA mimics can enhance native microRNA function. Certain antisense compounds alter splicing of pre-mRNA. Regardless of the specific mechanism, sequence-specificity makes antisense compounds attractive as tools for target validation and gene functionalization, as well as therapeutics to selectively modulate the expression of genes involved in the pathogenesis of diseases.
Antisense technology is an effective means for modulating the expression of one or more specific gene products and can therefore prove to be uniquely useful in a number of therapeutic, diagnostic, and research applications. Chemically modified nucleosides may be incorporated into antisense compounds to enhance one or more properties, such as nuclease resistance, pharmacokinetics or affinity for a target nucleic acid. In 1998, the antisense compound, Vitravene® (fomivirsen; developed by Isis Pharmaceuticals Inc., Carlsbad, Calif.) was the first antisense drug to achieve marketing clearance from the U.S. Food and Drug Administration (FDA), and is currently a treatment of cytomegalovirus (CMV)-induced retinitis in AIDS patients.
New chemical modifications have improved the potency and efficacy of antisense compounds, uncovering the potential for oral delivery as well as enhancing subcutaneous administration, decreasing potential for side effects, and leading to improvements in patient convenience. Chemical modifications increasing potency of antisense compounds allow administration of lower doses, which reduces the potential for toxicity, as well as decreasing overall cost of therapy. Modifications increasing the resistance to degradation result in slower clearance from the body, allowing for less frequent dosing. Different types of chemical modifications can be combined in one compound to further optimize the compounds efficacy.
SUMMARY OF THE INVENTION
In certain embodiments, the present disclosure provides conjugated antisense compounds. In certain embodiments, the present disclosure provides conjugated antisense compounds comprising an antisense oligonucleotide complementary to a nucleic acid transcript. In certain embodiments, the present disclosure provides methods comprising contacting a cell with a conjugated antisense compound comprising an antisense oligonucleotide complementary to a nucleic acid transcript. In certain embodiments, the present disclosure provides methods comprising contacting a cell with a conjugated antisense compound comprising an antisense oligonucleotide and reducing the amount or activity of a nucleic acid transcript in a cell.
The asialoglycoprotein receptor (ASGP-R) has been described previously. See e.g., Park et al., PNAS vol. 102, No. 47, pp 17125-17129 (2005). Such receptors are expressed on liver cells, particularly hepatocytes. Further, it has been shown that compounds comprising clusters of three N-acetylgalactosamine (GalNAc) ligands are capable of binding to the ASGP-R, resulting in uptake of the compound into the cell. See e.g., Khorev et al., Bioorganic and Medicinal Chemistry, 16, 9, pp 5216-5231 (May 2008). Accordingly, conjugates comprising such GalNAc clusters have been used to facilitate uptake of certain compounds into liver cells, specifically hepatocytes. For example it has been shown that certain GalNAc-containing conjugates increase activity of duplex siRNA compounds in liver cells in vivo. In such instances, the GalNAc-containing conjugate is typically attached to the sense strand of the siRNA duplex. Since the sense strand is discarded before the antisense strand ultimately hybridizes with the target nucleic acid, there is little concern that the conjugate will interfere with activity. Typically, the conjugate is attached to the 3′ end of the sense strand of the siRNA. See e.g., U.S. Pat. No. 8,106,022. Certain conjugate groups described herein are more active and/or easier to synthesize than conjugate groups previously described.
In certain embodiments of the present invention, conjugates are attached to single-stranded antisense compounds, including, but not limited to RNase H based antisense compounds and antisense compounds that alter splicing of a pre-mRNA target nucleic acid. In such embodiments, the conjugate should remain attached to the antisense compound long enough to provide benefit (improved uptake into cells) but then should either be cleaved, or otherwise not interfere with the subsequent steps necessary for activity, such as hybridization to a target nucleic acid and interaction with RNase H or enzymes associated with splicing or splice modulation. This balance of properties is more important in the setting of single-stranded antisense compounds than in siRNA compounds, where the conjugate may simply be attached to the sense strand. Disclosed herein are conjugated single-stranded antisense compounds having improved potency in liver cells in vivo compared with the same antisense compound lacking the conjugate. Given the required balance of properties for these compounds such improved potency is surprising.
In certain embodiments, conjugate groups herein comprise a cleavable moiety. As noted, without wishing to be bound by mechanism, it is logical that the conjugate should remain on the compound long enough to provide enhancement in uptake, but after that, it is desirable for some portion or, ideally, all of the conjugate to be cleaved, releasing the parent compound (e.g., antisense compound) in its most active form. In certain embodiments, the cleavable moiety is a cleavable nucleoside. Such embodiments take advantage of endogenous nucleases in the cell by attaching the rest of the conjugate (the cluster) to the antisense oligonucleotide through a nucleoside via one or more cleavable bonds, such as those of a phosphodiester linkage. In certain embodiments, the cluster is bound to the cleavable nucleoside through a phosphodiester linkage. In certain embodiments, the cleavable nucleoside is attached to the antisense oligonucleotide (antisense compound) by a phosphodiester linkage. In certain embodiments, the conjugate group may comprise two or three cleavable nucleosides. In such embodiments, such cleavable nucleosides are linked to one another, to the antisense compound and/or to the cluster via cleavable bonds (such as those of a phosphodiester linkage). Certain conjugates herein do not comprise a cleavable nucleoside and instead comprise a cleavable bond. It is shown that that sufficient cleavage of the conjugate from the oligonucleotide is provided by at least one bond that is vulnerable to cleavage in the cell (a cleavable bond).
In certain embodiments, conjugated antisense compounds are prodrugs. Such prodrugs are administered to an animal and are ultimately metabolized to a more active form. For example, conjugated antisense compounds are cleaved to remove all or part of the conjugate resulting in the active (or more active) form of the antisense compound lacking all or some of the conjugate.
In certain embodiments, conjugates are attached at the 5′ end of an oligonucleotide. Certain such 5′-conjugates are cleaved more efficiently than counterparts having a similar conjugate group attached at the 3′ end. In certain embodiments, improved activity may correlate with improved cleavage. In certain embodiments, oligonucleotides comprising a conjugate at the 5′ end have greater efficacy than oligonucleotides comprising a conjugate at the 3′ end (see, for example, Examples 56, 81, 83, and 84). Further, 5′-attachment allows simpler oligonucleotide synthesis. Typically, oligonucleotides are synthesized on a solid support in the 3′ to 5′ direction. To make a 3′-conjugated oligonucleotide, typically one attaches a pre-conjugated 3′ nucleoside to the solid support and then builds the oligonucleotide as usual. However, attaching that conjugated nucleoside to the solid support adds complication to the synthesis. Further, using that approach, the conjugate is then present throughout the synthesis of the oligonucleotide and can become degraded during subsequent steps or may limit the sorts of reactions and reagents that can be used. Using the structures and techniques described herein for 5′-conjugated oligonucleotides, one can synthesize the oligonucleotide using standard automated techniques and introduce the conjugate with the final (5′-most) nucleoside or after the oligonucleotide has been cleaved from the solid support.
In view of the art and the present disclosure, one of ordinary skill can easily make any of the conjugates and conjugated oligonucleotides herein. Moreover, synthesis of certain such conjugates and conjugated oligonucleotides disclosed herein is easier and/or requires few steps, and is therefore less expensive than that of conjugates previously disclosed, providing advantages in manufacturing. For example, the synthesis of certain conjugate groups consists of fewer synthetic steps, resulting in increased yield, relative to conjugate groups previously described. Conjugate groups such as GalNAc3-10 in Example 46 and GalNAc3-7 in Example 48 are much simpler than previously described conjugates such as those described in U.S. Pat. Nos. 8,106,022 or 7,262,177 that require assembly of more chemical intermediates. Accordingly, these and other conjugates described herein have advantages over previously described compounds for use with any oligonucleotide, including single-stranded oligonucleotides and either strand of double-stranded oligonucleotides (e.g., siRNA).
Similarly, disclosed herein are conjugate groups having only one or two GalNAc ligands. As shown, such conjugates groups improve activity of antisense compounds. Such compounds are much easier to prepare than conjugates comprising three GalNAc ligands. Conjugate groups comprising one or two GalNAc ligands may be attached to any antisense compounds, including single-stranded oligonucleotides and either strand of double-stranded oligonucleotides (e.g., siRNA).
In certain embodiments, the conjugates herein do not substantially alter certain measures of tolerability. For example, it is shown herein that conjugated antisense compounds are not more immunogenic than unconjugated parent compounds. Since potency is improved, embodiments in which tolerability remains the same (or indeed even if tolerability worsens only slightly compared to the gains in potency) have improved properties for therapy.
In certain embodiments, conjugation allows one to alter antisense compounds in ways that have less attractive consequences in the absence of conjugation. For example, in certain embodiments, replacing one or more phosphorothioate linkages of a fully phosphorothioate antisense compound with phosphodiester linkages results in improvement in some measures of tolerability. For example, in certain instances, such antisense compounds having one or more phosphodiester are less immunogenic than the same compound in which each linkage is a phosphorothioate. However, in certain instances, as shown in Example 26, that same replacement of one or more phosphorothioate linkages with phosphodiester linkages also results in reduced cellular uptake and/or loss in potency. In certain embodiments, conjugated antisense compounds described herein tolerate such change in linkages with little or no loss in uptake and potency when compared to the conjugated full-phosphorothioate counterpart. In fact, in certain embodiments, for example, in Examples 44, 57, 59, and 86, oligonucleotides comprising a conjugate and at least one phosphodiester internucleoside linkage actually exhibit increased potency in vivo even relative to a full phosphorothioate counterpart also comprising the same conjugate. Moreover, since conjugation results in substantial increases in uptake/potency a small loss in that substantial gain may be acceptable to achieve improved tolerability. Accordingly, in certain embodiments, conjugated antisense compounds comprise at least one phosphodiester linkage.
In certain embodiments, conjugation of antisense compounds herein results in increased delivery, uptake and activity in hepatocytes. Thus, more compound is delivered to liver tissue. However, in certain embodiments, that increased delivery alone does not explain the entire increase in activity. In certain such embodiments, more compound enters hepatocytes. In certain embodiments, even that increased hepatocyte uptake does not explain the entire increase in activity. In such embodiments, productive uptake of the conjugated compound is increased. For example, as shown in Example 102, certain embodiments of GalNAc-containing conjugates increase enrichment of antisense oligonucleotides in hepatocytes versus non-parenchymal cells. This enrichment is beneficial for oligonucleotides that target genes that are expressed in hepatocytes.
In certain embodiments, conjugated antisense compounds herein result in reduced kidney exposure. For example, as shown in Example 20, the concentrations of antisense oligonucleotides comprising certain embodiments of GalNAc-containing conjugates are lower in the kidney than that of antisense oligonucleotides lacking a GalNAc-containing conjugate. This has several beneficial therapeutic implications. For therapeutic indications where activity in the kidney is not sought, exposure to kidney risks kidney toxicity without corresponding benefit. Moreover, high concentration in kidney typically results in loss of compound to the urine resulting in faster clearance. Accordingly for non-kidney targets, kidney accumulation is undesired.
In certain embodiments, the present disclosure provides conjugated antisense compounds represented by the formula:

A-B-C-DE-F)q 

wherein
A is the antisense oligonucleotide;
B is the cleavable moiety
C is the conjugate linker
D is the branching group
each E is a tether;
each F is a ligand; and
q is an integer between 1 and 5.
In the above diagram and in similar diagrams herein, the branching group “D” branches as many times as is necessary to accommodate the number of (E-F) groups as indicated by “q”. Thus, where q=1, the formula is:

A-B-C-D-E-F

where q=2, the formula is:




where q=3, the formula is:




where q=4, the formula is:




where q=5, the formula is:




In certain embodiments, conjugated antisense compounds are provided having the structure:




In certain embodiments, conjugated antisense compounds are provided having the structure:




In certain embodiments, conjugated antisense compounds are provided having the structure:




In certain embodiments, conjugated antisense compounds are provided having the structure:





The present disclosure provides the following non-limiting numbered embodiments:
Embodiment 1. The conjugated antisense compound of any of embodiments 1179 to 1182, wherein the tether has a structure selected from among:




wherein each n is independently, 0, 1, 2, 3, 4, 5, 6, or 7.

Embodiment 2. The conjugated antisense compound of any of embodiments 1179 to 1182, wherein the tether has the structure:





Embodiment 3. The conjugated antisense compound of any of embodiments 1179 to 1182 or 1688 to 1689, wherein the linker has a structure selected from among:





Embodiment 4. The conjugated antisense compound of any of embodiments 1179 to 1182 or 1688 to 1689, wherein the linker has a structure selected from among:





wherein each n is independently, 0, 1, 2, 3, 4, 5, 6, or 7.
Embodiment 5. The conjugated antisense compound of any of embodiments 1179 to 1182 or 1688 to 1689, wherein the linker has the structure:




In embodiments having more than one of a particular variable (e.g., more than one “m” or “n”), unless otherwise indicated, each such particular variable is selected independently. Thus, for a structure having more than one n, each n is selected independently, so they may or may not be the same as one another.


DETAILED DESCRIPTION
It is to be understood that both the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive of the disclosure. Herein, the use of the singular includes the plural unless specifically stated otherwise. As used herein, the use of “or” means “and/or” unless stated otherwise. Furthermore, the use of the term “including” as well as other forms, such as “includes” and “included”, is not limiting. Also, terms such as “element” or “component” encompass both elements and components comprising one unit and elements and components that comprise more than one subunit, unless specifically stated otherwise.
The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described. All documents, or portions of documents, cited in this application, including, but not limited to, patents, patent applications, articles, books, and treatises, are hereby expressly incorporated by reference in their entirety for any purpose.
A. Definitions
Unless specific definitions are provided, the nomenclature used in connection with, and the procedures and techniques of, analytical chemistry, synthetic organic chemistry, and medicinal and pharmaceutical chemistry described herein are those well known and commonly used in the art. Standard techniques may be used for chemical synthesis, and chemical analysis. Certain such techniques and procedures may be found for example in “Carbohydrate Modifications in Antisense Research” Edited by Sangvi and Cook, American Chemical Society, Washington D.C., 1994; “Remington's Pharmaceutical Sciences,” Mack Publishing Co., Easton, Pa., 21st edition, 2005; and “Antisense Drug Technology, Principles, Strategies, and Applications” Edited by Stanley T. Crooke, CRC Press, Boca Raton, Fla.; and Sambrook et al., “Molecular Cloning, A laboratory Manual,” 2nd Edition, Cold Spring Harbor Laboratory Press, 1989, which are hereby incorporated by reference for any purpose. Where permitted, all patents, applications, published applications and other publications and other data referred to throughout in the disclosure are incorporated by reference herein in their entirety.
Unless otherwise indicated, the following terms have the following meanings:
As used herein, “2′-F nucleoside” refers to a nucleoside comprising a sugar comprising fluorine at the 2′ position. Unless otherwise indicated, the fluorine in a 2′-F nucleoside is in the ribo position (replacing the OH of a natural ribose).
“2′-O-methoxyethyl” (also 2′-MOE and 2′-O(CH2)2—OCH3) refers to an O-methoxy-ethyl modification of the 2′ position of a furosyl ring. A 2′-O-methoxyethyl modified sugar is a modified sugar.
“2′-O-methoxyethyl nucleotide” means a nucleotide comprising a 2′-O-methoxyethyl modified sugar moiety.
As used herein, “2′-substituted sugar moiety” means a furanosyl comprising a substituent at the 2′-position other than H or OH. Unless otherwise indicated, a 2′-substituted sugar moiety is not a bicyclic sugar moiety (i.e., the 2′-substituent of a 2′-substituted sugar moiety does not form a bridge to another atom of the furanosyl ring.
“3′ target site” refers to the nucleotide of a target nucleic acid which is complementary to the 3′-most nucleotide of a particular antisense compound.
“5′ target site” refers to the nucleotide of a target nucleic acid which is complementary to the 5′-most nucleotide of a particular antisense compound.
“5-methylcytosine” means a cytosine modified with a methyl group attached to the 5′ position. A 5-methylcytosine is a modified nucleobase.
“About” means within +10% of a value. For example, if it is stated, “a marker may be increased by about 50%”, it is implied that the marker may be increased between 45%-55%.
“Active pharmaceutical agent” means the substance or substances in a pharmaceutical composition that provide a therapeutic benefit when administered to an individual. For example, in certain embodiments an antisense oligonucleotide targeted to PTP1B is an active pharmaceutical agent.
“Active target region” or “target region” means a region to which one or more active antisense compounds is targeted. “Active antisense compounds” means antisense compounds that reduce target nucleic acid levels or protein levels.
“Adipogenesis” means the development of fat cells from preadipocytes. “Lipogenesis” means the production or formation of fat, either fatty degeneration or fatty infiltration.
“Adiposity” or “Obesity” refers to the state of being obese or an excessively high amount of body fat or adipose tissue in relation to lean body mass. The amount of body fat includes concern for both the distribution of fat throughout the body and the size and mass of the adipose tissue deposits. Body fat distribution can be estimated by skin-fold measures, waist-to-hip circumference ratios, or techniques such as ultrasound, computed tomography, or magnetic resonance imaging. According to the Center for Disease Control and Prevention, individuals with a body mass index (BMI) of 30 or more are considered obese. The term “Obesity” as used herein includes conditions where there is an increase in body fat beyond the physical requirement as a result of excess accumulation of adipose tissue in the body. The term “obesity” includes, but is not limited to, the following conditions: adult-onset obesity; alimentary obesity; endogenous or inflammatory obesity; endocrine obesity; familial obesity; hyperinsulinar obesity; hyperplastic-hypertrophic obesity; hypogonadal obesity; hypothyroid obesity; lifelong obesity; morbid obesity and exogenous obesity.
“Administered concomitantly” refers to the co-administration of two agents in any manner in which the pharmacological effects of both are manifest in the patient at the same time. Concomitant administration does not require that both agents be administered in a single pharmaceutical composition, in the same dosage form, or by the same route of administration. The effects of both agents need not manifest themselves at the same time. The effects need only be overlapping for a period of time and need not be coextensive.
“Administering” means providing an agent to an animal, and includes, but is not limited to, administering by a medical professional and self-administering.
“Agent” means an active substance that can provide a therapeutic benefit when administered to an animal “First Agent” means a therapeutic compound provided herein. For example, a first agent can be an antisense oligonucleotide targeting PTP1B. “Second agent” means a second therapeutic compound of the invention (e.g. a second antisense oligonucleotide targeting PTP1B) and/or a non-PTP1B therapeutic compound.
“Amelioration” refers to a lessening of at least one indicator, sign, or symptom of an associated disease, disorder, or condition. The severity of indicators can be determined by subjective or objective measures, which are known to those skilled in the art.
“Animal” refers to a human or non-human animal, including, but not limited to, mice, rats, rabbits, dogs, cats, pigs, and non-human primates, including, but not limited to, monkeys and chimpanzees.
“Antisense activity” means any detectable or measurable activity attributable to the hybridization of an antisense compound to its target nucleic acid. In certain embodiments, antisense activity is a decrease in the amount or expression of a target nucleic acid or protein encoded by such target nucleic acid.
“Antisense compound” means an oligomeric compound that is capable of undergoing hybridization to a target nucleic acid through hydrogen bonding.
“Antisense inhibition” means reduction of target nucleic acid levels or target protein levels in the presence of an antisense compound complementary to a target nucleic acid compared to target nucleic acid levels or target protein levels in the absence of the antisense compound.
“Antisense oligonucleotide” means a single-stranded oligonucleotide having a nucleobase sequence that permits hybridization to a corresponding region or segment of a target nucleic acid.
“Bicyclic sugar” means a furosyl ring modified by the bridging of two non-geminal ring atoms. A bicyclic sugar is a modified sugar.
“Bicyclic nucleic acid” or “BNA” refers to a nucleoside or nucleotide wherein the furanose portion of the nucleoside or nucleotide includes a bridge connecting two carbon atoms on the furanose ring, thereby forming a bicyclic ring system.
As used herein, “bicyclic sugar moiety” means a modified sugar moiety comprising a 4 to 7 membered ring (including but not limited to a furanosyl) comprising a bridge connecting two atoms of the 4 to 7 membered ring to form a second ring, resulting in a bicyclic structure. In certain embodiments, the 4 to 7 membered ring is a sugar ring. In certain embodiments the 4 to 7 membered ring is a furanosyl. In certain such embodiments, the bridge connects the 2′-carbon and the 4′-carbon of the furanosyl.
“Cap structure” or “terminal cap moiety” means chemical modifications, which have been incorporated at either terminus of an antisense compound.
“Chemically distinct region” refers to a region of an antisense compound that is in some way chemically different than another region of the same antisense compound. For example, a region having 2′-O-methoxyethyl nucleotides is chemically distinct from a region having nucleotides without 2′-O-methoxyethyl modifications.
As used herein, “chemical modification” means a chemical difference in a compound when compared to a naturally occurring counterpart. Chemical modifications of oligonucleotides include nucleoside modifications (including sugar moiety modifications and nucleobase modifications) and internucleoside linkage modifications. In reference to an oligonucleotide, chemical modification does not include differences only in nucleobase sequence.
“Chimeric antisense compound” means an antisense compound that has at least two chemically distinct regions.
“Co-administration” means administration of two or more agents to an individual. The two or more agents can be in a single pharmaceutical composition, or can be in separate pharmaceutical compositions. Each of the two or more agents can be administered through the same or different routes of administration. Co-administration encompasses parallel or sequential administration.
“Cholesterol” is a sterol molecule found in the cell membranes of all animal tissues. Cholesterol must be transported in an animal's blood plasma by lipoproteins including very low density lipoprotein (VLDL), intermediate density lipoprotein (IDL), low density lipoprotein (LDL), and high density lipoprotein (HDL). “Plasma cholesterol” refers to the sum of all lipoproteins (VDL, IDL, LDL, HDL) esterified and/or non-esterified cholesterol present in the plasma or serum.
“Cholesterol absorption inhibitor” means an agent that inhibits the absorption of exogenous cholesterol obtained from diet.
“Complementarity” means the capacity for pairing between nucleobases of a first nucleic acid and a second nucleic acid.
As used herein, “constrained ethyl nucleoside” or “cEt” means a nucleoside comprising a bicyclic sugar moiety comprising a 4′-CH(CH3)—O-2′bridge.
“Contiguous nucleobases” means nucleobases immediately adjacent to each other.
“Deoxyribonucleotide” means a nucleotide having a hydrogen at the 2′ position of the sugar portion of the nucleotide. Deoxyribonucleotides may be modified with any of a variety of substituents.
“Diabetes mellitus” or “diabetes” is a syndrome characterized by disordered metabolism and abnormally high blood sugar (hyperglycemia) resulting from insufficient levels of insulin or reduced insulin sensitivity. The characteristic symptoms are excessive urine production (polyuria) due to high blood glucose levels, excessive thirst and increased fluid intake (polydipsia) attempting to compensate for increased urination, blurred vision due to high blood glucose effects on the eye's optics, unexplained weight loss, and lethargy.
“Diabetic dyslipidemia” or “type 2 diabetes with dyslipidemia” means a condition characterized by Type 2 diabetes, reduced HDL-C, elevated triglycerides, and elevated small, dense LDL particles.
“Diluent” means an ingredient in a composition that lacks pharmacological activity, but is pharmaceutically necessary or desirable. For example, the diluent in an injected composition can be a liquid, e.g. saline solution.
“Dyslipidemia” refers to a disorder of lipid and/or lipoprotein metabolism, including lipid and/or lipoprotein overproduction or deficiency. Dyslipidemias may be manifested by elevation of lipids such as cholesterol and triglycerides as well as lipoproteins such as low-density lipoprotein (LDL) cholesterol.
“Dosage unit” means a form in which a pharmaceutical agent is provided, e.g. pill, tablet, or other dosage unit known in the art. In certain embodiments, a dosage unit is a vial containing lyophilized antisense oligonucleotide. In certain embodiments, a dosage unit is a vial containing reconstituted antisense oligonucleotide.
“Dose” means a specified quantity of a pharmaceutical agent provided in a single administration, or in a specified time period. In certain embodiments, a dose can be administered in one, two, or more boluses, tablets, or injections. For example, in certain embodiments where subcutaneous administration is desired, the desired dose requires a volume not easily accommodated by a single injection, therefore, two or more injections can be used to achieve the desired dose. In certain embodiments, the pharmaceutical agent is administered by infusion over an extended period of time or continuously. Doses can be stated as the amount of pharmaceutical agent per hour, day, week, or month.
“Effective amount” or “therapeutically effective amount” means the amount of active pharmaceutical agent sufficient to effectuate a desired physiological outcome in an individual in need of the agent. The effective amount can vary among individuals depending on the health and physical condition of the individual to be treated, the taxonomic group of the individuals to be treated, the formulation of the composition, assessment of the individual's medical condition, and other relevant factors.
“Fully complementary” or “100% complementary” means each nucleobase of a nucleobase sequence of a first nucleic acid has a complementary nucleobase in a second nucleobase sequence of a second nucleic acid. In certain embodiments, a first nucleic acid is an antisense compound and a target nucleic acid is a second nucleic acid.
As used herein, “furanosyl” means a structure comprising a 5-membered ring comprising four carbon atoms and one oxygen atom.
“Gapmer” means a chimeric antisense compound in which an internal region having a plurality of nucleosides that support RNase H cleavage is positioned between external regions having one or more nucleosides, wherein the nucleosides comprising the internal region are chemically distinct from the nucleoside or nucleosides comprising the external regions. The internal region can be referred to as a “gap segment” and the external regions can be referred to as “wing segments.”
“Gap-widened” means a chimeric antisense compound having a gap segment of 12 or more contiguous 2′-deoxyribonucleosides positioned between and immediately adjacent to 5′ and 3′ wing segments having from one to six nucleosides.
“Glucose” is a monosaccharide used by cells as a source of energy and inflammatory intermediate. “Plasma glucose” refers to glucose present in the plasma.
“HMG-CoA reductase inhibitor” means an agent that acts through the inhibition of the enzyme HMG-CoA reductase, such as atorvastatin, rosuvastatin, fluvastatin, lovastatin, pravastatin, and simvastatin.
“Hybridization” means the annealing of complementary nucleic acid molecules. In certain embodiments, complementary nucleic acid molecules include an antisense compound and a target nucleic acid.
“Hyperlipidemia” or “hyperlipemia” is a condition characterized by elevated serum lipids or circulating (plasma) lipids. This condition manifests an abnormally high concentration of fats. The lipid fractions in the circulating blood are cholesterol, low density lipoproteins, very low density lipoproteins and triglycerides.
“Hypertriglyceridemia” means a condition characterized by elevated triglyceride levels.
“Identifying” or “selecting an animal with metabolic” means identifying or selecting a subject having been diagnosed with a metabolic disease, or a metabolic disorder; or, identifying or selecting a subject having any symptom of a metabolic disease, including, but not limited to, metabolic syndrome, hyperglycemia, hypertriglyceridemia, hypertension increased insulin resistance, decreased insulin sensitivity, above normal body weight, and/or above normal body fat or any combination thereof. Such identification may be accomplished by any method, including but not limited to, standard clinical tests or assessments, such as measuring serum or circulating (plasma) blood-glucose, measuring serum or circulating (plasma) triglycerides, measuring blood-pressure, measuring body fat, measuring body weight, and the like.
“Immediately adjacent” means there are no intervening elements between the immediately adjacent elements.
“Individual” or “subject” or “animal” means a human or non-human animal selected for treatment or therapy.
“Inhibiting the expression or activity” refers to a reduction or blockade of the expression or activity of a RNA or protein and does not necessarily indicate a total elimination of expression or activity.
“Insulin resistance” is defined as the condition in which normal amounts of insulin are inadequate to produce a normal insulin response from fat, muscle and liver cells. Insulin resistance in fat cells results in hydrolysis of stored triglycerides, which elevates free fatty acids in the blood plasma. Insulin resistance in muscle reduces glucose uptake whereas insulin resistance in liver reduces glucose storage, with both effects serving to elevate blood glucose. High plasma levels of insulin and glucose due to insulin resistance often leads to metabolic syndrome and type 2 diabetes.
“Insulin sensitivity” is a measure of how effectively an individual processes glucose. An individual having high insulin sensitivity effectively processes glucose whereas an individual with low insulin sensitivity does not effectively process glucose.
“Internucleoside linkage” refers to the chemical bond between nucleosides.
“Intravenous administration” means administration into a vein.
“Linked nucleosides” means adjacent nucleosides which are bonded together.
As used herein, “locked nucleic acid nucleoside” or “LNA” means a nucleoside comprising a bicyclic sugar moiety comprising a 4′-CH2—O-2′bridge.
“Lipid-lowering therapy” or “lipid lowering agent” means a therapeutic regimen provided to a subject to reduce one or more lipids in a subject. In certain embodiments, a lipid-lowering therapy is provided to reduce one or more of ApoB, total cholesterol, LDL-C, VLDL-C, IDL-C, non-HDL-C, triglycerides, small dense LDL particles, and Lp(a) in a subject. Examples of lipid-lowering therapy include statins, fibrates, and MTP inhibitors.
“Major risk factors” refers to factors that contribute to a high risk for a particular disease or condition. In certain embodiments, major risk factors for coronary heart disease include, without limitation, cigarette smoking, hypertension, low HDL-C, family history of coronary heart disease, age, and other factors disclosed herein.
“Metabolic disease” or “metabolic disorder” refers to a condition characterized by an alteration or disturbance in metabolic function. “Metabolic” and “metabolism” are terms well known in the art and generally include the whole range of biochemical processes that occur within a living organism. Metabolic diseases or disorders include, but are not limited to, obesity, diabetes, hyperglycemia, prediabetes, non-alcoholic fatty liver disease (NAFLD), metabolic syndrome, insulin resistance, diabetic dyslipidemia, or hypertriglyceridemia or a combination thereof.
“Metabolic syndrome” means a condition characterized by a clustering of lipid and non-lipid cardiovascular risk factors of metabolic origin. In certain embodiments, metabolic syndrome is identified by the presence of any 3 of the following factors: waist circumference of greater than 102 cm in men or greater than 88 cm in women; serum triglyceride of at least 150 mg/dL; HDL-C less than 40 mg/dL in men or less than 50 mg/dL in women; blood pressure of at least 130/85 mmHg; and fasting glucose of at least 110 mg/dL. These determinants can be readily measured in clinical practice (JAMA, 2001, 285: 2486-2497).
“Mismatch” or “non-complementary nucleobase” refers to the case when a nucleobase of a first nucleic acid is not capable of pairing with the corresponding nucleobase of a second or target nucleic acid.
“Mixed dyslipidemia” means a condition characterized by elevated cholesterol and elevated triglycerides.
“Modified internucleoside linkage” refers to a substitution or any change from a naturally occurring internucleoside bond (i.e. a phosphodiester internucleoside bond).
“Modified nucleobase” refers to any nucleobase other than adenine, cytosine, guanine, thymidine, or uracil. An “unmodified nucleobase” means the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C), and uracil (U).
“Modified nucleoside” means a nucleoside having, independently, a modified sugar moiety or modified nucleobase.
“Modified nucleotide” means a nucleotide having, independently, a modified sugar moiety, modified internucleoside linkage, or modified nucleobase. A “modified nucleoside” means a nucleoside having, independently, a modified sugar moiety or modified nucleobase.
“Modified oligonucleotide” means an oligonucleotide comprising at least one modified nucleotide.
“Modified sugar” refers to a substitution or change from a natural sugar.
As used herein, “modified sugar moiety” means a substituted sugar moiety or a sugar surrogate.
As used herein, “MOE” means —OCH2CH2OCH3.
“Motif” means the pattern of chemically distinct regions in an antisense compound.
“MTP inhibitor” means an agent inhibits the enzyme, microsomal triglyceride transfer protein.
“Naturally occurring internucleoside linkage” means a 3′ to 5′ phosphodiester linkage.
As used herein, “naturally occurring sugar moiety” means a ribofuranosyl as found in naturally occurring RNA or a deoxyribofuranosyl as found in naturally occurring DNA.
“Natural sugar moiety” means a sugar found in DNA (2′-H) or RNA (2′-OH).
“Non-alcoholic fatty liver disease” or “NAFLD” means a condition characterized by fatty inflammation of the liver that is not due to excessive alcohol use (for example, alcohol consumption of over 20 g/day). In certain embodiments, NAFLD is related to insulin resistance and the metabolic syndrome. 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
“Nucleic acid” refers to molecules composed of monomeric nucleotides. A nucleic acid includes ribonucleic acids (RNA), deoxyribonucleic acids (DNA), single-stranded nucleic acids, double-stranded nucleic acids, small interfering ribonucleic acids (siRNA), and microRNAs (miRNA). A nucleic acid can also comprise a combination of these elements in a single molecule.
“Nucleobase” means a heterocyclic moiety capable of pairing with a base of another nucleic acid. As used herein, “nucleobase” means a group of atoms that can be linked to a sugar moiety to create a nucleoside that is capable of incorporation into an oligonucleotide, and wherein the group of atoms is capable of bonding with a complementary naturally occurring nucleobase of another oligonucleotide or nucleic acid. Nucleobases may be naturally occurring or may be modified.
“Nucleobase sequence” means the order of contiguous nucleobases independent of any sugar, linkage, or nucleobase modification.
As used herein, “nucleoside” means a compound comprising a nucleobase moiety and a sugar moiety. Nucleosides include, but are not limited to, naturally occurring nucleosides (as found in DNA and RNA) and modified nucleosides. Nucleosides may be linked to a phosphate moiety.
“Nucleoside mimetic” includes those structures used to replace the sugar or the sugar and the base and not necessarily the linkage at one or more positions of an oligomeric compound such as for example nucleoside mimetics having morpholino, cyclohexenyl, cyclohexyl, tetrahydropyranyl, bicyclo or tricyclo sugar mimetics e.g. non furanose sugar units.
“Nucleotide” means a nucleoside having a phosphate group covalently linked to the sugar portion of the nucleoside. As used herein, “nucleotide” means a nucleoside further comprising a phosphate linking group. As used herein, “linked nucleosides” may or may not be linked by phosphate linkages and thus includes, but is not limited to “linked nucleotides.” As used herein, “linked nucleosides” are nucleosides that are connected in a continuous sequence (i.e. no additional nucleosides are present between those that are linked).
“Nucleotide mimetic” includes those structures used to replace the nucleoside and the linkage at one or more positions of an oligomeric compound such as for example peptide nucleic acids or morpholinos (morpholinos linked by —N(H)—C(═O)—O— or other non-phosphodiester linkage).
“Oligomeric compound” or “oligomer” refers to a polymeric structure comprising two or more sub-structures and capable of hybridizing to a region of a nucleic acid molecule. In certain embodiments, oligomeric compounds are oligonucleosides. In certain embodiments, oligomeric compounds are oligonucleotides. In certain embodiments, oligomeric compounds are antisense compounds. In certain embodiments, oligomeric compounds are antisense oligonucleotides. In certain embodiments, oligomeric compounds are chimeric oligonucleotides.
“Oligonucleotide” means a polymer of linked nucleosides each of which can be modified or unmodified, independent one from another.
“Parenteral administration” means administration through injection or infusion. Parenteral administration includes subcutaneous administration, intravenous administration, intramuscular administration, intraarterial administration, intraperitoneal administration, or intracranial administration, e.g. intrathecal or intracerebroventricular administration. Administration can be continuous, or chronic, or short or intermittent.
“Peptide” means a molecule formed by linking at least two amino acids by amide bonds. Peptide refers to polypeptides and proteins.
“Pharmaceutical agent” means a substance that provides a therapeutic benefit when administered to an individual. For example, in certain embodiments, an antisense oligonucleotide targeted to PTP1B is pharmaceutical agent.
“Pharmaceutical composition” means a mixture of substances suitable for administering to an individual. For example, a pharmaceutical composition can comprise one or more active agents and a sterile aqueous solution.
“Pharmaceutically acceptable carrier” means a medium or diluent that does not interfere with the structure of the oligonucleotide. Certain, of such carries enable pharmaceutical compositions to be formulated as, for example, tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspension and lozenges for the oral ingestion by a subject. For example, a pharmaceutically acceptable carrier can be a sterile aqueous solution.
“Pharmaceutically acceptable derivative” encompasses pharmaceutically acceptable salts, conjugates, prodrugs or isomers of the compounds described herein.
“Pharmaceutically acceptable salts” means physiologically and pharmaceutically acceptable salts of antisense compounds, i.e., salts that retain the desired biological activity of the parent oligonucleotide and do not impart undesired toxicological effects thereto.
“Phosphorothioate linkage” means a linkage between nucleosides where the phosphodiester bond is modified by replacing one of the non-bridging oxygen atoms with a sulfur atom. A phosphorothioate linkage is a modified internucleoside linkage.
“Portion” means a defined number of contiguous (i.e. linked) nucleobases of a nucleic acid. In certain embodiments, a portion is a defined number of contiguous nucleobases of a target nucleic acid. In certain embodiments, a portion is a defined number of contiguous nucleobases of an antisense compound.
“Prevent” refers to delaying or forestalling the onset or development of a disease, disorder, or condition for a period of time from minutes to indefinitely. Prevent also means reducing risk of developing a disease, disorder, or condition.
“Prodrug” means a therapeutic agent that is prepared in an inactive form that is converted to an active form within the body or cells thereof by the action of endogenous enzymes or other chemicals or conditions.
“Protein tyrosine phosphatase 1B” or “PTP1B” (also known as PTPN1; protein tyrosine phosphatase, non-receptor type 1; PTP-1B; RKPTP) means any nucleic acid or protein of PTP1B.
“PTP1B expression” means the level of mRNA transcribed from the gene encoding PTP or the level of protein translated from the mRNA. PTP1B expression can be determined by art known methods such as a Northern or Western blot.
“PTP1B nucleic acid” means any nucleic acid encoding PTP1B. For example, in certain embodiments, a PTP1B nucleic acid includes a DNA sequence encoding PTP1B, a RNA sequence transcribed from DNA encoding PTP1B (including genomic DNA comprising introns and exons), and a mRNA sequence encoding PTP1B. “PTP1B mRNA” means a mRNA encoding a PTP1B protein.
“Side effects” means physiological responses attributable to a treatment other than the desired effects. In certain embodiments, side effects include injection site reactions, liver function test abnormalities, renal function abnormalities, liver toxicity, renal toxicity, central nervous system abnormalities, myopathies, and malaise. For example, increased aminotransferase levels in serum can indicate liver toxicity or liver function abnormality. For example, increased bilirubin can indicate liver toxicity or liver function abnormality.
“Single-stranded oligonucleotide” means an oligonucleotide which is not hybridized to a complementary strand.
“Specifically hybridizable” refers to an antisense compound having a sufficient degree of complementarity between an antisense oligonucleotide and a target nucleic acid to induce a desired effect, while exhibiting minimal or no effects on non-target nucleic acids under conditions in which specific binding is desired, i.e. under physiological conditions in the case of in vivo assays and therapeutic treatments.
“Statin” means an agent that inhibits the activity of HMG-CoA reductase.
“Subcutaneous administration” means administration just below the skin.
As used herein, “sugar moiety” means a naturally occurring sugar moiety or a modified sugar moiety of a nucleoside.
As used herein, “substituted sugar moiety” means a furanosyl that is not a naturally occurring sugar moiety. Substituted sugar moieties include, but are not limited to furanosyls comprising substituents at the 2′-position, the 3′-position, the 5′-position and/or the 4′-position. Certain substituted sugar moieties are bicyclic sugar moieties.
As used herein the term “sugar surrogate” means a structure that does not comprise a furanosyl and that is capable of replacing the naturally occurring sugar moiety of a nucleoside, such that the resulting nucleoside sub-units are capable of linking together and/or linking to other nucleosides to form an oligomeric compound which is capable of hybridizing to a complementary oligomeric compound. Such structures include rings comprising a different number of atoms than furanosyl (e.g., 4, 6, or 7-membered rings); replacement of the oxygen of a furanosyl with a non-oxygen atom (e.g., carbon, sulfur, or nitrogen); or both a change in the number of atoms and a replacement of the oxygen. Such structures may also comprise substitutions corresponding to those described for substituted sugar moieties (e.g., 6-membered carbocyclic bicyclic sugar surrogates optionally comprising additional substituents). Sugar surrogates also include more complex sugar replacements (e.g., the non-ring systems of peptide nucleic acid). Sugar surrogates include without limitation morpholines, cyclohexenyls and cyclohexitols.
“Targeting” or “targeted” means the process of design and selection of an antisense compound that will specifically hybridize to a target nucleic acid and induce a desired effect.
“Target nucleic acid,” “target RNA,” and “target RNA transcript” all refer to a nucleic acid capable of being targeted by antisense compounds.
“Target segment” means the sequence of nucleotides of a target nucleic acid to which an antisense compound is targeted. “5′ target site” refers to the 5′-most nucleotide of a target segment. “3′ target site” refers to the 3′-most nucleotide of a target segment.
“Therapeutically effective amount” means an amount of an agent that provides a therapeutic benefit to an individual.
“Therapeutic lifestyle change” means dietary and lifestyle changes intended to lower fat/adipose tissue mass and/or cholesterol. Such change can reduce the risk of developing heart disease, and may includes recommendations for dietary intake of total daily calories, total fat, saturated fat, polyunsaturated fat, monounsaturated fat, carbohydrate, protein, cholesterol, insoluble fiber, as well as recommendations for physical activity.
“Triglyceride” or “TG” means a lipid or neutral fat consisting of glycerol combined with three fatty acid molecules.
“Type 2 diabetes,” (also known as “type 2 diabetes mellitus” or “diabetes mellitus, type 2”, and formerly called “diabetes mellitus type 2”, “non-insulin-dependent diabetes (NIDDM)”, “obesity related diabetes”, or “adult-onset diabetes”) is a metabolic disorder that is primarily characterized by insulin resistance, relative insulin deficiency, and hyperglycemia.
“Treat” refers to administering a pharmaceutical composition to an animal to effect an alteration or improvement of a disease, disorder, or condition.
As used herein the terms, “unmodified nucleobase” or “naturally occurring nucleobase” means the naturally occurring heterocyclic nucleobases of RNA or DNA: the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) (including 5-methyl C), and uracil (U).
“Unmodified nucleotide” means a nucleotide composed of naturally occurring nucleobases, sugar moieties, and internucleoside linkages. In certain embodiments, an unmodified nucleotide is an RNA nucleotide (i.e. β-D-ribonucleosides) or a DNA nucleotide (i.e. β-D-deoxyribonucleoside).
As used herein, “2′-substituted nucleoside” means a nucleoside comprising a substituent at the 2′-position other than H or OH. Unless otherwise indicated, a 2′-substituted nucleoside is not a bicyclic nucleoside.
As used herein, “deoxynucleoside” means a nucleoside comprising 2′-H furanosyl sugar moiety, as found in naturally occurring deoxyribonucleosides (DNA). In certain embodiments, a 2′-deoxynucleoside may comprise a modified nucleobase or may comprise an RNA nucleobase (e.g., uracil).
As used herein, “oligonucleotide” means a compound comprising a plurality of linked nucleosides. In certain embodiments, an oligonucleotide comprises one or more unmodified ribonucleosides (RNA) and/or unmodified deoxyribonucleosides (DNA) and/or one or more modified nucleosides.
As used herein “oligonucleoside” means an oligonucleotide in which none of the internucleoside linkages contains a phosphorus atom. As used herein, oligonucleotides include oligonucleosides.
As used herein, “modified oligonucleotide” means an oligonucleotide comprising at least one modified nucleoside and/or at least one modified internucleoside linkage.
As used herein, “linkage” or “linking group” means a group of atoms that link together two or more other groups of atoms.
As used herein “internucleoside linkage” means a covalent linkage between adjacent nucleosides in an oligonucleotide.
As used herein “naturally occurring internucleoside linkage” means a 3′ to 5′ phosphodiester linkage.
As used herein, “modified internucleoside linkage” means any internucleoside linkage other than a naturally occurring internucleoside linkage.
As used herein, “terminal internucleoside linkage” means the linkage between the last two nucleosides of an oligonucleotide or defined region thereof.
As used herein, “phosphorus linking group” means a linking group comprising a phosphorus atom. Phosphorus linking groups include without limitation groups having the formula:




wherein:

Ra and Rd are each, independently, O, S, CH2, NH, or NJ1 wherein J1 is C1-C6 alkyl or substituted C1-C6 alkyl;
Rb is O or S;
Rc is OH, SH, C1-C6 alkyl, substituted C1-C6 alkyl, C1-C6 alkoxy, substituted C1-C6 alkoxy, amino or substituted amino; and
J1 is Rb is O or S.
Phosphorus linking groups include without limitation, phosphodiester, phosphorothioate, phosphorodithioate, phosphonate, phosphoramidate, phosphorothioamidate, thionoalkylphosphonate, phosphotriesters, thionoalkylphosphotriester and boranophosphate.
As used herein, “internucleoside phosphorus linking group” means a phosphorus linking group that directly links two nucleosides.
As used herein, “non-internucleoside phosphorus linking group” means a phosphorus linking group that does not directly link two nucleosides. In certain embodiments, a non-internucleoside phosphorus linking group links a nucleoside to a group other than a nucleoside. In certain embodiments, a non-internucleoside phosphorus linking group links two groups, neither of which is a nucleoside.
As used herein, “neutral linking group” means a linking group that is not charged. Neutral linking groups include without limitation phosphotriesters, methylphosphonates, MMI (—CH2—N(CH3)—O—), amide-3 (—CH2—C(═O)—N(H)—), amide-4 (—CH2—N(H)—C(═O)—), formacetal (—O—CH2—O—), and thioformacetal (—S—CH2—O—). Further neutral linking groups include nonionic linkages comprising siloxane (dialkylsiloxane), carboxylate ester, carboxamide, sulfide, sulfonate ester and amides (See for example: Carbohydrate Modifications in Antisense Research; Y. S. Sanghvi and P. D. Cook Eds. ACS Symposium Series 580; Chapters 3 and 4, (pp. 40-65)). Further neutral linking groups include nonionic linkages comprising mixed N, O, S and CH2 component parts.
As used herein, “internucleoside neutral linking group” means a neutral linking group that directly links two nucleosides.
As used herein, “non-internucleoside neutral linking group” means a neutral linking group that does not directly link two nucleosides. In certain embodiments, a non-internucleoside neutral linking group links a nucleoside to a group other than a nucleoside. In certain embodiments, a non-internucleoside neutral linking group links two groups, neither of which is a nucleoside.
As used herein, “oligomeric compound” means a polymeric structure comprising two or more sub-structures. In certain embodiments, an oligomeric compound comprises an oligonucleotide. In certain embodiments, an oligomeric compound comprises one or more conjugate groups and/or terminal groups. In certain embodiments, an oligomeric compound consists of an oligonucleotide. Oligomeric compounds also include naturally occurring nucleic acids. In certain embodiments, an oligomeric compound comprises a backbone of one or more linked monomeric subunits where each linked monomeric subunit is directly or indirectly attached to a heterocyclic base moiety. In certain embodiments, oligomeric compounds may also include monomeric subunits that are not linked to a heterocyclic base moiety, thereby providing abasic sites. In certain embodiments, the linkages joining the monomeric subunits, the sugar moieties or surrogates and the heterocyclic base moieties can be independently modified. In certain embodiments, the linkage-sugar unit, which may or may not include a heterocyclic base, may be substituted with a mimetic such as the monomers in peptide nucleic acids.
As used herein, “terminal group” means one or more atom attached to either, or both, the 3′ end or the 5′ end of an oligonucleotide. In certain embodiments a terminal group is a conjugate group. In certain embodiments, a terminal group comprises one or more terminal group nucleosides.
As used herein, “conjugate” or “conjugate group” means an atom or group of atoms bound to an oligonucleotide or oligomeric compound. In general, conjugate groups modify one or more properties of the compound to which they are attached, including, but not limited to pharmacodynamic, pharmacokinetic, binding, absorption, cellular distribution, cellular uptake, charge and/or clearance properties.
As used herein, “conjugate linker” or “linker” in the context of a conjugate group means a portion of a conjugate group comprising any atom or group of atoms and which covalently link (1) an oligonucleotide to another portion of the conjugate group or (2) two or more portions of the conjugate group.
Conjugate groups are shown herein as radicals, providing a bond for forming covalent attachment to an oligomeric compound such as an antisense oligonucleotide. In certain embodiments, the point of attachment on the oligomeric compound is the 3′-oxygen atom of the 3′-hydroxyl group of the 3′ terminal nucleoside of the oligomeric compound. In certain embodiments the point of attachment on the oligomeric compound is the 5′-oxygen atom of the 5′-hydroxyl group of the 5′ terminal nucleoside of the oligomeric compound. In certain embodiments, the bond for forming attachment to the oligomeric compound is a cleavable bond. In certain such embodiments, such cleavable bond constitutes all or part of a cleavable moiety.
In certain embodiments, conjugate groups comprise a cleavable moiety (e.g., a cleavable bond or cleavable nucleoside) and a carbohydrate cluster portion, such as a GalNAc cluster portion. Such carbohydrate cluster portion comprises: a targeting moiety and, optionally, a conjugate linker. In certain embodiments, the carbohydrate cluster portion is identified by the number and identity of the ligand. For example, in certain embodiments, the carbohydrate cluster portion comprises 3 GalNAc groups and is designated “GalNAc3”. In certain embodiments, the carbohydrate cluster portion comprises 4 GalNAc groups and is designated “GalNAc4”. Specific carbohydrate cluster portions (having specific tether, branching and conjugate linker groups) are described herein and designated by Roman numeral followed by subscript “a”. Accordingly “GalNac3-1,” refers to a specific carbohydrate cluster portion of a conjugate group having 3 GalNac groups and specifically identified tether, branching and linking groups. Such carbohydrate cluster fragment is attached to an oligomeric compound via a cleavable moiety, such as a cleavable bond or cleavable nucleoside.
As used herein, “cleavable moiety” means a bond or group that is capable of being split under physiological conditions. In certain embodiments, a cleavable moiety is cleaved inside a cell or sub-cellular compartments, such as a lysosome. In certain embodiments, a cleavable moiety is cleaved by endogenous enzymes, such as nucleases. In certain embodiments, a cleavable moiety comprises a group of atoms having one, two, three, four, or more than four cleavable bonds.
As used herein, “cleavable bond” means any chemical bond capable of being split. In certain embodiments, a cleavable bond is selected from among: an amide, a polyamide, an ester, an ether, one or both esters of a phosphodiester, a phosphate ester, a carbamate, a di-sulfide, or a peptide.
As used herein, “carbohydrate cluster” means a compound having one or more carbohydrate residues attached to a scaffold or linker group. (see, e.g., Maier et al., “Synthesis of Antisense Oligonucleotides Conjugated to a Multivalent Carbohydrate Cluster for Cellular Targeting,” Bioconjugate Chemistry, 2003, (14): 18-29, which is incorporated herein by reference in its entirety, or Rensen et al., “Design and Synthesis of Novel N-Acetylgalactosamine-Terminated Glycolipids for Targeting of Lipoproteins to the Hepatic Asiaglycoprotein Receptor,” J. Med. Chem. 2004, (47): 5798-5808, for examples of carbohydrate conjugate clusters).
As used herein, “modified carbohydrate” means any carbohydrate having one or more chemical modifications relative to naturally occurring carbohydrates.
As used herein, “carbohydrate derivative” means any compound which may be synthesized using a carbohydrate as a starting material or intermediate.
As used herein, “carbohydrate” means a naturally occurring carbohydrate, a modified carbohydrate, or a carbohydrate derivative.
As used herein “protecting group” means any compound or protecting group known to those having skill in the art. Non-limiting examples of protecting groups may be found in “Protective Groups in Organic Chemistry”, T. W. Greene, P. G. M. Wuts, ISBN 0-471-62301-6, John Wiley & Sons, Inc, New York, which is incorporated herein by reference in its entirety.
As used herein, “single-stranded” means an oligomeric compound that is not hybridized to its complement and which lacks sufficient self-complementarity to form a stable self-duplex.
As used herein, “double stranded” means a pair of oligomeric compounds that are hybridized to one another or a single self-complementary oligomeric compound that forms a hairpin structure. In certain embodiments, a double-stranded oligomeric compound comprises a first and a second oligomeric compound.
As used herein, “antisense compound” means a compound comprising or consisting of an oligonucleotide at least a portion of which is complementary to a target nucleic acid to which it is capable of hybridizing, resulting in at least one antisense activity.
As used herein, “antisense activity” means any detectable and/or measurable change attributable to the hybridization of an antisense compound to its target nucleic acid. In certain embodiments, antisense activity includes modulation of the amount or activity of a target nucleic acid transcript (e.g. mRNA). In certain embodiments, antisense activity includes modulation of the splicing of pre-mRNA.
As used herein, “RNase H based antisense compound” means an antisense compound wherein at least some of the antisense activity of the antisense compound is attributable to hybridization of the antisense compound to a target nucleic acid and subsequent cleavage of the target nucleic acid by RNase H.
As used herein, “RISC based antisense compound” means an antisense compound wherein at least some of the antisense activity of the antisense compound is attributable to the RNA Induced Silencing Complex (RISC).
As used herein, “detecting” or “measuring” means that a test or assay for detecting or measuring is performed. Such detection and/or measuring may result in a value of zero. Thus, if a test for detection or measuring results in a finding of no activity (activity of zero), the step of detecting or measuring the activity has nevertheless been performed.
As used herein, “detectable and/or measurable activity” means a statistically significant activity that is not zero.
As used herein, “essentially unchanged” means little or no change in a particular parameter, particularly relative to another parameter which changes much more. In certain embodiments, a parameter is essentially unchanged when it changes less than 5%. In certain embodiments, a parameter is essentially unchanged if it changes less than two-fold while another parameter changes at least ten-fold. For example, in certain embodiments, an antisense activity is a change in the amount of a target nucleic acid. In certain such embodiments, the amount of a non-target nucleic acid is essentially unchanged if it changes much less than the target nucleic acid does, but the change need not be zero.
As used herein, “expression” means the process by which a gene ultimately results in a protein. Expression includes, but is not limited to, transcription, post-transcriptional modification (e.g., splicing, polyadenlyation, addition of 5′-cap), and translation.
As used herein, “target nucleic acid” means a nucleic acid molecule to which an antisense compound is intended to hybridize to result in a desired antisense activity. Antisense oligonucleotides have sufficient complementarity to their target nucleic acids to allow hybridization under physiological conditions.
As used herein, “nucleobase complementarity” or “complementarity” when in reference to nucleobases means a nucleobase that is capable of base pairing with another nucleobase. For example, in DNA, adenine (A) is complementary to thymine (T). For example, in RNA, adenine (A) is complementary to uracil (U). In certain embodiments, complementary nucleobase means a nucleobase of an antisense compound that is capable of base pairing with a nucleobase of its target nucleic acid. For example, if a nucleobase at a certain position of an antisense compound is capable of hydrogen bonding with a nucleobase at a certain position of a target nucleic acid, then the position of hydrogen bonding between the oligonucleotide and the target nucleic acid is considered to be complementary at that nucleobase pair. Nucleobases comprising certain modifications may maintain the ability to pair with a counterpart nucleobase and thus, are still capable of nucleobase complementarity.
As used herein, “non-complementary” in reference to nucleobases means a pair of nucleobases that do not form hydrogen bonds with one another.
As used herein, “complementary” in reference to oligomeric compounds (e.g., linked nucleosides, oligonucleotides, or nucleic acids) means the capacity of such oligomeric compounds or regions thereof to hybridize to another oligomeric compound or region thereof through nucleobase complementarity. Complementary oligomeric compounds need not have nucleobase complementarity at each nucleoside. Rather, some mismatches are tolerated. In certain embodiments, complementary oligomeric compounds or regions are complementary at 70% of the nucleobases (70% complementary). In certain embodiments, complementary oligomeric compounds or regions are 80% complementary. In certain embodiments, complementary oligomeric compounds or regions are 90% complementary. In certain embodiments, complementary oligomeric compounds or regions are 95% complementary. In certain embodiments, complementary oligomeric compounds or regions are 100% complementary.
As used herein, “mismatch” means a nucleobase of a first oligomeric compound that is not capable of pairing with a nucleobase at a corresponding position of a second oligomeric compound, when the first and second oligomeric compound are aligned. Either or both of the first and second oligomeric compounds may be oligonucleotides.
As used herein, “hybridization” means the pairing of complementary oligomeric compounds (e.g., an antisense compound and its target nucleic acid). While not limited to a particular mechanism, the most common mechanism of pairing involves hydrogen bonding, which may be Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding, between complementary nucleobases.
As used herein, “specifically hybridizes” means the ability of an oligomeric compound to hybridize to one nucleic acid site with greater affinity than it hybridizes to another nucleic acid site.
As used herein, “fully complementary” in reference to an oligonucleotide or portion thereof means that each nucleobase of the oligonucleotide or portion thereof is capable of pairing with a nucleobase of a complementary nucleic acid or contiguous portion thereof. Thus, a fully complementary region comprises no mismatches or unhybridized nucleobases in either strand.
As used herein, “percent complementarity” means the percentage of nucleobases of an oligomeric compound that are complementary to an equal-length portion of a target nucleic acid. Percent complementarity is calculated by dividing the number of nucleobases of the oligomeric compound that are complementary to nucleobases at corresponding positions in the target nucleic acid by the total length of the oligomeric compound.
As used herein, “percent identity” means the number of nucleobases in a first nucleic acid that are the same type (independent of chemical modification) as nucleobases at corresponding positions in a second nucleic acid, divided by the total number of nucleobases in the first nucleic acid.
As used herein, “modulation” means a change of amount or quality of a molecule, function, or activity when compared to the amount or quality of a molecule, function, or activity prior to modulation. For example, modulation includes the change, either an increase (stimulation or induction) or a decrease (inhibition or reduction) in gene expression. As a further example, modulation of expression can include a change in splice site selection of pre-mRNA processing, resulting in a change in the absolute or relative amount of a particular splice-variant compared to the amount in the absence of modulation.
As used herein, “chemical motif” means a pattern of chemical modifications in an oligonucleotide or a region thereof. Motifs may be defined by modifications at certain nucleosides and/or at certain linking groups of an oligonucleotide.
As used herein, “nucleoside motif” means a pattern of nucleoside modifications in an oligonucleotide or a region thereof. The linkages of such an oligonucleotide may be modified or unmodified. Unless otherwise indicated, motifs herein describing only nucleosides are intended to be nucleoside motifs. Thus, in such instances, the linkages are not limited.
As used herein, “sugar motif” means a pattern of sugar modifications in an oligonucleotide or a region thereof.
As used herein, “linkage motif” means a pattern of linkage modifications in an oligonucleotide or region thereof. The nucleosides of such an oligonucleotide may be modified or unmodified. Unless otherwise indicated, motifs herein describing only linkages are intended to be linkage motifs. Thus, in such instances, the nucleosides are not limited.
As used herein, “nucleobase modification motif” means a pattern of modifications to nucleobases along an oligonucleotide. Unless otherwise indicated, a nucleobase modification motif is independent of the nucleobase sequence.
As used herein, “sequence motif” means a pattern of nucleobases arranged along an oligonucleotide or portion thereof. Unless otherwise indicated, a sequence motif is independent of chemical modifications and thus may have any combination of chemical modifications, including no chemical modifications.
As used herein, “type of modification” in reference to a nucleoside or a nucleoside of a “type” means the chemical modification of a nucleoside and includes modified and unmodified nucleosides. Accordingly, unless otherwise indicated, a “nucleoside having a modification of a first type” may be an unmodified nucleoside.
As used herein, “differently modified” mean chemical modifications or chemical substituents that are different from one another, including absence of modifications. Thus, for example, a MOE nucleoside and an unmodified DNA nucleoside are “differently modified,” even though the DNA nucleoside is unmodified. Likewise, DNA and RNA are “differently modified,” even though both are naturally-occurring unmodified nucleosides. Nucleosides that are the same but for comprising different nucleobases are not differently modified. For example, a nucleoside comprising a 2′-OMe modified sugar and an unmodified adenine nucleobase and a nucleoside comprising a 2′-OMe modified sugar and an unmodified thymine nucleobase are not differently modified.
As used herein, “the same type of modifications” refers to modifications that are the same as one another, including absence of modifications. Thus, for example, two unmodified DNA nucleosides have “the same type of modification,” even though the DNA nucleoside is unmodified. Such nucleosides having the same type modification may comprise different nucleobases.
As used herein, “separate regions” means portions of an oligonucleotide wherein the chemical modifications or the motif of chemical modifications of any neighboring portions include at least one difference to allow the separate regions to be distinguished from one another.
As used herein, “pharmaceutically acceptable carrier or diluent” means any substance suitable for use in administering to an animal. In certain embodiments, a pharmaceutically acceptable carrier or diluent is sterile saline. In certain embodiments, such sterile saline is pharmaceutical grade saline.
As used herein the term “metabolic disorder” means a disease or condition principally characterized by dysregulation of metabolism—the complex set of chemical reactions associated with breakdown of food to produce energy.
As used herein, the term “cardiovascular disorder” means a disease or condition principally characterized by impaired function of the heart or blood vessels.
As used herein the term “mono or polycyclic ring system” is meant to include all ring systems selected from single or polycyclic radical ring systems wherein the rings are fused or linked and is meant to be inclusive of single and mixed ring systems individually selected from aliphatic, alicyclic, aryl, heteroaryl, aralkyl, arylalkyl, heterocyclic, heteroaryl, heteroaromatic and heteroarylalkyl. Such mono and poly cyclic structures can contain rings that each have the same level of saturation or each, independently, have varying degrees of saturation including fully saturated, partially saturated or fully unsaturated. Each ring can comprise ring atoms selected from C, N, O and S to give rise to heterocyclic rings as well as rings comprising only C ring atoms which can be present in a mixed motif such as for example benzimidazole wherein one ring has only carbon ring atoms and the fused ring has two nitrogen atoms. The mono or polycyclic ring system can be further substituted with substituent groups such as for example phthalimide which has two ═O groups attached to one of the rings. Mono or polycyclic ring systems can be attached to parent molecules using various strategies such as directly through a ring atom, fused through multiple ring atoms, through a substituent group or through a bifunctional linking moiety.
As used herein, “prodrug” means an inactive or less active form of a compound which, when administered to a subject, is metabolized to form the active, or more active, compound (e.g., drug).
As used herein, “substituent” and “substituent group,” means an atom or group that replaces the atom or group of a named parent compound. For example a substituent of a modified nucleoside is any atom or group that differs from the atom or group found in a naturally occurring nucleoside (e.g., a modified 2′-substituent is any atom or group at the 2′-position of a nucleoside other than H or OH). Substituent groups can be protected or unprotected. In certain embodiments, compounds of the present disclosure have substituents at one or at more than one position of the parent compound. Substituents may also be further substituted with other substituent groups and may be attached directly or via a linking group such as an alkyl or hydrocarbyl group to a parent compound.
Likewise, as used herein, “substituent” in reference to a chemical functional group means an atom or group of atoms that differs from the atom or a group of atoms normally present in the named functional group. In certain embodiments, a substituent replaces a hydrogen atom of the functional group (e.g., in certain embodiments, the substituent of a substituted methyl group is an atom or group other than hydrogen which replaces one of the hydrogen atoms of an unsubstituted methyl group). Unless otherwise indicated, groups amenable for use as substituents include without limitation, halogen, hydroxyl, alkyl, alkenyl, alkynyl, acyl (—C(O)Raa), carboxyl (—C(O)O—Raa), aliphatic groups, alicyclic groups, alkoxy, substituted oxy (—O—Raa), aryl, aralkyl, heterocyclic radical, heteroaryl, heteroarylalkyl, amino (—N(Rbb)(Rcc)), imino(═NRbb), amido (—C(O)N(Rbb)(Rcc) or —N(Rbb)C(O)Raa), azido (—N3), nitro (—NO2), cyano (—CN), carbamido (—OC(O)N(Rbb)(Rcc) or —N(Rbb)C(O)ORaa), ureido (—N(Rbb)C(O)N(Rbb)(Rcc)), thioureido (—N(Rbb)C(S)N(Rbb)—(Rcc)), guanidinyl (—N(Rbb)C(═NRbb)N(Rbb)(Rcc)), amidinyl (—C(═NRbb)N(Rbb)(Rcc) or —N(Rbb)C(═NRbb)(Raa)), thiol (—SRbb), sulfinyl (—S(O)Rbb), sulfonyl (—S(O)2Rbb) and sulfonamidyl (—S(O)2N(Rbb)(Rcc) or —N(Rbb)S—(O)2Rbb). Wherein each Raa, Rbb and Rcc is, independently, H, an optionally linked chemical functional group or a further substituent group with a preferred list including without limitation, alkyl, alkenyl, alkynyl, aliphatic, alkoxy, acyl, aryl, aralkyl, heteroaryl, alicyclic, heterocyclic and heteroarylalkyl. Selected substituents within the compounds described herein are present to a recursive degree.
As used herein, “alkyl,” as used herein, means a saturated straight or branched hydrocarbon radical containing up to twenty four carbon atoms. Examples of alkyl groups include without limitation, methyl, ethyl, propyl, butyl, isopropyl, n-hexyl, octyl, decyl, dodecyl and the like. Alkyl groups typically include from 1 to about 24 carbon atoms, more typically from 1 to about 12 carbon atoms (C1-C12alkyl) with from 1 to about 6 carbon atoms being more preferred.
As used herein, “alkenyl,” means a straight or branched hydrocarbon chain radical containing up to twenty four carbon atoms and having at least one carbon-carbon double bond. Examples of alkenyl groups include without limitation, ethenyl, propenyl, butenyl, 1-methyl-2-buten-1-yl, dienes such as 1,3-butadiene and the like. Alkenyl groups typically include from 2 to about 24 carbon atoms, more typically from 2 to about 12 carbon atoms with from 2 to about 6 carbon atoms being more preferred. Alkenyl groups as used herein may optionally include one or more further substituent groups.
As used herein, “alkynyl,” means a straight or branched hydrocarbon radical containing up to twenty four carbon atoms and having at least one carbon-carbon triple bond. Examples of alkynyl groups include, without limitation, ethynyl, 1-propynyl, 1-butynyl, and the like. Alkynyl groups typically include from 2 to about 24 carbon atoms, more typically from 2 to about 12 carbon atoms with from 2 to about 6 carbon atoms being more preferred. Alkynyl groups as used herein may optionally include one or more further substituent groups.
As used herein, “acyl,” means a radical formed by removal of a hydroxyl group from an organic acid and has the general Formula —C(O)—X where X is typically aliphatic, alicyclic or aromatic. Examples include aliphatic carbonyls, aromatic carbonyls, aliphatic sulfonyls, aromatic sulfinyls, aliphatic sulfinyls, aromatic phosphates, aliphatic phosphates and the like. Acyl groups as used herein may optionally include further substituent groups.
As used herein, “alicyclic” means a cyclic ring system wherein the ring is aliphatic. The ring system can comprise one or more rings wherein at least one ring is aliphatic. Preferred alicyclics include rings having from about 5 to about 9 carbon atoms in the ring. Alicyclic as used herein may optionally include further substituent groups.
As used herein, “aliphatic” means a straight or branched hydrocarbon radical containing up to twenty four carbon atoms wherein the saturation between any two carbon atoms is a single, double or triple bond. An aliphatic group preferably contains from 1 to about 24 carbon atoms, more typically from 1 to about 12 carbon atoms with from 1 to about 6 carbon atoms being more preferred. The straight or branched chain of an aliphatic group may be interrupted with one or more heteroatoms that include nitrogen, oxygen, sulfur and phosphorus. Such aliphatic groups interrupted by heteroatoms include without limitation, polyalkoxys, such as polyalkylene glycols, polyamines, and polyimines Aliphatic groups as used herein may optionally include further substituent groups.
As used herein, “alkoxy” means a radical formed between an alkyl group and an oxygen atom wherein the oxygen atom is used to attach the alkoxy group to a parent molecule. Examples of alkoxy groups include without limitation, methoxy, ethoxy, propoxy, isopropoxy, n-butoxy, sec-butoxy, tert-butoxy, n-pentoxy, neopentoxy, n-hexoxy and the like. Alkoxy groups as used herein may optionally include further substituent groups.
As used herein, “aminoalkyl” means an amino substituted C1-C12 alkyl radical. The alkyl portion of the radical forms a covalent bond with a parent molecule. The amino group can be located at any position and the aminoalkyl group can be substituted with a further substituent group at the alkyl and/or amino portions.
As used herein, “aralkyl” and “arylalkyl” mean an aromatic group that is covalently linked to a C1-C12 alkyl radical. The alkyl radical portion of the resulting aralkyl (or arylalkyl) group forms a covalent bond with a parent molecule. Examples include without limitation, benzyl, phenethyl and the like. Aralkyl groups as used herein may optionally include further substituent groups attached to the alkyl, the aryl or both groups that form the radical group.
As used herein, “aryl” and “aromatic” mean a mono- or polycyclic carbocyclic ring system radicals having one or more aromatic rings. Examples of aryl groups include without limitation, phenyl, naphthyl, tetrahydronaphthyl, indanyl, idenyl and the like. Preferred aryl ring systems have from about 5 to about 20 carbon atoms in one or more rings. Aryl groups as used herein may optionally include further substituent groups.
As used herein, “halo” and “halogen,” mean an atom selected from fluorine, chlorine, bromine and iodine.
As used herein, “heteroaryl,” and “heteroaromatic,” mean a radical comprising a mono- or poly-cyclic aromatic ring, ring system or fused ring system wherein at least one of the rings is aromatic and includes one or more heteroatoms. Heteroaryl is also meant to include fused ring systems including systems where one or more of the fused rings contain no heteroatoms. Heteroaryl groups typically include one ring atom selected from sulfur, nitrogen or oxygen. Examples of heteroaryl groups include without limitation, pyridinyl, pyrazinyl, pyrimidinyl, pyrrolyl, pyrazolyl, imidazolyl, thiazolyl, oxazolyl, isooxazolyl, thiadiazolyl, oxadiazolyl, thiophenyl, furanyl, quinolinyl, isoquinolinyl, benzimidazolyl, benzooxazolyl, quinoxalinyl and the like. Heteroaryl radicals can be attached to a parent molecule directly or through a linking moiety such as an aliphatic group or hetero atom. Heteroaryl groups as used herein may optionally include further substituent groups.
As used herein, “conjugate compound” means any atoms, group of atoms, or group of linked atoms suitable for use as a conjugate group. In certain embodiments, conjugate compounds may possess or impart one or more properties, including, but not limited to pharmacodynamic, pharmacokinetic, binding, absorption, cellular distribution, cellular uptake, charge and/or clearance properties.
As used herein, unless otherwise indicated or modified, the term “double-stranded” refers to two separate oligomeric compounds that are hybridized to one another. Such double stranded compounds may have one or more or non-hybridizing nucleosides at one or both ends of one or both strands (overhangs) and/or one or more internal non-hybridizing nucleosides (mismatches) provided there is sufficient complementarity to maintain hybridization under physiologically relevant conditions.
B. Certain Compounds
In certain embodiments, the invention provides conjugated antisense compounds comprising antisense oligonucleotides and a conjugate.
a. Certain Antisense Oligonucleotides
In certain embodiments, the invention provides antisense oligonucleotides. Such antisense oligonucleotides comprise linked nucleosides, each nucleoside comprising a sugar moiety and a nucleobase. The structure of such antisense oligonucleotides may be considered in terms of chemical features (e.g., modifications and patterns of modifications) and nucleobase sequence (e.g., sequence of antisense oligonucleotide, identify and sequence of target nucleic acid).
i. Certain Chemistry Features
In certain embodiments, antisense oligonucleotide comprise one or more modification. In certain such embodiments, antisense oligonucleotides comprise one or more modified nucleosides and/or modified internucleoside linkages. In certain embodiments, modified nucleosides comprise a modified sugar moiety and/or modified nucleobase.
1. Certain Sugar Moieties
In certain embodiments, compounds of the disclosure comprise one or more modified nucleosides comprising a modified sugar moiety. Such compounds comprising one or more sugar-modified nucleosides may have desirable properties, such as enhanced nuclease stability or increased binding affinity with a target nucleic acid relative to an oligonucleotide comprising only nucleosides comprising naturally occurring sugar moieties. In certain embodiments, modified sugar moieties are substituted sugar moieties. In certain embodiments, modified sugar moieties are sugar surrogates. Such sugar surrogates may comprise one or more substitutions corresponding to those of substituted sugar moieties.
In certain embodiments, modified sugar moieties are substituted sugar moieties comprising one or more non-bridging sugar substituent, including but not limited to substituents at the 2′ and/or 5′ positions. Examples of sugar substituents suitable for the 2′-position, include, but are not limited to: 2′-F, 2′-OCH3 (“OMe” or “O-methyl”), and 2′-O(CH2)2O CH3 (“MOE”). In certain embodiments, sugar substituents at the 2′ position is selected from allyl, amino, azido, thio, O-allyl, O—C1-C10 alkyl, O—C1-C10 substituted alkyl; OCF3, O(CH2)2SCH3, O(CH2)2—O—N(Rm)(Rn), and O—CH2—C(═O)—N(Rm)(Rn), where each Rm and Rn is, independently, H or substituted or unsubstituted C1-C10 alkyl. Examples of sugar substituents at the 5′-position, include, but are not limited to: 5′-methyl (R or S); 5′-vinyl, and 5′-methoxy. In certain embodiments, substituted sugars comprise more than one non-bridging sugar substituent, for example, 2′-F-5′-methyl sugar moieties (see, e.g., PCT International Application WO 2008/101157, for additional 5′,2′-bis substituted sugar moieties and nucleosides).
Nucleosides comprising 2′-substituted sugar moieties are referred to as 2′-substituted nucleosides. In certain embodiments, a 2′-substituted nucleoside comprises a 2′-substituent group selected from halo, allyl, amino, azido, SH, CN, OCN, CF3, OCF3, O, S, or N(Rm)-alkyl; O, S, or N(Rm)-alkenyl; O, S or N(Rm)-alkynyl; O-alkylenyl-O-alkyl, alkynyl, alkaryl, aralkyl, O-alkaryl, O-aralkyl, O(CH2)2SCH3, O—(CH2)2—O—N(Rm)(Rn) or O—CH2—C(═O)—N(Rm)(Rn), where each Rm and Rn is, independently, H, an amino protecting group or substituted or unsubstituted C1-C10 alkyl. These 2′-substituent groups can be further substituted with one or more substituent groups independently selected from hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro (NO2), thiol, thioalkoxy (S-alkyl), halogen, alkyl, aryl, alkenyl and alkynyl.
In certain embodiments, a 2′-substituted nucleoside comprises a 2′-substituent group selected from F, NH2, N3, OCF3, O—CH3, O(CH2)3NH2, CH2—CH═CH2, O—CH2—CH═CH2, OCH2CH2OCH3, O(CH2)2SCH3, O—(CH2)2—O—N(Rm)(Rn), O(CH2)2O(CH2)2N(CH3)2, and N-substituted acetamide (O—CH2—C(═O)—N(Rm)(Rn) where each Rm and Rn is, independently, H, an amino protecting group or substituted or unsubstituted C1-C10 alkyl.
In certain embodiments, a 2′-substituted nucleoside comprises a sugar moiety comprising a 2′-substituent group selected from F, OCF3, O—CH3, OCH2CH2OCH3, O(CH2)2SCH3, O—(CH2)2—O—N(CH3)2, —O(CH2)2O(CH2)2N(CH3)2, and O—CH2—C(═O)—N(H)CH3.
In certain embodiments, a 2′-substituted nucleoside comprises a sugar moiety comprising a 2′-substituent group selected from F, O—CH3, and OCH2CH2OCH3.
Certain modified sugar moieties comprise a bridging sugar substituent that forms a second ring resulting in a bicyclic sugar moiety. In certain such embodiments, the bicyclic sugar moiety comprises a bridge between the 4′ and the 2′ furanose ring atoms. Examples of such 4′ to 2′ sugar substituents, include, but are not limited to: —[C(Ra)(Rb)]n—, —[C(Ra)(Rb)]n—O—, —C(RaRb)—N(R)—O— or, —C(RaRb)—O—N(R)—; 4′-CH2-2′, 4′-(CH2)2-2′, 4′-(CH2)3-2′, 4′-(CH2)—O-2′ (LNA); 4′-(CH2)—S-2′; 4′-(CH2)2—O-2′ (ENA); 4′-CH(CH3)—O-2′ (cEt) and 4′-CH(CH2OCH3)—O-2′, and analogs thereof (see, e.g., U.S. Pat. No. 7,399,845, issued on Jul. 15, 2008); 4′-C(CH3)(CH3)—O-2′ and analogs thereof, (see, e.g., WO2009/006478, published Jan. 8, 2009); 4′-CH2—N(OCH3)-2′ and analogs thereof (see, e.g., WO2008/150729, published Dec. 11, 2008); 4′-CH2—O—N(CH3)-2′ (see, e.g., US2004/0171570, published Sep. 2, 2004); 4′-CH2—O—N(R)-2′, and 4′-CH2—N(R)—O-2′-, wherein each R is, independently, H, a protecting group, or C1-C12 alkyl; 4′-CH2—N(R)—O-2′, wherein R is H, C1-C12 alkyl, or a protecting group (see, U.S. Pat. No. 7,427,672, issued on Sep. 23, 2008); 4′-CH2—C(H)(CH3)-2′ (see, e.g., Chattopadhyaya, et al., J. Org. Chem., 2009, 74, 118-134); and 4′-CH2—C(═CH2)-2′ and analogs thereof (see, published PCT International Application WO 2008/154401, published on Dec. 8, 2008).
In certain embodiments, such 4′ to 2′ bridges independently comprise from 1 to 4 linked groups independently selected from —[C(Ra)(Rb)]n—, —C(Ra)═C(Rb)—, —C(Ra)═N—, —C(═NRa)—, —C(═O)—, —C(═S)—, —O—, —Si(Ra)2—, —S(═O)x—, and —N(Ra)—;
wherein:
x is 0, 1, or 2;
n is 1, 2, 3, or 4;
each Ra and Rb is, independently, H, a protecting group, hydroxyl, C1-C12 alkyl, substituted C1-C12 alkyl, C2-C12 alkenyl, substituted C2-C12 alkenyl, C2-C12 alkynyl, substituted C2-C12 alkynyl, C5-C20 aryl, substituted C5-C20 aryl, heterocycle radical, substituted heterocycle radical, heteroaryl, substituted heteroaryl, C5-C7 alicyclic radical, substituted C5-C7 alicyclic radical, halogen, OJ1, NJ1J2, SJ1, N3, COOJ1, acyl (C(═O)—H), substituted acyl, CN, sulfonyl (S(═O)2-J1), or sulfoxyl (S(═O)-J1); and
each J1 and J2 is, independently, H, C1-C12 alkyl, substituted C1-C12 alkyl, C2-C12 alkenyl, substituted C2-C12 alkenyl, C2-C12 alkynyl, substituted C2-C12 alkynyl, C5-C20 aryl, substituted C5-C20 aryl, acyl (C(═O)—H), substituted acyl, a heterocycle radical, a substituted heterocycle radical, C1-C12 aminoalkyl, substituted C1-C12 aminoalkyl, or a protecting group.
Nucleosides comprising bicyclic sugar moieties are referred to as bicyclic nucleosides or BNAs. Bicyclic nucleosides include, but are not limited to, (A) α-L-Methyleneoxy (4′-CH2—O-2′) BNA, (B) β-D-Methyleneoxy (4′-CH2—O-2′) BNA (also referred to as locked nucleic acid or LNA), (C) Ethyleneoxy (4′-(CH2)2—O-2′) BNA, (D) Aminooxy (4′-CH2—O—N(R)-2′) BNA, (E) Oxyamino (4′-CH2—N(R)—O-2′) BNA, (F) Methyl(methyleneoxy) (4′-CH(CH3)—O-2′) BNA (also referred to as constrained ethyl or cEt), (G) methylene-thio (4′-CH2—S-2′) BNA, (H) methylene-amino (4′-CH2-N(R)-2′) BNA, (I) methyl carbocyclic (4′-CH2—CH(CH3)-2′) BNA, and (J) propylene carbocyclic (4′-(CH2)3-2′) BNA as depicted below.







wherein Bx is a nucleobase moiety and R is, independently, H, a protecting group, or C1-C12 alkyl.

Additional bicyclic sugar moieties are known in the art, for example: Singh et al., Chem. Commun., 1998, 4, 455-456; Koshkin et al., Tetrahedron, 1998, 54, 3607-3630; Wahlestedt et al., Proc. Natl. Acad. Sci. U.S.A, 2000, 97, 5633-5638; Kumar et al., Bioorg. Med. Chem. Lett., 1998, 8, 2219-2222; Singh et al., J. Org. Chem., 1998, 63, 10035-10039; Srivastava et al., J. Am. Chem. Soc., 129(26) 8362-8379 (Jul. 4, 2007); Elayadi et al., Curr. Opinion Invens. Drugs, 2001, 2, 558-561; Braasch et al., Chem. Biol., 2001, 8, 1-7; Orum et al., Curr. Opinion Mol. Ther., 2001, 3, 239-243; U.S. Pat. Nos. 7,053,207, 6,268,490, 6,770,748, 6,794,499, 7,034,133, 6,525,191, 6,670,461, and 7,399,845; WO 2004/106356, WO 1994/14226, WO 2005/021570, and WO 2007/134181; U.S. Patent Publication Nos. US2004/0171570, US2007/0287831, and US2008/0039618; U.S. patent Ser. No. 12/129,154, U.S. Provisional Applications 60/989,574, 61/026,995, 61/026,998, 61/056,564, 61/086,231, 61/097,787, and 61/099,844; and PCT International Applications Nos. PCT/US2008/064591, PCT/US2008/066154, and PCT/US2008/068922.
In certain embodiments, bicyclic sugar moieties and nucleosides incorporating such bicyclic sugar moieties are further defined by isomeric configuration. For example, a nucleoside comprising a 4′-2′ methylene-oxy bridge, may be in the α-L configuration or in the 3-D configuration. Previously, α-L-methyleneoxy (4′-CH2—O-2′) bicyclic nucleosides have been incorporated into antisense oligonucleotides that showed antisense activity (Frieden et al., Nucleic Acids Research, 2003, 21, 6365-6372).
In certain embodiments, substituted sugar moieties comprise one or more non-bridging sugar substituent and one or more bridging sugar substituent (e.g., 5′-substituted and 4′-2′ bridged sugars). (see, PCT International Application WO 2007/134181, published on Nov. 22, 2007, wherein LNA is substituted with, for example, a 5′-methyl or a 5′-vinyl group).
In certain embodiments, modified sugar moieties are sugar surrogates. In certain such embodiments, the oxygen atom of the naturally occurring sugar is substituted, e.g., with a sulfur, carbon or nitrogen atom. In certain such embodiments, such modified sugar moiety also comprises bridging and/or non-bridging substituents as described above. For example, certain sugar surrogates comprise a 4′-sulfur atom and a substitution at the 2′-position (see, e.g., published U.S. Patent Application US2005/0130923, published on Jun. 16, 2005) and/or the 5′ position. By way of additional example, carbocyclic bicyclic nucleosides having a 4′-2′ bridge have been described (see, e.g., Freier et al., Nucleic Acids Research, 1997, 25(22), 4429-4443 and Albaek et al., J. Org. Chem., 2006, 71, 7731-7740).
In certain embodiments, sugar surrogates comprise rings having other than 5-atoms. For example, in certain embodiments, a sugar surrogate comprises a morpholino. Morpholino compounds and their use in oligomeric compounds has been reported in numerous patents and published articles (see for example: Braasch et al., Biochemistry, 2002, 41, 4503-4510; and U.S. Pat. Nos. 5,698,685; 5,166,315; 5,185,444; and 5,034,506). As used here, the term “morpholino” means a sugar surrogate having the following structure:




In certain embodiments, morpholinos may be modified, for example by adding or altering various substituent groups from the above morpholino structure. Such sugar surrogates are referred to herein as “modified morpholinos.”

For another example, in certain embodiments, a sugar surrogate comprises a six-membered tetrahydropyran. Such tetrahydropyrans may be further modified or substituted. Nucleosides comprising such modified tetrahydropyrans include, but are not limited to, hexitol nucleic acid (HNA), anitol nucleic acid (ANA), manitol nucleic acid (MNA) (see Leumann, C J. Bioorg. & Med. Chem. (2002) 10:841-854), fluoro HNA (F-HNA), and those compounds having Formula VI:




wherein independently for each of said at least one tetrahydropyran nucleoside analog of Formula VI:

Bx is a nucleobase moiety;
T3 and T4 are each, independently, an internucleoside linking group linking the tetrahydropyran nucleoside analog to the antisense compound or one of T3 and T4 is an internucleoside linking group linking the tetrahydropyran nucleoside analog to the antisense compound and the other of T3 and T4 is H, a hydroxyl protecting group, a linked conjugate group, or a 5′ or 3′-terminal group;
q1, q2, q3, q4, q5, q6 and q7 are each, independently, H, C1-C6 alkyl, substituted C1-C6 alkyl, C2-C6 alkenyl, substituted C2-C6 alkenyl, C2-C6 alkynyl, or substituted C2-C6 alkynyl; and
each of R1 and R2 is independently selected from among: hydrogen, halogen, substituted or unsubstituted alkoxy, NJ1J2, SJ1, N3, OC(═X)J1, OC(═X)NJ1J2, NJ3C(═X)NJ1J2, and CN, wherein X is O, S or NJ1, and each J1, J2, and J3 is, independently, H or C1-C6 alkyl.
In certain embodiments, the modified THP nucleosides of Formula VI are provided wherein q1, q2, q3, q4, q5, q6 and q7 are each H. In certain embodiments, at least one of q1, q2, q3, q4, q5, q6 and q7 is other than H. In certain embodiments, at least one of q1, q2, q3, q4, q5, q6 and q7 is methyl. In certain embodiments, THP nucleosides of Formula VI are provided wherein one of R1 and R2 is F. In certain embodiments, R1 is fluoro and R2 is H, R1 is methoxy and R2 is H, and R1 is methoxyethoxy and R2 is H.
Many other bicyclo and tricyclo sugar surrogate ring systems are also known in the art that can be used to modify nucleosides for incorporation into antisense compounds (see, e.g., review article: Leumann, J. C, Bioorganic & Medicinal Chemistry, 2002, 10, 841-854).
Combinations of modifications are also provided without limitation, such as 2′-F-5′-methyl substituted nucleosides (see PCT International Application WO 2008/101157 Published on Aug. 21, 2008 for other disclosed 5′,2′-bis substituted nucleosides) and replacement of the ribosyl ring oxygen atom with S and further substitution at the 2′-position (see published U.S. Patent Application US2005-0130923, published on Jun. 16, 2005) or alternatively 5′-substitution of a bicyclic nucleic acid (see PCT International Application WO 2007/134181, published on Nov. 22, 2007 wherein a 4′-CH2—O-2′ bicyclic nucleoside is further substituted at the 5′ position with a 5′-methyl or a 5′-vinyl group). The synthesis and preparation of carbocyclic bicyclic nucleosides along with their oligomerization and biochemical studies have also been described (see, e.g., Srivastava et al., J. Am. Chem. Soc. 2007, 129(26), 8362-8379).
In certain embodiments, the present disclosure provides oligonucleotides comprising modified nucleosides. Those modified nucleotides may include modified sugars, modified nucleobases, and/or modified linkages. The specific modifications are selected such that the resulting oligonucleotides possess desirable characteristics. In certain embodiments, oligonucleotides comprise one or more RNA-like nucleosides. In certain embodiments, oligonucleotides comprise one or more DNA-like nucleotides.
2. Certain Nucleobase Modifications
In certain embodiments, nucleosides of the present disclosure comprise one or more unmodified nucleobases. In certain embodiments, nucleosides of the present disclosure comprise one or more modified nucleobases.
In certain embodiments, modified nucleobases are selected from: universal bases, hydrophobic bases, promiscuous bases, size-expanded bases, and fluorinated bases as defined herein. 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and O-6 substituted purines, including 2-aminopropyladenine, 5-propynyluracil; 5-propynylcytosine; 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 (—C≡C—CH3) uracil and cytosine and other alkynyl derivatives of pyrimidine bases, 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, 2-F-adenine, 2-amino-adenine, 8-azaguanine and 8-azaadenine, 7-deazaguanine and 7-deazaadenine, 3-deazaguanine and 3-deazaadenine, universal bases, hydrophobic bases, promiscuous bases, size-expanded bases, and fluorinated bases as defined herein. Further modified nucleobases include tricyclic pyrimidines such as phenoxazine cytidine ([5,4-b][1,4]benzoxazin-2(3H)-one), phenothiazine cytidine (1H-pyrimido[5,4-b][1,4]benzothiazin-2(3H)-one), G-clamps such as a substituted phenoxazine cytidine (e.g. 9-(2-aminoethoxy)-H-pyrimido[5,4-b][1,4]benzoxazin-2(3H)-one), carbazole cytidine (2H-pyrimido[4,5-b]indol-2-one), pyridoindole cytidine (H-pyrido[3′,2′:4,5]pyrrolo[2,3-d]pyrimidin-2-one). Modified nucleobases may also include those in which the purine or pyrimidine base is replaced with other heterocycles, for example 7-deaza-adenine, 7-deazaguanosine, 2-aminopyridine and 2-pyridone. Further nucleobases include those disclosed in U.S. Pat. No. 3,687,808, those disclosed in The Concise Encyclopedia Of Polymer Science And Engineering, Kroschwitz, J. I., Ed., John Wiley & Sons, 1990, 858-859; 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, Crooke, S. T. and Lebleu, B., Eds., CRC Press, 1993, 273-288.
Representative United States patents that teach the preparation of certain of the above noted modified nucleobases as well as other modified nucleobases include without limitation, U.S. Pat. Nos. 3,687,808; 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; 5,645,985; 5,681,941; 5,750,692; 5,763,588; 5,830,653 and 6,005,096, certain of which are commonly owned with the instant application, and each of which is herein incorporated by reference in its entirety.
3. Certain Internucleoside Linkages
In certain embodiments, the present disclosure provides oligonucleotides comprising linked nucleosides. In such embodiments, nucleosides may be linked together using any internucleoside linkage. The two main classes of internucleoside linking groups are defined by the presence or absence of a phosphorus atom. Representative phosphorus containing internucleoside linkages include, but are not limited to, phosphodiesters (PO), phosphotriesters, methylphosphonates, phosphoramidate, and phosphorothioates (PS). Representative non-phosphorus containing internucleoside linking groups include, but are not limited to, methylenemethylimino (—CH2—N(CH3)—O—CH2—), thiodiester (—O—C(O)—S—), thionocarbamate (—O—C(O)(NH)—S—); siloxane (—O—Si(H)2—O—); and N,N′-dimethylhydrazine (—CH2—N(CH3)—N(CH3)—). Modified linkages, compared to natural phosphodiester linkages, can be used to alter, typically increase, nuclease resistance of the oligonucleotide. In certain embodiments, internucleoside linkages having a chiral atom can be prepared as a racemic mixture, or as separate enantiomers. Representative chiral linkages include, but are not limited to, alkylphosphonates and phosphorothioates. Methods of preparation of phosphorous-containing and non-phosphorous-containing internucleoside linkages are well known to those skilled in the art.
The oligonucleotides described herein contain one or more asymmetric centers and thus give rise to enantiomers, diastereomers, and other stereoisomeric configurations that may be defined, in terms of absolute stereochemistry, as (R) or (S), α or β such as for sugar anomers, or as (D) or (L) such as for amino acids etc. Included in the antisense compounds provided herein are all such possible isomers, as well as their racemic and optically pure forms.
Neutral internucleoside linkages include without limitation, phosphotriesters, methylphosphonates, MMI (3′-CH2—N(CH3)—O-5′), amide-3 (3′-CH2—C(═O)—N(H)-5′), amide-4 (3′-CH2—N(H)—C(═O)-5′), formacetal (3′-O—CH2—O-5′), and thioformacetal (3′-S—CH2—O-5′). Further neutral internucleoside linkages include nonionic linkages comprising siloxane (dialkylsiloxane), carboxylate ester, carboxamide, sulfide, sulfonate ester and amides (See for example: Carbohydrate Modifications in Antisense Research; Y. S. Sanghvi and P. D. Cook, Eds., ACS Symposium Series 580; Chapters 3 and 4, 40-65). Further neutral internucleoside linkages include nonionic linkages comprising mixed N, O, S and CH2 component parts.
4. Certain Motifs
In certain embodiments, antisense oligonucleotides comprise one or more modified nucleoside (e.g., nucleoside comprising a modified sugar and/or modified nucleobase) and/or one or more modified internucleoside linkage. The pattern of such modifications on an oligonucleotide is referred to herein as a motif. In certain embodiments, sugar, nucleobase, and linkage motifs are independent of one another.
a. Certain Sugar Motifs
In certain embodiments, oligonucleotides comprise one or more type of modified sugar moieties and/or naturally occurring sugar moieties arranged along an oligonucleotide or region thereof in a defined pattern or sugar modification motif. Such motifs may include any of the sugar modifications discussed herein and/or other known sugar modifications.
In certain embodiments, the oligonucleotides comprise or consist of a region having a gapmer sugar motif, which comprises two external regions or “wings” and a central or internal region or “gap.” The three regions of a gapmer sugar motif (the 5′-wing, the gap, and the 3′-wing) form a contiguous sequence of nucleosides wherein at least some of the sugar moieties of the nucleosides of each of the wings differ from at least some of the sugar moieties of the nucleosides of the gap. Specifically, at least the sugar moieties of the nucleosides of each wing that are closest to the gap (the 3′-most nucleoside of the 5′-wing and the 5′-most nucleoside of the 3′-wing) differ from the sugar moiety of the neighboring gap nucleosides, thus defining the boundary between the wings and the gap. In certain embodiments, the sugar moieties within the gap are the same as one another. In certain embodiments, the gap includes one or more nucleoside having a sugar moiety that differs from the sugar moiety of one or more other nucleosides of the gap. In certain embodiments, the sugar motifs of the two wings are the same as one another (symmetric sugar gapmer). In certain embodiments, the sugar motifs of the 5′-wing differs from the sugar motif of the 3′-wing (asymmetric sugar gapmer).
i. Certain 5′-Wings
In certain embodiments, the 5′-wing of a gapmer consists of 1 to 8 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 1 to 7 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 1 to 6 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 1 to 5 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 2 to 5 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 3 to 5 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 4 or 5 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 1 to 4 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 1 to 3 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 1 or 2 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 2 to 4 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 2 or 3 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 3 or 4 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 1 nucleoside. In certain embodiments, the 5′-wing of a gapmer consists of 2 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 3 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 4 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 5 linked nucleosides. In certain embodiments, the 5′-wing of a gapmer consists of 6 linked nucleosides.
In certain embodiments, the 5′-wing of a gapmer comprises at least one bicyclic nucleoside. In certain embodiments, the 5′-wing of a gapmer comprises at least two bicyclic nucleosides. In certain embodiments, the 5′-wing of a gapmer comprises at least three bicyclic nucleosides. In certain embodiments, the 5′-wing of a gapmer comprises at least four bicyclic nucleosides. In certain embodiments, the 5′-wing of a gapmer comprises at least one constrained ethyl nucleoside. In certain embodiments, the 5′-wing of a gapmer comprises at least one LNA nucleoside. In certain embodiments, each nucleoside of the 5′-wing of a gapmer is a bicyclic nucleoside. In certain embodiments, each nucleoside of the 5′-wing of a gapmer is a constrained ethyl nucleoside. In certain embodiments, each nucleoside of the 5′-wing of a gapmer is a LNA nucleoside.
In certain embodiments, the 5′-wing of a gapmer comprises at least one non-bicyclic modified nucleoside. In certain embodiments, the 5′-wing of a gapmer comprises at least one 2′-substituted nucleoside. In certain embodiments, the 5′-wing of a gapmer comprises at least one 2′-MOE nucleoside. In certain embodiments, the 5′-wing of a gapmer comprises at least one 2′-OMe nucleoside. In certain embodiments, each nucleoside of the 5′-wing of a gapmer is a non-bicyclic modified nucleoside. In certain embodiments, each nucleoside of the 5′-wing of a gapmer is a 2′-substituted nucleoside. In certain embodiments, each nucleoside of the 5′-wing of a gapmer is a 2′-MOE nucleoside. In certain embodiments, each nucleoside of the 5′-wing of a gapmer is a 2′-OMe nucleoside.
In certain embodiments, the 5′-wing of a gapmer comprises at least one 2′-deoxynucleoside. In certain embodiments, each nucleoside of the 5′-wing of a gapmer is a 2′-deoxynucleoside. In a certain embodiments, the 5′-wing of a gapmer comprises at least one ribonucleoside. In certain embodiments, each nucleoside of the 5′-wing of a gapmer is a ribonucleoside. In certain embodiments, one, more than one, or each of the nucleosides of the 5′-wing is an RNA-like nucleoside.
In certain embodiments, the 5′-wing of a gapmer comprises at least one bicyclic nucleoside and at least one non-bicyclic modified nucleoside. In certain embodiments, the 5′-wing of a gapmer comprises at least one bicyclic nucleoside and at least one 2′-substituted nucleoside. In certain embodiments, the 5′-wing of a gapmer comprises at least one bicyclic nucleoside and at least one 2′-MOE nucleoside. In certain embodiments, the 5′-wing of a gapmer comprises at least one bicyclic nucleoside and at least one 2′-OMe nucleoside. In certain embodiments, the 5′-wing of a gapmer comprises at least one bicyclic nucleoside and at least one 2′-deoxynucleoside.
In certain embodiments, the 5′-wing of a gapmer comprises at least one constrained ethyl nucleoside and at least one non-bicyclic modified nucleoside. In certain embodiments, the 5′-wing of a gapmer comprises at least one constrained ethyl nucleoside and at least one 2′-substituted nucleoside. In certain embodiments, the 5′-wing of a gapmer comprises at least one constrained ethyl nucleoside and at least one 2′-MOE nucleoside. In certain embodiments, the 5′-wing of a gapmer comprises at least one constrained ethyl nucleoside and at least one 2′-OMe nucleoside. In certain embodiments, the 5′-wing of a gapmer comprises at least one constrained ethyl nucleoside and at least one 2′-deoxynucleoside.
ii. Certain 3′-Wings
In certain embodiments, the 3′-wing of a gapmer consists of 1 to 8 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 1 to 7 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 1 to 6 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 1 to 5 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 2 to 5 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 3 to 5 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 4 or 5 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 1 to 4 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 1 to 3 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 1 or 2 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 2 to 4 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 2 or 3 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 3 or 4 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 1 nucleoside. In certain embodiments, the 3′-wing of a gapmer consists of 2 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 3 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 4 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 5 linked nucleosides. In certain embodiments, the 3′-wing of a gapmer consists of 6 linked nucleosides.
In certain embodiments, the 3′-wing of a gapmer comprises at least one bicyclic nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one constrained ethyl nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one LNA nucleoside. In certain embodiments, each nucleoside of the 3′-wing of a gapmer is a bicyclic nucleoside. In certain embodiments, each nucleoside of the 3′-wing of a gapmer is a constrained ethyl nucleoside. In certain embodiments, each nucleoside of the 3′-wing of a gapmer is a LNA nucleoside.
In certain embodiments, the 3′-wing of a gapmer comprises at least one non-bicyclic modified nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least two non-bicyclic modified nucleosides. In certain embodiments, the 3′-wing of a gapmer comprises at least three non-bicyclic modified nucleosides. In certain embodiments, the 3′-wing of a gapmer comprises at least four non-bicyclic modified nucleosides. In certain embodiments, the 3′-wing of a gapmer comprises at least one 2′-substituted nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one 2′-MOE nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one 2′-OMe nucleoside. In certain embodiments, each nucleoside of the 3′-wing of a gapmer is a non-bicyclic modified nucleoside. In certain embodiments, each nucleoside of the 3′-wing of a gapmer is a 2′-substituted nucleoside. In certain embodiments, each nucleoside of the 3′-wing of a gapmer is a 2′-MOE nucleoside. In certain embodiments, each nucleoside of the 3′-wing of a gapmer is a 2′-OMe nucleoside.
In certain embodiments, the 3′-wing of a gapmer comprises at least one 2′-deoxynucleoside. In certain embodiments, each nucleoside of the 3′-wing of a gapmer is a 2′-deoxynucleoside. In a certain embodiments, the 3′-wing of a gapmer comprises at least one ribonucleoside. In certain embodiments, each nucleoside of the 3′-wing of a gapmer is a ribonucleoside. In certain embodiments, one, more than one, or each of the nucleosides of the 5′-wing is an RNA-like nucleoside.
In certain embodiments, the 3′-wing of a gapmer comprises at least one bicyclic nucleoside and at least one non-bicyclic modified nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one bicyclic nucleoside and at least one 2′-substituted nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one bicyclic nucleoside and at least one 2′-MOE nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one bicyclic nucleoside and at least one 2′-OMe nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one bicyclic nucleoside and at least one 2′-deoxynucleoside.
In certain embodiments, the 3′-wing of a gapmer comprises at least one constrained ethyl nucleoside and at least one non-bicyclic modified nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one constrained ethyl nucleoside and at least one 2′-substituted nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one constrained ethyl nucleoside and at least one 2′-MOE nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one constrained ethyl nucleoside and at least one 2′-OMe nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one constrained ethyl nucleoside and at least one 2′-deoxynucleoside.
In certain embodiments, the 3′-wing of a gapmer comprises at least one LNA nucleoside and at least one non-bicyclic modified nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one LNA nucleoside and at least one 2′-substituted nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one LNA nucleoside and at least one 2′-MOE nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one LNA nucleoside and at least one 2′-OMe nucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one LNA nucleoside and at least one 2′-deoxynucleoside.
In certain embodiments, the 3′-wing of a gapmer comprises at least one bicyclic nucleoside, at least one non-bicyclic modified nucleoside, and at least one 2′-deoxynucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one constrained ethyl nucleoside, at least one non-bicyclic modified nucleoside, and at least one 2′-deoxynucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one LNA nucleoside, at least one non-bicyclic modified nucleoside, and at least one 2′-deoxynucleoside.
In certain embodiments, the 3′-wing of a gapmer comprises at least one bicyclic nucleoside, at least one 2′-substituted nucleoside, and at least one 2′-deoxynucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one constrained ethyl nucleoside, at least one 2′-substituted nucleoside, and at least one 2′-deoxynucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one LNA nucleoside, at least one 2′-substituted nucleoside, and at least one 2′-deoxynucleoside.
In certain embodiments, the 3′-wing of a gapmer comprises at least one bicyclic nucleoside, at least one 2′-MOE nucleoside, and at least one 2′-deoxynucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one constrained ethyl nucleoside, at least one 2′-MOE nucleoside, and at least one 2′-deoxynucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one LNA nucleoside, at least one 2′-MOE nucleoside, and at least one 2′-deoxynucleoside.
In certain embodiments, the 3′-wing of a gapmer comprises at least one bicyclic nucleoside, at least one 2′-OMe nucleoside, and at least one 2′-deoxynucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one constrained ethyl nucleoside, at least one 2′-OMe nucleoside, and at least one 2′-deoxynucleoside. In certain embodiments, the 3′-wing of a gapmer comprises at least one LNA nucleoside, at least one 2′-OMe nucleoside, and at least one 2′-deoxynucleoside.
iii. Certain Central Regions (gaps)
In certain embodiments, the gap of a gapmer consists of 6 to 20 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 6 to 15 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 6 to 12 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 6 to 10 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 6 to 9 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 6 to 8 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 6 or 7 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 7 to 10 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 7 to 9 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 7 or 8 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 8 to 10 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 8 or 9 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 6 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 7 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 8 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 9 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 10 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 11 linked nucleosides. In certain embodiments, the gap of a gapmer consists of 12 linked nucleosides.
In certain embodiments, each nucleoside of the gap of a gapmer is a 2′-deoxynucleoside. In certain embodiments, the gap comprises one or more modified nucleosides. In certain embodiments, each nucleoside of the gap of a gapmer is a 2′-deoxynucleoside or is a modified nucleoside that is “DNA-like.” In such embodiments, “DNA-like” means that the nucleoside has similar characteristics to DNA, such that a duplex comprising the gapmer and an RNA molecule is capable of activating RNase H. For example, under certain conditions, 2′-(ara)-F have been shown to support RNase H activation, and thus is DNA-like. In certain embodiments, one or more nucleosides of the gap of a gapmer is not a 2′-deoxynucleoside and is not DNA-like. In certain such embodiments, the gapmer nonetheless supports RNase H activation (e.g., by virtue of the number or placement of the non-DNA nucleosides).
In certain embodiments, gaps comprise a stretch of unmodified 2′-deoxynucleoside interrupted by one or more modified nucleosides, thus resulting in three sub-regions (two stretches of one or more 2′-deoxynucleotides and a stretch of one or more interrupting modified nucleosides). In certain embodiments, no stretch of unmodified 2′-deoxynucleotides is longer than 5, 6, or 7 nucleosides. In certain embodiments, such short stretches is achieved by using short gap regions. In certain embodiments, short stretches are achieved by interrupting a longer gap region.
In certain embodiments, the gap comprises one or more modified nucleosides. In certain embodiments, the gap comprises one or more modified nucleosides selected from among cEt, FHNA, LNA, and 2-thio-thymidine. In certain embodiments, the gap comprises one modified nucleoside. In certain embodiments, the gap comprises a 5′-substituted sugar moiety selected from among 5′-Me, and 5′-(R)-Me. In certain embodiments, the gap comprises two modified nucleosides. In certain embodiments, the gap comprises three modified nucleosides. In certain embodiments, the gap comprises four modified nucleosides. In certain embodiments, the gap comprises two or more modified nucleosides and each modified nucleoside is the same. In certain embodiments, the gap comprises two or more modified nucleosides and each modified nucleoside is different.
In certain embodiments, the gap comprises one or more modified linkages. In certain embodiments, the gap comprises one or more methyl phosphonate linkages. In certain embodiments the gap comprises two or more modified linkages. In certain embodiments, the gap comprises one or more modified linkages and one or more modified nucleosides. In certain embodiments, the gap comprises one modified linkage and one modified nucleoside. In certain embodiments, the gap comprises two modified linkages and two or more modified nucleosides.
b. Certain Internucleoside Linkage Motifs
In certain embodiments, oligonucleotides comprise modified internucleoside linkages arranged along the oligonucleotide or region thereof in a defined pattern or modified internucleoside linkage motif. In certain embodiments, oligonucleotides comprise a region having an alternating internucleoside linkage motif. In certain embodiments, oligonucleotides of the present disclosure comprise a region of uniformly modified internucleoside linkages. In certain such embodiments, the oligonucleotide comprises a region that is uniformly linked by phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide is uniformly linked by phosphorothioate internucleoside linkages. In certain embodiments, each internucleoside linkage of the oligonucleotide is selected from phosphodiester and phosphorothioate. In certain embodiments, each internucleoside linkage of the oligonucleotide is selected from phosphodiester and phosphorothioate and at least one internucleoside linkage is phosphorothioate.
In certain embodiments, the oligonucleotide comprises at least 6 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least 7 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least 8 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least 9 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least 10 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least 11 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least 12 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least 13 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least 14 phosphorothioate internucleoside linkages.
In certain embodiments, the oligonucleotide comprises at least one block of at least 6 consecutive phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least one block of at least 7 consecutive phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least one block of at least 8 consecutive phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least one block of at least 9 consecutive phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least one block of at least 10 consecutive phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises at least block of at least one 12 consecutive phosphorothioate internucleoside linkages. In certain such embodiments, at least one such block is located at the 3′ end of the oligonucleotide. In certain such embodiments, at least one such block is located within 3 nucleosides of the 3′ end of the oligonucleotide. In certain embodiments, the oligonucleotide comprises less than 15 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises less than 14 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises less than 13 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises less than 12 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises less than 11 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises less than 10 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises less than 9 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises less than 8 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises less than 7 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises less than 6 phosphorothioate internucleoside linkages. In certain embodiments, the oligonucleotide comprises less than 5 phosphorothioate internucleoside linkages.
c. Certain Nucleobase Modification Motifs
In certain embodiments, oligonucleotides comprise chemical modifications to nucleobases arranged along the oligonucleotide or region thereof in a defined pattern or nucleobases modification motif. In certain such embodiments, nucleobase modifications are arranged in a gapped motif. In certain embodiments, nucleobase modifications are arranged in an alternating motif. In certain embodiments, each nucleobase is modified. In certain embodiments, none of the nucleobases is chemically modified.
In certain embodiments, oligonucleotides comprise a block of modified nucleobases. In certain such embodiments, the block is at the 3′-end of the oligonucleotide. In certain embodiments the block is within 3 nucleotides of the 3′-end of the oligonucleotide. In certain such embodiments, the block is at the 5′-end of the oligonucleotide. In certain embodiments the block is within 3 nucleotides of the 5′-end of the oligonucleotide.
In certain embodiments, nucleobase modifications are a function of the natural base at a particular position of an oligonucleotide. For example, in certain embodiments each purine or each pyrimidine in an oligonucleotide is modified. In certain embodiments, each adenine is modified. In certain embodiments, each guanine is modified. In certain embodiments, each thymine is modified. In certain embodiments, each cytosine is modified. In certain embodiments, each uracil is modified.
In certain embodiments, some, all, or none of the cytosine moieties in an oligonucleotide are 5-methyl cytosine moieties. Herein, 5-methyl cytosine is not a “modified nucleobase.” Accordingly, unless otherwise indicated, unmodified nucleobases include both cytosine residues having a 5-methyl and those lacking a 5 methyl. In certain embodiments, the methylation state of all or some cytosine nucleobases is specified.
In certain embodiments, chemical modifications to nucleobases comprise attachment of certain conjugate groups to nucleobases. In certain embodiments, each purine or each pyrimidine in an oligonucleotide may be optionally modified to comprise a conjugate group.
d. Certain Overall Lengths
In certain embodiments, the present disclosure provides oligonucleotides of any of a variety of ranges of lengths. In certain embodiments, oligonucleotides consist of X to Y linked nucleosides, where X represents the fewest number of nucleosides in the range and Y represents the largest number of nucleosides in the range. In certain such embodiments, X and Y are each independently selected from 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, and 50; provided that X≦Y. For example, in certain embodiments, the oligonucleotide may consist of 8 to 9, 8 to 10, 8 to 11, 8 to 12, 8 to 13, 8 to 14, 8 to 15, 8 to 16, 8 to 17, 8 to 18, 8 to 19, 8 to 20, 8 to 21, 8 to 22, 8 to 23, 8 to 24, 8 to 25, 8 to 26, 8 to 27, 8 to 28, 8 to 29, 8 to 30, 9 to 10, 9 to 11, 9 to 12, 9 to 13, 9 to 14, 9 to 15, 9 to 16, 9 to 17, 9 to 18, 9 to 19, 9 to 20, 9 to 21, 9 to 22, 9 to 23, 9 to 24, 9 to 25, 9 to 26, 9 to 27, 9 to 28, 9 to 29, 9 to 30, 10 to 11, 10 to 12, 10 to 13, 10 to 14, 10 to 15, 10 to 16, 10 to 17, 10 to 18, 10 to 19, 10 to 20, 10 to 21, 10 to 22, 10 to 23, 10 to 24, 10 to 25, 10 to 26, 10 to 27, 10 to 28, 10 to 29, 10 to 30, 11 to 12, 11 to 13, 11 to 14, 11 to 15, 11 to 16, 11 to 17, 11 to 18, 11 to 19, 11 to 20, 11 to 21, 11 to 22, 11 to 23, 11 to 24, 11 to 25, 11 to 26, 11 to 27, 11 to 28, 11 to 29, 11 to 30, 12 to 13, 12 to 14, 12 to 15, 12 to 16, 12 to 17, 12 to 18, 12 to 19, 12 to 20, 12 to 21, 12 to 22, 12 to 23, 12 to 24, 12 to 25, 12 to 26, 12 to 27, 12 to 28, 12 to 29, 12 to 30, 13 to 14, 13 to 15, 13 to 16, 13 to 17, 13 to 18, 13 to 19, 13 to 20, 13 to 21, 13 to 22, 13 to 23, 13 to 24, 13 to 25, 13 to 26, 13 to 27, 13 to 28, 13 to 29, 13 to 30, 14 to 15, 14 to 16, 14 to 17, 14 to 18, 14 to 19, 14 to 20, 14 to 21, 14 to 22, 14 to 23, 14 to 24, 14 to 25, 14 to 26, 14 to 27, 14 to 28, 14 to 29, 14 to 30, 15 to 16, 15 to 17, 15 to 18, 15 to 19, 15 to 20, 15 to 21, 15 to 22, 15 to 23, 15 to 24, 15 to 25, 15 to 26, 15 to 27, 15 to 28, 15 to 29, 15 to 30, 16 to 17, 16 to 18, 16 to 19, 16 to 20, 16 to 21, 16 to 22, 16 to 23, 16 to 24, 16 to 25, 16 to 26, 16 to 27, 16 to 28, 16 to 29, 16 to 30, 17 to 18, 17 to 19, 17 to 20, 17 to 21, 17 to 22, 17 to 23, 17 to 24, 17 to 25, 17 to 26, 17 to 27, 17 to 28, 17 to 29, 17 to 30, 18 to 19, 18 to 20, 18 to 21, 18 to 22, 18 to 23, 18 to 24, 18 to 25, 18 to 26, 18 to 27, 18 to 28, 18 to 29, 18 to 30, 19 to 20, 19 to 21, 19 to 22, 19 to 23, 19 to 24, 19 to 25, 19 to 26, 19 to 29, 19 to 28, 19 to 29, 19 to 30, 20 to 21, 20 to 22, 20 to 23, 20 to 24, 20 to 25, 20 to 26, 20 to 27, 20 to 28, 20 to 29, 20 to 30, 21 to 22, 21 to 23, 21 to 24, 21 to 25, 21 to 26, 21 to 27, 21 to 28, 21 to 29, 21 to 30, 22 to 23, 22 to 24, 22 to 25, 22 to 26, 22 to 27, 22 to 28, 22 to 29, 22 to 30, 23 to 24, 23 to 25, 23 to 26, 23 to 27, 23 to 28, 23 to 29, 23 to 30, 24 to 25, 24 to 26, 24 to 27, 24 to 28, 24 to 29, 24 to 30, 25 to 26, 25 to 27, 25 to 28, 25 to 29, 25 to 30, 26 to 27, 26 to 28, 26 to 29, 26 to 30, 27 to 28, 27 to 29, 27 to 30, 28 to 29, 28 to 30, or 29 to 30 linked nucleosides. In embodiments where the number of nucleosides of an oligonucleotide of a compound is limited, whether to a range or to a specific number, the compound may, nonetheless further comprise additional other substituents. For example, an oligonucleotide comprising 8-30 nucleosides excludes oligonucleotides having 31 nucleosides, but, unless otherwise indicated, such an oligonucleotide may further comprise, for example one or more conjugate groups, terminal groups, or other substituents.
Further, where an oligonucleotide is described by an overall length range and by regions having specified lengths, and where the sum of specified lengths of the regions is less than the upper limit of the overall length range, the oligonucleotide may have additional nucleosides, beyond those of the specified regions, provided that the total number of nucleosides does not exceed the upper limit of the overall length range.
5. Certain Antisense Oligonucleotide Chemistry Motifs
In certain embodiments, the chemical structural features of antisense oligonucleotides are characterized by their sugar motif, internucleoside linkage motif, nucleobase modification motif and overall length. In certain embodiments, such parameters are each independent of one another. Thus, each internucleoside linkage of an oligonucleotide having a gapmer sugar motif may be modified or unmodified and may or may not follow the gapmer modification pattern of the sugar modifications. Thus, the internucleoside linkages within the wing regions of a sugar-gapmer may be the same or different from one another and may be the same or different from the internucleoside linkages of the gap region. Likewise, such sugar-gapmer oligonucleotides may comprise one or more modified nucleobase independent of the gapmer pattern of the sugar modifications. One of skill in the art will appreciate that such motifs may be combined to create a variety of oligonucleotides.
In certain embodiments, the selection of internucleoside linkage and nucleoside modification are not independent of one another.
i. Certain Sequences and Targets
In certain embodiments, the invention provides antisense oligonucleotides having a sequence complementary to a target nucleic acid. Such antisense compounds are capable of hybridizing to a target nucleic acid, resulting in at least one antisense activity. In certain embodiments, antisense compounds specifically hybridize to one or more target nucleic acid. In certain embodiments, a specifically hybridizing antisense compound has a nucleobase sequence comprising a region having sufficient complementarity to a target nucleic acid to allow hybridization and result in antisense activity and insufficient complementarity to any non-target so as to avoid or reduce non-specific hybridization to non-target nucleic acid sequences under conditions in which specific hybridization is desired (e.g., under physiological conditions for in vivo or therapeutic uses, and under conditions in which assays are performed in the case of in vitro assays). In certain embodiments, oligonucleotides are selective between a target and non-target, even though both target and non-target comprise the target sequence. In such embodiments, selectivity may result from relative accessibility of the target region of one nucleic acid molecule compared to the other.
In certain embodiments, the present disclosure provides antisense compounds comprising oligonucleotides that are fully complementary to the target nucleic acid over the entire length of the oligonucleotide. In certain embodiments, oligonucleotides are 99% complementary to the target nucleic acid. In certain embodiments, oligonucleotides are 95% complementary to the target nucleic acid. In certain embodiments, such oligonucleotides are 90% complementary to the target nucleic acid.
In certain embodiments, such oligonucleotides are 85% complementary to the target nucleic acid. In certain embodiments, such oligonucleotides are 80% complementary to the target nucleic acid. In certain embodiments, an antisense compound comprises a region that is fully complementary to a target nucleic acid and is at least 80% complementary to the target nucleic acid over the entire length of the oligonucleotide. In certain such embodiments, the region of full complementarity is from 6 to 14 nucleobases in length.
In certain embodiments, oligonucleotides comprise a hybridizing region and a terminal region. In certain such embodiments, the hybridizing region consists of 12-30 linked nucleosides and is fully complementary to the target nucleic acid. In certain embodiments, the hybridizing region includes one mismatch relative to the target nucleic acid. In certain embodiments, the hybridizing region includes two mismatches relative to the target nucleic acid. In certain embodiments, the hybridizing region includes three mismatches relative to the target nucleic acid. In certain embodiments, the terminal region consists of 1-4 terminal nucleosides. In certain embodiments, the terminal nucleosides are at the 3′ end. In certain embodiments, one or more of the terminal nucleosides are not complementary to the target nucleic acid.
Antisense mechanisms include any mechanism involving the hybridization of an oligonucleotide with target nucleic acid, wherein the hybridization results in a biological effect. In certain embodiments, such hybridization results in either target nucleic acid degradation or occupancy with concomitant inhibition or stimulation of the cellular machinery involving, for example, translation, transcription, or splicing of the target nucleic acid.
One type of antisense mechanism involving degradation of target RNA is RNase H mediated antisense. RNase H is a cellular endonuclease which cleaves the RNA strand of an RNA:DNA duplex. It is known in the art that single-stranded antisense compounds which are “DNA-like” elicit RNase H activity in mammalian cells. Activation of RNase H, therefore, results in cleavage of the RNA target, thereby greatly enhancing the efficiency of DNA-like oligonucleotide-mediated inhibition of gene expression.
In certain embodiments, a conjugate group comprises a cleavable moiety. In certain embodiments, a conjugate group comprises one or more cleavable bond. In certain embodiments, a conjugate group comprises a linker. In certain embodiments, a linker comprises a protein binding moiety. In certain embodiments, a conjugate group comprises a cell-targeting moiety (also referred to as a cell-targeting group). In certain embodiments a cell-targeting moiety comprises a branching group. In certain embodiments, a cell-targeting moiety comprises one or more tethers. In certain embodiments, a cell-targeting moiety comprises a carbohydrate or carbohydrate cluster.
ii. Certain Cleavable Moieties
In certain embodiments, a cleavable moiety is a cleavable bond. In certain embodiments, a cleavable moiety comprises a cleavable bond. In certain embodiments, the conjugate group comprises a cleavable moiety. In certain such embodiments, the cleavable moiety attaches to the antisense oligonucleotide. In certain such embodiments, the cleavable moiety attaches directly to the cell-targeting moiety. In certain such embodiments, the cleavable moiety attaches to the conjugate linker. In certain embodiments, the cleavable moiety comprises a phosphate or phosphodiester. In certain embodiments, the cleavable moiety is a cleavable nucleoside or nucleoside analog. In certain embodiments, the nucleoside or nucleoside analog comprises an optionally protected heterocyclic base selected from a purine, substituted purine, pyrimidine or substituted pyrimidine. In certain embodiments, the cleavable moiety is a nucleoside comprising an optionally protected heterocyclic base selected from uracil, thymine, cytosine, 4-N-benzoylcytosine, 5-methylcytosine, 4-N-benzoyl-5-methylcytosine, adenine, 6-N-benzoyladenine, guanine and 2-N-isobutyrylguanine. In certain embodiments, the cleavable moiety is 2′-deoxy nucleoside that is attached to the 3′ position of the antisense oligonucleotide by a phosphodiester linkage and is attached to the linker by a phosphodiester or phosphorothioate linkage. In certain embodiments, the cleavable moiety is 2′-deoxy adenosine that is attached to the 3′ position of the antisense oligonucleotide by a phosphodiester linkage and is attached to the linker by a phosphodiester or phosphorothioate linkage. In certain embodiments, the cleavable moiety is 2′-deoxy adenosine that is attached to the 3′ position of the antisense oligonucleotide by a phosphodiester linkage and is attached to the linker by a phosphodiester linkage.
In certain embodiments, the cleavable moiety is attached to the 3′ position of the antisense oligonucleotide. In certain embodiments, the cleavable moiety is attached to the 5′ position of the antisense oligonucleotide. In certain embodiments, the cleavable moiety is attached to a 2′ position of the antisense oligonucleotide. In certain embodiments, the cleavable moiety is attached to the antisense oligonucleotide by a phosphodiester linkage. In certain embodiments, the cleavable moiety is attached to the linker by either a phosphodiester or a phosphorothioate linkage. In certain embodiments, the cleavable moiety is attached to the linker by a phosphodiester linkage. In certain embodiments, the conjugate group does not include a cleavable moiety.
In certain embodiments, the cleavable moiety is cleaved after the complex has been administered to an animal only after being internalized by a targeted cell. Inside the cell the cleavable moiety is cleaved thereby releasing the active antisense oligonucleotide. While not wanting to be bound by theory it is believed that the cleavable moiety is cleaved by one or more nucleases within the cell. In certain embodiments, the one or more nucleases cleave the phosphodiester linkage between the cleavable moiety and the linker. In certain embodiments, the cleavable moiety has a structure selected from among the following:




wherein each of Bx, Bx1, Bx2, and Bx3 is independently a heterocyclic base moiety. In certain embodiments, the cleavable moiety has a structure selected from among the following:





iii. Certain Linkers
In certain embodiments, the conjugate groups comprise a linker. In certain such embodiments, the linker is covalently bound to the cleavable moiety. In certain such embodiments, the linker is covalently bound to the antisense oligonucleotide. In certain embodiments, the linker is covalently bound to a cell-targeting moiety. In certain embodiments, the linker further comprises a covalent attachment to a solid support. In certain embodiments, the linker further comprises a covalent attachment to a protein binding moiety. In certain embodiments, the linker further comprises a covalent attachment to a solid support and further comprises a covalent attachment to a protein binding moiety. In certain embodiments, the linker includes multiple positions for attachment of tethered ligands. In certain embodiments, the linker includes multiple positions for attachment of tethered ligands and is not attached to a branching group. In certain embodiments, the linker further comprises one or more cleavable bond. In certain embodiments, the conjugate group does not include a linker.
In certain embodiments, the linker includes at least a linear group comprising groups selected from alkyl, amide, disulfide, polyethylene glycol, ether, thioether (—S—) and hydroxylamino (—O—N(H)—) groups. In certain embodiments, the linear group comprises groups selected from alkyl, amide and ether groups. In certain embodiments, the linear group comprises groups selected from alkyl and ether groups. In certain embodiments, the linear group comprises at least one phosphorus linking group. In certain embodiments, the linear group comprises at least one phosphodiester group. In certain embodiments, the linear group includes at least one neutral linking group. In certain embodiments, the linear group is covalently attached to the cell-targeting moiety and the cleavable moiety. In certain embodiments, the linear group is covalently attached to the cell-targeting moiety and the antisense oligonucleotide. In certain embodiments, the linear group is covalently attached to the cell-targeting moiety, the cleavable moiety and a solid support. In certain embodiments, the linear group is covalently attached to the cell-targeting moiety, the cleavable moiety, a solid support and a protein binding moiety. In certain embodiments, the linear group includes one or more cleavable bond.
In certain embodiments, the linker includes the linear group covalently attached to a scaffold group. In certain embodiments, the scaffold includes a branched aliphatic group comprising groups selected from alkyl, amide, disulfide, polyethylene glycol, ether, thioether and hydroxylamino groups. In certain embodiments, the scaffold includes a branched aliphatic group comprising groups selected from alkyl, amide and ether groups. In certain embodiments, the scaffold includes at least one mono or polycyclic ring system. In certain embodiments, the scaffold includes at least two mono or polycyclic ring systems. In certain embodiments, the linear group is covalently attached to the scaffold group and the scaffold group is covalently attached to the cleavable moiety and the linker. In certain embodiments, the linear group is covalently attached to the scaffold group and the scaffold group is covalently attached to the cleavable moiety, the linker and a solid support. In certain embodiments, the linear group is covalently attached to the scaffold group and the scaffold group is covalently attached to the cleavable moiety, the linker and a protein binding moiety. In certain embodiments, the linear group is covalently attached to the scaffold group and the scaffold group is covalently attached to the cleavable moiety, the linker, a protein binding moiety and a solid support. In certain embodiments, the scaffold group includes one or more cleavable bond.
In certain embodiments, the linker includes a protein binding moiety. In certain embodiments, the protein binding moiety is a lipid such as for example including but not limited to cholesterol, cholic acid, adamantane acetic acid, 1-pyrene butyric acid, dihydrotestosterone, 1,3-Bis-O(hexadecyl)glycerol, geranyloxyhexyl group, hexadecylglycerol, borneol, menthol, 1,3-propanediol, heptadecyl group, palmitic acid, myristic acid, O3-(oleoyl)lithocholic acid, O3-(oleoyl)cholenic acid, dimethoxytrityl, or phenoxazine), a vitamin (e.g., folate, vitamin A, vitamin E, biotin, pyridoxal), a peptide, a carbohydrate (e.g., monosaccharide, disaccharide, trisaccharide, tetrasaccharide, oligosaccharide, polysaccharide), an endosomolytic component, a steroid (e.g., uvaol, hecigenin, diosgenin), a terpene (e.g., triterpene, e.g., sarsasapogenin, friedelin, epifriedelanol derivatized lithocholic acid), or a cationic lipid. In certain embodiments, the protein binding moiety is a C16 to C22 long chain saturated or unsaturated fatty acid, cholesterol, cholic acid, vitamin E, adamantane or 1-pentafluoropropyl.
In certain embodiments, a linker has a structure selected from among:










wherein each n is, independently, from 1 to 20; and p is from 1 to 6.
In certain embodiments, a linker has a structure selected from among:







wherein each n is, independently, from 1 to 20.
In certain embodiments, a linker has a structure selected from among:







wherein n is from 1 to 20.
In certain embodiments, a linker has a structure selected from among:







wherein each L is, independently, a phosphorus linking group or a neutral linking group; and
each n is, independently, from 1 to 20.
In certain embodiments, a linker has a structure selected from among:










In certain embodiments, a linker has a structure selected from among:







In certain embodiments, a linker has a structure selected from among:







In certain embodiments, a linker has a structure selected from among:




wherein n is from 1 to 20.
In certain embodiments, a linker has a structure selected from among:




In certain embodiments, a linker has a structure selected from among:




In certain embodiments, a linker has a structure selected from among:




In certain embodiments, the conjugate linker has the structure:




In certain embodiments, the conjugate linker has the structure:




In certain embodiments, a linker has a structure selected from among:




In certain embodiments, a linker has a structure selected from among:




wherein each n is independently, 0, 1, 2, 3, 4, 5, 6, or 7.
iv. Certain Cell-Targeting Moieties
In certain embodiments, conjugate groups comprise cell-targeting moieties. Certain such cell-targeting moieties increase cellular uptake of antisense compounds. In certain embodiments, cell-targeting moieties comprise a branching group, one or more tether, and one or more ligand. In certain embodiments, cell-targeting moieties comprise a branching group, one or more tether, one or more ligand and one or more cleavable bond.
1. Certain Branching Groups
In certain embodiments, the conjugate groups comprise a targeting moiety comprising a branching group and at least two tethered ligands. In certain embodiments, the branching group attaches the conjugate linker. In certain embodiments, the branching group attaches the cleavable moiety. In certain embodiments, the branching group attaches the antisense oligonucleotide. In certain embodiments, the branching group is covalently attached to the linker and each of the tethered ligands. In certain embodiments, the branching group comprises a branched aliphatic group comprising groups selected from alkyl, amide, disulfide, polyethylene glycol, ether, thioether and hydroxylamino groups. In certain embodiments, the branching group comprises groups selected from alkyl, amide and ether groups. In certain embodiments, the branching group comprises groups selected from alkyl and ether groups. In certain embodiments, the branching group comprises a mono or polycyclic ring system. In certain embodiments, the branching group comprises one or more cleavable bond. In certain embodiments, the conjugate group does not include a branching group.
In certain embodiments, a branching group has a structure selected from among:










wherein each n is, independently, from 1 to 20;
j is from 1 to 3; and
m is from 2 to 6.
In certain embodiments, a branching group has a structure selected from among:







wherein each n is, independently, from 1 to 20; and
m is from 2 to 6.
In certain embodiments, a branching group has a structure selected from among:










In certain embodiments, a branching group has a structure selected from among:




wherein each A1 is independently, O, S, C═O or NH; and
each n is, independently, from 1 to 20.
In certain embodiments, a branching group has a structure selected from among:




wherein each A1 is independently, O, S, C═O or NH; and
each n is, independently, from 1 to 20.
In certain embodiments, a branching group has a structure selected from among:




wherein A1 is O, S, C═O or NH; and
each n is, independently, from 1 to 20.
In certain embodiments, a branching group has a structure selected from among:




In certain embodiments, a branching group has a structure selected from among:




In certain embodiments, a branching group has a structure selected from among:




2. Certain Tethers
In certain embodiments, conjugate groups comprise one or more tethers covalently attached to the branching group. In certain embodiments, conjugate groups comprise one or more tethers covalently attached to the linking group. In certain embodiments, each tether is a linear aliphatic group comprising one or more groups selected from alkyl, ether, thioether, disulfide, amide and polyethylene glycol groups in any combination. In certain embodiments, each tether is a linear aliphatic group comprising one or more groups selected from alkyl, substituted alkyl, ether, thioether, disulfide, amide, phosphodiester and polyethylene glycol groups in any combination. In certain embodiments, each tether is a linear aliphatic group comprising one or more groups selected from alkyl, ether and amide groups in any combination. In certain embodiments, each tether is a linear aliphatic group comprising one or more groups selected from alkyl, substituted alkyl, phosphodiester, ether and amide groups in any combination. In certain embodiments, each tether is a linear aliphatic group comprising one or more groups selected from alkyl and phosphodiester in any combination. In certain embodiments, each tether comprises at least one phosphorus linking group or neutral linking group.
In certain embodiments, the tether includes one or more cleavable bond. In certain embodiments, the tether is attached to the branching group through either an amide or an ether group. In certain embodiments, the tether is attached to the branching group through a phosphodiester group. In certain embodiments, the tether is attached to the branching group through a phosphorus linking group or neutral linking group. In certain embodiments, the tether is attached to the branching group through an ether group. In certain embodiments, the tether is attached to the ligand through either an amide or an ether group. In certain embodiments, the tether is attached to the ligand through an ether group. In certain embodiments, the tether is attached to the ligand through either an amide or an ether group. In certain embodiments, the tether is attached to the ligand through an ether group.
In certain embodiments, each tether comprises from about 8 to about 20 atoms in chain length between the ligand and the branching group. In certain embodiments, each tether group comprises from about 10 to about 18 atoms in chain length between the ligand and the branching group. In certain embodiments, each tether group comprises about 13 atoms in chain length.
In certain embodiments, a tether has a structure selected from among:




wherein each n is, independently, from 1 to 20; and
each p is from 1 to about 6.
In certain embodiments, a tether has a structure selected from among:




In certain embodiments, a tether has a structure selected from among:




    
    
        wherein each n is, independently, from 1 to 20.
    
    


In certain embodiments, a tether has a structure selected from among:




    
    
        wherein L is either a phosphorus linking group or a neutral linking group;
        Z1 is C(═O)O—R2 
        Z2 is H, C1-C6 alkyl or substituted C1-C6 alkyl;
        R2 is H, C1-C6 alkyl or substituted C1-C6 alkyl; and
        each m1 is, independently, from 0 to 20 wherein at least one m1 is greater than 0 for each tether.
    
    


In certain embodiments, a tether has a structure selected from among:




In certain embodiments, a tether has a structure selected from among:




    
    
        wherein Z2 is H or CH3; and
        each m1 is, independently, from 0 to 20 wherein at least one m1 is greater than 0 for each tether.
    
    


In certain embodiments, a tether has a structure selected from among:




wherein each n is independently, 0, 1, 2, 3, 4, 5, 6, or 7.

In certain embodiments, a tether comprises a phosphorus linking group. In certain embodiments, a tether does not comprise any amide bonds. In certain embodiments, a tether comprises a phosphorus linking group and does not comprise any amide bonds.
3. Certain Ligands
In certain embodiments, the present disclosure provides ligands wherein each ligand is covalently attached to a tether. In certain embodiments, each ligand is selected to have an affinity for at least one type of receptor on a target cell. In certain embodiments, ligands are selected that have an affinity for at least one type of receptor on the surface of a mammalian liver cell. In certain embodiments, ligands are selected that have an affinity for the hepatic asialoglycoprotein receptor (ASGP-R). In certain embodiments, each ligand is a carbohydrate. In certain embodiments, each ligand is, independently selected from galactose, N-acetyl galactoseamine, mannose, glucose, glucosamone and fucose. In certain embodiments, each ligand is N-acetyl galactoseamine (GalNAc). In certain embodiments, the targeting moiety comprises 2 to 6 ligands. In certain embodiments, the targeting moiety comprises 3 ligands. In certain embodiments, the targeting moiety comprises 3 N-acetyl galactoseamine ligands.
In certain embodiments, the ligand is a carbohydrate, carbohydrate derivative, modified carbohydrate, multivalent carbohydrate cluster, polysaccharide, modified polysaccharide, or polysaccharide derivative. In certain embodiments, the ligand is an amino sugar or a thio sugar. For example, amino sugars may be selected from any number of compounds known in the art, for example glucosamine, sialic acid, α-D-galactosamine, N-Acetylgalactosamine, 2-acetamido-2-deoxy-D-galactopyranose (GalNAc), 2-Amino-3-O—[(R)-1-carboxyethyl]-2-deoxy-β-D-glucopyranose (β-muramic acid), 2-Deoxy-2-methylamino-L-glucopyranose, 4,6-Dideoxy-4-formamido-2,3-di-O-methyl-D-mannopyranose, 2-Deoxy-2-sulfoamino-D-glucopyranose and N-sulfo-D-glucosamine, and N-Glycoloyl-α-neuraminic acid. For example, thio sugars may be selected from the group consisting of 5-Thio-β-D-glucopyranose, Methyl 2,3,4-tri-O-acetyl-1-thio-6-O-trityl-α-D-glucopyranoside, 4-Thio-β-D-galactopyranose, and ethyl 3,4,6,7-tetra-O-acetyl-2-deoxy-1,5-dithio-α-D-gluco-heptopyranoside.
In certain embodiments, “GalNac” or “Gal-NAc” refers to 2-(Acetylamino)-2-deoxy-D-galactopyranose, commonly referred to in the literature as N-acetyl galactosamine. In certain embodiments, “N-acetyl galactosamine” refers to 2-(Acetylamino)-2-deoxy-D-galactopyranose. In certain embodiments, “GalNac” or “Gal-NAc” refers to 2-(Acetylamino)-2-deoxy-D-galactopyranose. In certain embodiments, “GalNac” or “Gal-NAc” refers to 2-(Acetylamino)-2-deoxy-D-galactopyranose, which includes both the β-form: 2-(Acetylamino)-2-deoxy-β-D-galactopyranose and α-form: 2-(Acetylamino)-2-deoxy-D-galactopyranose. In certain embodiments, both the β-form: 2-(Acetylamino)-2-deoxy-β-D-galactopyranose and α-form: 2-(Acetylamino)-2-deoxy-D-galactopyranose may be used interchangeably. Accordingly, in structures in which one form is depicted, these structures are intended to include the other form as well. For example, where the structure for an α-form: 2-(Acetylamino)-2-deoxy-D-galactopyranose is shown, this structure is intended to include the other form as well. In certain embodiments, In certain preferred embodiments, the β-form 2-(Acetylamino)-2-deoxy-D-galactopyranose is the preferred embodiment.




In certain embodiments one or more ligand has a structure selected from among:




wherein each R1 is selected from OH and NHCOOH.
In certain embodiments one or more ligand has a structure selected from among:







In certain embodiments one or more ligand has a structure selected from among:




In certain embodiments one or more ligand has a structure selected from among:




i. Certain Conjugates
In certain embodiments, conjugate groups comprise the structural features above. In certain such embodiments, conjugate groups have the following structure:




wherein each n is, independently, from 1 to 20.
In certain such embodiments, conjugate groups have the following structure:




In certain such embodiments, conjugate groups have the following structure:




wherein each n is, independently, from 1 to 20;
Z is H or a linked solid support;
Q is an antisense compound;
X is O or S; and
Bx is a heterocyclic base moiety.
In certain such embodiments, conjugate groups have the following structure:




In certain such embodiments, conjugate groups have the following structure:




In certain such embodiments, conjugate groups have the following structure:




In certain such embodiments, conjugate groups have the following structure:




In certain such embodiments, conjugate groups have the following structure:




In certain such embodiments, conjugate groups have the following structure:




In certain such embodiments, conjugate groups have the following structure:




In certain such embodiments, conjugate groups have the following structure:




In certain embodiments, conjugates do not comprise a pyrrolidine.
In certain such embodiments, conjugate groups have the following structure:




In certain such embodiments, conjugate groups have the following structure:




In certain such embodiments, conjugate groups have the following structure:




In certain such embodiments, conjugate groups have the following structure:




In certain such embodiments, conjugate groups have the following structure:




In certain such embodiments, conjugate groups have the following structure:




In certain such embodiments, conjugate groups have the following structure:




In certain such embodiments, conjugate groups have the following structure:




In certain such embodiments, conjugate groups have the following structure:




In certain such embodiments, conjugate groups have the following structure:




In certain such embodiments, conjugate groups have the following structure:




In certain embodiments, the cell-targeting moiety of the conjugate group has the following structure:




wherein X is a substituted or unsubstituted tether of six to eleven consecutively bonded atoms.
In certain embodiments, the cell-targeting moiety of the conjugate group has the following structure:




wherein X is a substituted or unsubstituted tether of ten consecutively bonded atoms.
In certain embodiments, the cell-targeting moiety of the conjugate group has the following structure:




wherein X is a substituted or unsubstituted tether of four to eleven consecutively bonded atoms and wherein the tether comprises exactly one amide bond.
In certain embodiments, the cell-targeting moiety of the conjugate group has the following structure:




wherein Y and Z are independently selected from a C1-C12 substituted or unsubstituted alkyl, alkenyl, or alkynyl group, or a group comprising an ether, a ketone, an amide, an ester, a carbamate, an amine, a piperidine, a phosphate, a phosphodiester, a phosphorothioate, a triazole, a pyrrolidine, a disulfide, or a thioether.
In certain such embodiments, the cell-targeting moiety of the conjugate group has the following structure:




wherein Y and Z are independently selected from a C1-C12 substituted or unsubstituted alkyl group, or a group comprising exactly one ether or exactly two ethers, an amide, an amine, a piperidine, a phosphate, a phosphodiester, or a phosphorothioate.
In certain such embodiments, the cell-targeting moiety of the conjugate group has the following structure:




wherein Y and Z are independently selected from a C1-C12 substituted or unsubstituted alkyl group.
In certain such embodiments, the cell-targeting moiety of the conjugate group has the following structure:




wherein m and n are independently selected from 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, and 12.
In certain such embodiments, the cell-targeting moiety of the conjugate group has the following structure:




wherein m is 4, 5, 6, 7, or 8, and n is 1, 2, 3, or 4.
In certain embodiments, the cell-targeting moiety of the conjugate group has the following structure:




wherein X is a substituted or unsubstituted tether of four to thirteen consecutively bonded atoms, and wherein X does not comprise an ether group.
In certain embodiments, the cell-targeting moiety of the conjugate group has the following structure:




wherein X is a substituted or unsubstituted tether of eight consecutively bonded atoms, and wherein X does not comprise an ether group.
In certain embodiments, the cell-targeting moiety of the conjugate group has the following structure:




wherein X is a substituted or unsubstituted tether of four to thirteen consecutively bonded atoms, and wherein the tether comprises exactly one amide bond, and wherein X does not comprise an ether group.
In certain embodiments, the cell-targeting moiety of the conjugate group has the following structure:




wherein X is a substituted or unsubstituted tether of four to thirteen consecutively bonded atoms and wherein the tether consists of an amide bond and a substituted or unsubstituted C2-C11 alkyl group.
In certain embodiments, the cell-targeting moiety of the conjugate group has the following structure:




wherein Y is selected from a C1-C12 substituted or unsubstituted alkyl, alkenyl, or alkynyl group, or a group comprising an ether, a ketone, an amide, an ester, a carbamate, an amine, a piperidine, a phosphate, a phosphodiester, a phosphorothioate, a triazole, a pyrrolidine, a disulfide, or a thioether.
In certain such embodiments, the cell-targeting moiety of the conjugate group has the following structure:




wherein Y is selected from a C1-C12 substituted or unsubstituted alkyl group, or a group comprising an ether, an amine, a piperidine, a phosphate, a phosphodiester, or a phosphorothioate.
In certain such embodiments, the cell-targeting moiety of the conjugate group has the following structure:




wherein Y is selected from a C1-C12 substituted or unsubstituted alkyl group.
In certain such embodiments, the cell-targeting moiety of the conjugate group has the following structure:




Wherein n is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12.
In certain such embodiments, the cell-targeting moiety of the conjugate group has the following structure:




wherein n is 4, 5, 6, 7, or 8.
In certain embodiments, conjugates do not comprise a pyrrolidine.
b. Certain Conjugated Antisense Compounds
In certain embodiments, the conjugates are bound to a nucleoside of the antisense oligonucleotide at the 2′, 3′, of 5′ position of the nucleoside. In certain embodiments, a conjugated antisense compound has the following structure:

A-B-C-DE-F)q 

wherein
A is the antisense oligonucleotide;
B is the cleavable moiety
C is the conjugate linker
D is the branching group
each E is a tether;
each F is a ligand; and
q is an integer between 1 and 5.
In certain embodiments, a conjugated antisense compound has the following structure:

A-C-DE-F)q 

wherein
A is the antisense oligonucleotide;
C is the conjugate linker
D is the branching group
each E is a tether;
each F is a ligand; and
q is an integer between 1 and 5.
In certain such embodiments, the conjugate linker comprises at least one cleavable bond.
In certain such embodiments, the branching group comprises at least one cleavable bond.
In certain embodiments each tether comprises at least one cleavable bond.
In certain embodiments, the conjugates are bound to a nucleoside of the antisense oligonucleotide at the 2′, 3′, of 5′ position of the nucleoside.
In certain embodiments, a conjugated antisense compound has the following structure:

A-B-CE-F)q 

wherein
A is the antisense oligonucleotide;
B is the cleavable moiety
C is the conjugate linker
each E is a tether;
each F is a ligand; and
q is an integer between 1 and 5.
In certain embodiments, the conjugates are bound to a nucleoside of the antisense oligonucleotide at the 2′, 3′, of 5′ position of the nucleoside. In certain embodiments, a conjugated antisense compound has the following structure:

A-CE-F)q 

wherein
A is the antisense oligonucleotide;
C is the conjugate linker
each E is a tether;
each F is a ligand; and
q is an integer between 1 and 5.
In certain embodiments, a conjugated antisense compound has the following structure:

A-B-DE-F)q 

wherein
A is the antisense oligonucleotide;
B is the cleavable moiety
D is the branching group
each E is a tether;
each F is a ligand; and
q is an integer between 1 and 5.
In certain embodiments, a conjugated antisense compound has the following structure:

A-DE-F)q 

wherein
A is the antisense oligonucleotide;
D is the branching group
each E is a tether;
each F is a ligand; and
q is an integer between 1 and 5.
In certain such embodiments, the conjugate linker comprises at least one cleavable bond.
In certain embodiments each tether comprises at least one cleavable bond.
In certain embodiments, a conjugated antisense compound has a structure selected from among the following:




In certain embodiments, a conjugated antisense compound has a structure selected from among the following:




In certain embodiments, a conjugated antisense compound has a structure selected from among the following:




Representative United States patents, United States patent application publications, and international patent application publications that teach the preparation of certain of the above noted conjugates, conjugated antisense compounds, tethers, linkers, branching groups, ligands, cleavable moieties as well as other modifications include without limitation, U.S. Pat. Nos. 5,994,517, 6,300,319, 6,660,720, 6,906,182, 7,262,177, 7,491,805, 8,106,022, 7,723,509, US 2006/0148740, US 2011/0123520, WO 2013/033230 and WO 2012/037254, each of which is incorporated by reference herein in its entirety.
Representative publications that teach the preparation of certain of the above noted conjugates, conjugated antisense compounds, tethers, linkers, branching groups, ligands, cleavable moieties as well as other modifications include without limitation, BIESSEN et al., “The Cholesterol Derivative of a Triantennary Galactoside with High Affinity for the Hepatic Asialoglycoprotein Receptor: a Potent Cholesterol Lowering Agent” J. Med. Chem. (1995) 38:1846-1852, BIESSEN et al., “Synthesis of Cluster Galactosides with High Affinity for the Hepatic Asialoglycoprotein Receptor” J. Med. Chem. (1995) 38:1538-1546, LEE et al., “New and more efficient multivalent glyco-ligands for asialoglycoprotein receptor of mammalian hepatocytes” Bioorganic & Medicinal Chemistry (2011) 19:2494-2500, RENSEN et al., “Determination of the Upper Size Limit for Uptake and Processing of Ligands by the Asialoglycoprotein Receptor on Hepatocytes in Vitro and in Vivo” J. Biol. Chem. (2001) 276(40):37577-37584, RENSEN et al., “Design and Synthesis of Novel N-Acetylgalactosamine-Terminated Glycolipids for Targeting of Lipoproteins to the Hepatic Asialoglycoprotein Receptor” J. Med. Chem. (2004) 47:5798-5808, SLIEDREGT et al., “Design and Synthesis of Novel Amphiphilic Dendritic Galactosides for Selective Targeting of Liposomes to the Hepatic Asialoglycoprotein Receptor” J. Med. Chem. (1999) 42:609-618, and Valentijn et al., “Solid-phase synthesis of lysine-based cluster galactosides with high affinity for the Asialoglycoprotein Receptor” Tetrahedron, 1997, 53(2), 759-770, each of which is incorporated by reference herein in its entirety.
In certain embodiments, conjugated antisense compounds comprise an RNase H based oligonucleotide (such as a gapmer) or a splice modulating oligonucleotide (such as a fully modified oligonucleotide) and any conjugate group comprising at least one, two, or three GalNAc groups. In certain embodiments a conjugated antisense compound comprises any conjugate group found in any of the following references: Lee, Carbohydr Res, 1978, 67, 509-514; Connolly et al., J Biol Chem, 1982, 257, 939-945; Pavia et al., Int J Pep Protein Res, 1983, 22, 539-548; Lee et al., Biochem, 1984, 23, 4255-4261; Lee et al., Glycoconjugate J, 1987, 4, 317-328; Toyokuni et al., Tetrahedron Lett, 1990, 31, 2673-2676; Biessen et al., J Med Chem, 1995, 38, 1538-1546; Valentijn et al., Tetrahedron, 1997, 53, 759-770; Kim et al., Tetrahedron Lett, 1997, 38, 3487-3490; Lee et al., Bioconjug Chem, 1997, 8, 762-765; Kato et al., Glycobiol, 2001, 11, 821-829; Rensen et al., J Biol Chem, 2001, 276, 37577-37584; Lee et al., Methods Enzymol, 2003, 362, 38-43; Westerlind et al., Glycoconj J, 2004, 21, 227-241; Lee et al., Bioorg Med Chem Lett, 2006, 16(19), 5132-5135; Maierhofer et al., Bioorg Med Chem, 2007, 15, 7661-7676; Khorev et al., Bioorg Med Chem, 2008, 16, 5216-5231; Lee et al., Bioorg Med Chem, 2011, 19, 2494-2500; Kornilova et al., Analyt Biochem, 2012, 425, 43-46; Pujol et al., Angew Chemie Int Ed Engl, 2012, 51, 7445-7448; Biessen et al., J Med Chem, 1995, 38, 1846-1852; Sliedregt et al., J Med Chem, 1999, 42, 609-618; Rensen et al., J Med Chem, 2004, 47, 5798-5808; Rensen et al., Arterioscler Thromb Vasc Biol, 2006, 26, 169-175; van Rossenberg et al., Gene Ther, 2004, 11, 457-464; Sato et al., J Am Chem Soc, 2004, 126, 14013-14022; Lee et al., J Org Chem, 2012, 77, 7564-7571; Biessen et al., FASEB J, 2000, 14, 1784-1792; Rajur et al., Bioconjug Chem, 1997, 8, 935-940; Duff et al., Methods Enzymol, 2000, 313, 297-321; Maier et al., Bioconjug Chem, 2003, 14, 18-29; Jayaprakash et al., Org Lett, 2010, 12, 5410-5413; Manoharan, Antisense Nucleic Acid Drug Dev, 2002, 12, 103-128; Merwin et al., Bioconjug Chem, 1994, 5, 612-620; Tomiya et al., Bioorg Med Chem, 2013, 21, 5275-5281; International applications WO1998/013381; WO2011/038356; WO1997/046098; WO2008/098788; WO2004/101619; WO2012/037254; WO2011/120053; WO2011/100131; WO2011/163121; WO2012/177947; WO2013/033230; WO2013/075035; WO2012/083185; WO2012/083046; WO2009/082607; WO2009/134487; WO2010/144740; WO2010/148013; WO1997/020563; WO2010/088537; WO2002/043771; WO2010/129709; WO2012/068187; WO2009/126933; WO2004/024757; WO2010/054406; WO2012/089352; WO2012/089602; WO2013/166121; WO2013/165816; U.S. Pat. Nos. 4,751,219; 8,552,163; 6,908,903; 7,262,177; 5,994,517; 6,300,319; 8,106,022; 7,491,805; 7,491,805; 7,582,744; 8,137,695; 6,383,812; 6,525,031; 6,660,720; 7,723,509; 8,541,548; 8,344,125; 8,313,772; 8,349,308; 8,450,467; 8,501,930; 8,158,601; 7,262,177; 6,906,182; 6,620,916; 8,435,491; 8,404,862; 7,851,615; Published U.S. Patent Application Publications US2011/0097264; US2011/0097265; US2013/0004427; US2005/0164235; US2006/0148740; US2008/0281044; US2010/0240730; US2003/0119724; US2006/0183886; US2008/0206869; US2011/0269814; US2009/0286973; US2011/0207799; US2012/0136042; US2012/0165393; US2008/0281041; US2009/0203135; US2012/0035115; US2012/0095075; US2012/0101148; US2012/0128760; US2012/0157509; US2012/0230938; US2013/0109817; US2013/0121954; US2013/0178512; US2013/0236968; US2011/0123520; US2003/0077829; US2008/0108801; and US2009/0203132; each of which is incorporated by reference in its entirety.
C. Certain Uses And Features
In certain embodiments, conjugated antisense compounds exhibit potent target RNA reduction in vivo. In certain embodiments, unconjugated antisense compounds accumulate in the kidney. In certain embodiments, conjugated antisense compounds accumulate in the liver. In certain embodiments, conjugated antisense compounds are well tolerated. Such properties render conjugated antisense compounds particularly useful for inhibition of many target RNAs, including, but not limited to those involved in metabolic, cardiovascular and other diseases, disorders or conditions. Thus, provided herein are methods of treating such diseases, disorders or conditions by contacting liver tissues with the conjugated antisense compounds targeted to RNAs associated with such diseases, disorders or conditions. Thus, also provided are methods for ameliorating any of a variety of metabolic, cardiovascular and other diseases, disorders or conditions with the conjugated antisense compounds of the present invention.
In certain embodiments, conjugated antisense compounds are more potent than unconjugated counterpart at a particular tissue concentration. Without wishing to be bound by any theory or mechanism, in certain embodiments, the conjugate may allow the conjugated antisense compound to enter the cell more efficiently or to enter the cell more productively. For example, in certain embodiments conjugated antisense compounds may exhibit greater target reduction as compared to its unconjugated counterpart wherein both the conjugated antisense compound and its unconjugated counterpart are present in the tissue at the same concentrations. For example, in certain embodiments conjugated antisense compounds may exhibit greater target reduction as compared to its unconjugated counterpart wherein both the conjugated antisense compound and its unconjugated counterpart are present in the liver at the same concentrations.
Productive and non-productive uptake of oligonucleotides has been discussed previously (See e.g. Geary, R. S., E. Wancewicz, et al. (2009). “Effect of Dose and Plasma Concentration on Liver Uptake and Pharmacologic Activity of a 2′-Methoxyethyl Modified Chimeric Antisense Oligonucleotide Targeting PTEN.” Biochem. Pharmacol. 78(3): 284-91; & Koller, E., T. M. Vincent, et al. (2011). “Mechanisms of single-stranded phosphorothioate modified antisense oligonucleotide accumulation in hepatocytes.” Nucleic Acids Res. 39(11): 4795-807). Conjugate groups described herein may improve productive uptake.
In certain embodiments, the conjugate groups described herein may further improve potency by increasing the affinity of the conjugated antisense compound for a particular type of cell or tissue. In certain embodiments, the conjugate groups described herein may further improve potency by increasing recognition of the conjugated antisense compound by one or more cell-surface receptors. In certain embodiments, the conjugate groups described herein may further improve potency by facilitating endocytosis of the conjugated antisense compound.
In certain embodiments, the cleavable moiety may further improve potency by allowing the conjugate to be cleaved from the antisense oligonucleotide after the conjugated antisense compound has entered the cell. Accordingly, in certain embodiments, conjugated antisense compounds can be administered at doses lower than would be necessary for unconjugated antisense oligonucleotides.
Phosphorothioate linkages have been incorporated into antisense oligonucleotides previously. Such phosphorothioate linkages are resistant to nucleases and so improve stability of the oligonucleotide. Further, phosphorothioate linkages also bind certain proteins, which results in accumulation of antisense oligonucleotide in the liver. Oligonucleotides with fewer phosphorothioate linkages accumulate less in the liver and more in the kidney (see, for example, Geary, R., “Pharmacokinetic Properties of 2′-O-(2-Methoxyethyl)-Modified Oligonucleotide Analogs in Rats,” Journal of Pharmacology and Experimental Therapeutics, Vol. 296, No. 3, 890-897; & Pharmacological Properties of 2′-O-Methoxyethyl Modified Oligonucleotides in Antisense a Drug Technology, Chapter 10, Crooke, S. T., ed., 2008) In certain embodiments, oligonucleotides with fewer phosphorothioate internucleoside linkages and more phosphodiester internucleoside linkages accumulate less in the liver and more in the kidney. When treating diseases in the liver, this is undesirable for several reasons (1) less drug is getting to the site of desired action (liver); (2) drug is escaping into the urine; and (3) the kidney is exposed to relatively high concentration of drug which can result in toxicities in the kidney. Thus, for liver diseases, phosphorothioate linkages provide important benefits.
In certain embodiments, however, administration of oligonucleotides uniformly linked by phosphorothioate internucleoside linkages induces one or more proinflammatory reactions. (see for example: J Lab Clin Med. 1996 September; 128(3):329-38. “Amplification of antibody production by phosphorothioate oligodeoxynucleotides”. Branda et al.; and see also for example: Toxicologic Properties in Antisense a Drug Technology, Chapter 12, pages 342-351, Crooke, S. T., ed., 2008). In certain embodiments, administration of oligonucleotides wherein most of the internucleoside linkages comprise phosphorothioate internucleoside linkages induces one or more proinflammatory reactions.
In certain embodiments, the degree of proinflammatory effect may depend on several variables (e.g. backbone modification, off-target effects, nucleobase modifications, and/or nucleoside modifications) see for example: Toxicologic Properties in Antisense a Drug Technology, Chapter 12, pages 342-351, Crooke, S. T., ed., 2008). In certain embodiments, the degree of proinflammatory effect may be mitigated by adjusting one or more variables. For example the degree of proinflammatory effect of a given oligonucleotide may be mitigated by replacing any number of phosphorothioate internucleoside linkages with phosphodiester internucleoside linkages and thereby reducing the total number of phosphorothioate internucleoside linkages.
In certain embodiments, it would be desirable to reduce the number of phosphorothioate linkages, if doing so could be done without losing stability and without shifting the distribution from liver to kidney. For example, in certain embodiments, the number of phosphorothioate linkages may be reduced by replacing phosphorothioate linkages with phosphodiester linkages. In such an embodiment, the antisense compound having fewer phosphorothioate linkages and more phosphodiester linkages may induce less proinflammatory reactions or no proinflammatory reaction. Although the the antisense compound having fewer phosphorothioate linkages and more phosphodiester linkages may induce fewer proinflammatory reactions, the antisense compound having fewer phosphorothioate linkages and more phosphodiester linkages may not accumulate in the liver and may be less efficacious at the same or similar dose as compared to an antisense compound having more phosphorothioate linkages. In certain embodiments, it is therefore desirable to design an antisense compound that has a plurality of phosphodiester bonds and a plurality of phosphorothioate bonds but which also possesses stability and good distribution to the liver.
In certain embodiments, conjugated antisense compounds accumulate more in the liver and less in the kidney than unconjugated counterparts, even when some of the phosporothioate linkages are replaced with less proinflammatory phosphodiester internucleoside linkages. In certain embodiments, conjugated antisense compounds accumulate more in the liver and are not excreted as much in the urine compared to its unconjugated counterparts, even when some of the phosporothioate linkages are replaced with less proinflammatory phosphodiester internucleoside linkages. In certain embodiments, the use of a conjugate allows one to design more potent and better tolerated antisense drugs. Indeed, in certain embodiments, conjugated antisense compounds have larger therapeutic indexes than unconjugated counterparts. This allows the conjugated antisense compound to be administered at a higher absolute dose, because there is less risk of proinflammatory response and less risk of kidney toxicity. This higher dose, allows one to dose less frequently, since the clearance (metabolism) is expected to be similar. Further, because the compound is more potent, as described above, one can allow the concentration to go lower before the next dose without losing therapeutic activity, allowing for even longer periods between dosing.
In certain embodiments, the inclusion of some phosphorothioate linkages remains desirable. For example, the terminal linkages are vulnerable to exonucleases and so in certain embodiments, those linkages are phosphorothioate or other modified linkage. Internucleoside linkages linking two deoxynucleosides are vulnerable to endonucleases and so in certain embodiments those those linkages are phosphorothioate or other modified linkage. Internucleoside linkages between a modified nucleoside and a deoxynucleoside where the deoxynucleoside is on the 5′ side of the linkage deoxynucleosides are vulnerable to endonucleases and so in certain embodiments those those linkages are phosphorothioate or other modified linkage. Internucleoside linkages between two modified nucleosides of certain types and between a deoxynucleoside and a modified nucleoside of certain type where the modified nucleoside is at the 5′ side of the linkage are sufficiently resistant to nuclease digestion, that the linkage can be phosphodiester.
In certain embodiments, the antisense oligonucleotide of a conjugated antisense compound comprises fewer than 16 phosphorthioate linkages. In certain embodiments, the antisense oligonucleotide of a conjugated antisense compound comprises fewer than 15 phosphorthioate linkages. In certain embodiments, the antisense oligonucleotide of a conjugated antisense compound comprises fewer than 14 phosphorthioate linkages. In certain embodiments, the antisense oligonucleotide of a conjugated antisense compound comprises fewer than 13 phosphorthioate linkages. In certain embodiments, the antisense oligonucleotide of a conjugated antisense compound comprises fewer than 12 phosphorthioate linkages. In certain embodiments, the antisense oligonucleotide of a conjugated antisense compound comprises fewer than 11 phosphorthioate linkages. In certain embodiments, the antisense oligonucleotide of a conjugated antisense compound comprises fewer than 10 phosphorthioate linkages. In certain embodiments, the antisense oligonucleotide of a conjugated antisense compound comprises fewer than 9 phosphorthioate linkages. In certain embodiments, the antisense oligonucleotide of a conjugated antisense compound comprises fewer than 8 phosphorthioate linkages.
In certain embodiments, antisense compounds comprising one or more conjugate group described herein has increased activity and/or potency and/or tolerability compared to a parent antisense compound lacking such one or more conjugate group. Accordingly, in certain embodiments, attachment of such conjugate groups to an oligonucleotide is desirable. Such conjugate groups may be attached at the 5′-, and/or 3′-end of an oligonucleotide. In certain instances, attachment at the 5′-end is synthetically desirable. Typically, oligonucleotides are synthesized by attachment of the 3′ terminal nucleoside to a solid support and sequential coupling of nucleosides from 3′ to 5′ using techniques that are well known in the art. Accordingly if a conjugate group is desired at the 3′-terminus, one may (1) attach the conjugate group to the 3′-terminal nucleoside and attach that conjugated nucleoside to the solid support for subsequent preparation of the oligonucleotide or (2) attach the conjugate group to the 3′-terminal nucleoside of a completed oligonucleotide after synthesis. Neither of these approaches is very efficient and thus both are costly. In particular, attachment of the conjugated nucleoside to the solid support, while demonstrated in the Examples herein, is an inefficient process. In certain embodiments, attaching a conjugate group to the 5′-terminal nucleoside is synthetically easier than attachment at the 3′-end. One may attach a non-conjugated 3′ terminal nucleoside to the solid support and prepare the oligonucleotide using standard and well characterized reactions. One then needs only to attach a 5′nucleoside having a conjugate group at the final coupling step. In certain embodiments, this is more efficient than attaching a conjugated nucleoside directly to the solid support as is typically done to prepare a 3′-conjugated oligonucleotide. The Examples herein demonstrate attachment at the 5′-end. In addition, certain conjugate groups have synthetic advantages. For Example, certain conjugate groups comprising phosphorus linkage groups are synthetically simpler and more efficiently prepared than other conjugate groups, including conjugate groups reported previously (e.g., WO/2012/037254).
In certain embodiments, conjugated antisense compounds are administered to a subject. In such embodiments, antisense compounds comprising one or more conjugate group described herein has increased activity and/or potency and/or tolerability compared to a parent antisense compound lacking such one or more conjugate group. Without being bound by mechanism, it is believed that the conjugate group helps with distribution, delivery, and/or uptake into a target cell or tissue. In certain embodiments, once inside the target cell or tissue, it is desirable that all or part of the conjugate group to be cleaved to release the active oligonucleotide. In certain embodiments, it is not necessary that the entire conjugate group be cleaved from the oligonucleotide. For example, in Example 20 a conjugated oligonucleotide was administered to mice and a number of different chemical species, each comprising a different portion of the conjugate group remaining on the oligonucleotide, were detected (Table 10a). This conjugated antisense compound demonstrated good potency (Table 10). Thus, in certain embodiments, such metabolite profile of multiple partial cleavage of the conjugate group does not interfere with activity/potency. Nevertheless, in certain embodiments it is desirable that a prodrug (conjugated oligonucleotide) yield a single active compound. In certain instances, if multiple forms of the active compound are found, it may be necessary to determine relative amounts and activities for each one. In certain embodiments where regulatory review is required (e.g., USFDA or counterpart) it is desirable to have a single (or predominantly single) active species. In certain such embodiments, it is desirable that such single active species be the antisense oligonucleotide lacking any portion of the conjugate group. In certain embodiments, conjugate groups at the 5′-end are more likely to result in complete metabolism of the conjugate group. Without being bound by mechanism it may be that endogenous enzymes responsible for metabolism at the 5′ end (e.g., 5′ nucleases) are more active/efficient than the 3′ counterparts. In certain embodiments, the specific conjugate groups are more amenable to metabolism to a single active species. In certain embodiments, certain conjugate groups are more amenable to metabolism to the oligonucleotide.
D. Antisense
In certain embodiments, oligomeric compounds of the present invention are antisense compounds. In such embodiments, the oligomeric compound is complementary to a target nucleic acid. In certain embodiments, a target nucleic acid is an RNA. In certain embodiments, a target nucleic acid is a non-coding RNA. In certain embodiments, a target nucleic acid encodes a protein. In certain embodiments, a target nucleic acid is selected from a mRNA, a pre-mRNA, a microRNA, a non-coding RNA, including small non-coding RNA, and a promoter-directed RNA. In certain embodiments, oligomeric compounds are at least partially complementary to more than one target nucleic acid. For example, oligomeric compounds of the present invention may be microRNA mimics, which typically bind to multiple targets.
In certain embodiments, antisense compounds comprise a portion having a nucleobase sequence at least 70% complementary to the nucleobase sequence of a target nucleic acid. In certain embodiments, antisense compounds comprise a portion having a nucleobase sequence at least 80% complementary to the nucleobase sequence of a target nucleic acid. In certain embodiments, antisense compounds comprise a portion having a nucleobase sequence at least 90% complementary to the nucleobase sequence of a target nucleic acid. In certain embodiments, antisense compounds comprise a portion having a nucleobase sequence at least 95% complementary to the nucleobase sequence of a target nucleic acid. In certain embodiments, antisense compounds comprise a portion having a nucleobase sequence at least 98% complementary to the nucleobase sequence of a target nucleic acid. In certain embodiments, antisense compounds comprise a portion having a nucleobase sequence that is 100% complementary to the nucleobase sequence of a target nucleic acid. In certain embodiments, antisense compounds are at least 70%, 80%, 90%, 95%, 98%, or 100% complementary to the nucleobase sequence of a target nucleic acid over the entire length of the antisense compound.
Antisense mechanisms include any mechanism involving the hybridization of an oligomeric compound with target nucleic acid, wherein the hybridization results in a biological effect. In certain embodiments, such hybridization results in either target nucleic acid degradation or occupancy with concomitant inhibition or stimulation of the cellular machinery involving, for example, translation, transcription, or polyadenylation of the target nucleic acid or of a nucleic acid with which the target nucleic acid may otherwise interact.
One type of antisense mechanism involving degradation of target RNA is RNase H mediated antisense. RNase H is a cellular endonuclease which cleaves the RNA strand of an RNA:DNA duplex. It is known in the art that single-stranded antisense compounds which are “DNA-like” elicit RNase H activity in mammalian cells. Activation of RNase H, therefore, results in cleavage of the RNA target, thereby greatly enhancing the efficiency of DNA-like oligonucleotide-mediated inhibition of gene expression.
Antisense mechanisms also include, without limitation RNAi mechanisms, which utilize the RISC pathway. Such RNAi mechanisms include, without limitation siRNA, ssRNA and microRNA mechanisms. Such mechanisms include creation of a microRNA mimic and/or an anti-microRNA.
Antisense mechanisms also include, without limitation, mechanisms that hybridize or mimic non-coding RNA other than microRNA or mRNA. Such non-coding RNA includes, but is not limited to promoter-directed RNA and short and long RNA that effects transcription or translation of one or more nucleic acids.
In certain embodiments, oligonucleotides comprising conjugates described herein are RNAi compounds. In certain embodiments, oligomeric oligonucleotides comprising conjugates described herein are ssRNA compounds. In certain embodiments, oligonucleotides comprising conjugates described herein are paired with a second oligomeric compound to form an siRNA. In certain such embodiments, the second oligomeric compound also comprises a conjugate. In certain embodiments, the second oligomeric compound is any modified or unmodified nucleic acid. In certain embodiments, the oligonucleotides comprising conjugates described herein is the antisense strand in an siRNA compound. In certain embodiments, the oligonucleotides comprising conjugates described herein is the sense strand in an siRNA compound. In embodiments in which the conjugated oligomeric compound is double-stranded siRnA, the conjugate may be on the sense strand, the antisense strand or both the sense strand and the antisense strand.
D. Target Nucleic Acids, Regions and Segments
In certain embodiments, conjugated antisense compounds target any nucleic acid. In certain embodiments, the target nucleic acid encodes a target protein that is clinically relevant. In such embodiments, modulation of the target nucleic acid results in clinical benefit. Certain target nucleic acids include, but are not limited to, the target nucleic acids illustrated in Table 1.







TABLE 1







Certain Human Target Nucleic Acids











SEQ ID


Target
GENBANK ® Accession Number
NO












PTP1B
NM_002827.2
1



NT_011362.9 truncated from nucleotides
2



14178000 to 14256000


FGFR4
NM_002011.3
3



NT_023133.11 truncated from nucleosides
4



21323018 to 21335213



AB209631.1
5



NM_022963.2
6


GCCR
the complement of GENBANK Accession
7



No. NT_029289.10 truncated from



nucleotides 3818000 to 3980000


GCGR
NM_000160.3
8



NW_926918.1 truncated from nucleotides
9



16865000 to 16885000


Factor VII
NT_027140.6 truncated from nucleotides
10



1255000 to 1273000



NM_019616.2
11



DB184141.1
12



NW_001104507.1 truncated from
13



nucleotides 691000 to 706000


Factor XI
NM_000128.3
14



NT_022792.17, truncated from 19598000
15



to 19624000



NM_028066.1
16



NW_001118167.1
17









The targeting process usually includes determination of at least one target region, segment, or site within the target nucleic acid for the antisense interaction to occur such that the desired effect will result.
In certain embodiments, a target region is a structurally defined region of the nucleic acid. For example, in certain such embodiments, a target region may encompass a 3′ UTR, a 5′ UTR, an exon, an intron, a coding region, a translation initiation region, translation termination region, or other defined nucleic acid region or target segment.
In certain embodiments, a target segment is at least about an 8-nucleobase portion of a target region to which a conjugated antisense compound is targeted. Target segments can include DNA or RNA sequences that comprise at least 8 consecutive nucleobases from the 5′-terminus of one of the target segments (the remaining nucleobases being a consecutive stretch of the same DNA or RNA beginning immediately upstream of the 5′-terminus of the target segment and continuing until the DNA or RNA comprises about 8 to about 30 nucleobases). Target segments are also represented by DNA or RNA sequences that comprise at least 8 consecutive nucleobases from the 3′-terminus of one of the target segments (the remaining nucleobases being a consecutive stretch of the same DNA or RNA beginning immediately downstream of the 3′-terminus of the target segment and continuing until the DNA or RNA comprises about 8 to about 30 nucleobases). Target segments can also be represented by DNA or RNA sequences that comprise at least 8 consecutive nucleobases from an internal portion of the sequence of a target segment, and may extend in either or both directions until the conjugated antisense compound comprises about 8 to about 30 nucleobases.
In certain embodiments, antisense compounds targeted to the nucleic acids listed in Table 1 can be modified as described herein. In certain embodiments, the antisense compounds can have a modified sugar moiety, an unmodified sugar moiety or a mixture of modified and unmodified sugar moieties as described herein. In certain embodiments, the antisense compounds can have a modified internucleoside linkage, an unmodified internucleoside linkage or a mixture of modified and unmodified internucleoside linkages as described herein. In certain embodiments, the antisense compounds can have a modified nucleobase, an unmodified nucleobase or a mixture of modified and unmodified nucleobases as described herein. In certain embodiments, the antisense compounds can have a motif as described herein.
In certain embodiments, antisense compounds targeted to the nucleic acids listed in Table 1 can be conjugated as described herein.
1. Protein Tyrosine Phosphatase 1B (PTP1B)
Protein tyrosine phosphatase 1B (PTP1B) is a member of a family of PTPs (Barford, et al., Science 1994. 263: 1397-1404) and is a cytosolic enzyme (Neel and Tonks, Curr. Opin. Cell Biol. 1997. 9: 193-204). PTP1B is expressed ubiquitously including tissues that are key regulators of insulin metabolism such as liver, muscle and fat (Goldstein, Receptor 1993. 3: 1-15), where it is the main PTP enzyme.
PTP1B is considered to be a negative regulator of insulin signaling. PTP1B interacts with and dephosphorylates the insulin receptor, thus attenuating and potentially terminating the insulin signaling transduction (Goldstein et al., J. Biol. Chem. 2000. 275: 4383-4389). The physiological role of PTP1B in insulin signaling has been demonstrated in knockout mice models. Mice lacking the PTP1B gene were protected against insulin resistance and obesity (Elchebly et al., Science 1999. 283: 1544-1548). PTP1B-deficient mice had low adiposity, increased basal metabolic rate as well as total energy expenditure and were protected from diet-induced obesity. Insulin-stimulated glucose uptake was elevated in skeletal muscle, whereas adipose tissue was unaffected providing evidence that increased insulin sensitivity in PTP1B-deficient mice was tissue-specific (Klaman et al., Mol. Cell. Biol. 2000. 20: 5479-5489). These mice were phenotypically normal and were also resistant to diet-induced obesity, insulin resistance and had significantly lower triglyceride levels on a high-fat diet. Therefore, inhibition of PTP1B in patients suffering from Type II diabetes, metabolic syndrome, diabetic dyslipidemia, or related metabolic diseases would be beneficial.
Antisense inhibition of PTP1B provides a unique advantage over traditional small molecule inhibitors in that antisense inhibitors do not rely on competitive binding of the compound to the protein and inhibit activity directly by reducing the expression of PTP1B. Antisense technology is emerging as an effective means for reducing the expression of certain gene products and may therefore prove to be uniquely useful in a number of therapeutic, diagnostic, and research applications for the modulation of PTP1B.
There is a currently a lack of acceptable options for treating metabolic disorders. It is therefore an object herein to provide compounds and methods for the treatment of such diseases and disorder.
All documents, or portions of documents, cited in this application, including, but not limited to, patents, patent applications, articles, books, and treatises, are hereby expressly incorporated-by-reference for the portions of the document discussed herein, as well as in their entirety.
Certain Conjugated Antisense Compounds Targeted to a PTP1B Nucleic Acid
In certain embodiments, conjugated antisense compounds are targeted to a PTP1B nucleic acid having the sequence of GENBANK® Accession No. NM_002827.2, incorporated herein as SEQ ID NO: 1 or GENBANK Accession No. NT_011362.9 truncated from nucleotides 14178000 to Ser. No. 14/256,000, incorporated herein as SEQ ID NO: 2. In certain such embodiments, a conjugated antisense compound targeted to SEQ ID NO: 1 is at least 90%, at least 95%, or 100% complementary to SEQ ID NOs: 1 and/or 2.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 1 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 54. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 1 comprises a nucleobase sequence of SEQ ID NO: 54.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 1 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 55. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 1 comprises a nucleobase sequence of SEQ ID NO: 55.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 1 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 56. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 1 comprises a nucleobase sequence of SEQ ID NO: 56.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 1 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 57. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 1 comprises a nucleobase sequence of SEQ ID NO: 57.







TABLE 2 







Antisense Compounds targeted to PTP1B SEQ ID NO: 1












Target


SEQ


ISIS
Start


ID


No
Site
Sequence (5′-3′)
Motif
NO





142082
3291
AAATGGTTTATTCCATGGCC
5-10-5 MOE
54


 


404173
3290
AATGGTTTATTCCATGGCCA
5-10-5 MOE
55


 


409826
3287
GGTTTATTCCATGGCCATTG
5-10-5 MOE
56


 


446431
3292
AATGGTTTATTCCATGGC
4-10-4 MOE
57









In certain embodiments, a compound comprises or consists of ISIS 142082 and a conjugate group. ISIS 142082 is a modified oligonucleotide having the formula: Aes Aes Aes Tes Ges Gds Tds Tds Tds Ads Tds Tds mCds mCds Ads Tes Ges Ges mCes mCe, wherein,
A=an adenine,
mC=a 5′-methylcytosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside,
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises or consists of ISIS 404173 and a conjugate group. ISIS 404173 is a modified oligonucleotide having the formula: Aes Aes Tes Ges Ges Tds Tds Tds Ads Tds Tds mCds mCds Ads Tds Ges Ges mCes mCes Ae, wherein,
A=an adenine,
mC=a 5′-methylcytosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside,
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises or consists of ISIS 409826 and a conjugate group. ISIS 409826 is a modified oligonucleotide having the formula: Ges Ges Tes Tes Tes Ads Tds Tds mCds mCds Ads Tds Gds Gds mCds mCes Aes Tes Tes Ge, wherein,
A=an adenine,
mC=a 5′-methylcytosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside,
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises or consists of ISIS 446431 and a conjugate group. ISIS 446431 is a modified oligonucleotide having the formula: Aes Aes Tes Ges Gds Tds Tds Tds Ads Tds Tds mCds mCds Ads Tes Ges Ges mCe, wherein,
A=an adenine,
mC=a 5′-methylcytosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside,
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises an antisense oligonucleotide disclosed in U.S. Pat. No. 7,563,884 and WO 2007/131237, which is incorporated by reference in its entirety herein, and a conjugate group described herein. In certain embodiments, a compound comprises an antisense oligonucleotide having a nucleobase sequence of any of SEQ ID NOs 17-96 and 244-389 disclosed in U.S. Pat. No. 7,563,884 and a conjugate group described herein. In certain embodiments, a compound comprises an antisense oligonucleotide having a nucleobase sequence of any of SEQ ID NOs 886-1552 of SEQ ID Nos WO 2007/131237 and a conjugate group described herein. In certain embodiments, a compound comprises an antisense oligonucleotide disclosed in U.S. Pat. No. 7,563,884 and WO 2007/131237, which is incorporated by reference in its entirety herein, and a conjugate group described herein. In certain embodiments, a compound comprises an antisense oligonucleotide having a nucleobase sequence of any of SEQ ID NOs disclosed in U.S. Pat. No. 7,563,884 and WO 2007/131237 and a conjugate group described herein. The nucleobase sequences of all of the aforementioned referenced SEQ ID NOs are incorporated by reference herein.
PTP1B Therapeutic Indications
In certain embodiments, provided herein are methods of treating an individual comprising administering one or more conjugated pharmaceutical compositions as described herein. In certain embodiments, the individual has metabolic related disease.
As shown in the examples below, conjugated compounds targeted to PTP1B, as described herein, have been shown to reduce the severity of physiological symptoms of metabolic related diseases, including metabolic syndrome, diabetes mellitus, insulin resistance, diabetic dyslipidemia, hypertriglyceridemia, obesity and weight gain. In certain of the experiments, the conjugated compounds reduced blood glucose levels, e.g., the animals continued to experience symptoms, but the symptoms were less severe compared to untreated animals. In other of the experiments, however, the conjugated compounds appear to reduce the symptoms of diabetes; e g., animals treated for a longer period of time experienced less severe symptoms than those administered the compounds for a shorter period of time. In other of the experiments, however, the conjugated compounds appear to inhibit weight gain; e g., animals treated for a longer period of time experienced less severe symptoms than those administered the compounds for a shorter period of time. In other of the experiments, however, the conjugated compounds appear to inhibit hypertriglyceridemia; e.g., animals treated for a longer period of time experienced less severe symptoms than those administered the compounds for a shorter period of time. The ability of the conjugated compounds exemplified below to restore function therefore demonstrates that symptoms of the disease may be reversed by treatment with a compound as described herein.
Diabetes mellitus is characterized by numerous physical and physiological symptoms. Any symptom known to one of skill in the art to be associated with Type 2 diabetes can be ameliorated or otherwise modulated as set forth above in the methods described above. In certain embodiments, the symptom is a physical symptom selected from the group consisting of increased glucose levels, increased weight gain, frequent urination, unusual thirst, extreme hunger, extreme fatigue, blurred vision, frequent infections, tingling or numbness at the extremities, dry and itchy skin, weight loss, slow-healing sores, and swollen gums
In certain embodiments, the symptom is a physiological symptom selected from the group consisting of increased insulin resistance, increased glucose levels, increased fat mass, decreased metabolic rate, decreased glucose clearance, decreased glucose tolerance, decreased insulin sensitivity, decreased hepatic insulin sensitivity, increased adipose tissue size and weight, increased body fat, and increased body weight.
Liu and Chernoff have shown that PTP1B binds to and serves as a substrate for the epidermal growth factor receptor (EGFR) (Liu and Chernoff, Biochem. J., 1997, 327, 139-145). Furthermore, in A431 human epidermoid carcinoma cells, PT1B was found to be inactivated by the presence of H2O2 generated by the addition of EGF. These studies indicate that PTP1B can be negatively regulated by the oxidation state of the cell, which is often deregulated during tumorigenesis (Lee et al., J. Biol. Chem., 1998, 273, 15366-15372).
Overexpression of PTP1B has been demonstrated in malignant ovarian cancers and this correlation was accompanied by a concomitant increase in the expression of the associated growth factor receptor (Wiener et al., Am. J. Obstet. Gynecol., 1994, 170, 1177-1183).
PTP1B has been shown to suppress transformation in NIH3T3 cells induced by the neu oncogene (Brown-Shimer et al., Cancer Res., 1992, 52, 478-482), as well as in rat 3Y1 fibroblasts induced by v-srk, v-src, and v-ras (Liu et al., Mol. Cell. Biol., 1998, 18, 250-259) and rat-1 fibroblasts induced by bcr-abl (LaMontagne et al., Proc. Natl. Acad. Sci. U.S.A, 1998, 95, 14094-14099). It has also been shown that PTP1B promotes differentiation of K562 cells, a chronic myelogenous leukemia cell line, in a similar manner as does an inhibitor of the bcr-abl oncoprotein. These studies describe the possible role of PTP1B in controlling the pathogenesis of chronic myeloid leukemia (LaMontagne et al., Proc. Natl. Acad. Sci. U.S.A, 1998, 95, 14094-14099).
Accordingly, provided herein are methods for ameliorating a symptom associated with hyperproliferative disorders in a subject in need thereof. In certain embodiments, the hyperproliferative disorder is cancer. In certain embodiments, provided herein are methods for ameliorating a symptom associated with cancer. In certain embodiments, provided is a method for reducing the rate of onset of a symptom associated with hyperproliferative disorders. In certain embodiments, provided is a method for reducing the rate of onset of a symptom associated with cancer. In certain embodiments, provided is a method for reducing the severity of a symptom associated with hyperproliferative disorders. In certain embodiments, provided is a method for reducing the severity of a symptom associated with cancer. In such embodiments, the methods comprise administering to an individual in need thereof a therapeutically effective amount of a compound targeted to a PTP1B nucleic acid.
In certain embodiments, provided are methods of treating an individual comprising administering one or more conjugated pharmaceutical compositions as described herein. In certain embodiments, the individual has metabolic related disease.
In certain embodiments, administration of a conjugated antisense compound targeted to a PTP1B nucleic acid results in reduction of PTP1B expression by at least about 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or 99%, or a range defined by any two of these values.
In certain embodiments, pharmaceutical compositions comprising a conjugated antisense compound targeted to PTP1B are used for the preparation of a medicament for treating a patient suffering or susceptible to metabolic related disease.
In certain embodiments, the methods described herein include administering a compound comprising a conjugate group and a modified oligonucleotide having a contiguous nucleobases portion as described herein of a sequence recited in SEQ ID NOs: 54-57.
It will be understood that any of the compounds described herein can be used in the aforementioned methods and uses. For example, in certain embodiments a conjugated antisense compound targeted to a PTP1B nucleic acid in the aforementioned methods and uses can include, but is not limited to, a conjugated antisense compound targeted to SEQ ID NO: 1 comprising an at least 8 consecutive nucleobase sequence of any of SEQ ID NOs: 54-57; a conjugated antisense compound targeted to SEQ ID NO: 1 comprising a nucleobase sequence of any of SEQ ID NOs: 54-57; a compound comprising or consisting of ISIS 142082, ISIS 404173, ISIS 409826, or ISIS 446431 and a conjugate group; a compound comprising an antisense oligonucleotide disclosed in U.S. Pat. No. 7,563,884 and WO 2007/131237, which is incorporated by reference in its entirety herein, and a conjugate group; a compound comprising an antisense oligonucleotide having a nucleobase sequence of any of SEQ ID NOs 17-96 and 244-389 disclosed in U.S. Pat. No. 7,563,884 and a conjugate group described herein; or a compound comprising an antisense oligonucleotide having a nucleobase sequence of any of—SEQ ID NOs 886-1552 disclosed in WO 2007/131237 and a conjugate group described herein.
2. FGFR4
Obesity is considered a long-term metabolic disease. There are several serious medical sequelae related to obesity. There are over 1 billion overweight individuals worldwide with 100 million clinically obese. The increasing health care costs of treating obesity related diseases in the US alone are estimated at over $100 billion annually. Current methods for treating obesity include behavioral modification, diet, surgery (gastroplasty), administering pharmaceutical agents that block appetite stimulating signals or absorption of nutrients (fat), and administering agents that increase thermogenesis or fat metabolism. Some of these methods have disadvantages in that they rely on patient resolve, are invasive, or have unwanted side effects. An understanding of the mechanisms by which obesity is regulated may provide important therapeutic information.
Obesity is frequently associated with insulin resistance and together constitutes risk factors for later development of type 2 diabetes and cardiovascular diseases. Insulin resistance occurs well before development of type 2 diabetes, and insulin is overproduced to compensate for the insulin resistance and to maintain normal glucose levels. Type 2 diabetes ensues, as the pancreas can no longer produce enough insulin to maintain normal glucose levels. Early stages of type 2 diabetes are associated with elevated levels of insulin but as the disease progresses the pancreas may fail to produce insulin, resulting in increased blood glucose levels. Diabetes is a significant risk factor for both heart disease and stroke and is the leading cause of blindness and end-stage renal failure.
Diabetes is a disorder characterized by hyperglycemia due to deficient insulin action that may result from reduced insulin production or insulin resistance or both. Diabetes mellitus is a polygenic disorder affecting a significant portion of the people in the world. It is divided into two types. In type I diabetes, or insulin-dependent diabetes mellitus (IDDM), patients produce little or no insulin, the hormone that regulates glucose utilization. In type 2 diabetes, or noninsulin-dependent diabetes mellitus (NIDDM), patients often have plasma insulin levels that are the same compared to nondiabetic humans; however, these patients have developed a resistance to the insulin stimulating effect of glucose and lipid metabolism in the main insulin-sensitive tissues, i.e., muscle, liver and adipose tissues, and the plasma insulin levels are insufficient to overcome the pronounced insulin resistance. Additionally, glucotoxicity, which results from long-term hyperglycemia, induces tissue-dependent insulin resistance (Nawano et al., Am. J. Physiol. Endocrinol. Metab., 278, E535-543) exacerbating the disease. Type 2 diabetes accounts for over 90% of all diabetes cases. It is a metabolic disorder characterized by hyperglycemia leading to secondary complications such as neuropathy, nephropathy, retinopathy, hypertriglyceridemia, obesity, and other cardiovascular diseases generally referred to as metabolic syndrome.
Metabolic syndrome is a combination of medical disorders that increase one's risk for cardiovascular disease and diabetes. The symptoms, including high blood pressure, high triglycerides, decreased HDL and obesity, tend to appear together in some individuals. Metabolic syndrome is known under various other names, such as (metabolic) syndrome X, insulin resistance syndrome or Reaven's syndrome.
Diabetes and obesity (sometimes now collectively referred to as “diabesity”) are interrelated in that obesity is known to exacerbate the pathology of diabetes and greater than 60% of diabetics are obese. Most human obesity is associated with insulin resistance and leptin resistance. In fact, it has been suggested that obesity may have an even greater impact on insulin action than diabetes itself (Sindelka et al., Physiol Res., 51, 85-91). Additionally, several compounds on the market for the treatment of diabetes are known to induce weight gain, a very undesirable side effect to the treatment of this disease. Therefore, a compound that has the potential to treat both diabetes and obesity would provide a significant improvement over current treatments.
Fibroblast growth factor receptor 4 (also known as FGF receptor-4, TKF; tyrosine kinase related to fibroblast growth factor receptor; hydroxyaryl-protein kinase; tyrosylprotein kinase; Fgfr4; FGFR-4; FGFR4; CD334, FGFR4_HUMAN and JTK2) has high affinity for the acidic and/or basic fibroblast growth factors. (Armstrong et al., Genes Chromosomes Cancer, 4, 94-98).
Although FGFRs generally have been shown to have wide distribution throughout the body, to date, FGFR4 has only been found in a few tissues. Among a wide variety of cells and tissues tested, including human lymphocytes and macrophages, FGFR4 was found to be expressed in the lung and in some tumors of lung origin as well as in malignancies not derived from lung tissues. (Holtrich et al., Proc. Nat. Acad. Sci., 88, 10411-10415). FGFR4 has also been found to be expressed in the liver and in adipose tissues. (Patel et al., JCEM, 90(2), 1226-1232). FGFR4 has also been found to be expressed in certain carcinoma cell lines. (Bange et al., Cancer Res., 62, 840-847).
Additionally, FGFR4 has been shown to play a role in systemic lipid and glucose homeostasis. FGFR4-deficient mice on a normal diet exhibited features of metabolic syndrome that include increase mass of insulin resistance, in addition to hypercholesterolemia. FGFR4 deficiency was shown to alleviate high-fat diet-induced fatty liver in a certain obese mouse model, which is also a correlate of metabolic syndrome. Restoration of FGFR4, specifically in hepatocytes of FGFR4 deficient mice, decrease plasma lipid level and restored the high fat diet-induced fatty liver but failed to restore glucose tolerance and sensitivity to insulin. (Huang et al., Diabetes, 56, 2501-2510).
Antisense inhibition of FGFR4 provides a unique advantage over traditional small molecule inhibitors in that antisense inhibitors do not rely on competitive binding of the compound to the protein and inhibit activity directly by reducing the expression of FGFR4. A representative United States patent that teaches FGFR4 antisense inhibitors includes US. Pat. Publication No. US2010/0292140, of which is herein incorporated by reference in its entirety. Antisense technology is emerging as an effective means for reducing the expression of certain gene products and may therefore prove to be uniquely useful in a number of therapeutic, diagnostic, and research applications for the modulation of FGFR4.
There is a currently a lack of acceptable options for treating metabolic disorders. It is therefore an object herein to provide compounds and methods for the treatment of such diseases and disorder. This invention relates to the discovery of novel, highly potent inhibitors of FGFR4 gene expression.
All documents, or portions of documents, cited in this application, including, but not limited to, patents, patent applications, articles, books, and treatises, are hereby expressly incorporated-by-reference for the portions of the document discussed herein, as well as in their entirety.
Certain Conjugated Antisense Compounds Targeted to a FGFR4 Nucleic Acid
In certain embodiments, conjugated antisense compounds are targeted to a FGFR4 nucleic acid having the sequence GENBANK Accession No. NM_002011.3 (incorporated herein as SEQ ID NO: 3), GENBANK Accession No: NT_023133.11 truncated from nucleosides 21323018 to 21335213 (incorporated herein as SEQ ID NO: 4); and GENBANK Accession No. AB209631.1 (incorporated herein as SEQ ID NO: 5); and GENBANK Accession No NM_022963.2 (incorporated herein as SEQ ID NO: 6). In certain such embodiments, a conjugated antisense compound targeted to SEQ ID NOs: 3-6 is at least 90%, at least 95%, or 100% complementary to SEQ ID NOs: 3-6.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 3 comprises an at least 8 consecutive nucleobase sequence of any one of SEQ ID NOs: 58-65. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 3 comprises a nucleobase sequence of any one of SEQ ID NO: 12-19.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 3 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 58. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 3 comprises a nucleobase sequence of SEQ ID NO: 59.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 3 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 59. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 3 comprises a nucleobase sequence of SEQ ID NO: 59.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 3 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 60. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 3 comprises a nucleobase sequence of SEQ ID NO: 60.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 3 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 61. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 3 comprises a nucleobase sequence of SEQ ID NO: 61.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 3 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 62. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 3 comprises a nucleobase sequence of SEQ ID NO: 62.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 3 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 63. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 3 comprises a nucleobase sequence of SEQ ID NO: 63.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 3 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 64. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 3 comprises a nucleobase sequence of SEQ ID NO: 64.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 3 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 65. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 3 comprises a nucleobase sequence of SEQ ID NO: 65.







TABLE 3 







Antisense Compounds targeted to FGFR4 SEQ ID NO: 3












Target


SEQ


ISIS
Start


ID


No
Site
Sequence (5′-3′)
Motif
NO














299005
192
GGCACACTCAGCAGGACCCC
5-10-5 MOE
58


 


463588
191
GCACACTCAGCAGGACCCCC
5-10-5 MOE
59


 


463589
193
AGGCACACTCAGCAGGACCC
5-10-5 MOE
60


 


463690
369
GCCAGGCGACTGCCCTCCTT
5-10-5 MOE
61


 


463691
370
TGCCAGGCGACTGCCCTCCT
5-10-5 MOE
62


 


463835
788
CGCTCTCCATCACGAGACTC
5-10-5 MOE
63


 


463837
790
CACGCTCTCCATCACGAGAC
5-10-5 MOE
64


 


464225
2954
CTTCCAGCTTCTCTGGGCTC
5-10-5 MOE
65









In certain embodiments, a compound comprises or consists of ISIS 299005 and a conjugate group. ISIS 299005 is a modified oligonucleotide having the formula: Ges Ges mCes Aes mCes Ads mCds Tds mCds Ads Gds mCds Ads Gds Gds Aes mCes mCes mCes mCe, wherein
A=an adenine,
mC=a 5′-methylcytosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside,
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises or consists of ISIS 463588 and a conjugate group. ISIS 463588 is a modified oligonucleotide having the formula: Ges mCes Aes mCes Aes mCds Tds mCds Ads Gds mCds Ads Gds Gds Ads mCes mCes mCes mCes mCe, wherein
A=an adenine,
mC=a 5′-methylcytosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside,
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises or consists of ISIS 463589 and a conjugate group. ISIS 463589 is a modified oligonucleotide having the formula: Aes Ges Ges mCes Aes mCds Ads mCds Tds mCds Ads Gds mCds Ads Gds Ges Aes mCes mCes mCe, wherein
A=an adenine,
mC=a 5′-methylcytosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside,
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises or consists of ISIS 463690 and a conjugate group. ISIS 463690 is a modified oligonucleotide having the formula: Ges mCes mCes Aes Ges Gds mCds Gds Ads mCds Tds Gds mCds mCds mCds Tes mCes mCes Tes Te, wherein
A=an adenine,
mC=a 5′-methylcytosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside,
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises or consists of ISIS 463691 and a conjugate group. ISIS 463691 is a modified oligonucleotide having the formula: Tes Ges mCes mCes Aes Gds Gds mCds Gds Ads mCds Tds Gds mCds mCds mCes Tes mCes mCes Te, wherein
A=an adenine,
mC=a 5′-methylcytosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside,
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises or consists of ISIS 463835 and a conjugate group. ISIS 463835 is a modified oligonucleotide having the formula: mCes Ges mCes Tes mCes Tds mCds mCds Ads Tds mCds Ads mCds Gds Ads Ges Aes mCes Tes mCe, wherein
A=an adenine,
mC=a 5′-methylcytosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside,
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises or consists of ISIS 463837 and a conjugate group. ISIS 463837 is a modified oligonucleotide having the formula: mCes Aes mCes Ges mCes Tds mCds Tds mCds mCds Ads Tds mCds Ads mCds Ges Aes Ges Aes mCe, wherein
A=an adenine,
mC=a 5′-methylcytosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside,
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises or consists of ISIS 464225 and a conjugate group. ISIS 464225 is a modified oligonucleotide having the formula: mCes Tes Tes mCes mCes Ads Gds mCds Tds Tds mCds Tds mCds Tds Gds Ges Ges mCes Tes mCe, wherein
A=an adenine,
mC=a 5′-methylcytosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside,
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises an antisense oligonucleotide disclosed in WO 2009/046141, which are incorporated by reference in their entireties herein, and a conjugate group. In certain embodiments, a compound comprises an antisense oligonucleotide having a nucleobase sequence of any of SEQ ID NOs 21-24, 28, 29, 36, 38, 39, 43, 48, 51, 54-56, 58-60, 64-66, 92-166 disclosed in WO 2009/046141 and a conjugate group described herein. In certain embodiments, a compound comprises an antisense oligonucleotide having a nucleobase sequence complementary to a preferred target segment of any of SEQ ID NOs 21-24, 28, 29, 36, 38, 39, 43, 48, 51, 54-56, 58-60, 64-66, 92-166 disclosed in WO 2009/046141 and a conjugate group described herein. The nucleobase sequences of all of the aforementioned referenced SEQ ID NOs are incorporated by reference herein.
FGFR4 Therapeutic Indications
In certain embodiments, provided herein are methods of treating an individual comprising administering one or more pharmaceutical compositions as described herein. In certain embodiments, the individual has a metabolic disease.
As shown in the examples below, conjugated compounds targeted to FGFR4, as described herein, have been shown to reduce the severity of physiological symptoms of a metabolic disease, including obesity or adiposity, metabolic syndrome, diabetes mellitus, insulin resistance, diabetic dyslipidemia, and hypertriglyceridemia. In certain of the experiments, the conjugated compounds reduced body weight, e.g., the animals continued to experience symptoms, but the symptoms were less severe compared to untreated animals. In certain of the experiments, the conjugated compounds reduced body fat, e.g., the animals continued to experience symptoms, but the symptoms were less severe compared to untreated animals. In certain of the experiments, the conjugated compounds reduced adipose tissue, e.g., the animals continued to experience symptoms, but the symptoms were less severe compared to untreated animals. In other of the experiments, however, the conjugated compounds appear to reduce the symptoms of obesity; e.g., animals treated for a longer period of time experienced less severe symptoms than those administered the compounds for a shorter period of time. In other of the experiments, however, the conjugated compounds appear to reduce the symptoms of diabetes; e g., animals treated for a longer period of time experienced less severe symptoms than those administered the compounds for a shorter period of time. In other of the experiments, however, the conjugated compounds appear to inhibit weight gain; e.g., animals treated for a longer period of time experienced less severe symptoms than those administered the compounds for a shorter period of time. In other of the experiments, however, the conjugated compounds appear to reduce glucose levels; e.g., animals treated for a longer period of time experienced less severe symptoms than those administered the compounds for a shorter period of time. In other of the experiments, however, the conjugated compounds appear to increase fatty acid oxidation; e.g., animals treated for a longer period of time experienced less severe symptoms than those administered the compounds for a shorter period of time. The ability of the conjugated compounds exemplified below to restore function therefore demonstrates that symptoms of the disease may be reversed by treatment with a compound as described herein.
Obesity is characterized by numerous physical and physiological symptoms. Any symptom known to one of skill in the art to be associated with obesity can be ameliorated or otherwise modulated as set forth above in the methods described above. In certain embodiments, the symptom is a physical symptom selected from the group consisting of increased adipose tissue mass or weight, increased weight gain, increased fat pad weight, imbalance with caloric intake and energy expenditure, increase in body fat, increase in body mass, having a body mass index (BMI) of 30 or higher, increase in body frame, increased sweating, sleep apnea, difficulty in sleeping, inability to cope with sudden physical activity, lethargy, back and joint problems, increase in breathlessness, increase in breast region adiposity, increase in abdomen size or fat, extreme hunger, or extreme fatigue.
In certain embodiments, the symptom is a physiological symptom selected from the group consisting of high blood pressure, hypertension, high cholesterol levels, type 2 diabetes, stroke, cardiac insufficiency, heart disease, coronary artery obstruction, breast cancer in women, gastro-oesophageal reflux disease, hip and knee arthrosis, and reduced life expectancy.
In certain embodiments, the physical symptom is excess body weight. In certain embodiments, the symptom is excess fat mass. In certain embodiments, the symptom is a body mass index of 30 or higher. In certain embodiments, the symptom is breathlessness. In certain embodiments, the symptom is increased sweating. In certain embodiments, the symptom is sleep apnea. In certain embodiments, the symptom is difficulty in sleeping. In certain embodiments, the symptom is inability to cope with sudden physical activity. In certain embodiments, the symptom is lethargy. In certain embodiments, the symptom is back and joint problems.
In certain embodiments, the physiological symptom is high blood pressure. In certain embodiments, the symptom is hypertension. In certain embodiments, the symptom is high cholesterol levels. In certain embodiments, the symptom is type 2 diabetes. In certain embodiments, the symptom is stroke. In certain embodiments, the symptom is cardiac insufficiency. In certain embodiments, the symptom is heart disease. In certain embodiments, the symptom is coronary artery obstruction. In certain embodiments, the symptom is breast cancer in women. In certain embodiments, the symptom is gastro-oesophageal reflux disease. In certain embodiments, the symptom is hip and knee arthrosis. In certain embodiments, the symptom is reduced life expectancy.
Diabetes mellitus is characterized by numerous physical and physiological symptoms. Any symptom known to one of skill in the art to be associated with Type 2 diabetes can be ameliorated or otherwise modulated as set forth above in the methods described above. In certain embodiments, the symptom is a physical symptom selected from the group consisting of increased glucose levels, increased weight gain, frequent urination, unusual thirst, extreme hunger, extreme fatigue, blurred vision, frequent infections, tingling or numbness at the extremities, dry and itchy skin, weight loss, slow-healing sores, and swollen gums
In certain embodiments, the symptom is a physiological symptom selected from the group consisting of increased insulin resistance, increased glucose levels, increased fat mass, decreased metabolic rate, decreased glucose clearance, decreased glucose tolerance, decreased insulin sensitivity, decreased hepatic insulin sensitivity, increased adipose tissue size and weight, increased body fat, and increased body weight.
In certain embodiments, the physical symptom is increased weight gain. In certain embodiments, the symptom is frequent urination. In certain embodiments, the symptom is unusual thirst. In certain embodiments, the symptom is extreme hunger. In certain embodiments, the symptom is extreme fatigue. In certain embodiments, the symptom is blurred vision. In certain embodiments, the symptom is frequent infections. In certain embodiments, the symptom is tingling or numbness at the extremities. In certain embodiments, the symptom is dry and itchy skin. In certain embodiments, the symptom is weight loss. In certain embodiments, the symptom is slow-healing sores. In certain embodiments, the symptom is swollen gums. In certain embodiments, the symptom is increased insulin resistance. In certain embodiments, the symptom is increased fat mass. In certain embodiments, the symptom is decreased metabolic rate. In certain embodiments, the symptom is decreased glucose clearance. In certain embodiments, the symptom is decreased glucose tolerance. In certain embodiments, the symptom is decreased insulin sensitivity. In certain embodiments, the symptom is decreased hepatic insulin sensitivity. In certain embodiments, the symptom is increased adipose tissue size and weight. In certain embodiments, the symptom is increased body fat. In certain embodiments, the symptom is increased body weight.
In certain embodiments, provided are methods of treating an individual comprising administering one or more pharmaceutical compositions as described herein. In certain embodiments, the individual has metabolic related disease.
In certain embodiments, administration of a conjugated antisense compound targeted to a FGFR4 nucleic acid results in reduction of FGFR4 expression by at least about 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or 99%, or a range defined by any two of these values.
In certain embodiments, pharmaceutical compositions comprising a conjugated antisense compound targeted to FGFR4 are used for the preparation of a medicament for treating a patient suffering or susceptible to a metabolic disease.
In certain embodiments, the methods described herein include administering a conjugated compound comprising a modified oligonucleotide having a contiguous nucleobases portion as described herein of a sequence recited in SEQ ID NO: 58-65.
It will be understood that any of the compounds described herein can be used in the aforementioned methods and uses. For example, in certain embodiments a conjugated antisense compound targeted to a FGFR4 nucleic acid in the aforementioned methods and uses can include, but is not limited to, a conjugated antisense compound targeted to SEQ ID NO: 3 comprising an at least 8 consecutive nucleobase sequence of any one of SEQ ID NOs: 58-65; a conjugated antisense compound targeted to SEQ ID NO: 3 comprising a nucleobase sequence of any one of SEQ ID NO: 58-65; a compound comprising or consisting of ISIS 299005, ISIS 463588, ISIS 463589, ISIS 463690, ISIS 463691, ISIS 463835, ISIS 463837, or ISIS 464225 and a conjugate group; a compound comprising an antisense oligonucleotide disclosed in WO 2009/046141, which are incorporated by reference in their entireties herein, and a conjugate group; a compound comprising an antisense oligonucleotide having a nucleobase sequence of any of SEQ ID NOs SEQ ID NOs 21-24, 28, 29, 36, 38, 39, 43, 48, 51, 54-56, 58-60, 64-66, 92-166 disclosed in WO 2009/046141 and a conjugate group described herein; or a compound comprising an antisense oligonucleotide having a nucleobase sequence complementary to a preferred target segment of any of SEQ ID NOs 21-24, 28, 29, 36, 38, 39, 43, 48, 51, 54-56, 58-60, 64-66, 92-166 disclosed in WO 2009/046141 and a conjugate group described herein. The nucleobase sequences of all of the aforementioned referenced SEQ ID NOs are incorporated by reference herein.
3. GCCR
Diabetes is a chronic metabolic disorder characterized by impaired insulin secretion and/or action. In type 2 diabetes (T2DM), insulin resistance leads to an inability of insulin to control the activity of gluconeogenic enzymes, and many subjects also exhibit inappropriate levels of circulating glucagon (GC) in the fasting and postprandial state. Glucagon is secreted from the α-cells of the pancreatic islets and regulates glucose homeostasis through modulation of hepatic glucose production (Quesada et al., J. Endocrinol. 2008. 199: 5-19).
Glucagon exerts its action on target tissues via the activation of glucocorticoid receptor (GCCR). The glucocorticoid receptor is a 62 kDa protein that is a member of the class B G-protein coupled family of receptors (Brubaker et al., Recept. Channels. 2002. 8: 179-88). GCCR activation leads to signal transduction by G proteins (Gsα and Gq), whereby Gsα activates adenylate cyclase, which causes cAMP production, resulting in an increase in levels of protein kinase A. GCCR signaling in the liver results in increased hepatic glucose production by induction of glycogenolysis and gluconeogenesis along with inhibition of glycogenesis (Jiang and Zhang. Am. J. Physiol. Endocrinol. Metab. 2003. 284: E671-E678). GCCR is also expressed in extrahepatic tissues, which includes heart, intestinal smooth muscle, kidney, brain, and adipose tissue (Hansen et al., Peptides. 1995. 16: 1163-1166).
Development of GCCR inhibitors have been hampered by the unfavorable side effects associated with systemic GCCR inhibition, including activation of the hypothalamic-pituitary adrenal (HPA) axis. Inhibition of GCCR activity in the brain can lead to an increase in circulating adrenocorticotropic hormone due to feedback regulation and a consequent increase in secretion of adrenal steroids (Philibert et al., Front. Horm. Res. 1991. 19: 1-17). This, in turn, can produce a myriad of negative chronic steroid-related side-effects. Other studies have demonstrated that specific inactivation of GCCR resulted in hypoglycemia upon prolonged fasting (Opherk et al., Mol. Endocronol. 2004. 18: 1346-1353).
It has previously been demonstrated in pre-clinical models that administration of GCCR antisense oligonucleotides results in tissue-specific accumulation and reduced GCCR expression in liver and adipose tissue (PCT Pub. No. WO2005/071080; PCT Pub. No. WO2007/035759) without affecting GCCR mRNA levels in the CNS or adrenal glands. Thus, antisense inhibition of GCCR mRNA expression has be shown to improve hyperglycemia and hyperlipidemia without activating the HPA axis. The present invention provides compositions and methods for modulating GCCR expression. Antisense compounds for modulating expression of GCCR are disclosed in the aforementioned published patent applications. However, there remains a need for additional improved compounds. The compounds and treatment methods described herein provide significant advantages over the treatments options currently available for GCCR related disorders. All documents, or portions of documents, cited in this application, including, but not limited to, patents, patent applications, articles, books, and treatises, are hereby expressly incorporated-by-reference for the portions of the document discussed herein, as well as in their entirety.
Certain Conjugated Antisense Compounds Targeted to a GCCR Nucleic Acid
In certain embodiments, conjugated antisense compounds are targeted to a GCCR nucleic acid having the sequence the complement of GENBANK Accession No. NT_029289.10 truncated from nucleotides 3818000 to U.S. Pat. No. 3,980,000 (incorporated herein as SEQ ID NO: 7). In certain such embodiments, a conjugated antisense compound targeted to SEQ ID NO: 7 is at least 90%, at least 95%, or 100% complementary to SEQ ID NO: 7.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 7 comprises an at least 8 consecutive nucleobase sequence of any one of SEQ ID NOs: 66-77. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 7 comprises a nucleobase sequence of any one of SEQ ID NO: 66-77.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 7 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 66. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 7 comprises a nucleobase sequence of SEQ ID NO: 66.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 7 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 67. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 7 comprises a nucleobase sequence of SEQ ID NO: 67.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 7 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 68. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 7 comprises a nucleobase sequence of SEQ ID NO: 68.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 7 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 69. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 7 comprises a nucleobase sequence of SEQ ID NO: 69.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 7 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 70. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 7 comprises a nucleobase sequence of SEQ ID NO: 70.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 7 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 71. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 7 comprises a nucleobase sequence of SEQ ID NO: 71.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 7 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 72. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 7 comprises a nucleobase sequence of SEQ ID NO: 72.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 7 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 73. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 7 comprises a nucleobase sequence of SEQ ID NO: 73.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 7 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 74. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 7 comprises a nucleobase sequence of SEQ ID NO: 74.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 7 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 75. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 7 comprises a nucleobase sequence of SEQ ID NO: 75.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 7 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 76. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 7 comprises a nucleobase sequence of SEQ ID NO: 76.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 7 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 77. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 7 comprises a nucleobase sequence of SEQ ID NO: 77.







TABLE 4







 Antisense Compounds targeted to GCCR SEQ ID NO: 7












Target


SEQ


ISIS
Start


ID


No
Site
Sequence (5′-3′)
Motif
NO





420470
57825
GGTAGAAATATAGTTGTTCC
5-10-5 MOE
66


 


420476
59956
TTCATGTGTCTGCATCATGT
5-10-5 MOE
67


 


426115
65940
GCAGCCATGGTGATCAGGAG
5-10-5 MOE
68


 


426130
63677
GCATCCAGCGAGCACCAAAG
5-10-5 MOE
69


 


426168
76224
GTCTGGATTACAGCATAAAC
5-10-5 MOE
70


 


426172
76229
CCTTGGTCTGGATTACAGCA
5-10-5 MOE
71


 


426183
65938
AGCCATGGTGATCAGGAGGC
3-14-3 MOE
72


 


426246
76225
GGTCTGGATTACAGCATAAA
3-14-3 MOE
73


 


426261
65938
AGCCATGGTGATCAGGAGGC
2-13-5 MOE
74


 


426262
65939
CAGCCATGGTGATCAGGAGG
2-13-5 MOE
75


 


426267
95513
GTGCTTGTCCAGGATGATGC
2-13-5 MOE
76


 


426325
76229
CCTTGGTCTGGATTACAGCA
2-13-5 MOE
77









In certain embodiments, a compound comprises or consists of ISIS 420470 and a conjugate group. ISIS 420470 is a modified oligonucleotide having the formula: Ges Ges Tes Aes Ges Ads Ads Ads Tds Ads Tds Ads Gds Tds Tds Ges Tes Tes mCes mCe, wherein
A=an adenine,
mC=a 5′-methylctosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside,
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises or consists of ISIS 420476 and a conjugate group. ISIS 420476 is a modified oligonucleotide having the formula: Tes Tes mCes Aes Tes Gds Tds Gds Tds mCds Tds Gds mCds Ads Tds mCes Aes Tes Ges Te, wherein
A=an adenine,
mC=a 5′-methylctosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside,
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises or consists of ISIS 426115 and a conjugate group. ISIS 426115 is a modified oligonucleotide having the formula: Ges mCes Aes Ges mCes mCds Ads Tds Gds Gds Tds Gds Ads Tds mCds Aes Ges Ges Aes Ge, wherein
A=an adenine,
mC=a 5′-methylcytosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside.,
d=a 2′-deoxynucleoside., and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises or consists of ISIS 426130 and a conjugate group. ISIS 426130 is a modified oligonucleotide having the formula: Ges mCes Aes Tes mCes mCds Ads Gds mCds Gds Ads Gds mCds Ads mCds mCes Aes Aes Aes Ge, wherein
A=an adenine,
mC=a 5′-methylctosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside,
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises or consists of ISIS 426168 and a conjugate group. ISIS 426168 is a modified oligonucleotide having the formula: Ges Tes mCes Tes Ges Gds Ads Tds Tds Ads mCds Ads Gds mCds Ads Tes Aes Aes Aes mCe, wherein
A=an adenine,
mC=a 5′-methylcytosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside,
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises or consists of ISIS 426172 and a conjugate group. ISIS 426172 is a modified oligonucleotide having the formula: mCes mCes Tes Tes Ges Gds Tds mCds Tds Gds Gds Ads Tds Tds Ads mCes Aes Ges mCes Ae, wherein
A=an adenine,
mC=a 5′-methylcytosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside,
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises or consists of ISIS 426183 and a conjugate group. ISIS 426183 is a modified oligonucleotide having the formula: Aes Ges mCes mCds Ads Tds Gds Gds Tds Gds Ads Tds mCds Ads Gds Gds Ads Ges Ges mCe, wherein
A=an adenine,
mC=a 5′-methylcytosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside,
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises or consists of ISIS 426246 and a conjugate group. ISIS 426246 is a modified oligonucleotide having the formula: Ges Ges Tes mCds Tds Gds Gds Ads Tds Tds Ads mCds Ads Gds mCds Ads Tds Aes Aes Ae, wherein
A=an adenine,
mC=a 5′-methylcytosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside,
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises or consists of ISIS 426261 and a conjugate group. ISIS 426261 is a modified oligonucleotide having the formula: Aes Ges mCds mCds Ads Tds Gds Gds Tds Gds Ads Tds mCds Ads Gds Ges Aes Ges Ges mCe, wherein
A=an adenine,
mC=a 5′-methylcytosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside,
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises or consists of ISIS 426262 and a conjugate group. ISIS 426262 is a modified oligonucleotide having the formula: mCes Aes Gds mCds mCds Ads Tds Gds Gds Tds Gds Ads Tds mCds Ads Ges Ges Aes Ges Ge, wherein
A=an adenine,
mC=a 5′-methylcytosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside.
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises or consists of ISIS 426267 and a conjugate group. ISIS 426267 is a modified oligonucleotide having the formula: Ges Tes Gds mCds Tds Tds Gds Tds mCds mCds Ads Gds Gds Ads Tds Ges Aes Tes Ges mCe, wherein
A=an adenine,
mC=a 5′-methylcytosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside.
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises or consists of ISIS 426325 and a conjugate group. ISIS 426325 is a modified oligonucleotide having the formula: mCes mCes Tds Tds Gds Gds Tds mCds Tds Gds Gds Ads Tds Tds Ads mCes Aes Ges mCes Ae, wherein
A=an adenine,
mC=a 5′-methylcytosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside.
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises an antisense oligonucleotide disclosed in WO 2005/071080, WO 2007/035759, or WO 2007/136988, which are incorporated by reference in their entireties herein, and a conjugate group. In certain embodiments, a compound comprises an antisense oligonucleotide having a nucleobase sequence of any of SEQ ID NOs 30-216, and 306-310 disclosed in WO 2005/071080 and a conjugate group described herein. In certain embodiments, a compound comprises an antisense oligonucleotide having a nucleobase sequence of any of SEQ ID NOs 26-113 disclosed in WO 2007/035759 and a conjugate group described herein. In certain embodiments, a compound comprises an antisense oligonucleotide having a nucleobase sequence of any of SEQ ID NOs 413-485 disclosed in WO 2007/136988 and a conjugate group described herein. In certain embodiments, a compound comprises an antisense oligonucleotide having a nucleobase sequence complementary to a preferred target segment of any of SEQ ID NOs 30-216, and 306-310 disclosed in WO 2005/071080, 26-113 disclosed in WO 2007/035759, and 413-485 disclosed in WO 2007/136988, and a conjugate group described herein. The nucleobase sequences of all of the aforementioned referenced SEQ ID NOs are incorporated by reference herein.
GCCR Therapeutic Indications
In certain embodiments, provided herein are methods of treating an individual comprising administering one or more pharmaceutical compositions as described herein. In certain embodiments, the individual has metabolic related disease.
As shown in the examples below, conjugated compounds targeted to GCCR, as described herein, have been shown to reduce the severity of physiological symptoms of metabolic related diseases, including metabolic syndrome, diabetes mellitus, insulin resistance, diabetic dyslipidemia, hypertriglyceridemia, obesity and weight gain e.g., the animals continued to experience symptoms, but the symptoms were less severe compared to untreated animals. In certain experiments, the conjugated compounds reduced blood glucose levels. In other experiments, the conjugated compounds reduce the symptoms of diabetes. In other experiments, the conjugated compounds inhibit weight gain. In other experiments, the conjugated compounds inhibit hypertriglyceridemia. In certain embodiements, the conjugated compounds restore function therefore demonstratingreversal of disease by treatment with a compound as described herein. In certain embodiments, animals treated for a longer period of time experience less severe symptoms than those administered the compounds for a shorter period of time.
Diabetes mellitus is characterized by numerous physical and physiological signs and/or symptoms. Any symptom known to one of skill in the art to be associated with Type 2 diabetes can be ameliorated or otherwise modulated as set forth above in the methods described above. In certain embodiments, the sign or symptom is a physical symptom such as increased glucose levels, increased weight gain, frequent urination, unusual thirst, extreme hunger, extreme fatigue, blurred vision, frequent infections, tingling or numbness at the extremities, dry and itchy skin, weight loss, slow-healing sores, and swollen gums. In certain embodiments, the sign or symptom is a physiological symptom such as increased insulin resistance, increased glucose levels, increased fat mass, decreased metabolic rate, decreased glucose clearance, decreased glucose tolerance, decreased insulin sensitivity, decreased hepatic insulin sensitivity, increased adipose tissue size and weight, increased body fat, and increased body weight.
In certain embodiments, the physical sign or symptom is increased glucose levels. In certain embodiments, the sign or symptom is weight gain. In certain embodiments, the sign or symptom is frequent urination. In certain embodiments, the sign or symptom is unusual thirst. In certain embodiments, the sign or symptom is extreme hunger. In certain embodiments, the sign or symptom is extreme fatigue. In certain embodiments, the sign or symptom is blurred vision. In certain embodiments, the sign or symptom is frequent infections. In certain embodiments, the sign or symptom is tingling or numbness at the extremities. In certain embodiments, the sign or symptom is dry and itchy skin. In certain embodiments, the sign or symptom is weight loss. In certain embodiments, the sign or symptom is slow-healing sores. In certain embodiments, the sign or symptom is swollen gums. In certain embodiments, the sign or symptom is increased insulin resistance. In certain embodiments, the sign or symptom is increased glucose levels. In certain embodiments, the sign or symptom is increased fat mass. In certain embodiments, the sign or symptom is decreased metabolic rate. In certain embodiments, the sign or symptom is decreased glucose clearance. In certain embodiments, the sign or symptom is decreased glucose tolerance. In certain embodiments, the sign or symptom is decreased insulin sensitivity. In certain embodiments, the sign or symptom is decreased hepatic insulin sensitivity. In certain embodiments, the sign or symptom is increased adipose tissue size and weight.
In certain embodiments, the sign or symptom is increased body fat. In certain embodiments, the sign or symptom is increased body weight.
In certain embodiments, provided are methods of treating an individual comprising administering one or more pharmaceutical compositions as described herein. In certain embodiments, the individual has metabolic related disease.
In certain embodiments, administration of a conjugated antisense compound targeted to a GCCR nucleic acid results in reduction of GCCR expression by at least about 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or 99%, or a range defined by any two of these values.
In certain embodiments, pharmaceutical compositions comprising a conjugated antisense compound targeted to GCCR are used for the preparation of a medicament for treating a patient suffering or susceptible to metabolic related disease.
In certain embodiments, the methods described herein include administering a conjugated compound comprising a modified oligonucleotide having a contiguous nucleobases portion as described herein of a sequence recited in SEQ ID NO: 66-77.
It will be understood that any of the compounds described herein can be used in the aforementioned methods and uses. For example, in certain embodiments a conjugated antisense compound targeted to a GCCR nucleic acid in the aforementioned methods and uses can include, but is not limited to a conjugated antisense compound targeted to SEQ ID NO: 7 comprising an at least 8 consecutive nucleobase sequence of any one of SEQ ID NOs: 66-77; a conjugated antisense compound targeted to SEQ ID NO: 7 comprising a nucleobase sequence of any one of SEQ ID NO: 66-77; a compound comprising or consisting of ISIS 420470, ISIS 420476, ISIS 426115, ISIS 426130, ISIS 426168, ISIS 426172, ISIS 426183, ISIS 426246, ISIS 426262, ISIS 426267, or ISIS 426325 and a conjugate group: a compound comprising an antisense oligonucleotide disclosed in WO 2005/071080, WO 20071035759, or WO 2007/136988, which are incorporated by reference in their entireties herein, and a conjugate group; a compound comprising an antisense oligonucleotide having a nucleobase sequence of any of SEQ ID NOs 26-113 disclosed in WO 2007/035759 and a conjugate group described herein; a compound comprising an antisense oligonucleotide having a nucleobase sequence of any of SEQ ID NOs 26-113 disclosed in WO 2007/035759 and a conjugate group described herein; or a compound comprising an antisense oligonucleotide having a nucleobase sequence of any of SEQ ID NOs 413-485 disclosed in WO 2007/136988 and a conjugate group described herein; The nucleobase sequences of all of the aforementioned referenced SEQ ID NOs are incorporated by reference herein.
4. GCGR
Insulin and glucagon are two pancreatic hormones involved in regulating glucose homeostasis and metabolism. Glucagon is secreted from the α-cells of the pancreatic islets and regulates glucose homeostasis through modulation of hepatic glucose production (Quesada et al., J. Endocrinol. 2008. 199: 5-19). The main function of glucagon is to counteract the actions of insulin.
Dysregulation of glucose metabolism may be caused either by defective insulin secretion and/or action, or by impaired postprandial glucagon suppression (Shah et al., Am. J. Physiol. Endocrinol. Metab. 1999. 277: E283-E290). Inhibition of postprandial glucagon secretion in diabetic subjects has been shown to substantially reduce blood glucose, suggesting that glucagon contributes significantly to the hyperglycemia seen in subjects with type 2 diabetes mellitus (Shah et al., J. Clin. Endocrinol. Metab. 2000. 85: 4053-4059).
Type 2 diabetes is characterized by impaired insulin secretion and/or action, and many subjects also exhibit inappropriate levels of circulating glucagon in the fasting and postprandial state. An increase in the glucagon/insulin ratio is likely an important determinant of the hyperglycemia seen in type 2 diabetes patients (Baron et al., Diabetes. 1987. 36: 274-283). Lack of suppression of postprandial glucagon secretion in subjects with T2DM also plays an important role in the pathogenesis of postprandial hyperglycemia (Henkel et al., Metabolism. 2005. 54: 1168-1173).
Glucagon exerts its action on target tissues via the activation of its receptor, GCGR. The glucagon receptor is a 62 kDa protein that is a member of the class B G-protein coupled family of receptors (Brubaker et al., Recept. Channels. 2002. 8: 179-88). GCGR activation leads to signal transduction by G proteins (Gsα and Gq), whereby Gsα activates adenylate cyclase, which causes cAMP production, resulting in an increase in levels of protein kinase A. GCGR signaling in the liver results in increased hepatic glucose production by induction of glycogenolysis and gluconeogenesis along with inhibition of glycogenesis (Jiang and Zhang. Am. J. Physiol. Endocrinol. Metab. 2003. 284: E671-E678). GCGR is also expressed in extrahepatic tissues, which includes heart, intestinal smooth muscle, kidney, brain, and adipose tissue (Hansen et al., Peptides. 1995. 16: 1163-1166).
Antisense inhibition of GCGR provides a unique advantage over traditional small molecule inhibitors in that antisense inhibitors do not rely on competitive binding of the compound to the protein and inhibit activity directly by reducing the expression of GCGR. A representative United States patent that teaches
GCGR antisense inhibitors includes U.S. Pat. No. 7,750,142, of which is herein incorporated by reference in its entirety. Antisense technology is emerging as an effective means for reducing the expression of certain gene products and may therefore prove to be uniquely useful in a number of therapeutic, diagnostic, and research applications for the modulation of GCGR.
There is a currently a lack of acceptable options for treating metabolic disorders. It is therefore an object herein to provide compounds and methods for the treatment of such diseases and disorder. This invention relates to the discovery of novel, highly potent inhibitors of GCGR gene expression. All documents, or portions of documents, cited in this application, including, but not limited to, patents, patent applications, articles, books, and treatises, are hereby expressly incorporated-by-reference for the portions of the document discussed herein, as well as in their entirety.
Certain Conjugated Antisense Compounds Targeted to a GCGR Nucleic Acid
In certain embodiments, conjugated antisense compounds are targeted to a GCGR nucleic acid having the sequence GENBANK Accession No. NM_000160.3 (incorporated herein as SEQ ID NO: 8) or GENBANK Accession No: NW_926918.1 truncated from nucleotides 16865000 to Ser. No. 16/885,000 (incorporated herein as SEQ ID NO: 9). In certain such embodiments, a conjugated antisense compound targeted to SEQ ID NOs: 8 and/or 9 is at least 90%, at least 95%, or 100% complementary to SEQ ID NOs: 8 and/or 9.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 8 and/or 9 comprises an at least 8 consecutive nucleobase sequence of any one of SEQ ID NOs: 78-83. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 8 and/or 9 comprises a nucleobase sequence of any one of SEQ ID NO: 78-83.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 8 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 78. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 8 comprises a nucleobase sequence of SEQ ID NO: 78.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 9 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 79. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 9 comprises a nucleobase sequence of SEQ ID NO: 79.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 9 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 80. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 9 comprises a nucleobase sequence of SEQ ID NO: 80.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 9 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 81. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 9 comprises a nucleobase sequence of SEQ ID NO: 81.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 8 and 9 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 82. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 8 and 9 comprises a nucleobase sequence of SEQ ID NO: 82.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 9 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 83. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 9 comprises a nucleobase sequence of SEQ ID NO: 83.







TABLE 5 







Antisense Compounds targeted to GCGR


SEQ ID NOs: 8 and 9













Target
Target






Start
Start






Site
Site






to
to


SEQ


ISIS
SEQ ID
SEQ ID


ID


No
NO: 8
NO: 9
Sequence (5′-3′)
Motif
NO





325568
548
n/a
GCACTTTGTGGTGCCAAGGC
2-16-2
78






MOE



 


398471
n/a
8133
TCCACAGGCCACAGGTGGGC
5-10-5
79






MOE



 


448766
n/a
9804
GCAAGGCTCGGTTGGGCTTC
5-10-5
80






MOE



 


449884
n/a
7270
GGTTCCCGAGGTGCCCA
3-10-4
81




7295

MOE





7319







7344







7368







7392







7416







7440





 


459014
227
10718
GGGCAATGCAGTCCTGG
3-10-4
82






MOE



 


459157
n/a
7267
GGGTTCCCGAGGTGCCCAATG
5-10-6
83




7292

MOE





7316







7341







7365







7389







7437









In certain embodiments, a compound comprises or consists of ISIS 325568 and a conjugate group, ISIS 325568 is a modified oligonucleotide having the formula: Ges mCes Ads mCds Tds Tds Tcds Gds Tds Gds Gds Tds Gds mCds mCds Ads Ads Gds Ges mCe, wherein
A=an adenine,
mC=a 5-methylcytosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside,
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises or consists of ISIS 398471 and a conjugate group, ISIS 398471 is a modified oligonucleotide having the formula: Tee mCes mCes Aes mCes Ads Gds Gds mCds mCds Ads mCds Ads Gds Gds Tes Ges Ges Ges mCe, wherein
A=an adenine,
mC=a 5′-methylcytosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside,
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises or consists of ISIS 448766 and a conjugate group, ISIS 448766 is a modified oligonucleotide having the formula: Ges mCes Aes Aes Ges Gds mCds Tds mCds Gds Gds Tds Tds Gds Gds Ges mCes Tes Tes mCe, wherein
A=an adenine,
mC=a 5′-methylcytosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside.
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises or consists of ISIS 449884 and a conjugate group. ISIS 449884 is a modified oligonucleotide having the formula: Ges Ges Tes Tds mCds mCds mCds Gds Ads Gds Gds Tds Gds mCes mCes mCes Ae, wherein
A=an adenine,
mC=a 5′-methylcytosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside.
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises or consists of ISIS 459014 and a conjugate group. ISIS 459014 is a modified oligonucleotide having the formula: Ges Ges Ges mCds Ads Ads Tds Gds mCds Ads Gds Tds mCds mCes Tes Ges Ge, wherein
A=an adenine,
mC=a 5′-methylcytosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside,
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises or consists of ISIS 459157 and a conjugate group. ISIS 459157 is a modified oligonucleotide having the formula: Ges Ges Ges Tes Tes mCds mCds mCds Gds Ads Gds Gds Tds Gds mCds mCes mCes Aes Aes Tes Ge, wherein
A=an adenine,
mC=a 5′-methylcytosine
G=a guanine,
T=a thymine,
e=a 2′-O-methoxyethyl modified nucleoside,
d=a 2′-deoxynucleoside, and
s=a phosphorothioate internucleoside linkage.
In certain embodiments, a compound comprises an antisense oligonucleotide disclosed in U.S. Pat. No. 7,750,142, U.S. Pat. No. 7,399,853, WO 2007/035771, or WO 2007/134014, which are incorporated by reference in their entireties herein, and a conjugate group. In certain embodiments, a compound comprises an antisense oligonucleotide having a nucleobase sequence of any of SEQ ID NOs 20-399 disclosed in U.S. Pat. No. 7,750,142 and a conjugate group described herein. In certain embodiments, a compound comprises an antisense oligonucleotide having a nucleobase sequence of any of SEQ ID NOs 20-399 disclosed in U.S. Pat. No. 7,399,853 and a conjugate group described herein. In certain embodiments, a compound comprises an antisense oligonucleotide having a nucleobase sequence of any of SEQ ID NOs 2 disclosed in WO 2007/035771 and a conjugate group described herein. In certain embodiments, a compound comprises an antisense oligonucleotide having a nucleobase sequence of any of SEQ ID NOs: 486-680 disclosed in WO 2007/134014 and a conjugate group described herein. In certain embodiments, a compound comprises an antisense oligonucleotide having a nucleobase sequence complementary to a preferred target segment of any of SEQ ID NOs 20-399 of U.S. Pat. No. 7,750,142, SEQ ID NO: 20-399 of U.S. Pat. No. 7,399,853, SEQ ID NO 2 of WO 2007/035771, or SEQ ID NOs. 486-680 of WO 2007/134014, and a conjugate group described herein. The nucleobase sequences of all of the aforementioned referenced SEQ ID NOs are incorporated by reference herein.
GCGR Therapeutic Indications
In certain embodiments, provided herein are methods of treating an individual comprising administering one or more pharmaceutical compositions as described herein. In certain embodiments, the individual has metabolic related disease.
As shown in the examples below, conjugated compounds targeted to GCGR, as described herein, have been shown to reduce the severity of physiological symptoms of metabolic related diseases, including metabolic syndrome, diabetes mellitus, insulin resistance, diabetic dyslipidemia, hypertriglyceridemia, obesity and weight gain. In certain of the experiments, the conjugated compounds reduced blood glucose levels, e.g., the animals continued to experience symptoms, but the symptoms were less severe compared to untreated animals. In other experiments, however, the conjugated compounds appear to reduce the symptoms of diabetes; e.g., animals treated for a longer period of time experienced less severe symptoms than those administered the compounds for a shorter period of time. In other experiments, however, the conjugated compounds appear to inhibit weight gain; e.g., animals treated for a longer period of time experienced less severe symptoms than those administered the compounds for a shorter period of time. In other experiments, however, the conjugated compounds appear to inhibit hypertriglyceridemia; e.g., animals treated for a longer period of time experienced less severe signs and/or symptoms than those administered the compounds for a shorter period of time. The ability of the conjugated compounds exemplified below to restore function therefore demonstrates that symptoms of the disease may be reversed by treatment with a compound as described herein.
Diabetes mellitus is characterized by numerous physical and physiological signs and/or symptoms. Any symptom known to one of skill in the art to be associated with Type 2 diabetes can be ameliorated or otherwise modulated as set forth above in the methods described above. In certain embodiments, the symptom or sign is a physical symptom or sign ssuch as increased glucose levels, increased weight gain, frequent urination, unusual thirst, extreme hunger, extreme fatigue, blurred vision, frequent infections, tingling or numbness at the extremities, dry and itchy skin, weight loss, slow-healing sores, and swollen gums. In certain embodiments, the symptom or sign is a physiological symptom or sign selected from the group consisting of increased insulin resistance, increased glucose levels, increased fat mass, decreased metabolic rate, decreased glucose clearance, decreased glucose tolerance, decreased insulin sensitivity, decreased hepatic insulin sensitivity, increased adipose tissue size and weight, increased body fat, and increased body weight.
In certain embodiments, the physical symptom or sign is increased glucose levels. In certain embodiments, the sign or symptom is weight gain. In certain embodiments, the symptom is frequent urination. In certain embodiments, the symptom is unusual thirst. In certain embodiments, the symptom is extreme hunger. In certain embodiments, the symptom is extreme fatigue. In certain embodiments, the symptom is blurred vision. In certain embodiments, the symptom is frequent infections. In certain embodiments, the symptom is tingling or numbness at the extremities. In certain embodiments, the symptom is dry and itchy skin. In certain embodiments, the sign or symptom is weight loss. In certain embodiments, the symptom is slow-healing sores. In certain embodiments, the symptom is swollen gums. In certain embodiments, the symptom or sign is increased insulin resistance. In certain embodiments, the symptom or sign is increased glucose levels. In certain embodiments, the symptom or sign is increased fat mass. In certain embodiments, the symptom or sign is decreased metabolic rate. In certain embodiments, the symptom o resign is decreased glucose clearance. In certain embodiments, the symptom or sign is decreased glucose tolerance. In certain embodiments, the symptom or sign is decreased insulin sensitivity. In certain embodiments, the symptom or sign is decreased hepatic insulin sensitivity. In certain embodiments, the symptom or sign is increased adipose tissue size and weight. In certain embodiments, the symptom or sign is increased body fat. In certain embodiments, the sign or symptom is increased body weight.
In certain embodiments, provided are methods of treating an individual comprising administering one or more pharmaceutical compositions as described herein. In certain embodiments, the individual has metabolic related disease.
In certain embodiments, administration of a conjugated antisense compound targeted to a GCGR nucleic acid results in reduction of GCGR expression by at least about 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or 99%, or a range defined by any two of these values.
In certain embodiments, pharmaceutical compositions comprising a conjugated antisense compound targeted to GCGR are used for the preparation of a medicament for treating a patient suffering or susceptible to metabolic related disease.
In certain embodiments, the methods described herein include administering a conjugated compound comprising a modified oligonucleotide having a contiguous nucleobases portion as described herein of a sequence recited in SEQ ID NO: 78-83.
It will be understood that any of the compounds described herein can be used in the aforementioned methods and uses. For example, in certain embodiments a conjugated antisense compound targeted to a GCGR nucleic acid in the aforementioned methods and uses can include, but is not limited to, a conjugated antisense compound targeted to SEQ ID NO: 8 and/or 9 comprising an at least 8 consecutive nucleobase sequence of any one of SEQ ID NOs: 78-83; a conjugated antisense compound targeted to SEQ ID NO: 8 and/or 9 comprising a nucleobase sequence of any one of SEQ ID NO: 78-83; a compound comprising or consisting of ISIS 325568, ISIS 398471, ISIS 448766, ISIS 449884, ISIS 459014, or ISIS 459157 and a conjugate group; a compound comprising an antisense oligonucleotide disclosed in U.S. Pat. No. 7,750,142; U.S. Pat. No. 7,399,853, WO 2007/035771, or WO 2007/134014, which are incorporated by reference in their entireties herein, and a conjugate group; The nucleobase sequences of all of the aforementioned referenced SEQ ID NOs are incorporated by reference herein.
4. 4. Coagulation Factor 7
The circulatory system requires mechanisms that prevent blood loss, as well as those that counteract inappropriate intravascular obstructions. Generally, coagulation comprises a cascade of reactions culminating in the conversion of soluble fibrinogen to an insoluble fibrin gel. The steps of the cascade involve the conversion of an inactive zymogen to an activated enzyme. The active enzyme then catalyzes the next step in the cascade.
Coagulation Cascade
The coagulation cascade may be initiated through two branches, the tissue factor pathway (also “extrinsic pathway”), which is the primary pathway, and the contact activation pathway (also “intrinsic pathway”).
The tissue factor pathway is initiated by the cell surface receptor tissue factor (TF, also referred to as factor III), which is expressed constitutively by extravascular cells (pericytes, cardiomyocytes, smooth muscle cells, and keratinocytes) and expressed by vascular monocytes and endothelial cells upon induction by inflammatory cytokines or endotoxin. (Drake et al., Am J Pathol 1989, 134:1087-1097). TF is the high affinity cellular receptor for coagulation factor VIIa, a serine protease. In the absence of TF, VIIa has very low catalytic activity, and binding to TF is necessary to render VIIa functional through an allosteric mechanism. (Drake et al., Am J Pathol 1989, 134:1087-1097). The TF-VIIa complex activates factor X to Xa. Xa in turn associates with its co-factor factor Va into a prothrombinase complex which in turn activates prothrombin, (also known as factor II or factor 2) to thrombin (also known as factor IIa, or factor 2a). Thrombin activates platelets, converts fibrinogen to fibrin and promotes fibrin cross-linking by activating factor XIII, thus forming a stable plug at sites where TF is exposed on extravascular cells. In addition, thrombin reinforces the coagulation cascade response by activating factors V and VIII.
The contact activation pathway is triggered by activation of factor XII to XIIa. Factor XIIa converts XI to XIa, and XIa converts IX to IXa. IXa associates with its cofactor Villa to convert X to Xa. The two pathways converge at this point as factor Xa associates factor Va to activate prothrombin (factor II) to thrombin (factor IIa).
Inhibition of Coagulation
At least three mechanisms keep the coagulation cascade in check, namely the action of activated protein C, antithrombin, and tissue factor pathway inhibitor. Activated protein C is a serine protease that degrades cofactors Va and VIIIa. Protein C is activated by thrombin with thrombomodulin, and requires coenzyme Protein S to function. Antithrombin is a serine protease inhibitor (serpin) that inhibits serine proteases: thrombin, Xa, XIIa, XIa and IXa. Tissue factor pathway inhibitor inhibits the action of Xa and the TF-VIIa complex. (Schwartz A L et al., Trends Cardiovasc Med. 1997; 7:234-239.)
Disease
Thrombosis is the pathological development of blood clots, and an embolism occurs when a blood clot migrates to another part of the body and interferes with organ function. Thromboembolism may cause conditions such as deep vein thrombosis, pulmonary embolism, myocardial infarction, and stroke. Significantly, thromboembolism is a major cause of morbidity affecting over 2 million Americans every year. (Adcock et al. American Journal of Clinical Pathology. 1997; 108:434-49). While most cases of thrombosis are due to acquired extrinsic problems, for example, surgery, cancer, immobility, some cases are due to a genetic predisposition, for example, antiphospholipid syndrome and the autosomal dominant condition, Factor V Leiden. (Bertina R M et al. Nature 1994; 369:64-67.)
Treatment
The most commonly used anticoagulants, warfarin, heparin, and low molecular weight heparin (LMWH) all possess significant drawbacks.
Warfarin is typically used to treat patients suffering from atrial fibrillation. The drug interacts with vitamin K-dependent coagulation factors which include factors II, VII, IX and X. Anticoagulant proteins C and S are also inhibited by warfarin. Drug therapy using warfarin is further complicated by the fact that warfarin interacts with other medications, including drugs used to treat atrial fibrillation, such as amiodarone. Because therapy with warfarin is difficult to predict, patients must be carefully monitored in order to detect any signs of anomalous bleeding.
Heparin functions by activating antithrombin which inhibits both thrombin and factor X. (Bjork I, Lindahl U. Mol Cell Biochem. 1982 48: 161-182.) Treatment with heparin may cause an immunological reaction that makes platelets aggregate within blood vessels that can lead to thrombosis. This side effect is known as heparin-induced thrombocytopenia (HIT) and requires patient monitoring. Prolonged treatment with heparin may also lead to osteoporosis. LMWH can also inhibit Factor 2, but to a lesser degree than unfractioned heparin (UFH). LMWH has been implicated in the development of HIT.
Thus, current anticoagulant agents lack predictability and specificity and, therefore, require careful patient monitoring to prevent adverse side effects, such as bleeding complications. There are currently no anticoagulants which target only the intrinsic or extrinsic pathway.
Antisense compounds targeting Factor VII have been previously disclosed in WO 2013/119979 and WO 2009/061851, each herein incorporated by reference in its entirety. Clinical studies are ongoing to assess the effect of antisense compounds targeting Factor VII in patients. However, there is still a need to provide patients with additional and more potent treatment options.
Certain Conjugated Antisense Compounds Targeted to a Factor VII Nucleic Acid
In certain embodiments, conjugated antisense compounds are targeted to a Factor VII nucleic acid having the sequence GENBANK Accession No. NT_027140.6 truncated from nucleotides 1255000 to 1273000, incorporated herein as SEQ ID NO: 10; GENBANK Accession No. NM_019616.2, incorporated herein as SEQ ID NO: 11; DB184141.1, designated herein as SEQ ID NO: 12; and GENBANK Accession No. NW_001104507.1 truncated from nucleotides 691000 to 706000, designated herein as SEQ ID NO: 13. In certain such embodiments, a conjugated antisense compound targeted to SEQ ID NO: 11 is at least 90%, at least 95%, or 100% complementary to SEQ ID NO: 11.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 11 comprises an at least 8 consecutive nucleobase sequence of any one of SEQ ID NOs: 84-92. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 11 comprises a nucleobase sequence of any one of SEQ ID NO: 84-92.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 11 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 84. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 11 comprises a nucleobase sequence of SEQ ID NO: 84.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 11 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 85. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 11 comprises a nucleobase sequence of SEQ ID NO: 85.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 11 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 86. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 11 comprises a nucleobase sequence of SEQ ID NO: 86.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 11 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 87. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 11 comprises a nucleobase sequence of SEQ ID NO: 87.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 11 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 88. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 11 comprises a nucleobase sequence of SEQ ID NO: 88.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 11 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 89. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 11 comprises a nucleobase sequence of SEQ ID NO: 89.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 11 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 90. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 11 comprises a nucleobase sequence of SEQ ID NO: 90.







TABLE 3 







Antisense Compounds targeted to Factor VII


SEQ ID NO: 11












Target


SEQ


ISIS
Start


ID


No
Site
Sequence (5′-3′)
Motif
NO





407935
15191
ATGCATGGTGATGCTT
eeeeeddddddd
84




CTGA
dddeeeee



 


473589
15128
GCTAAACAACCGCCTT
kdkdkddddddd
85





ddee



 


490279
 1387
CCCTCCTGTGCCTGGA
eeeeeddddddd
86




TGCT
dddeeeee



 


529804
15192
CATGGTGATGCTTCTG
kddddddddddk
87





ekee



 


534796
15131
AGAGCTAAACAACCGC
ekkddddddddd
88





dkke



 


540162
2565;
ACTCCCGGGACACCCA
eekddddddddd
89



2633;

dkke




2667





 


540175

GGACACCCACGCCCCC

90


 


540182

ACACCCTCGCCTCCGG

91


 


540191

GCCTCCGGAACACCCA

92









In certain embodiments, a compound comprises or consists of ISIS 420915 and a conjugate group. ISIS 407935 is a modified oligonucleotide having the formula: Aes Tes Ges mCes Aes Tds Gds Gds Tds Gds Ads Tds Gds mCds Tds Tes mCes Tes Ges Ae, wherein

    A=adenine
    T=thymine
    G=guanine;
    mC=5-methylcytosine; wherein

each sugar moiety is indicated according to the following:

    k=cEt;
    d=2′-deoxyribose;
    e=2′-MOE; wherein

each internucleoside linkage is indicated according to the following:

    s=phosphorothioate.


In certain embodiments, a compound comprises or consists of ISIS 304299 and a conjugate group. ISIS 473589 is a modified oligonucleotide having the formula: Gks mCds Tks Ads Aks Ads mCds Ads Ads mCds mCds Gds mCds mCds Tes Te; wherein,
each nucleobase is indicated according to the following:


    A=adenine
    T=thymine
    G=guanine;
    mC=5-methylcytosine; wherein

each sugar moiety is indicated according to the following:

    k=cEt;
    d=2′-deoxyribose;
    e=2′-MOE; wherein

each internucleoside linkage is indicated according to the following:

    s=phosphorothioate.


In certain embodiments, a compound comprises or consists of ISIS 420921 and a conjugate group. ISIS 490279 is a modified oligonucleotide having the formula: mCes mCes mCes Tes mCes mCds Tds Gds Tds Gds mCds mCds Tds Gds Gds Aes Tes Ges mCes Te; wherein, each nucleobase is indicated according to the following:

    A=adenine
    T=thymine
    G=guanine;
    mC=5-methylcytosine; wherein

each sugar moiety is indicated according to the following:

    k=cEt;
    d=2′-deoxyribose;
    e=2′-MOE; wherein

each internucleoside linkage is indicated according to the following:

    s=phosphorothioate.


In certain embodiments, a compound comprises or consists of ISIS 420922 and a conjugate group. ISIS 529804 is a modified oligonucleotide having the formula: mCks Ads Tds Gds Gds Tds Gds Ads Tds Gds mCds Tks Tes mCks Tes Ge, wherein

    A=adenine
    T=thymine
    G=guanine;
    mC=5-methylcytosine; wherein

each sugar moiety is indicated according to the following:

    k=cEt;
    d=2′-deoxyribose;
    e=2′-MOE; wherein

each internucleoside linkage is indicated according to the following:

    s=phosphorothioate.


In certain embodiments, a compound comprises or consists of ISIS 420950 and a conjugate group. ISIS 534796 is a modified oligonucleotide having the formula: Aes Gks Aks Gds mCds Tds Ads Ads Ads mCds Ads Ads mCds mCks Gks mCe, wherein

    A=adenine
    T=thymine
    G=guanine;
    mC=5-methylcytosine; wherein

each sugar moiety is indicated according to the following:

    k=cEt;
    d=2′-deoxyribose;
    e=2′-MOE; wherein

each internucleoside linkage is indicated according to the following:

    s=phosphorothioate.


In certain embodiments, a compound comprises or consists of ISIS 420955 and a conjugate group. ISIS 540162 is a modified oligonucleotide having the formula: Ges Aes Aes Tes Ges Tds Tds Tds Tds Ads Tds Tds Gds Tds mCds Tes mCes Tes Ges mCe, wherein

    A=adenine
    T=thymine
    G=guanine;
    mC=5-methylcytosine; wherein

each sugar moiety is indicated according to the following:

    k=cEt;
    d=2′-deoxyribose;
    e=2′-MOE; wherein

each internucleoside linkage is indicated according to the following:

    s=phosphorothioate.


In certain embodiments, a compound comprises or consists of ISIS 420957 and a conjugate group. ISIS 540175 is a modified oligonucleotide having the formula: Ges Ges Aks mCds Ads mCds mCds mCds Ads mCds Gds mCds mCds mCks mCks mCe; wherein, each nucleobase is indicated according to the following:

    A=adenine
    T=thymine
    G=guanine;
    mC=5-methylcytosine; wherein

each sugar moiety is indicated according to the following:

    k=cEt;
    d=2′-deoxyribose;
    e=2′-MOE; wherein

each internucleoside linkage is indicated according to the following:

    s=phosphorothioate.


In certain embodiments, a compound comprises or consists of ISIS 420959 and a conjugate group. ISIS 540182 is a modified oligonucleotide having the formula: Aes mCes Aks mCds mCds mCds Tds mCds Gds mCds mCds Tds mCds mCks Gks Ge, wherein

    A=adenine
    T=thymine
    G=guanine;
    mC=5-methylcytosine; wherein

each sugar moiety is indicated according to the following:

    k=cEt;
    d=2′-deoxyribose;
    e=2′-MOE; wherein

each internucleoside linkage is indicated according to the following:

    s=phosphorothioate.


In certain embodiments, a compound comprises or consists of ISIS 420959 and a conjugate group. ISIS 540191 is a modified oligonucleotide having the formula: Ges mCes mCks Tds mCds mCds Gds Gds Ads Ads mCds Ads mCds mCks mCks Ae, wherein

    A=adenine
    T=thymine
    G=guanine;
    mC=5-methylcytosine; wherein

each sugar moiety is indicated according to the following:

    k=cEt;
    d=2′-deoxyribose;
    e=2′-MOE; wherein

each internucleoside linkage is indicated according to the following:

    s=phosphorothioate.


In certain embodiments, a compound comprises an antisense oligonucleotide disclosed in WO 2013/119979 and WO 2009/061851, which are incorporated by reference in their entireties herein. In certain embodiments, a compound comprises an antisense oligonucleotide having a nucleobase sequence of any of SEQ ID NOs 21-659 disclosed in WO 2013/119979 and a conjugate group described herein. In certain embodiments, a compound comprises an antisense oligonucleotide having a nucleobase sequence of any of SEQ ID NOs 4-159 and 168-611 disclosed in WO 2009/061851 and a conjugate group described herein. The nucleobase sequences of all of the aforementioned referenced SEQ ID NOs are incorporated by reference herein.
Factor VII Therapeutic Indications
In certain embodiments, provided herein are compounds and compositions as described herein for use in therapy.
In certain embodiments, provided herein are conjugated antisense compounds and compositions as described herein for use in treating, preventing, or slowing progression of a thromboembolic complication.
In certain embodiments, provided herein are conjugated antisense compounds and compositions as described herein for use in treating, preventing, or slowing progression of a hyperproliferative disorder.
In certain embodiments, provided herein are conjugated antisense compounds and compositions as described herein for use in treating, preventing, or slowing progression of an inflammatory condition.
In certain embodiments, the invention provides methods for using a conjugated antisense compound targeted to a Factor VII nucleic acid for modulating the expression of Factor VII in a subject. In certain embodiments, the expression of Factor VII is reduced.
In certain embodiments, the invention provides methods for using a conjugated antisense compound targeted to a Factor VII nucleic acid in a pharmaceutical composition for treating a subject. In certain embodiments, the subject has a Factor VII related disease, disorder or condition, or symptom thereof. In certain embodiments, the Factor VII related disease, disorder or condition is a thromboembolic complication, a hyperproliferative disorder or an inflammatory condition.
In certain embodiments, the invention provides methods for using a conjugated antisense compound targeted to a Factor VII nucleic acid in the preparation of a medicament.
In certain embodiments, the invention provides a conjugated antisense compound targeted to a Factor VII nucleic acid, or a pharmaceutically acceptable salt thereof, for use in therapy.
Certain embodiments provide a conjugated antisense compound targeted to a Factor VII nucleic acid for use in the treatment of a Factor VII related disease, disorder or condition, or symptom thereof. In certain embodiments, the Factor VII related disease, disorder or condition is a thromboembolic complication, a hyperproliferative disorder or an inflammatory condition.
In certain embodiments, provided herein are conjugated antisense compounds and compositions as described herein for use in treating, preventing, or slowing progression of a thromboembolic complication.
In certain embodiments, provided herein are conjugated antisense compounds and compositions as described herein for use in treating, preventing, or slowing progression of a hyperproliferative disorder.
In certain embodiments, provided herein are conjugated antisense compounds and compositions as described herein for use in treating, preventing, or slowing progression of an inflammatory condition.
It will be understood that any of the compounds described herein can be used in the aforementioned methods and uses. For example, in certain embodiments a conjugated antisense compound targeted to a Factor VII nucleic acid in the aforementioned methods and uses can include, but is not limited to, a conjugated antisense compound targeted to SEQ ID NO: 11 comprising an at least 8 consecutive nucleobase sequence of any one of SEQ ID NOs: 84-92: a conjugated antisense compound targeted to SEQ ID NO: 11 comprising a nucleobase sequence of any one of SEQ ID NO: 84-92: a compound comprising or consisting of ISIS 407935. ISIS 473589 ISIS 490279 ISIS 529804 ISIS 534796 ISIS 540162 ISIS 540175, ISIS 540182, or ISIS 540191 and a conjugate group; a compound comprising an antisense oligonucleotide disclosed in WO 2013/119979 and WO 2009/061851, which are incorporated by reference in their entireties herein, and a conjugate group; a compound comprising an antisense oligonucleotide having a nucleobase sequence of any of SEQ ID NOs 21-659 disclosed in WO 2013/119979 and a conjugate group described herein; an antisense oligonucleotide having a nucleobase sequence of any of SEQ ID NOs 4-159 and 168-611 disclosed in WO 2009/061851 and a conjugate group described herein. The nucleobase sequences of all of the aforementioned referenced SEQ ID NOs are incorporated by reference herein.
4. Coagulation Factor 11
The circulatory system requires mechanisms that prevent blood loss, as well as those that counteract inappropriate intravascular obstructions. Generally, coagulation comprises a cascade of reactions culminating in the conversion of soluble fibrinogen to an insoluble fibrin gel. The steps of the cascade involve the conversion of an inactive zymogen to an activated enzyme. The active enzyme then catalyzes the next step in the cascade.
Coagulation Cascade
The coagulation cascade may be initiated through two branches, the tissue factor pathway (also “extrinsic pathway”), which is the primary pathway, and the contact activation pathway (also “intrinsic pathway”).
The tissue factor pathway is initiated by the cell surface receptor tissue factor (TF, also referred to as factor III), which is expressed constitutively by extravascular cells (pericytes, cardiomyocytes, smooth muscle cells, and keratinocytes) and expressed by vascular monocytes and endothelial cells upon induction by inflammatory cytokines or endotoxin. (Drake et al., Am J Pathol 1989, 134:1087-1097). TF is the high affinity cellular receptor for coagulation factor VIIa, a serine protease. In the absence of TF, VIIa has very low catalytic activity, and binding to TF is necessary to render VIIa functional through an allosteric mechanism. (Drake et al., Am J Pathol 1989, 134:1087-1097). The TF-VIIa complex activates factor X to Xa. Xa in turn associates with its co-factor factor Va into a prothrombinase complex which in turn activates prothrombin, (also known as factor II or factor 2) to thrombin (also known as factor IIa, or factor 2a). Thrombin activates platelets, converts fibrinogen to fibrin and promotes fibrin cross-linking by activating factor XIII, thus forming a stable plug at sites where TF is exposed on extravascular cells. In addition, thrombin reinforces the coagulation cascade response by activating factors V and VIII.
The contact activation pathway is triggered by activation of factor XII to XIIa. Factor XIIa converts XI to XIa, and XIa converts IX to IXa. IXa associates with its cofactor Villa to convert X to Xa. The two pathways converge at this point as factor Xa associates factor Va to activate prothrombin (factor II) to thrombin (factor IIa).
Inhibition of Coagulation.
At least three mechanisms keep the coagulation cascade in check, namely the action of activated protein C, antithrombin, and tissue factor pathway inhibitor. Activated protein C is a serine protease that degrades cofactors Va and Villa. Protein C is activated by thrombin with thrombomodulin, and requires coenzyme Protein S to function. Antithrombin is a serine protease inhibitor (serpin) that inhibits serine proteases: thrombin, Xa, XIIa, XIa and IXa. Tissue factor pathway inhibitor inhibits the action of Xa and the TF-VIIa complex. (Schwartz A L et al., Trends Cardiovasc Med. 1997; 7:234-239.)
Disease
Thrombosis is the pathological development of blood clots, and an embolism occurs when a blood clot migrates to another part of the body and interferes with organ function. Thromboembolism may cause conditions such as deep vein thrombosis, pulmonary embolism, myocardial infarction, and stroke. Significantly, thromboembolism is a major cause of morbidity affecting over 2 million Americans every year. (Adcock et al. American Journal of Clinical Pathology. 1997; 108:434-49). While most cases of thrombosis are due to acquired extrinsic problems, for example, surgery, cancer, immobility, some cases are due to a genetic predisposition, for example, antiphospholipid syndrome and the autosomal dominant condition, Factor V Leiden. (Bertina R M et al. Nature 1994; 369:64-67.)
Treatment.
The most commonly used anticoagulants, warfarin, heparin, and low molecular weight heparin (LMWH) all possess significant drawbacks.
Warfarin is typically used to treat patients suffering from atrial fibrillation. The drug interacts with vitamin K-dependent coagulation factors which include factors II, VII, IX and X. Anticoagulant proteins C and S are also inhibited by warfarin. Drug therapy using warfarin is further complicated by the fact that warfarin interacts with other medications, including drugs used to treat atrial fibrillation, such as amiodarone. Because therapy with warfarin is difficult to predict, patients must be carefully monitored in order to detect any signs of anomalous bleeding.
Heparin functions by activating antithrombin which inhibits both thrombin and factor X. (Bjork I, Lindahl U. Mol Cell Biochem. 1982 48: 161-182.) Treatment with heparin may cause an immunological reaction that makes platelets aggregate within blood vessels that can lead to thrombosis. This side effect is known as heparin-induced thrombocytopenia (HIT) and requires patient monitoring. Prolonged treatment with heparin may also lead to osteoporosis. LMWH can also inhibit Factor 2, but to a lesser degree than unfractioned heparin (UFH). LMWH has been implicated in the development of HIT.
Thus, current anticoagulant agents lack predictability and specificity and, therefore, require careful patient monitoring to prevent adverse side effects, such as bleeding complications. There are currently no anticoagulants which target only the intrinsic or extrinsic pathway.
Antisense compounds targeting Factor XI have been previously disclosed in WO 2010/045509 and WO 2010/121074, each herein incorporated by reference in its entirety. Clinical studies are ongoing to assess the effect of antisense compounds targeting Factor XI in patients. However, there is still a need to provide patients with additional and more potent treatment options.
Certain Conjugated Antisense Compounds Targeted to a Factor XI Nucleic Acid
In certain embodiments, conjugated antisense compounds are targeted to a Factor XI nucleic acid having the sequence GENBANK Accession No. NM_000128.3 (incorporated herein as SEQ ID NO: 14), GENBANK Accession No. NT_022792.17, truncated from Ser. No. 19/598,000 to Ser. No. 19/624,000, (incorporated herein as SEQ ID NO: 15), GENBANK Accession No. NM_028066.1 (incorporated herein as SEQ ID NO: 16), exons 1-15 GENBANK Accession No. NW_001118167.1 (incorporated herein as SEQ ID NO: 17). In certain such embodiments, a conjugated antisense compound targeted to SEQ ID NO: 2 is at least 90%, at least 95%, or 100% complementary to SEQ ID NO: 2.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 2 comprises an at least 8 consecutive nucleobase sequence of any one of SEQ ID NOs: 12-19. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 2 comprises a nucleobase sequence of any one of SEQ ID NO: 12-19.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 14 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 93. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 14 comprises a nucleobase sequence of SEQ ID NO: 93.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 14 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 94. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 14 comprises a nucleobase sequence of SEQ ID NO: 94:
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 14 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 95. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 14 comprises a nucleobase sequence of SEQ ID NO: 95.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 14 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 96. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 14 comprises a nucleobase sequence of SEQ ID NO: 96.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 14 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 97. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 14 comprises a nucleobase sequence of SEQ ID NO: 97.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 14 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 98. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 14 comprises a nucleobase sequence of SEQ ID NO: 98.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 14 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 99. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 14 comprises a nucleobase sequence of SEQ ID NO: 99.
In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 14 comprises an at least 8 consecutive nucleobase sequence of SEQ ID NO: 100. In certain embodiments, a conjugated antisense compound targeted to SEQ ID NO: 14 comprises a nucleobase sequence of SEQ ID NO: 100.







TABLE 7 







Antisense Compounds targeted to Factor 11


SEQ ID NO: 14-17












Target


SEQ


ISIS
Start


ID


No
Site
Sequence (5′-3′)
Motif
NO














416850

TGCACAGTTTCTGGCAGGCC

93


 


416858

ACGGCATTGGTGCACAGTTT

94


 


445522

GCACAGTTTCTGGCAGGC

95


 


445531

GGCATTGGTGCACAGTTT

96


 


449707

CACAGTTTCTGGCAGG

97


 


449708

ACAGTTTCTGGCAG

98


 


449709

GCACAGTTTCTGGCAGGC

99


 


449710

CACAGTTTCTGGCAGG

100


 


449711

ACAGTTTCTGGCAG

101









In certain embodiments, a compound comprises an antisense oligonucleotide disclosed in WO 2010/045509 and WO 2010/121074, which are incorporated by reference in their entireties herein, and a conjugate group. In certain embodiments, a compound comprises an antisense oligonucleotide having a nucleobase sequence of any of SEQ ID NOs 15-270 disclosed in WO 2010/045509 and a conjugate group described herein. In certain embodiments, a compound comprises an antisense oligonucleotide having a nucleobase sequence of any of SEQ ID NOs 15-270 disclosed in WO 2010/121074 and a conjugate group described herein. The nucleobase sequences of all of the aforementioned referenced SEQ ID NOs are incorporated by reference herein.
E. Certain Pharmaceutical Compositions
In certain embodiments, the present disclosure provides pharmaceutical compositions comprising one or more antisense compound. In certain embodiments, such pharmaceutical composition comprises a suitable pharmaceutically acceptable diluent or carrier. In certain embodiments, a pharmaceutical composition comprises a sterile saline solution and one or more antisense compound. In certain embodiments, such pharmaceutical composition consists of a sterile saline solution and one or more antisense compound. In certain embodiments, the sterile saline is pharmaceutical grade saline. In certain embodiments, a pharmaceutical composition comprises one or more antisense compound and sterile water. In certain embodiments, a pharmaceutical composition consists of one or more antisense compound and sterile water.
In certain embodiments, the sterile saline is pharmaceutical grade water. In certain embodiments, a pharmaceutical composition comprises one or more antisense compound and phosphate-buffered saline (PBS). In certain embodiments, a pharmaceutical composition consists of one or more antisense compound and sterile phosphate-buffered saline (PBS). In certain embodiments, the sterile saline is pharmaceutical grade PBS.
In certain embodiments, antisense compounds may be admixed with pharmaceutically acceptable active and/or inert substances for the preparation of pharmaceutical compositions or formulations. Compositions and methods for the formulation of pharmaceutical compositions depend on a number of criteria, including, but not limited to, route of administration, extent of disease, or dose to be administered.
Pharmaceutical compositions comprising antisense compounds encompass any pharmaceutically acceptable salts, esters, or salts of such esters. In certain embodiments, pharmaceutical compositions comprising antisense compounds comprise one or more oligonucleotide 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 pharmaceutically acceptable salts of antisense compounds, prodrugs, pharmaceutically acceptable salts of such prodrugs, and other bioequivalents. Suitable pharmaceutically acceptable salts include, but are not limited to, sodium and potassium salts.
A prodrug can include the incorporation of additional nucleosides at one or both ends of an oligonucleotide which are cleaved by endogenous nucleases within the body, to form the active antisense oligonucleotide.
Lipid moieties have been used in nucleic acid therapies in a variety of methods. In certain such methods, the nucleic acid is introduced into preformed liposomes or lipoplexes made of mixtures of cationic lipids and neutral lipids. In certain methods, DNA complexes with mono- or poly-cationic lipids are formed without the presence of a neutral lipid. In certain embodiments, a lipid moiety is selected to increase distribution of a pharmaceutical agent to a particular cell or tissue. In certain embodiments, a lipid moiety is selected to increase distribution of a pharmaceutical agent to fat tissue. In certain embodiments, a lipid moiety is selected to increase distribution of a pharmaceutical agent to muscle tissue.
In certain embodiments, pharmaceutical compositions provided herein comprise one or more modified oligonucleotides and one or more excipients. In certain such embodiments, excipients are selected from water, salt solutions, alcohol, polyethylene glycols, gelatin, lactose, amylase, magnesium stearate, talc, silicic acid, viscous paraffin, hydroxymethylcellulose and polyvinylpyrrolidone.
In certain embodiments, a pharmaceutical composition provided herein comprises a delivery system. Examples of delivery systems include, but are not limited to, liposomes and emulsions. Certain delivery systems are useful for preparing certain pharmaceutical compositions including those comprising hydrophobic compounds. In certain embodiments, certain organic solvents such as dimethylsulfoxide are used.
In certain embodiments, a pharmaceutical composition provided herein comprises one or more tissue-specific delivery molecules designed to deliver the one or more pharmaceutical agents of the present disclosure to specific tissues or cell types. For example, in certain embodiments, pharmaceutical compositions include liposomes coated with a tissue-specific antibody.
In certain embodiments, a pharmaceutical composition provided herein comprises a co-solvent system. Certain of such co-solvent systems comprise, for example, benzyl alcohol, a nonpolar surfactant, a water-miscible organic polymer, and an aqueous phase. In certain embodiments, such co-solvent systems are used for hydrophobic compounds. A non-limiting example of such a co-solvent system is the VPD co-solvent system, which is a solution of absolute ethanol comprising 3% w/v benzyl alcohol, 8% w/v of the nonpolar surfactant Polysorbate 80TM and 65% w/v polyethylene glycol 300. The proportions of such co-solvent systems may be varied considerably without significantly altering their solubility and toxicity characteristics. Furthermore, the identity of co-solvent components may be varied: for example, other surfactants may be used instead of Polysorbate 80TM; the fraction size of polyethylene glycol may be varied; other biocompatible polymers may replace polyethylene glycol, e.g., polyvinyl pyrrolidone; and other sugars or polysaccharides may substitute for dextrose.
In certain embodiments, a pharmaceutical composition provided herein is prepared for oral administration. In certain embodiments, pharmaceutical compositions are prepared for buccal administration.
In certain embodiments, a pharmaceutical composition is prepared for administration by injection (e.g., intravenous, subcutaneous, intramuscular, etc.). In certain of such embodiments, a pharmaceutical composition comprises a carrier and is formulated in aqueous solution, such as water or physiologically compatible buffers such as Hanks's solution, Ringer's solution, or physiological saline buffer. In certain embodiments, other ingredients are included (e.g., ingredients that aid in solubility or serve as preservatives). In certain embodiments, injectable suspensions are prepared using appropriate liquid carriers, suspending agents and the like. Certain pharmaceutical compositions for injection are presented in unit dosage form, e.g., in ampoules or in multi-dose containers. Certain pharmaceutical compositions for injection are suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents. Certain solvents suitable for use in pharmaceutical compositions for injection include, but are not limited to, lipophilic solvents and fatty oils, such as sesame oil, synthetic fatty acid esters, such as ethyl oleate or triglycerides, and liposomes. Aqueous injection suspensions may contain substances that increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran. Optionally, such suspensions may also contain suitable stabilizers or agents that increase the solubility of the pharmaceutical agents to allow for the preparation of highly concentrated solutions.
In certain embodiments, a pharmaceutical composition is prepared for transmucosal administration. In certain of such embodiments penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art.
In certain embodiments, a pharmaceutical composition provided herein comprises an oligonucleotide in a therapeutically effective amount. In certain embodiments, the therapeutically effective amount is sufficient to prevent, alleviate or ameliorate symptoms of a disease or to prolong the survival of the subject being treated. Determination of a therapeutically effective amount is well within the capability of those skilled in the art.
In certain embodiments, one or more modified oligonucleotide provided herein is formulated as a prodrug. In certain embodiments, upon in vivo administration, a prodrug is chemically converted to the biologically, pharmaceutically or therapeutically more active form of an oligonucleotide. In certain embodiments, prodrugs are useful because they are easier to administer than the corresponding active form. For example, in certain instances, a prodrug may be more bioavailable (e.g., through oral administration) than is the corresponding active form. In certain instances, a prodrug may have improved solubility compared to the corresponding active form. In certain embodiments, prodrugs are less water soluble than the corresponding active form. In certain instances, such prodrugs possess superior transmittal across cell membranes, where water solubility is detrimental to mobility. In certain embodiments, a prodrug is an ester. In certain such embodiments, the ester is metabolically hydrolyzed to carboxylic acid upon administration. In certain instances the carboxylic acid containing compound is the corresponding active form. In certain embodiments, a prodrug comprises a short peptide (polyaminoacid) bound to an acid group. In certain of such embodiments, the peptide is cleaved upon administration to form the corresponding active form.
In certain embodiments, the present disclosure provides compositions and methods for reducing the amount or activity of a target nucleic acid in a cell. In certain embodiments, the cell is in an animal. In certain embodiments, the animal is a mammal. In certain embodiments, the animal is a rodent. In certain embodiments, the animal is a primate. In certain embodiments, the animal is a non-human primate. In certain embodiments, the animal is a human.
In certain embodiments, the present disclosure provides methods of administering a pharmaceutical composition comprising an oligonucleotide of the present disclosure to an animal. Suitable administration routes include, but are not limited to, oral, rectal, transmucosal, intestinal, enteral, topical, suppository, through inhalation, intrathecal, intracerebroventricular, intraperitoneal, intranasal, intraocular, intratumoral, and parenteral (e.g., intravenous, intramuscular, intramedullary, and subcutaneous). In certain embodiments, pharmaceutical intrathecals are administered to achieve local rather than systemic exposures. For example, pharmaceutical compositions may be injected directly in the area of desired effect (e.g., into the liver).
Nonlimiting Disclosure and Incorporation by Reference
While certain compounds, compositions and methods described herein have been described with specificity in accordance with certain embodiments, the following examples serve only to illustrate the compounds described herein and are not intended to limit the same. Each of the references, GenBank accession numbers, and the like recited in the present application is incorporated herein by reference in its entirety.
Although the sequence listing accompanying this filing identifies each sequence as either “RNA” or “DNA” as required, in reality, those sequences may be modified with any combination of chemical modifications. One of skill in the art will readily appreciate that such designation as “RNA” or “DNA” to describe modified oligonucleotides is, in certain instances, arbitrary. For example, an oligonucleotide comprising a nucleoside comprising a 2′-OH sugar moiety and a thymine base could be described as a DNA having a modified sugar (2′-OH for the natural 2′-H of DNA) or as an RNA having a modified base (thymine (methylated uracil) for natural uracil of RNA).
Accordingly, nucleic acid sequences provided herein, including, but not limited to those in the sequence listing, are intended to encompass nucleic acids containing any combination of natural or modified
RNA and/or DNA, including, but not limited to such nucleic acids having modified nucleobases. By way of further example and without limitation, an oligonucleotide having the nucleobase sequence “ATCGATCG” encompasses any oligonucleotides having such nucleobase sequence, whether modified or unmodified, including, but not limited to, such compounds comprising RNA bases, such as those having sequence “AUCGAUCG” and those having some DNA bases and some RNA bases such as “AUCGATCG” and oligonucleotides having other modified bases, such as “ATmeCGAUCG,” wherein meC indicates a cytosine base comprising a methyl group at the 5-position.
EXAMPLES
The following examples illustrate certain embodiments of the present disclosure and are not limiting. Moreover, where specific embodiments are provided, the inventors have contemplated generic application of those specific embodiments. For example, disclosure of an oligonucleotide having a particular motif provides reasonable support for additional oligonucleotides having the same or similar motif And, for example, where a particular high-affinity modification appears at a particular position, other high-affinity modifications at the same position are considered suitable, unless otherwise indicated.
Example 1
General Method for the Preparation of Phosphoramidites, Compounds 1, 1a and 2




    
    
        Bx is a heterocyclic base;
    
    


Compounds 1, 1a and 2 were prepared as per the procedures well known in the art as described in the specification herein (see Seth et al., Bioorg. Med. Chem., 2011, 21(4), 1122-1125, J. Org. Chem., 2010, 75(5), 1569-1581, Nucleic Acids Symposium Series, 2008, 52(1), 553-554); and also see published PCT International Applications (WO 2011/115818, WO 2010/077578, WO2010/036698, WO2009/143369, WO 2009/006478, and WO 2007/090071), and U.S. Pat. No. 7,569,686).
Example 2
Preparation of Compound 7




Compounds 3 (2-acetamido-1,3,4,6-tetra-O-acetyl-2-deoxy-β-D-galactopyranose or galactosamine pentaacetate) is commercially available. Compound 5 was prepared according to published procedures (Weber et al., J. Med. Chem., 1991, 34, 2692).
Example 3
Preparation of Compound 11




Compounds 8 and 9 are commercially available.
Example 4
Preparation of Compound 18







Compound 11 was prepared as per the procedures illustrated in Example 3. Compound 14 is commercially available. Compound 17 was prepared using similar procedures reported by Rensen et al., J. Med. Chem., 2004, 47, 5798-5808.
Example 5
Preparation of Compound 23




Compounds 19 and 21 are commercially available.
Example 6
Preparation of Compound 24




Compounds 18 and 23 were prepared as per the procedures illustrated in Examples 4 and 5.
Example 7
Preparation of Compound 25




Compound 24 was prepared as per the procedures illustrated in Example 6.
Example 8
Preparation of Compound 26




Compound 24 is prepared as per the procedures illustrated in Example 6.
Example 9
General Preparation of Conjugated ASOs Comprising GalNAc3-1 at the 3′ Terminus, Compound 29







    
    
        Wherein the protected GalNAc3-1 has the structure:
    
    






The GalNAc3 cluster portion of the conjugate group GalNAc3-1 (GalNAc3-1a) can be combined with any cleavable moiety to provide a variety of conjugate groups. Wherein GalNAc3-1a has the formula:




The solid support bound protected GalNAc3-1, Compound 25, was prepared as per the procedures illustrated in Example 7. Oligomeric Compound 29 comprising GalNAc3-1 at the 3′ terminus was prepared using standard procedures in automated DNA/RNA synthesis (see Dupouy et al., Angew. Chem. Int. Ed., 2006, 45, 3623-3627). Phosphoramidite building blocks, Compounds 1 and 1a were prepared as per the procedures illustrated in Example 1. The phosphoramidites illustrated are meant to be representative and not intended to be limiting as other phosphoramidite building blocks can be used to prepare oligomeric compounds having a predetermined sequence and composition. The order and quantity of phosphoramidites added to the solid support can be adjusted to prepare gapped oligomeric compounds as described herein. Such gapped oligomeric compounds can have predetermined composition and base sequence as dictated by any given target.
Example 10
General Preparation Conjugated ASOs Comprising GalNAc3-1 at the 5′ Terminus, Compound 34







The UnylinkerTM 30 is commercially available. Oligomeric Compound 34 comprising a GalNAc3-1 cluster at the 5′ terminus is prepared using standard procedures in automated DNA/RNA synthesis (see Dupouy et al., Angew. Chem. Int. Ed., 2006, 45, 3623-3627). Phosphoramidite building blocks, Compounds 1 and 1a were prepared as per the procedures illustrated in Example 1. The phosphoramidites illustrated are meant to be representative and not intended to be limiting as other phosphoramidite building blocks can be used to prepare an oligomeric compound having a predetermined sequence and composition. The order and quantity of phosphoramidites added to the solid support can be adjusted to prepare gapped oligomeric compounds as described herein. Such gapped oligomeric compounds can have predetermined composition and base sequence as dictated by any given target.
Example 11
Preparation of Compound 39







Compounds 4, 13 and 23 were prepared as per the procedures illustrated in Examples 2, 4, and 5. Compound 35 is prepared using similar procedures published in Rouchaud et al., Eur. J. Org. Chem., 2011, 12, 2346-2353.
Example 12
Preparation of Compound 40




Compound 38 is prepared as per the procedures illustrated in Example 11.
Example 13
Preparation of Compound 44







Compounds 23 and 36 are prepared as per the procedures illustrated in Examples 5 and 11. Compound 41 is prepared using similar procedures published in WO 2009082607.
Example 14
Preparation of Compound 45




Compound 43 is prepared as per the procedures illustrated in Example 13.
Example 15
Preparation of Compound 47




Compound 46 is commercially available.
Example 16
Preparation of Compound 53







Compounds 48 and 49 are commercially available. Compounds 17 and 47 are prepared as per the procedures illustrated in Examples 4 and 15.
Example 17
Preparation of Compound 54




Compound 53 is prepared as per the procedures illustrated in Example 16.
Example 18
Preparation of Compound 55




Compound 53 is prepared as per the procedures illustrated in Example 16.
Example 19
General Method for the Preparation of Conjugated ASOs Comprising GalNAc3-1 at the 3′ Position Via Solid Phase Techniques (Preparation of ISIS 647535, 647536 and 651900)
Unless otherwise stated, all reagents and solutions used for the synthesis of oligomeric compounds are purchased from commercial sources. Standard phosphoramidite building blocks and solid support are used for incorporation nucleoside residues which include for example T, A, G, and mC residues. A 0.1 M solution of phosphoramidite in anhydrous acetonitrile was used for β-D-2′-deoxyribonucleoside and 2′-MOE.
The ASO syntheses were performed on ABI 394 synthesizer (1-2 μmol scale) or on GE Healthcare Bioscience ÄKTA oligopilot synthesizer (40-200 μmol scale) by the phosphoramidite coupling method on an GalNAc3-1 loaded VIMAD solid support (110 μmol/g, Guzaev et al., 2003) packed in the column. For the coupling step, the phosphoramidites were delivered 4 fold excess over the loading on the solid support and phosphoramidite condensation was carried out for 10 min. All other steps followed standard protocols supplied by the manufacturer. A solution of 6% dichloroacetic acid in toluene was used for removing dimethoxytrityl (DMT) group from 5′-hydroxyl group of the nucleotide. 4,5-Dicyanoimidazole (0.7 M) in anhydrous CH3CN was used as activator during coupling step. Phosphorothioate linkages were introduced by sulfurization with 0.1 M solution of xanthane hydride in 1:1 pyridine/CH3CN for a contact time of 3 minutes. A solution of 20% tert-butylhydroperoxide in CH3CN containing 6% water was used as an oxidizing agent to provide phosphodiester internucleoside linkages with a contact time of 12 minutes.
After the desired sequence was assembled, the cyanoethyl phosphate protecting groups were deprotected using a 1:1 (v/v) mixture of triethylamine and acetonitrile with a contact time of 45 minutes. The solid-support bound ASOs were suspended in aqueous ammonia (28-30 wt %) and heated at 55° C. for 6 h.
The unbound ASOs were then filtered and the ammonia was boiled off. The residue was purified by high pressure liquid chromatography on a strong anion exchange column (GE Healthcare Bioscience, Source 30Q, 30 μm, 2.54×8 cm, A=100 mM ammonium acetate in 30% aqueous CH3CN, B=1.5 M NaBr in A, O-40% of B in 60 min, flow 14 mL min-1, λ=260 nm). The residue was desalted by HPLC on a reverse phase column to yield the desired ASOs in an isolated yield of 15-30% based on the initial loading on the solid support. The ASOs were characterized by ion-pair-HPLC coupled MS analysis with Agilent 1100 MSD system.
Antisense oligonucleotides not comprising a conjugate were synthesized using standard oligonucleotide synthesis procedures well known in the art.
Using these methods, three separate antisense compounds targeting ApoC III were prepared. As summarized in Table 4, below, each of the three antisense compounds targeting ApoC III had the same nucleobase sequence; ISIS 304801 is a 5-10-5 MOE gapmer having all phosphorothioate linkages; ISIS 647535 is the same as ISIS 304801, except that it had a GalNAc3-1 conjugated at its 3′end; and ISIS 647536 is the same as ISIS 647535 except that certain internucleoside linkages of that compound are phosphodiester linkages. As further summarized in Table 4, two separate antisense compounds targeting SRB-1 were synthesized. ISIS 440762 was a 2-10-2 cEt gapmer with all phosphorothioate internucleoside linkages; ISIS 651900 is the same as ISIS 440762, except that it included a GalNAc3-1 at its 3′-end.







TABLE 4 







Modified ASO targeting ApoC III and SRB-1
















Ob-
SEQ



Sequence 

CalCd
served
ID


ASO
(5′ to 3′)
Target
Mass
Mass
No.





ISIS
AesGesmCesTesTesmCds
ApoC
7165.4
7164.4
20


304801
TdsTdsGdsTdsmCdsmCds
III






AdsGdsmCdsTesTesTes







AesTe






 


ISIS
AesGesmCesTesTesmCds
ApoC
9239.5
9237.8
21


647535
TdsTdsGdsTdsmCdsmCds
III






AdsGdsmCdsTesTesTesAes







Teo  






 


ISIS
AesGeomCeoTeoTeomCds
ApoC
9142.9
9140.8
21


647536
TdsTdsGdsTdsmCdsmCds
III






AdsGdsmCdsTeoTeoTesAes







Teo  






 


ISIS
TksmCksAdsGdsTdsmCds
SRB-1
4647.0
4646.4
22


440762
AdsTdsGdsAdsmCdsTds







TksmCk






 


ISIS
TksmCksAdsGdsTdsmCds
SRB-1
6721.1
6719.4
23


651900
AdsTdsGdsAdsmCdsTdsTdsm







Cko  









Subscripts: “e” indicates 2′-MOE modified nucleoside; “d” indicates β-D-2′-deoxyribonucleoside; “k” indicates 6′-(S)—CH3 bicyclic nucleoside (e.g. cEt); “s” indicates phosphorothioate internucleoside linkages (PS); “o” indicates phosphodiester internucleoside linkages (PO); and “o” indicates —O—P(═O)(OH)—. Superscript “m” indicates 5-methylcytosines. “GalNAc3-1” indicates a conjugate group having the structure shown previously in Example 9. Note that GalNAc3-1 comprises a cleavable adenosine which links the ASO to remainder of the conjugate, which is designated “GalNAc3-1a.” This nomenclature is used in the above table to show the full nucleobase sequence, including the adenosine, which is part of the conjugate. Thus, in the above table, the sequences could also be listed as ending with “GalNAc3-1” with the “Ado” omitted. This convention of using the subscript “a” to indicate the portion of a conjugate group lacking a cleavable nucleoside or cleavable moiety is used throughout these Examples. This portion of a conjugate group lacking the cleavable moiety is referred to herein as a “cluster” or “conjugate cluster” or “GalNAc3 cluster.” In certain instances it is convenient to describe a conjugate group by separately providing its cluster and its cleavable moiety.

Example 20
Dose-Dependent Antisense Inhibition of Human ApoC III in huApoC III Transgenic Mice
ISIS 304801 and ISIS 647535, each targeting human ApoC III and described above, were separately tested and evaluated in a dose-dependent study for their ability to inhibit human ApoC III in human ApoC III transgenic mice.
Treatment
Human ApoCIII transgenic mice were maintained on a 12-hour light/dark cycle and fed ad libitum Teklad lab chow. Animals were acclimated for at least 7 days in the research facility before initiation of the experiment. ASOs were prepared in PBS and sterilized by filtering through a 0.2 micron filter. ASOs were dissolved in 0.9% PBS for injection.
Human ApoC III transgenic mice were injected intraperitoneally once a week for two weeks with ISIS 304801 or 647535 at 0.08, 0.25. 0.75, 2.25 or 6.75 μmol/kg or with PBS as a control. Each treatment group consisted of 4 animals. Forty-eight hours after the administration of the last dose, blood was drawn from each mouse and the mice were sacrificed and tissues were collected.
ApoC III mRNA Analysis
ApoC III mRNA levels in the mice's livers were determined using real-time PCR and RIBOGREEN® RNA quantification reagent (Molecular Probes, Inc. Eugene, Oreg.) according to standard protocols. ApoC III mRNA levels were determined relative to total RNA (using Ribogreen), prior to normalization to PBS-treated control. The results below are presented as the average percent of ApoC III mRNA levels for each treatment group, normalized to PBS-treated control and are denoted as “% PBS”. The half maximal effective dosage (ED50) of each ASO is also presented in Table 5, below.
As illustrated, both antisense compounds reduced ApoC III RNA relative to the PBS control. Further, the antisense compound conjugated to GalNAc3-1 (ISIS 647535) was substantially more potent than the antisense compound lacking the GalNAc3-1 conjugate (ISIS 304801).







TABLE 5







Effect of ASO treatment on ApoC III mRNA levels


in human ApoC III transgenic mice


















Inter-








nucleoside
SEQ



Dose
%
ED50

linkage/
ID


ASO
(μmol/kg)
PBS
(μmol/kg)
3′ Conjugate
Length
No.
















PBS
0
100
—
—
—



ISIS
0.08
95
0.77
None
PS/20
20


304801
0.75
42



2.25
32



6.75
19


ISIS
0.08
50
0.074
GalNAc3-1
PS/20
21


647535
0.75
15



2.25
17



6.75
8









ApoC III Protein Analysis (Turbidometric Assay)

Plasma ApoC III protein analysis was determined using procedures reported by Graham et al, Circulation Research, published online before print Mar. 29, 2013.
Approximately 100 μl of plasma isolated from mice was analyzed without dilution using an Olympus Clinical Analyzer and a commercially available turbidometric ApoC III assay (Kamiya, Cat#KAI-006, Kamiya Biomedical, Seattle, Wash.). The assay protocol was performed as described by the vendor.
As shown in the Table 6 below, both antisense compounds reduced ApoC III protein relative to the PBS control. Further, the antisense compound conjugated to GalNAc3-1 (ISIS 647535) was substantially more potent than the antisense compound lacking the GalNAc3-1 conjugate (ISIS 304801).







TABLE 6







Effect of ASO treatment on ApoC III plasma protein


levels in human ApoC III transgenic mice


















Inter-




Dose

ED50

nucleoside



(μmol/
%
(μmol/
3′
Linkage/
SEQ


ASO
kg)
PBS
kg)
Conjugate
Length
ID No.
















PBS
0
100
—
—
—



ISIS
0.08
86
0.73
None
PS/20
20


304801
0.75
51



2.25
23



6.75
13


ISIS
0.08
72
0.19
GalNAc3-1
PS/20
21


647535
0.75
14



2.25
12



6.75
11









Plasma triglycerides and cholesterol were extracted by the method of Bligh and Dyer (Bligh, E. G. and Dyer, W. J. Can. J. Biochem. Physiol. 37: 911-917, 1959)(Bligh, E and Dyer, W, Can J Biochem Physiol, 37, 911-917, 1959)(Bligh, E and Dyer, W, Can J Biochem Physiol, 37, 911-917, 1959) and measured by using a Beckmann Coulter clinical analyzer and commercially available reagents.
The triglyceride levels were measured relative to PBS injected mice and are denoted as “% PBS”. Results are presented in Table 7. As illustrated, both antisense compounds lowered triglyceride levels. Further, the antisense compound conjugated to GalNAc3-1 (ISIS 647535) was substantially more potent than the antisense compound lacking the GalNAc3-1 conjugate (ISIS 304801).







TABLE 7







Effect of ASO treatment on triglyceride levels in transgenic mice


















Inter-




Dose

ED50

nucleoside



(μmol/
%
(μmol/
3′
Linkage/
SEQ


ASO
kg)
PBS
kg)
Conjugate
Length
ID No.
















PBS
0
100
—
—
—



ISIS
0.08
87
0.63
None
PS/20
20


304801
0.75
46



2.25
21



6.75
12


ISIS
0.08
65
0.13
GalNAc3-1
PS/20
21


647535
0.75
9



2.25
8



6.75
9









Plasma samples were analyzed by HPLC to determine the amount of total cholesterol and of different fractions of cholesterol (HDL and LDL). Results are presented in Tables 8 and 9. As illustrated, both antisense compounds lowered total cholesterol levels; both lowered LDL; and both raised HDL. Further, the antisense compound conjugated to GalNAc3-1 (ISIS 647535) was substantially more potent than the antisense compound lacking the GalNAc3-1 conjugate (ISIS 304801). An increase in HDL and a decrease in LDL levels is a cardiovascular beneficial effect of antisense inhibition of ApoC III.







TABLE 8







Effect of ASO treatment on total cholesterol levels in transgenic mice














Total


SEQ



Dose
Cholesterol
3′
Internucleoside
ID


ASO
(μmol/kg)
(mg/dL)
Conjugate
Linkage/Length
No.















PBS
0
257
—
—



ISIS
0.08
226
None
PS/20
20


304801
0.75
164



2.25
110



6.75
82


ISIS
0.08
230
GalNAc3-1
PS/20
21


647535
0.75
82



2.25
86



6.75
99
















TABLE 9







Effect of ASO treatment on HDL and LDL


cholesterol levels in transgenic mice


















Inter-




Dose



nucleoside



(μmol/
HDL
LDL
3′
Linkage/
SEQ


ASO
kg)
(mg/dL)
(mg/dL)
Conjugate
Length
ID No.
















PBS
0
17
28
—
—



ISIS
0.08
17
23
None
PS/20
32


304801
0.75
27
12



2.25
50
4



6.75
45
2


ISIS
0.08
21
21
GalNAc3-1
PS/20
111


647535
0.75
44
2



2.25
50
2



6.75
58
2









Pharmacokinetics Analysis (PK)

The PK of the ASOs was also evaluated. Liver and kidney samples were minced and extracted using standard protocols. Samples were analyzed on MSD1 utilizing IP-HPLC-MS. The tissue level (μg/g) of full-length ISIS 304801 and 647535 was measured and the results are provided in Table 10. As illustrated, liver concentrations of total full-length antisense compounds were similar for the two antisense compounds. Thus, even though the GalNAc3-1-conjugated antisense compound is more active in the liver (as demonstrated by the RNA and protein data above), it is not present at substantially higher concentration in the liver. Indeed, the calculated EC50 (provided in Table 10) confirms that the observed increase in potency of the conjugated compound cannot be entirely attributed to increased accumulation. This result suggests that the conjugate improved potency by a mechanism other than liver accumulation alone, possibly by improving the productive uptake of the antisense compound into cells.
The results also show that the concentration of GalNAc3-1 conjugated antisense compound in the kidney is lower than that of antisense compound lacking the GalNAc conjugate. This has several beneficial therapeutic implications. For therapeutic indications where activity in the kidney is not sought, exposure to kidney risks kidney toxicity without corresponding benefit. Moreover, high concentration in kidney typically results in loss of compound to the urine resulting in faster clearance. Accordingly, for non-kidney targets, kidney accumulation is undesired. These data suggest that GalNAc3-1 conjugation reduces kidney accumulation.







TABLE 10







PK analysis of ASO treatment in transgenic mice

















Kid-
Liver

Inter-




Dose
Liver
ney
EC50

nucleoside
SEQ



(μmol/
(μg/
(μg/
(μg/
3′
Linkage/
ID


ASO
kg)
g)
g)
g)
Conjugate
Length
No.

















ISIS
0.1
5.2
2.1
53
None
PS/20
20


304801
0.8
62.8
119.6



2.3
142.3
191.5



6.8
202.3
337.7


ISIS
0.1
3.8
0.7
3.8
GalNAc3-1
PS/20
21


647535
0.8
72.7
34.3



2.3
106.8
111.4



6.8
237.2
179.3









Metabolites of ISIS 647535 were also identified and their masses were confirmed by high resolution mass spectrometry analysis. The cleavage sites and structures of the observed metabolites are shown below. The relative % of full length ASO was calculated using standard procedures and the results are presented in Table 10a. The major metabolite of ISIS 647535 was full-length ASO lacking the entire conjugate (i.e. ISIS 304801), which results from cleavage at cleavage site A, shown below. Further, additional metabolites resulting from other cleavage sites were also observed. These results suggest that introducing other cleabable bonds such as esters, peptides, disulfides, phosphoramidates or acyl-hydrazones between the GalNAc3-1 sugar and the ASO, which can be cleaved by enzymes inside the cell, or which may cleave in the reductive environment of the cytosol, or which are labile to the acidic pH inside endosomes and lyzosomes, can also be useful.







TABLE 10a







Observed full length metabolites of ISIS 647535










Metabolite
ASO
Cleavage site
Relative %













1
ISIS 304801
A
36.1


2
ISIS 304801 + dA
B
10.5


3
ISIS 647535 minus [3 GalNAc]
C
16.1


4
ISIS 647535 minus
D
17.6



[3 GalNAc + 1 5-hydroxy-



pentanoic acid tether]


5
ISIS 647535 minus
D
9.9



[2 GalNAc + 2 5-hydroxy-



pentanoic acid tether]


6
ISIS 647535 minus
D
9.8



[3 GalNAc + 3 5-hydroxy-



pentanoic acid tether]









Cleavage Sites










Example 21
Antisense Inhibition of Human ApoC III in Human ApoC III Transgenic Mice in Single Administration Study
ISIS 304801, 647535 and 647536 each targeting human ApoC III and described in Table 4, were further evaluated in a single administration study for their ability to inhibit human ApoC III in human ApoC III transgenic mice.
Treatment
Human ApoCIII transgenic mice were maintained on a 12-hour light/dark cycle and fed ad libitum Teklad lab chow. Animals were acclimated for at least 7 days in the research facility before initiation of the experiment. ASOs were prepared in PBS and sterilized by filtering through a 0.2 micron filter. ASOs were dissolved in 0.9% PBS for injection.
Human ApoC III transgenic mice were injected intraperitoneally once at the dosage shown below with ISIS 304801, 647535 or 647536 (described above) or with PBS treated control. The treatment group consisted of 3 animals and the control group consisted of 4 animals. Prior to the treatment as well as after the last dose, blood was drawn from each mouse and plasma samples were analyzed. The mice were sacrificed 72 hours following the last administration.
Samples were collected and analyzed to determine the ApoC III mRNA and protein levels in the liver; plasma triglycerides; and cholesterol, including HDL and LDL fractions were assessed as described above (Example 20). Data from those analyses are presented in Tables 11-15, below. Liver transaminase levels, alanine aminotransferase (ALT) and aspartate aminotransferase (AST), in serum were measured relative to saline injected mice using standard protocols. The ALT and AST levels showed that the antisense compounds were well tolerated at all administered doses.
These results show improvement in potency for antisense compounds comprising a GalNAc3-1 conjugate at the 3′ terminus (ISIS 647535 and 647536) compared to the antisense compound lacking a GalNAc3-1 conjugate (ISIS 304801). Further, ISIS 647536, which comprises a GalNAc3-1 conjugate and some phosphodiester linkages was as potent as ISIS 647535, which comprises the same conjugate and all internucleoside linkages within the ASO are phosphorothioate.







TABLE 11







Effect of ASO treatment on ApoC III mRNA levels


in human ApoC III transgenic mice



















SEQ



Dose
%
ED50
3′
Internucleoside
ID


ASO
(mg/kg)
PBS
(mg/kg)
Conjugate
linkage/Length
No.
















PBS
0
99
—
—
—



ISIS
1
104
13.2
None
PS/20
20


304801
3
92



10
71



30
40


ISIS
0.3
98
1.9
GalNAc3-1
PS/20
21


647535
1
70



3
33



10
20


ISIS
0.3
103
1.7
GalNAc3-1
PS/PO/20
21


647536
1
60



3
31



10
21
















TABLE 12







Effect of ASO treatment on ApoC III plasma


protein levels in human ApoC III transgenic mice



















SEQ



Dose
%
ED50
3′
Internucleoside
ID


ASO
(mg/kg)
PBS
(mg/kg)
Conjugate
Linkage/Length
No.
















PBS
0
99
—
—
—



ISIS
1
104
23.2
None
PS/20
20


304801
3
92



10
71



30
40


ISIS
0.3
98
2.1
GalNAc3-1
PS/20
21


647535
1
70



3
33



10
20


ISIS
0.3
103
1.8
GalNAc3-1
PS/PO/20
21


647536
1
60



3
31



10
21
















TABLE 13







Effect of ASO treatment on triglyceride levels in transgenic mice



















SEQ



Dose
%
ED50

Internucleoside
ID


ASO
(mg/kg)
PBS
(mg/kg)
3′ Conjugate
Linkage/Length
No.
















PBS
0
98
—
—
—



ISIS
1
80
29.1
None
PS/20
20


304801
3
92



10
70



30
47


ISIS
0.3
100
2.2
GalNAc3-1
PS/20
21


647535
1
70



3
34



10
23


ISIS
0.3
95
1.9
GalNAc3-1
PS/PO/20
21


647536
1
66



3
31



10
23
















TABLE 14







Effect of ASO treatment on total cholesterol levels in transgenic mice













Dose


Internucleoside



ASO
(mg/kg)
% PBS
3′ Conjugate
Linkage/Length
SEQ ID No.















PBS
0
96
—
—



ISIS
1
104
None
PS/20
20


304801
3
96



10
86



30
72


ISIS
0.3
93
GalNAc3-1
PS/20
21


647535
1
85



3
61



10
53


ISIS
0.3
115
GalNAc3-1
PS/PO/20
21


647536
1
79



3
51



10
54
















TABLE 15







Effect of ASO treatment on HDL and LDL


cholesterol levels in transgenic mice















HDL
LDL






Dose
%
%
3′
Internucleoside
SEQ ID


ASO
(mg/kg)
PBS
PBS
Conjugate
Linkage/Length
No.
















PBS
0
131
90
—
—



ISIS
1
130
72
None
PS/20
20


304801
3
186
79



10
226
63



30
240
46


ISIS
0.3
98
86
GalNAc3-1
PS/20
21


647535
1
214
67



3
212
39



10
218
35


ISIS
0.3
143
89
GalNAc3-1
PS/PO/20
21


647536
1
187
56



3
213
33



10
221
34









These results confirm that the GalNAc3-1 conjugate improves potency of an antisense compound. The results also show equal potency of a GalNAc3-1 conjugated antisense compounds where the antisense oligonucleotides have mixed linkages (ISIS 647536 which has six phosphodiester linkages) and a full phosphorothioate version of the same antisense compound (ISIS 647535).
Phosphorothioate linkages provide several properties to antisense compounds. For example, they resist nuclease digestion and they bind proteins resulting in accumulation of compound in the liver, rather than in the kidney/urine. These are desirable properties, particularly when treating an indication in the liver. However, phosphorothioate linkages have also been associated with an inflammatory response. Accordingly, reducing the number of phosphorothioate linkages in a compound is expected to reduce the risk of inflammation, but also lower concentration of the compound in liver, increase concentration in the kidney and urine, decrease stability in the presence of nucleases, and lower overall potency. The present results show that a GalNAc3-1 conjugated antisense compound where certain phosphorothioate linkages have been replaced with phosphodiester linkages is as potent against a target in the liver as a counterpart having full phosphorothioate linkages. Such compounds are expected to be less proinflammatory (See Example 24 describing an experiment showing reduction of PS results in reduced inflammatory effect).
Example 22
Effect of GalNAc3-1 Conjugated Modified ASO Targeting SRB-1 In Vivo
ISIS 440762 and 651900, each targeting SRB-1 and described in Table 4 were evaluated in a dose-dependent study for their ability to inhibit SRB-1 in Balb/c mice.
Treatment
Six week old male Balb/c mice (Jackson Laboratory, Bar Harbor, Me.) were injected subcutaneously once at the dosage shown below with ISIS 440762, 651900 or with PBS treated control. Each treatment group consisted of 4 animals. The mice were sacrificed 48 hours following the final administration to determine the SRB-1 mRNA levels in liver using real-time PCR and RIBOGREEN® RNA quantification reagent (Molecular Probes, Inc. Eugene, Oreg.) according to standard protocols. SRB-1 mRNA levels were determined relative to total RNA (using Ribogreen), prior to normalization to PBS-treated control. The results below are presented as the average percent of SRB-1 mRNA levels for each treatment group, normalized to PBS-treated control and is denoted as “% PBS”.
As illustrated in Table 16, both antisense compounds lowered SRB-1 mRNA levels. Further, the antisense compound comprising the GalNAc3-1 conjugate (ISIS 651900) was substantially more potent than the antisense compound lacking the GalNAc3-1 conjugate (ISIS 440762). These results demonstrate that the potency benefit of GalNAc3-1 conjugates are observed using antisense oligonucleotides complementary to a different target and having different chemically modified nucleosides, in this instance modified nucleosides comprise constrained ethyl sugar moieties (a bicyclic sugar moiety).







TABLE 16







Effect of ASO treatment on SRB-1 mRNA levels in Balb/c mice















Liver



SEQ



Dose
%
ED50

Internucleoside
ID


ASO
(mg/kg)
PBS
(mg/kg)
3′ Conjugate
linkage/Length
No.
















PBS
0
100

—
—



ISIS
0.7
85
2.2
None
PS/14
22


440762
2
55



7
12



20
3


ISIS
0.07
98
0.3
GalNAc3-1
PS/14
23


651900
0.2
63



0.7
20



2
6



7
5









Example 23
Human Peripheral Blood Mononuclear Cells (hPBMC) Assay Protocol
The hPBMC assay was performed using BD Vautainer CPT tube method. A sample of whole blood from volunteered donors with informed consent at US HealthWorks clinic (Faraday & El Camino Real, Carlsbad) was obtained and collected in 4-15 BD Vacutainer CPT 8 ml tubes (VWR Cat.#BD362753). The approximate starting total whole blood volume in the CPT tubes for each donor was recorded using the PBMC assay data sheet.
The blood sample was remixed immediately prior to centrifugation by gently inverting tubes 8-10 times. CPT tubes were centrifuged at rt (18-25° C.) in a horizontal (swing-out) rotor for 30 min at 1500-1800 RCF with brake off (2700 RPM Beckman Allegra 6R). The cells were retrieved from the buffy coat interface (between Ficoll and polymer gel layers); transferred to a sterile 50 ml conical tube and pooled up to 5 CPT tubes/50 ml conical tube/donor. The cells were then washed twice with PBS (Ca++, Mg++ free; GIBCO). The tubes were topped up to 50 ml and mixed by inverting several times. The sample was then centrifuged at 330×g for 15 minutes at rt (1215 RPM in Beckman Allegra 6R) and aspirated as much supernatant as possible without disturbing pellet. The cell pellet was dislodged by gently swirling tube and resuspended cells in RPMI+10% FBS+pen/strep ( ̃1 ml/10 ml starting whole blood volume). A 60 μl sample was pipette into a sample vial (Beckman Coulter) with 600 μl VersaLyse reagent (Beckman Coulter Cat#A09777) and was gently vortexed for 10-15 sec. The sample was allowed to incubate for 10 min at rt and being mixed again before counting. The cell suspension was counted on Vicell XR cell viability analyzer (Beckman Coulter) using PBMC cell type (dilution factor of 1:11 was stored with other parameters). The live cell/ml and viability were recorded. The cell suspension was diluted to 1×107 live PBMC/ml in RPMI+ 10% FBS+pen/strep.
The cells were plated at 5×105 in 50 μl/well of 96-well tissue culture plate (Falcon Microtest). 50 μl/well of 2× concentration oligos/controls diluted in RPMI+10% FBS+pen/strep. was added according to experiment template (100 μl/well total). Plates were placed on the shaker and allowed to mix for approx. 1 min After being incubated for 24 hrs at 37° C.; 5% CO2, the plates were centrifuged at 400×g for 10 minutes before removing the supernatant for MSD cytokine assay (i.e. human IL-6, IL-10, IL-8 and MCP-1).
Example 24
Evaluation of Proinflammatory Effects in hPBMC Assay for GalNAc3-1 Conjugated ASOs
The antisense oligonucleotides (ASOs) listed in Table 17 were evaluated for proinflammatory effect in hPBMC assay using the protocol described in Example 23. ISIS 353512 is an internal standard known to be a high responder for IL-6 release in the assay. The hPBMCs were isolated from fresh, volunteered donors and were treated with ASOs at 0, 0.0128, 0.064, 0.32, 1.6, 8, 40 and 200 μM concentrations. After a 24 hr treatment, the cytokine levels were measured.
The levels of IL-6 were used as the primary readout. The EC50 and Emax was calculated using standard procedures. Results are expressed as the average ratio of Emax/EC50 from two donors and is denoted as “Emax/EC50.” The lower ratio indicates a relative decrease in the proinflammatory response and the higher ratio indicates a relative increase in the proinflammatory response.
With regard to the test compounds, the least proinflammatory compound was the PS/PO linked ASO (ISIS 616468). The GalNAc3-1 conjugated ASO, ISIS 647535 was slightly less proinflammatory than its non-conjugated counterpart ISIS 304801. These results indicate that incorporation of some PO linkages reduces proinflammatory reaction and addition of a GalNAc3-1 conjugate does not make a compound more proinflammatory and may reduce proinflammatory response. Accordingly, one would expect that an antisense compound comprising both mixed PS/PO linkages and a GalNAc3-1 conjugate would produce lower proinflammatory responses relative to full PS linked antisense compound with or without a GalNAc3-1 conjugate. These results show that GalNAc3-1 conjugated antisense compounds, particularly those having reduced PS content are less proinflammatory.
Together, these results suggest that a GalNAc3-1 conjugated compound, particularly one with reduced PS content, can be administered at a higher dose than a counterpart full PS antisense compound lacking a GalNAc3-1 conjugate. Since half-life is not expected to be substantially different for these compounds, such higher administration would result in less frequent dosing. Indeed such administration could be even less frequent, because the GalNAc3-1 conjugated compounds are more potent (See Examples 20-22) and re-dosing is necessary once the concentration of a compound has dropped below a desired level, where such desired level is based on potency.







TABLE 17 







Modified ASOs













SEQ





ID


ASO
Sequence (5′ to 3′)
Target
No.





ISIS
GesmCesTesGesAesTdsTdsAdsGdsAdsGds
TNFα
24


104838
AdsGdsAdsGdsGesTesmCesmCesmCe




 


ISIS
TesmCesmCesmCdsAdsTdsTdsTdsmCdsAdsGds
CRP
25


353512
GdsAdsGdsAdsmCdsmCdsTesGesGe




 


ISIS
AesGesmCesTesTesmCdsTdsTdsGdsTdsm
ApoC
20


304801
CdsmCdsAdsGdsmCdsTesTesTesAesTe
III



 


ISIS
AesGesmCesTesTesmCdsTdsTdsGdsTdsm
ApoC
21


647535
CdsmCdsAdsGdsmCdsTesTesTesAes
III




Teo 




 


ISIS
AesGeomCeoTeoTeomCdsTdsTdsGdsTdsm
ApoC
20


616468
CdsmCdsAdsGdsmCdsTeoTeoTesAesTe
III









Subscripts: “e” indicates 2′-MOE modified nucleoside; “d” indicates β-D-2′-deoxyribonucleoside; “k” indicates 6′-(S)—CH3 bicyclic nucleoside (e.g. cEt); “s” indicates phosphorothioate internucleoside linkages (PS); “o” indicates phosphodiester internucleoside linkages (PO); and “o” indicates —O—P(═O)(OH)—. Superscript “m” indicates 5-methylcytosines. “Ado′GalNAc3-1.” indicates a conjugate having the structure GalNAc3-1 shown in Example 9 attached to the 3′-end of the antisense oligonucleotide, as indicated.







TABLE 18







Proinflammatory Effect of ASOs targeting ApoC III in hPBMC assay














EC50
Emax

3′
Internucleoside
SEQ ID


ASO
(μM)
(μM)
Emax/EC50
Conjugate
Linkage/Length
No.
















ISIS 353512
0.01
265.9
26,590
None
PS/20
25


(high responder)


ISIS 304801
0.07
106.55
1,522
None
PS/20
20


ISIS 647535
0.12
138
1,150
GalNAc3-1
PS/20
21


ISIS 616468
0.32
71.52
224
None
PS/PO/20
20









Example 25
Effect of GalNAc3-1 Conjugated Modified ASO Targeting Human ApoC III In Vitro
ISIS 304801 and 647535 described above were tested in vitro. Primary hepatocyte cells from transgenic mice at a density of 25,000 cells per well were treated with 0.03, 0.08, 0.24, 0.74, 2.22, 6.67 and 20 μM concentrations of modified oligonucleotides. After a treatment period of approximately 16 hours, RNA was isolated from the cells and mRNA levels were measured by quantitative real-time PCR and the hApoC III mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN.
The IC50 was calculated using the standard methods and the results are presented in Table 19. As illustrated, comparable potency was observed in cells treated with ISIS 647535 as compared to the control, ISIS 304801.







TABLE 19







Modified ASO targeting human ApoC III in primary hepatocytes














Internucleoside
SEQ


ASO
IC50 (μM)
3′ Conjugate
linkage/Length
ID No.





ISIS
0.44
None
PS/20
20


304801


ISIS
0.31
GalNAc3-1
PS/20
21


647535









In this experiment, the large potency benefits of GalNAc3-1 conjugation that are observed in vivo were not observed in vitro. Subsequent free uptake experiments in primary hepatocytes in vitro did show increased potency of oligonucleotides comprising various GalNAc conjugates relative to oligonucleotides that lacking the GalNAc conjugate. (see Examples 60, 82, and 92)
Example 26
Effect of PO/PS Linkages on ApoC III ASO Activity
Human ApoC III transgenic mice were injected intraperitoneally once at 25 mg/kg of ISIS 304801, or ISIS 616468 (both described above) or with PBS treated control once per week for two weeks. The treatment group consisted of 3 animals and the control group consisted of 4 animals. Prior to the treatment as well as after the last dose, blood was drawn from each mouse and plasma samples were analyzed. The mice were sacrificed 72 hours following the last administration.
Samples were collected and analyzed to determine the ApoC III protein levels in the liver as described above (Example 20). Data from those analyses are presented in Table 20, below.
These results show reduction in potency for antisense compounds with PO/PS (ISIS 616468) in the wings relative to full PS (ISIS 304801).







TABLE 20







Effect of ASO treatment on ApoC III protein levels


in human ApoC III transgenic mice













Dose

3′
Internucleoside
SEQ ID


ASO
(mg/kg)
% PBS
Conjugate
linkage/Length
No.





PBS
0
99
—
—



ISIS
25 mg/kg/wk
24
None
Full PS
20


304801
for 2 wks


ISIS
25 mg/kg/wk
40
None
14 PS/6 PO
20


616468
for 2 wks









Example 27
Compound 56




Compound 56 is commercially available from Glen Research or may be prepared according to published procedures reported by Shchepinov et al., Nucleic Acids Research, 1997, 25(22), 4447-4454.
Example 28
Preparation of Compound 60




Compound 4 was prepared as per the procedures illustrated in Example 2. Compound 57 is commercially available. Compound 60 was confirmed by structural analysis.
Compound 57 is meant to be representative and not intended to be limiting as other monoprotected substituted or unsubstituted alkyl diols including but not limited to those presented in the specification herein can be used to prepare phosphoramidites having a predetermined composition.
Example 29
Preparation of Compound 63




Compounds 61 and 62 are prepared using procedures similar to those reported by Tober et al., Eur. J. Org. Chem., 2013, 3, 566-577; and Jiang et al., Tetrahedron, 2007, 63(19), 3982-3988.
Alternatively, Compound 63 is prepared using procedures similar to those reported in scientific and patent literature by Kim et al., Synlett, 2003, 12, 1838-1840; and Kim et al., published PCT International Application. WO 2004063208.
Example 30
Preparation of Compound 63b




Compound 63a is prepared using procedures similar to those reported by Hanessian et al., Canadian Journal of Chemistry, 1996, 74(9), 1731-1737.
Example 31
Preparation of Compound 63d




Compound 63c is prepared using procedures similar to those reported by Chen et al., Chinese Chemical Letters, 1998, 9(5), 451-453.
Example 32
Preparation of Compound 67




Compound 64 was prepared as per the procedures illustrated in Example 2. Compound 65 is prepared using procedures similar to those reported by Or et al., published PCT International Application, WO 2009003009. The protecting groups used for Compound 65 are meant to be representative and not intended to be limiting as other protecting groups including but not limited to those presented in the specification herein can be used.
Example 33
Preparation of Compound 70




Compound 64 was prepared as per the procedures illustrated in Example 2. Compound 68 is commercially available. The protecting group used for Compound 68 is meant to be representative and not intended to be limiting as other protecting groups including but not limited to those presented in the specification herein can be used.
Example 34
Preparation of Compound 75a




Compound 75 is prepared according to published procedures reported by Shchepinov et al., Nucleic Acids Research, 1997, 25(22), 4447-4454.
Example 35
Preparation of Compound 79




Compound 76 was prepared according to published procedures reported by Shchepinov et al., Nucleic Acids Research, 1997, 25(22), 4447-4454.
Example 36
Preparation of Compound 79a




Compound 77 is prepared as per the procedures illustrated in Example 35.
Example 37
General Method for the Preparation of Conjugated Oligomeric Compound 82 Comprising a Phosphodiester Linked GalNAc3-2 Conjugate at 5′ Terminus Via Solid Support (Method I)







The GalNAc3 cluster portion of the conjugate group GalNAc3-2 (GalNAc3-2a) can be combined with any cleavable moiety to provide a variety of conjugate groups. Wherein GalNAc3-2a has the formula:




The VIMAD-bound oligomeric compound 79b was prepared using standard procedures for automated DNA/RNA synthesis (see Dupouy et al., Angew. Chem. Int. Ed, 2006, 45, 3623-3627). The phosphoramidite Compounds 56 and 60 were prepared as per the procedures illustrated in Examples 27 and 28, respectively. The phosphoramidites illustrated are meant to be representative and not intended to be limiting as other phosphoramidite building blocks including but not limited those presented in the specification herein can be used to prepare an oligomeric compound having a phosphodiester linked conjugate group at the 5′ terminus. The order and quantity of phosphoramidites added to the solid support can be adjusted to prepare the oligomeric compounds as described herein having any predetermined sequence and composition.
Example 38
Alternative Method for the Preparation of Oligomeric Compound 82 Comprising a Phosphodiester Linked GalNAc3-2 Conjugate at 5′ Terminus (Method II)




The VIMAD-bound oligomeric compound 79b was prepared using standard procedures for automated DNA/RNA synthesis (see Dupouy et al., Angew. Chem. Int. Ed, 2006, 45, 3623-3627). The GalNAc3-2 cluster phosphoramidite, Compound 79 was prepared as per the procedures illustrated in Example 35. This alternative method allows a one-step installation of the phosphodiester linked GalNAc3-2 conjugate to the oligomeric compound at the final step of the synthesis. The phosphoramidites illustrated are meant to be representative and not intended to be limiting, as other phosphoramidite building blocks including but not limited to those presented in the specification herein can be used to prepare oligomeric compounds having a phosphodiester conjugate at the 5′ terminus. The order and quantity of phosphoramidites added to the solid support can be adjusted to prepare the oligomeric compounds as described herein having any predetermined sequence and composition.
Example 39
General Method for the Preparation of Oligomeric Compound 83 h Comprising a GalNAc3-3 Conjugate at the 5′ Terminus (GalNAc3-1 Modified for 5′ End Attachment) Via Solid Support







Compound 18 was prepared as per the procedures illustrated in Example 4. Compounds 83a and 83b are commercially available. Oligomeric Compound 83e comprising a phosphodiester linked hexylamine was prepared using standard oligonucleotide synthesis procedures. Treatment of the protected oligomeric compound with aqueous ammonia provided the 5′-GalNAc3-3 conjugated oligomeric compound (83 h).
Wherein GalNAc3-3 has the structure:




The GalNAc3 cluster portion of the conjugate group GalNAc3-3 (GalNAc3-3a) can be combined with any cleavable moiety to provide a variety of conjugate groups. Wherein GalNAc3-3a has the formula:




Example 40
General Method for the Preparation of Oligomeric Compound 89 Comprising a Phosphodiester Linked GalNAc3-4 Conjugate at the 3′ Terminus Via Solid Support










Wherein GalNAc3-4 has the structure:





Wherein CM is a cleavable moiety. In certain embodiments, cleavable moiety is:




The GalNAc3 cluster portion of the conjugate group GalNAc3-4 (GalNAc3-4a) can be combined with any cleavable moiety to provide a variety of conjugate groups. Wherein GalNAc3-4a has the formula:




The protected Unylinker functionalized solid support Compound 30 is commercially available. Compound 84 is prepared using procedures similar to those reported in the literature (see Shchepinov et al., Nucleic Acids Research, 1997, 25(22), 4447-4454; Shchepinov et al., Nucleic Acids Research, 1999, 27, 3035-3041; and Hornet et al., Nucleic Acids Research, 1997, 25, 4842-4849).
The phosphoramidite building blocks, Compounds 60 and 79a are prepared as per the procedures illustrated in Examples 28 and 36. The phosphoramidites illustrated are meant to be representative and not intended to be limiting as other phosphoramidite building blocks can be used to prepare an oligomeric compound having a phosphodiester linked conjugate at the 3′ terminus with a predetermined sequence and composition. The order and quantity of phosphoramidites added to the solid support can be adjusted to prepare the oligomeric compounds as described herein having any predetermined sequence and composition.
Example 41
General Method for the Preparation of ASOs Comprising a Phosphodiester Linked GalNAc3-2 (See Example 37, Bx is Adenine) Conjugate at the 5′ Position Via Solid Phase Techniques (Preparation of ISIS 661134)
Unless otherwise stated, all reagents and solutions used for the synthesis of oligomeric compounds are purchased from commercial sources. Standard phosphoramidite building blocks and solid support are used for incorporation nucleoside residues which include for example T, A, G, and mC residues. Phosphoramidite compounds 56 and 60 were used to synthesize the phosphodiester linked GalNAc3-2 conjugate at the 5′ terminus. A 0.1 M solution of phosphoramidite in anhydrous acetonitrile was used for β-D-2′-deoxyribonucleoside and 2′-MOE.
The ASO syntheses were performed on ABI 394 synthesizer (1-2 μmol scale) or on GE Healthcare Bioscience ÄKTA oligopilot synthesizer (40-200 μmol scale) by the phosphoramidite coupling method on VIMAD solid support (110 μmol/g, Guzaev et al., 2003) packed in the column. For the coupling step, the phosphoramidites were delivered at a 4 fold excess over the initial loading of the solid support and phosphoramidite coupling was carried out for 10 min. All other steps followed standard protocols supplied by the manufacturer. A solution of 6% dichloroacetic acid in toluene was used for removing the dimethoxytrityl (DMT) groups from 5′-hydroxyl groups of the nucleotide. 4,5-Dicyanoimidazole (0.7 M) in anhydrous CH3CN was used as activator during the coupling step. Phosphorothioate linkages were introduced by sulfurization with 0.1 M solution of xanthane hydride in 1:1 pyridine/CH3CN for a contact time of 3 minutes. A solution of 20% tert-butylhydroperoxide in CH3CN containing 6% water was used as an oxidizing agent to provide phosphodiester internucleoside linkages with a contact time of 12 minutes.
After the desired sequence was assembled, the cyanoethyl phosphate protecting groups were deprotected using a 20% diethylamine in toluene (v/v) with a contact time of 45 minutes. The solid-support bound ASOs were suspended in aqueous ammonia (28-30 wt %) and heated at 55° C. for 6 h. The unbound ASOs were then filtered and the ammonia was boiled off. The residue was purified by high pressure liquid chromatography on a strong anion exchange column (GE Healthcare Bioscience, Source 30Q, 30 μm, 2.54×8 cm, A=100 mM ammonium acetate in 30% aqueous CH3CN, B=1.5 M NaBr in A, 0-40% of B in 60 min, flow 14 mL min-1,λ=260 nm). The residue was desalted by HPLC on a reverse phase column to yield the desired ASOs in an isolated yield of 15-30% based on the initial loading on the solid support. The ASOs were characterized by ion-pair-HPLC coupled MS analysis with Agilent 1100 MSD system.







TABLE 21 







ASO comprising a phosphodiester linked GalNAc3-2


conjugate at the 5′ position targeting SRB-1















SEQ




CalCd
Observed
ID


ISIS No.
Sequence (5′ to 3′)
Mass
Mass
No.














661134
 TksmCks
6482.2
6481.6
26



AdsGdsTdsmCdsAdsTdsGds






AdsmCdsTdsTksmCk









Subscripts: “e” indicates 2′-MOE modified nucleoside; “d” indicates β-D-2′-deoxyribonucleoside; “k” indicates 6′-(S)—CH3 bicyclic nucleoside (e.g. cEt); “s” indicates phosphorothioate internucleoside linkages (PS); “o” indicates phosphodiester internucleoside linkages (PO); and “o′” indicates —O—P(═O)(OH)—. Superscript “m” indicates 5-methylcytosines. The structure of GalNAc3-2a is shown in Example 37.
Example 42
General Method for the Preparation of ASOs Comprising a GalNAc3-3 Conjugate at the 5′ Position Via Solid Phase Techniques (Preparation of ISIS 661166)
The synthesis for ISIS 661166 was performed using similar procedures as illustrated in Examples 39 and 41.
ISIS 661166 is a 5-10-5 MOE gapmer, wherein the 5′ position comprises a GalNAc3-3 conjugate. The ASO was characterized by ion-pair-HPLC coupled MS analysis with Agilent 1100 MSD system.







TABLE 21a 







ASO comprising a GalNAc3-3 conjugate at the


5′ position via a hexylamino


phosphodiester linkage targeting Malat-1













Sequence 

Calcd
Observed
SEQ ID


ISIS No.
(5′ to 3′)
Conjugate
Mass
Mass
No.





661166
5′- 
 
8992.16
8990.51
27



mCesGesGesTes







GesmCdsAdsAdsGds







GdsmCdsTdssTdsAds







GdsGesAesAeTesTe









Subscripts: “e” indicates 2′-MOE modified nucleoside; “d” indicates β-D-2′-deoxyribonucleoside; “s” indicates phosphorothioate internucleoside linkages (PS); “o” indicates phosphodiester internucleoside linkages (PO); and “o′” indicates —O—P(═O)(OH)—. Superscript “m” indicates 5-methylcytosines. The structure of “5′-GalNAc3-3a” is shown in Example 39.
Example 43
Dose-Dependent Study of Phosphodiester Linked GalNAc3-2 (See Examples 37 and 41, Bx is Adenine) at the 5′ Terminus Targeting SRB-1 In Vivo
ISIS 661134 (see Example 41) comprising a phosphodiester linked GalNAc3-2 conjugate at the 5′ terminus was tested in a dose-dependent study for antisense inhibition of SRB-1 in mice. Unconjugated ISIS 440762 and 651900 (GalNAc3-1 conjugate at 3′ terminus, see Example 9) were included in the study for comparison and are described previously in Table 4.
Treatment
Six week old male Balb/c mice (Jackson Laboratory, Bar Harbor, Me.) were injected subcutaneously once at the dosage shown below with ISIS 440762, 651900, 661134 or with PBS treated control. Each treatment group consisted of 4 animals. The mice were sacrificed 72 hours following the final administration to determine the liver SRB-1 mRNA levels using real-time PCR and RIBOGREEN® RNA quantification reagent (Molecular Probes, Inc. Eugene, Oreg.) according to standard protocols. SRB-1 mRNA levels were determined relative to total RNA (using Ribogreen), prior to normalization to PBS-treated control. The results below are presented as the average percent of SRB-1 mRNA levels for each treatment group, normalized to PBS-treated control and is denoted as “% PBS”. The ED50s were measured using similar methods as described previously and are presented below.
As illustrated in Table 22, treatment with antisense oligonucleotides lowered SRB-1 mRNA levels in a dose-dependent manner. Indeed, the antisense oligonucleotides comprising the phosphodiester linked GalNAc3-2 conjugate at the 5′ terminus (ISIS 661134) or the GalNAc3-1 conjugate linked at the 3′ terminus (ISIS 651900) showed substantial improvement in potency compared to the unconjugated antisense oligonucleotide (ISIS 440762). Further, ISIS 661134, which comprises the phosphodiester linked GalNAc3-2 conjugate at the 5′ terminus was equipotent compared to ISIS 651900, which comprises the GalNAc3-1 conjugate at the 3′ terminus.







TABLE 22







ASOs containing GalNAc3-1 or GalNAc3-2 targeting SRB-1












ISIS
Dosage
SRB-1 mRNA
ED50

SEQ ID


No.
(mg/kg)
levels (% PBS)
(mg/kg)
Conjugate
No.















PBS
0
100
—
—



440762
0.2
116
2.58
No conjugate
22



0.7
91



2
69



7
22



20
5


651900
0.07
95
0.26
3′ GalNAc3-1
23



0.2
77



0.7
28



2
11



7
8


661134
0.07
107
0.25
5′ GalNAc3-2
26



0.2
86



0.7
28



2
10



7
6









Structures for 3′ GalNAc3-1 and 5′ GalNAc3-2 were described previously in Examples 9 and 37.
Pharmacokinetics Analysis (PK)
The PK of the ASOs from the high dose group (7 mg/kg) was examined and evaluated in the same manner as illustrated in Example 20. Liver sample was minced and extracted using standard protocols. The full length metabolites of 661134 (5′ GalNAc3-2) and ISIS 651900 (3′ GalNAc3-1) were identified and their masses were confirmed by high resolution mass spectrometry analysis. The results showed that the major metabolite detected for the ASO comprising a phosphodiester linked GalNAc3-2 conjugate at the 5′ terminus (ISIS 661134) was ISIS 440762 (data not shown). No additional metabolites, at a detectable level, were observed. Unlike its counterpart, additional metabolites similar to those reported previously in Table 10a were observed for the ASO having the GalNAc3-1 conjugate at the 3′ terminus (ISIS 651900). These results suggest that having the phosphodiester linked GalNAc3-1 or GalNAc3-2 conjugate may improve the PK profile of ASOs without compromising their potency.
Example 44
Effect of PO/PS Linkages on Antisense Inhibition of ASOs Comprising GalNAc3-1 Conjugate (See Example 9) at the 3′ Terminus Targeting SRB-1
ISIS 655861 and 655862 comprising a GalNAc3-1 conjugate at the 3′ terminus each targeting SRB-1 were tested in a single administration study for their ability to inhibit SRB-1 in mice. The parent unconjugated compound, ISIS 353382 was included in the study for comparison.
The ASOs are 5-10-5 MOE gapmers, wherein the gap region comprises ten 2′-deoxyribonucleosides and each wing region comprises five 2′-MOE modified nucleosides. The ASOs were prepared using similar methods as illustrated previously in Example 19 and are described Table a 23, below.







TABLE 23 







Modified ASOs comprising GalNAc3-1 conjugate


at the 3′ terminus targeting SRB-1













SEQ





ID


ISIS No.
Sequence (5′ to 3′)
Chemistry
No.













353382
GesmCesTesTesmCesAdsGds
Full PS no 
28


(parent)
TdsmCdsAdsTdsGdsAdsmCds
conjugate




TdsTesmCesmCesTesTe




 


655861
GesmCesTesTesmCesAdsGds
Full PS with
29



TdsmCdsAdsTdsGdsAdsmCds
 




TdsTesmCesmCesTesTeo
conjugate




 




 


655862
GesmCeoTeoTeomCeoAdsGds
Mixed PS/PO
29



TdsmCdsAdsTdsGdsAdsmCds
with  




TdsTeomCeomCesTesTeo
conjugate




 









Subscripts: “e” indicates 2′-MOE modified nucleoside; “d” indicates β-D-2′-deoxyribonucleoside; “s” indicates phosphorothioate internucleoside linkages (PS); “o” indicates phosphodiester internucleoside linkages (PO); and “o′” indicates —O—P(═O)(OH)—. Superscript “m” indicates 5-methylcytosines. The structure of “GalNAc3-1” is shown in Example 9.
Treatment
Six week old male Balb/c mice (Jackson Laboratory, Bar Harbor, Me.) were injected subcutaneously once at the dosage shown below with ISIS 353382, 655861, 655862 or with PBS treated control. Each treatment group consisted of 4 animals. Prior to the treatment as well as after the last dose, blood was drawn from each mouse and plasma samples were analyzed. The mice were sacrificed 72 hours following the final administration to determine the liver SRB-1 mRNA levels using real-time PCR and RIBOGREEN® RNA quantification reagent (Molecular Probes, Inc. Eugene, Oreg.) according to standard protocols. SRB-1 mRNA levels were determined relative to total RNA (using Ribogreen), prior to normalization to PBS-treated control. The results below are presented as the average percent of SRB-1 mRNA levels for each treatment group, normalized to PBS-treated control and is denoted as “% PBS”. The ED50s were measured using similar methods as described previously and are reported below.
As illustrated in Table 24, treatment with antisense oligonucleotides lowered SRB-1 mRNA levels in a dose-dependent manner compared to PBS treated control. Indeed, the antisense oligonucleotides comprising the GalNAc3-1 conjugate at the 3′ terminus (ISIS 655861 and 655862) showed substantial improvement in potency comparing to the unconjugated antisense oligonucleotide (ISIS 353382). Further, ISIS 655862 with mixed PS/PO linkages showed an improvement in potency relative to full PS (ISIS 655861).







TABLE 24







Effect of PO/PS linkages on antisense inhibition of ASOs


comprising GalNAc3-1 conjugate at 3′ terminus targeting SRB-1














SRB-1







mRNA


SEQ


ISIS
Dosage
levels
ED50

ID


No.
(mg/kg)
(% PBS)
(mg/kg)
Chemistry
No.















PBS
0
100
—
—



353382
3
76.65
10.4
Full PS without
28


(parent)
10
52.40
10.4
conjugate



30
24.95


655861
0.5
81.22
2.2
Full PS with GalNAc3-1
29



1.5
63.51

conjugate



5
24.61



15
14.80


655862
0.5
69.57
1.3
Mixed PS/PO with
29



1.5
45.78

GalNAc3-1 conjugate



5
19.70



15
12.90









Liver transaminase levels, alanine aminotransferase (ALT) and aspartate aminotransferase (AST), in serum were measured relative to saline injected mice using standard protocols. Organ weights were also evaluated. The results demonstrated that no elevation in transaminase levels (Table 25) or organ weights (data not shown) were observed in mice treated with ASOs compared to PBS control. Further, the ASO with mixed PS/PO linkages (ISIS 655862) showed similar transaminase levels compared to full PS (ISIS 655861).







TABLE 25







Effect of PO/PS linkages on transaminase levels of ASOs


comprising GalNAc3-1 conjugate at 3′ terminus targeting SRB-1












ISIS
Dosage
ALT
AST




No.
(mg/kg)
(U/L)
(U/L)
Chemistry
SEQ ID No.















PBS
0
28.5
65
—



353382
3
50.25
89
Full PS without
28


(parent)
10
27.5
79.3
conjugate



30
27.3
97


655861
0.5
28
55.7
Full PS with
29



1.5
30
78
GalNAc3-1



5
29
63.5



15
28.8
67.8


655862
0.5
50
75.5
Mixed PS/PO with
29



1.5
21.7
58.5
GalNAc3-1



5
29.3
69



15
22
61









Example 45
Preparation of PFP Ester, Compound 110a







Compound 4 (9.5 g, 28.8 mmoles) was treated with compound 103a or 103b (38 mmoles), individually, and TMSOTf (0.5 eq.) and molecular sieves in dichloromethane (200 mL), and stirred for 16 hours at room temperature. At that time, the organic layer was filtered thru celite, then washed with sodium bicarbonate, water and brine. The organic layer was then separated and dried over sodium sulfate, filtered and reduced under reduced pressure. The resultant oil was purified by silica gel chromatography (2%→10% methanol dichloromethane) to give compounds 104a and 104b in >80% yield. LCMS and proton NMR was consistent with the structure.
Compounds 104a and 104b were treated to the same conditions as for compounds 100a-d (Example 47), to give compounds 105a and 105b in >90% yield. LCMS and proton NMR was consistent with the structure.
Compounds 105a and 105b were treated, individually, with compound 90 under the same conditions as for compounds 901a-d, to give compounds 106a (80%) and 106b (20%). LCMS and proton NMR was consistent with the structure.
Compounds 106a and 106b were treated to the same conditions as for compounds 96a-d (Example 47), to give 107a (60%) and 107b (20%). LCMS and proton NMR was consistent with the structure.
Compounds 107a and 107b were treated to the same conditions as for compounds 97a-d (Example 47), to give compounds 108a and 108b in 40-60% yield. LCMS and proton NMR was consistent with the structure.
Compounds 108a (60%) and 108b (40%) were treated to the same conditions as for compounds 100a-d (Example 47), to give compounds 109a and 109b in >80% yields. LCMS and proton NMR was consistent with the structure.
Compound 109a was treated to the same conditions as for compounds 101a-d (Example 47), to give Compound 110a in 30-60% yield. LCMS and proton NMR was consistent with the structure. Alternatively, Compound 110b can be prepared in a similar manner starting with Compound 109b.
Example 46
General Procedure for Conjugation with PFP Esters (Oligonucleotide 111); Preparation of ISIS 666881 (GalNAc3-10)
A 5′-hexylamino modified oligonucleotide was synthesized and purified using standard solid-phase oligonucleotide procedures. The 5′-hexylamino modified oligonucleotide was dissolved in 0.1 M sodium tetraborate, pH 8.5 (200 μL) and 3 equivalents of a selected PFP esterified GalNAc3 cluster dissolved in DMSO (50 μL) was added. If the PFP ester precipitated upon addition to the ASO solution DMSO was added until all PFP ester was in solution. The reaction was complete after about 16 h of mixing at room temperature. The resulting solution was diluted with water to 12 mL and then spun down at 3000 rpm in a spin filter with a mass cut off of 3000 Da. This process was repeated twice to remove small molecule impurities. The solution was then lyophilized to dryness and redissolved in concentrated aqueous ammonia and mixed at room temperature for 2.5 h followed by concentration in vacuo to remove most of the ammonia. The conjugated oligonucleotide was purified and desalted by RP-HPLC and lyophilized to provide the GalNAc3 conjugated oligonucleotide.




Oligonucleotide 111 is conjugated with GalNAc3-10. The GalNAc3 cluster portion of the conjugate group GalNAc3-10 (GalNAc3-10a) can be combined with any cleavable moiety to provide a variety of conjugate groups. In certain embodiments, the cleavable moiety is —P(═O)(OH)-Ad-P(═O)(OH)— as shown in the oligonucleotide (ISIS 666881) synthesized with GalNAc3-10 below. The structure of GalNAc3-10 (GalNAc3-10a-CM-) is shown below:




Following this general procedure ISIS 666881 was prepared. 5′-hexylamino modified oligonucleotide, ISIS 660254, was synthesized and purified using standard solid-phase oligonucleotide procedures. ISIS 660254 (40 mg, 5.2 μmol) was dissolved in 0.1 M sodium tetraborate, pH 8.5 (200 μL) and 3 equivalents PFP ester (Compound 110a) dissolved in DMSO (50 μL) was added. The PFP ester precipitated upon addition to the ASO solution requiring additional DMSO (600 μL) to fully dissolve the PFP ester. The reaction was complete after 16 h of mixing at room temperature. The solution was diluted with water to 12 mL total volume and spun down at 3000 rpm in a spin filter with a mass cut off of 3000 Da. This process was repeated twice to remove small molecule impurities. The solution was lyophilized to dryness and redissolved in concentrated aqueous ammonia with mixing at room temperature for 2.5 h followed by concentration in vacuo to remove most of the ammonia. The conjugated oligonucleotide was purified and desalted by RP-HPLC and lyophilized to give ISIS 666881 in 90% yield by weight (42 mg, 4.7 μmol).










GalNAc3-10 conjugated oligonucleotide













SEQ





ID


ASO
Sequence (5′ to 3′)
5′ group
No.













ISIS
NH2(CH2)6-oAdoGesmCesTes
Hexylamine
30


660254
TesmCesAdsGdsTdsmCdsAdsTdsGds





AdsmCdsTdsTesmCesmCesTesTe




 


ISIS
 GesmCes
 
30


666881
TesTesmCesAdsGdsTdsmCdsAdsTds





GdsAdsmCdsTdsTesmCesmCesTesTe









Capital letters indicate the nucleobase for each nucleoside and mC indicates a 5-methyl cytosine. Subscripts: “e” indicates a 2′-MOE modified nucleoside; “d” indicates a β-D-2′-deoxyribonucleoside; “s” indicates a phosphorothioate internucleoside linkage (PS); “o” indicates a phosphodiester internucleoside linkage (PO); and “o”′ indicates —O—P(═O)(OH)—. Conjugate groups are in bold.
Example 47
Preparation of Oligonucleotide 102 Comprising GalNAc3-8










The triacid 90 (4 g, 14.43 mmol) was dissolved in DMF (120 mL) and N,N-Diisopropylethylamine (12.35 mL, 72 mmoles). Pentafluorophenyl trifluoroacetate (8.9 mL, 52 mmoles) was added dropwise, under argon, and the reaction was allowed to stir at room temperature for 30 minutes. Boc-diamine 91a or 91b (68.87 mmol) was added, along with N,N-Diisopropylethylamine (12.35 mL, 72 mmoles), and the reaction was allowed to stir at room temperature for 16 hours. At that time, the DMF was reduced by >75% under reduced pressure, and then the mixture was dissolved in dichloromethane. The organic layer was washed with sodium bicarbonate, water and brine. The organic layer was then separated and dried over sodium sulfate, filtered and reduced to an oil under reduced pressure. The resultant oil was purified by silica gel chromatography (2%→10% methanol dichloromethane) to give compounds 92a and 92b in an approximate 80% yield. LCMS and proton NMR were consistent with the structure.
Compound 92a or 92b (6.7 mmoles) was treated with 20 mL of dichloromethane and 20 mL of trifluoroacetic acid at room temperature for 16 hours. The resultant solution was evaporated and then dissolved in methanol and treated with DOWEX-OH resin for 30 minutes. The resultant solution was filtered and reduced to an oil under reduced pressure to give 85-90% yield of compounds 93a and 93b.
Compounds 7 or 64 (9.6 mmoles) were treated with HBTU (3.7 g, 9.6 mmoles) and N,N-Diisopropylethylamine (5 mL) in DMF (20 mL) for 15 minutes. To this was added either compounds 93a or 93b (3 mmoles), and allowed to stir at room temperature for 16 hours. At that time, the DMF was reduced by >75% under reduced pressure, and then the mixture was dissolved in dichloromethane. The organic layer was washed with sodium bicarbonate, water and brine. The organic layer was then separated and dried over sodium sulfate, filtered and reduced to an oil under reduced pressure. The resultant oil was purified by silica gel chromatography (5%→20% methanol dichloromethane) to give compounds 96a-d in 20-40% yield. LCMS and proton NMR was consistent with the structure.
Compounds 96a-d (0.75 mmoles), individually, were hydrogenated over Raney Nickel for 3 hours in Ethanol (75 mL). At that time, the catalyst was removed by filtration thru celite, and the ethanol removed under reduced pressure to give compounds 97a-d in 80-90% yield. LCMS and proton NMR were consistent with the structure.
Compound 23 (0.32 g, 0.53 mmoles) was treated with HBTU (0.2 g, 0.53 mmoles) and N,N-Diisopropylethylamine (0.19 mL, 1.14 mmoles) in DMF (30 mL) for 15 minutes. To this was added compounds 97a-d (0.38 mmoles), individually, and allowed to stir at room temperature for 16 hours. At that time, the DMF was reduced by >75% under reduced pressure, and then the mixture was dissolved in dichloromethane. The organic layer was washed with sodium bicarbonate, water and brine. The organic layer was then separated and dried over sodium sulfate, filtered and reduced to an oil under reduced pressure. The resultant oil was purified by silica gel chromatography (2%→20% methanol/dichloromethane) to give compounds 98a-d in 30-40% yield. LCMS and proton NMR was consistent with the structure.
Compound 99 (0.17 g, 0.76 mmoles) was treated with HBTU (0.29 g, 0.76 mmoles) and N,N-Diisopropylethylamine (0.35 mL, 2.0 mmoles) in DMF (50 mL) for 15 minutes. To this was added compounds 97a-d (0.51 mmoles), individually, and allowed to stir at room temperature for 16 hours. At that time, the DMF was reduced by >75% under reduced pressure, and then the mixture was dissolved in dichloromethane. The organic layer was washed with sodium bicarbonate, water and brine. The organic layer was then separated and dried over sodium sulfate, filtered and reduced to an oil under reduced pressure. The resultant oil was purified by silica gel chromatography (5%→20% methanol/dichloromethane) to give compounds 100a-d in 40-60% yield. LCMS and proton NMR was consistent with the structure.
Compounds 100a-d (0.16 mmoles), individually, were hydrogenated over 10% Pd(OH)2/C for 3 hours in methanol/ethyl acetate (1:1, 50 mL). At that time, the catalyst was removed by filtration thru celite, and the organics removed under reduced pressure to give compounds 101a-d in 80-90% yield. LCMS and proton NMR was consistent with the structure.
Compounds 101a-d (0.15 mmoles), individually, were dissolved in DMF (15 mL) and pyridine (0.016 mL, 0.2 mmoles). Pentafluorophenyl trifluoroacetate (0.034 mL, 0.2 mmoles) was added dropwise, under argon, and the reaction was allowed to stir at room temperature for 30 minutes. At that time, the DMF was reduced by >75% under reduced pressure, and then the mixture was dissolved in dichloromethane. The organic layer was washed with sodium bicarbonate, water and brine. The organic layer was then separated and dried over sodium sulfate, filtered and reduced to an oil under reduced pressure. The resultant oil was purified by silica gel chromatography (2%→5% methanol dichloromethane) to give compounds 102a-d in an approximate 80% yield. LCMS and proton NMR were consistent with the structure.




Oligomeric Compound 102, comprising a GalNAc3-8 conjugate group, was prepared using the general procedures illustrated in Example 46. The GalNAc3 cluster portion of the conjugate group GalNAc3-8 (GalNAc3-8a) can be combined with any cleavable moiety to provide a variety of conjugate groups. In a preferred embodiment, the cleavable moiety is —P(═O)(OH)-Ad-P(═O)(OH)—.
The structure of GalNAc3-8 (GalNAc3-8a-CM-) is shown below:




Example 48
Preparation of Oligonucleotide 119 Comprising GalNAc3-7







Compound 112 was synthesized following the procedure described in the literature (J. Med. Chem. 2004, 47, 5798-5808).
Compound 112 (5 g, 8.6 mmol) was dissolved in 1:1 methanol/ethyl acetate (22 mL/22 mL). Palladium hydroxide on carbon (0.5 g) was added. The reaction mixture was stirred at room temperature under hydrogen for 12 h. The reaction mixture was filtered through a pad of celite and washed the pad with 1:1 methanol/ethyl acetate. The filtrate and the washings were combined and concentrated to dryness to yield Compound 105a (quantitative). The structure was confirmed by LCMS.
Compound 113 (1.25 g, 2.7 mmol), HBTU (3.2 g, 8.4 mmol) and DIEA (2.8 mL, 16.2 mmol) were dissolved in anhydrous DMF (17 mL) and the reaction mixture was stirred at room temperature for 5 min To this a solution of Compound 105a (3.77 g, 8.4 mmol) in anhydrous DMF (20 mL) was added. The reaction was stirred at room temperature for 6 h. Solvent was removed under reduced pressure to get an oil. The residue was dissolved in CH2Cl2 (100 mL) and washed with aqueous saturated NaHCO3 solution (100 mL) and brine (100 mL). The organic phase was separated, dried (Na2SO4), filtered and evaporated. The residue was purified by silica gel column chromatography and eluted with 10 to 20% MeOH in dichloromethane to yield Compound 114 (1.45 g, 30%). The structure was confirmed by LCMS and 1H NMR analysis.
Compound 114 (1.43 g, 0.8 mmol) was dissolved in 1:1 methanol/ethyl acetate (4 mL/4 mL). Palladium on carbon (wet, 0.14 g) was added. The reaction mixture was flushed with hydrogen and stirred at room temperature under hydrogen for 12 h. The reaction mixture was filtered through a pad of celite. The celite pad was washed with methanol/ethyl acetate (1:1). The filtrate and the washings were combined together and evaporated under reduced pressure to yield Compound 115 (quantitative). The structure was confirmed by LCMS and 1H NMR analysis.
Compound 83a (0.17 g, 0.75 mmol), HBTU (0.31 g, 0.83 mmol) and DIEA (0.26 mL, 1.5 mmol) were dissolved in anhydrous DMF (5 mL) and the reaction mixture was stirred at room temperature for 5 min To this a solution of Compound 115 (1.22 g, 0.75 mmol) in anhydrous DMF was added and the reaction was stirred at room temperature for 6 h. The solvent was removed under reduced pressure and the residue was dissolved in CH2Cl2. The organic layer was washed aqueous saturated NaHCO3 solution and brine and dried over anhydrous Na2SO4 and filtered. The organic layer was concentrated to dryness and the residue obtained was purified by silica gel column chromatography and eluted with 3 to 15% MeOH in dichloromethane to yield Compound 116 (0.84 g, 61%). The structure was confirmed by LC MS and 1H NMR analysis.




Compound 116 (0.74 g, 0.4 mmol) was dissolved in 1:1 methanol/ethyl acetate (5 mL/5 mL). Palladium on carbon (wet, 0.074 g) was added. The reaction mixture was flushed with hydrogen and stirred at room temperature under hydrogen for 12 h. The reaction mixture was filtered through a pad of celite. The celite pad was washed with methanol/ethyl acetate (1:1). The filtrate and the washings were combined together and evaporated under reduced pressure to yield compound 117 (0.73 g, 98%). The structure was confirmed by LCMS and 1H NMR analysis.
Compound 117 (0.63 g, 0.36 mmol) was dissolved in anhydrous DMF (3 mL). To this solution N,N-Diisopropylethylamine (70 μL, 0.4 mmol) and pentafluorophenyl trifluoroacetate (72 μL, 0.42 mmol) were added. The reaction mixture was stirred at room temperature for 12 h and poured into a aqueous saturated NaHCO3 solution. The mixture was extracted with dichloromethane, washed with brine and dried over anhydrous Na2SO4. The dichloromethane solution was concentrated to dryness and purified with silica gel column chromatography and eluted with 5 to 10% MeOH in dichloromethane to yield compound 118 (0.51 g, 79%). The structure was confirmed by LCMS and 1H and 1H and 19F NMR.




Oligomeric Compound 119, comprising a GalNAc3-7 conjugate group, was prepared using the general procedures illustrated in Example 46. The GalNAc3 cluster portion of the conjugate group GalNAc3-7 (GalNAc3-7a) can be combined with any cleavable moiety to provide a variety of conjugate groups. In certain embodiments, the cleavable moiety is —P(═O)(OH)-Ad-P(═O)(OH)—.
The structure of GalNAc3-7 (GalNAc3-7a-CM-) is shown below:




Example 49
Preparation of Oligonucleotide 132 Comprising GalNAc3-5




Compound 120 (14.01 g, 40 mmol) and HBTU (14.06 g, 37 mmol) were dissolved in anhydrous DMF (80 mL). Triethylamine (11.2 mL, 80.35 mmol) was added and stirred for 5 min. The reaction mixture was cooled in an ice bath and a solution of compound 121 (10 g, mmol) in anhydrous DMF (20 mL) was added. Additional triethylamine (4.5 mL, 32.28 mmol) was added and the reaction mixture was stirred for 18 h under an argon atmosphere. The reaction was monitored by TLC (ethyl acetate:hexane; 1:1; Rf=0.47). The solvent was removed under reduced pressure. The residue was taken up in EtOAc (300 mL) and washed with 1M NaHSO4 (3×150 mL), aqueous saturated NaHCO3 solution (3×150 mL) and brine (2×100 mL). Organic layer was dried with Na2SO4. Drying agent was removed by filtration and organic layer was concentrated by rotary evaporation. Crude mixture was purified by silica gel column chromatography and eluted by using 35-50% EtOAc in hexane to yield a compound 122 (15.50 g, 78.13%). The structure was confirmed by LCMS and 1H NMR analysis. Mass m/z 589.3 [M+H]+.
A solution of LiOH (92.15 mmol) in water (20 mL) and THF (10 mL) was added to a cooled solution of Compound 122 (7.75 g, 13.16 mmol) dissolved in methanol (15 mL). The reaction mixture was stirred at room temperature for 45 min and monitored by TLC (EtOAc:hexane; 1:1). The reaction mixture was concentrated to half the volume under reduced pressure. The remaining solution was cooled an ice bath and neutralized by adding concentrated HCl. The reaction mixture was diluted, extracted with EtOAc (120 mL) and washed with brine (100 mL). An emulsion formed and cleared upon standing overnight. The organic layer was separated dried (Na2SO4), filtered and evaporated to yield Compound 123 (8.42 g). Residual salt is the likely cause of excess mass. LCMS is consistent with structure. Product was used without any further purification. M.W.cal:574.36; M.W.fd:575.3 [M+H]+.




Compound 126 was synthesized following the procedure described in the literature (J. Am. Chem. Soc. 2011, 133, 958-963).







Compound 123 (7.419 g, 12.91 mmol), HOBt (3.49 g, 25.82 mmol) and compound 126 (6.33 g, 16.14 mmol) were dissolved in and DMF (40 mL) and the resulting reaction mixture was cooled in an ice bath. To this N,N-Diisopropylethylamine (4.42 mL, 25.82 mmol), PyBop (8.7 g, 16.7 mmol) followed by Bop coupling reagent (1.17 g, 2.66 mmol) were added under an argon atmosphere. The ice bath was removed and the solution was allowed to warm to room temperature. The reaction was completed after 1 h as determined by TLC (DCM:MeOH:AA; 89:10:1). The reaction mixture was concentrated under reduced pressure. The residue was dissolved in EtOAc (200 mL) and washed with 1 M NaHSO4 (3×100 mL), aqueous saturated NaHCO3 (3×100 mL) and brine (2×100 mL). The organic phase separated dried (Na2SO4), filtered and concentrated. The residue was purified by silica gel column chromatography with a gradient of 50% hexanes/EtOAC to 100% EtOAc to yield Compound 127 (9.4 g) as a white foam. LCMS and 1H NMR were consistent with structure. Mass m/z 778.4 [M+H]+.
Trifluoroacetic acid (12 mL) was added to a solution of compound 127 (1.57 g, 2.02 mmol) in dichloromethane (12 mL) and stirred at room temperature for 1 h. The reaction mixture was co-evaporated with toluene (30 mL) under reduced pressure to dryness. The residue obtained was co-evaporated twice with acetonitrile (30 mL) and toluene (40 mL) to yield Compound 128 (1.67 g) as trifluoro acetate salt and used for next step without further purification. LCMS and 1H NMR were consistent with structure. Mass m/z 478.2 [M+H]+.
Compound 7 (0.43 g, 0.963 mmol), HATU (0.35 g, 0.91 mmol), and HOAt (0.035 g, 0.26 mmol) were combined together and dried for 4 h over P2O5 under reduced pressure in a round bottom flask and then dissolved in anhydrous DMF (1 mL) and stirred for 5 min To this a solution of compound 128 (0.20 g, 0.26 mmol) in anhydrous DMF (0.2 mL) and N,N-Diisopropylethylamine (0.2 mL) was added. The reaction mixture was stirred at room temperature under an argon atmosphere. The reaction was complete after 30 min as determined by LCMS and TLC (7% MeOH/DCM). The reaction mixture was concentrated under reduced pressure. The residue was dissolved in DCM (30 mL) and washed with 1 M NaHSO4 (3×20 mL), aqueous saturated NaHCO3 (3×20 mL) and brine (3×20 mL). The organic phase was separated, dried over Na2SO4, filtered and concentrated. The residue was purified by silica gel column chromatography using 5-15% MeOH in dichloromethane to yield Compound 129 (96.6 mg). LC MS and 1H NMR are consistent with structure. Mass m/z 883.4 [M+2H]+.
Compound 129 (0.09 g, 0.051 mmol) was dissolved in methanol (5 mL) in 20 mL scintillation vial. To this was added a small amount of 10% Pd/C (0.015 mg) and the reaction vessel was flushed with H2 gas. The reaction mixture was stirred at room temperature under H2 atmosphere for 18 h. The reaction mixture was filtered through a pad of Celite and the Celite pad was washed with methanol. The filtrate washings were pooled together and concentrated under reduced pressure to yield Compound 130 (0.08 g). LCMS and 1H NMR were consistent with structure. The product was used without further purification. Mass m/z 838.3 [M+2H]+.
To a 10 mL pointed round bottom flask were added compound 130 (75.8 mg, 0.046 mmol), 0.37 M pyridine/DMF (200 μL) and a stir bar. To this solution was added 0.7 M pentafluorophenyl trifluoroacetate/DMF (100 μL) drop wise with stirring. The reaction was completed after 1 h as determined by LC MS. The solvent was removed under reduced pressure and the residue was dissolved in CHCl3 ( ̃10 mL). The organic layer was partitioned against NaHSO4 (1 M, 10 mL), aqueous saturated NaHCO3 (10 mL) and brine (10 mL) three times each. The organic phase separated and dried over Na2SO4, filtered and concentrated to yield Compound 131 (77.7 mg). LCMS is consistent with structure. Used without further purification. Mass m/z 921.3 [M+2H]+.




Oligomeric Compound 132, comprising a GalNAc3-5 conjugate group, was prepared using the general procedures illustrated in Example 46. The GalNAc3 cluster portion of the conjugate group GalNAc3-5 (GalNAc3-5a) can be combined with any cleavable moiety to provide a variety of conjugate groups. In certain embodiments, the cleavable moiety is —P(═O)(OH)-Ad-P(═O)(OH)—.
The structure of GalNAc3-5 (GalNAc3-5a-CM-) is shown below:




Example 50
Preparation of Oligonucleotide 144 Comprising GalNAc4-11







Synthesis of Compound 134. To a Merrifield flask was added aminomethyl VIMAD resin (2.5 g, 450 μmol/g) that was washed with acetonitrile, dimethylformamide, dichloromethane and acetonitrile. The resin was swelled in acetonitrile (4 mL). Compound 133 was pre-activated in a 100 mL round bottom flask by adding 20 (1.0 mmol, 0.747 g), TBTU (1.0 mmol, 0.321 g), acetonitrile (5 mL) and DIEA (3.0 mmol, 0.5 mL). This solution was allowed to stir for 5 min and was then added to the Merrifield flask with shaking. The suspension was allowed to shake for 3 h. The reaction mixture was drained and the resin was washed with acetonitrile, DMF and DCM. New resin loading was quantitated by measuring the absorbance of the DMT cation at 500 nm (extinction coefficient=76000) in DCM and determined to be 238 μmol/g. The resin was capped by suspending in an acetic anhydride solution for ten minutes three times.
The solid support bound compound 141 was synthesized using iterative Fmoc-based solid phase peptide synthesis methods. A small amount of solid support was withdrawn and suspended in aqueous ammonia (28-30 wt %) for 6 h. The cleaved compound was analyzed by LC-MS and the observed mass was consistent with structure. Mass m/z 1063.8 [M+2H]+.
The solid support bound compound 142 was synthesized using solid phase peptide synthesis methods.




The solid support bound compound 143 was synthesized using standard solid phase synthesis on a DNA synthesizer.
The solid support bound compound 143 was suspended in aqueous ammonia (28-30 wt %) and heated at 55° C. for 16 h. The solution was cooled and the solid support was filtered. The filtrate was concentrated and the residue dissolved in water and purified by HPLC on a strong anion exchange column. The fractions containing full length compound 144 were pooled together and desalted. The resulting GalNAc4-11 conjugated oligomeric compound was analyzed by LC-MS and the observed mass was consistent with structure.
The GalNAc4 cluster portion of the conjugate group GalNAc4-11 (GalNAc4-11a) can be combined with any cleavable moiety to provide a variety of conjugate groups. In certain embodiments, the cleavable moiety is —P(═O)(OH)-Ad-P(═O)(OH)—.
The structure of GalNAc4-11 (GalNAc4-11a-CM) is shown below:




Example 51
Preparation of Oligonucleotide 155 Comprising GalNAc3-6




Compound 146 was synthesized as described in the literature (Analytical Biochemistry 1995, 229, 54-60).




Compound 4 (15 g, 45.55 mmol) and compound 35b (14.3 grams, 57 mmol) were dissolved in CH2Cl2 (200 ml). Activated molecular sieves (4 Å. 2 g, powdered) were added, and the reaction was allowed to stir for 30 minutes under nitrogen atmosphere. TMS-OTf was added (4.1 ml, 22.77 mmol) and the reaction was allowed to stir at room temp overnight. Upon completion, the reaction was quenched by pouring into solution of saturated aqueous NaHCO3 (500 ml) and crushed ice ( ̃150 g). The organic layer was separated, washed with brine, dried over MgSO4, filtered, and was concentrated to an orange oil under reduced pressure. The crude material was purified by silica gel column chromatography and eluted with 2-10% MeOH in CH2Cl2 to yield Compound 112 (16.53 g, 63%). LCMS and 1H NMR were consistent with the expected compound.
Compound 112 (4.27 g, 7.35 mmol) was dissolved in 1:1 MeOH/EtOAc (40 ml). The reaction mixture was purged by bubbling a stream of argon through the solution for 15 minutes. Pearlman's catalyst (palladium hydroxide on carbon, 400 mg) was added, and hydrogen gas was bubbled through the solution for 30 minutes. Upon completion (TLC 10% MeOH in CH2Cl2, and LCMS), the catalyst was removed by filtration through a pad of celite. The filtrate was concentrated by rotary evaporation, and was dried briefly under high vacuum to yield Compound 105a (3.28 g). LCMS and 1H NMR were consistent with desired product.
Compound 147 (2.31 g, 11 mmol) was dissolved in anhydrous DMF (100 mL). N,N-Diisopropylethylamine (DIEA, 3.9 mL, 22 mmol) was added, followed by HBTU (4 g, 10.5 mmol). The reaction mixture was allowed to stir for  ̃15 minutes under nitrogen. To this a solution of compound 105a (3.3 g, 7.4 mmol) in dry DMF was added and stirred for 2 h under nitrogen atmosphere. The reaction was diluted with EtOAc and washed with saturated aqueous NaHCO3 and brine. The organics phase was separated, dried (MgSO4), filtered, and concentrated to an orange syrup. The crude material was purified by column chromatography 2-5% MeOH in CH2Cl2 to yield Compound 148 (3.44 g, 73%). LCMS and 1H NMR were consistent with the expected product.
Compound 148 (3.3 g, 5.2 mmol) was dissolved in 1:1 MeOH/EtOAc (75 ml). The reaction mixture was purged by bubbling a stream of argon through the solution for 15 minutes. Pearlman's catalyst (palladium hydroxide on carbon) was added (350 mg). Hydrogen gas was bubbled through the solution for 30 minutes. Upon completion (TLC 10% MeOH in DCM, and LCMS), the catalyst was removed by filtration through a pad of celite. The filtrate was concentrated by rotary evaporation, and was dried briefly under high vacuum to yield Compound 149 (2.6 g). LCMS was consistent with desired product. The residue was dissolved in dry DMF (10 ml) was used immediately in the next step.




Compound 146 (0.68 g, 1.73 mmol) was dissolved in dry DMF (20 ml). To this DIEA (450 μL, 2.6 mmol, 1.5 eq.) and HBTU (1.96 g, 0.5.2 mmol) were added. The reaction mixture was allowed to stir for 15 minutes at room temperature under nitrogen. A solution of compound 149 (2.6 g) in anhydrous DMF (10 mL) was added. The pH of the reaction was adjusted to pH=9-10 by addition of DIEA (if necessary). The reaction was allowed to stir at room temperature under nitrogen for 2 h. Upon completion the reaction was diluted with EtOAc (100 mL), and washed with aqueous saturated aqueous NaHCO3, followed by brine. The organic phase was separated, dried over MgSO4, filtered, and concentrated. The residue was purified by silica gel column chromatography and eluted with 2-10% MeOH in CH2Cl2 to yield Compound 150 (0.62 g, 20%). LCMS and 1H NMR were consistent with the desired product.
Compound 150 (0.62 g) was dissolved in 1:1 MeOH/EtOAc (5 L). The reaction mixture was purged by bubbling a stream of argon through the solution for 15 minutes. Pearlman's catalyst (palladium hydroxide on carbon) was added (60 mg). Hydrogen gas was bubbled through the solution for 30 minutes. Upon completion (TLC 10% MeOH in DCM, and LCMS), the catalyst was removed by filtration (syringe-tip Teflon filter, 0.45 μm). The filtrate was concentrated by rotary evaporation, and was dried briefly under high vacuum to yield Compound 151 (0.57 g). The LCMS was consistent with the desired product. The product was dissolved in 4 mL dry DMF and was used immediately in the next step.




Compound 83a (0.11 g, 0.33 mmol) was dissolved in anhydrous DMF (5 mL) and N,N-Diisopropylethylamine (75 μL, 1 mmol) and PFP-TFA (90 μL, 0.76 mmol) were added. The reaction mixture turned magenta upon contact, and gradually turned orange over the next 30 minutes. Progress of reaction was monitored by TLC and LCMS. Upon completion (formation of the PFP ester), a solution of compound 151 (0.57 g, 0.33 mmol) in DMF was added. The pH of the reaction was adjusted to pH=9-10 by addition of N,N-Diisopropylethylamine (if necessary). The reaction mixture was stirred under nitrogen for  ̃30 min Upon completion, the majority of the solvent was removed under reduced pressure. The residue was diluted with CH2Cl2 and washed with aqueous saturated NaHCO3, followed by brine. The organic phase separated, dried over MgSO4, filtered, and concentrated to an orange syrup. The residue was purified by silica gel column chromatography (2-10% MeOH in CH2Cl2) to yield Compound 152 (0.35 g, 55%). LCMS and 1H NMR were consistent with the desired product.
Compound 152 (0.35 g, 0.182 mmol) was dissolved in 1:1 MeOH/EtOAc (10 mL). The reaction mixture was purged by bubbling a stream of argon thru the solution for 15 minutes. Pearlman's catalyst (palladium hydroxide on carbon) was added (35 mg). Hydrogen gas was bubbled thru the solution for 30 minutes. Upon completion (TLC 10% MeOH in DCM, and LCMS), the catalyst was removed by filtration (syringe-tip Teflon filter, 0.45 μm). The filtrate was concentrated by rotary evaporation, and was dried briefly under high vacuum to yield Compound 153 (0.33 g, quantitative). The LCMS was consistent with desired product.
Compound 153 (0.33 g, 0.18 mmol) was dissolved in anhydrous DMF (5 mL) with stirring under nitrogen. To this N,N-Diisopropylethylamine (65 μL, 0.37 mmol) and PFP-TFA (35 μL, 0.28 mmol) were added. The reaction mixture was stirred under nitrogen for  ̃30 min. The reaction mixture turned magenta upon contact, and gradually turned orange. The pH of the reaction mixture was maintained at pH=9-10 by adding more N,-Diisopropylethylamine. The progress of the reaction was monitored by TLC and LCMS. Upon completion, the majority of the solvent was removed under reduced pressure. The residue was diluted with CH2Cl2 (50 mL), and washed with saturated aqueous NaHCO3, followed by brine. The organic layer was dried over MgSO4, filtered, and concentrated to an orange syrup. The residue was purified by column chromatography and eluted with 2-10% MeOH in CH2Cl2 to yield Compound 154 (0.29 g, 79%). LCMS and 1H NMR were consistent with the desired product.




Oligomeric Compound 155, comprising a GalNAc3-6 conjugate group, was prepared using the general procedures illustrated in Example 46. The GalNAc3 cluster portion of the conjugate group GalNAc3-6 (GalNAc3-6a) can be combined with any cleavable moiety to provide a variety of conjugate groups. In certain embodiments, the cleavable moiety is —P(═O)(OH)-Ad-P(═O)(OH)—.
The structure of GalNAc3-6 (GalNAc3-6a-CM-) is shown below:




Example 52
Preparation of Oligonucleotide 160 Comprising GalNAc3-9




Compound 156 was synthesized following the procedure described in the literature (J. Med. Chem. 2004, 47, 5798-5808).
Compound 156, (18.60 g, 29.28 mmol) was dissolved in methanol (200 mL). Palladium on carbon (6.15 g, 10 wt %, loading (dry basis), matrix carbon powder, wet) was added. The reaction mixture was stirred at room temperature under hydrogen for 18 h. The reaction mixture was filtered through a pad of celite and the celite pad was washed thoroughly with methanol. The combined filtrate was washed and concentrated to dryness. The residue was purified by silica gel column chromatography and eluted with 5-10% methanol in dichloromethane to yield Compound 157 (14.26 g, 89%). Mass m/z 544.1 [M−H]−.
Compound 157 (5 g, 9.17 mmol) was dissolved in anhydrous DMF (30 mL). HBTU (3.65 g, 9.61 mmol) and N,N-Diisopropylethylamine (13.73 mL, 78.81 mmol) were added and the reaction mixture was stirred at room temperature for 5 minutes. To this a solution of compound 47 (2.96 g, 7.04 mmol) was added. The reaction was stirred at room temperature for 8 h. The reaction mixture was poured into a saturated NaHCO3 aqueous solution. The mixture was extracted with ethyl acetate and the organic layer was washed with brine and dried (Na2SO4), filtered and evaporated. The residue obtained was purified by silica gel column chromatography and eluted with 50% ethyl acetate in hexane to yield compound 158 (8.25 g, 73.3%). The structure was confirmed by MS and 1H NMR analysis.
Compound 158 (7.2 g, 7.61 mmol) was dried over P2O5 under reduced pressure. The dried compound was dissolved in anhydrous DMF (50 mL). To this 1H-tetrazole (0.43 g, 6.09 mmol) and N-methylimidazole (0.3 mL, 3.81 mmol) and 2-cyanoethyl-N,N,N′,N′-tetraisopropyl phosphorodiamidite (3.65 mL, 11.50 mmol) were added. The reaction mixture was stirred t under an argon atmosphere for 4 h. The reaction mixture was diluted with ethyl acetate (200 mL). The reaction mixture was washed with saturated NaHCO3 and brine. The organic phase was separated, dried (Na2SO4), filtered and evaporated. The residue was purified by silica gel column chromatography and eluted with 50-90% ethyl acetate in hexane to yield Compound 159 (7.82 g, 80.5%). The structure was confirmed by LCMS and 31P NMR analysis.




Oligomeric Compound 160, comprising a GalNAc3-9 conjugate group, was prepared using standard oligonucleotide synthesis procedures. Three units of compound 159 were coupled to the solid support, followed by nucleotide phosphoramidites. Treatment of the protected oligomeric compound with aqueous ammonia yielded compound 160. The GalNAc3 cluster portion of the conjugate group GalNAc3-9 (GalNAc3-9a) can be combined with any cleavable moiety to provide a variety of conjugate groups. In certain embodiments, the cleavable moiety is —P(═O)(OH)-Ad-P(═O)(OH)—. The structure of GalNAc3-9 (GalNAc3-9a-CM) is shown below:




Example 53
Alternate Procedure for Preparation of Compound 18 (GalNAc3-1a and GalNAc3-3a)




Lactone 161 was reacted with diamino propane (3-5 eq) or Mono-Boc protected diamino propane (1 eq) to provide alcohol 162a or 162b. When unprotected propanediamine was used for the above reaction, the excess diamine was removed by evaporation under high vacuum and the free amino group in 162a was protected using CbzCl to provide 162b as a white solid after purification by column chromatography. Alcohol 162b was further reacted with compound 4 in the presence of TMSOTf to provide 163a which was converted to 163b by removal of the Cbz group using catalytic hydrogenation. The pentafluorophenyl (PFP) ester 164 was prepared by reacting triacid 113 (see Example 48) with PFPTFA (3.5 eq) and pyridine (3.5 eq) in DMF (0.1 to 0.5 M). The triester 164 was directly reacted with the amine 163b (3-4 eq) and DIPEA (3-4 eq) to provide Compound 18. The above method greatly facilitates purification of intermediates and minimizes the formation of byproducts which are formed using the procedure described in Example 4.
Example 54
Alternate Procedure for Preparation of Compound 18 (GalNAc3-1a and GalNAc3-3a)




The triPFP ester 164 was prepared from acid 113 using the procedure outlined in example 53 above and reacted with mono-Boc protected diamine to provide 165 in essentially quantitative yield. The Boc groups were removed with hydrochloric acid or trifluoroacetic acid to provide the triamine which was reacted with the PFP activated acid 166 in the presence of a suitable base such as DIPEA to provide Compound 18.
The PFP protected Gal-NAc acid 166 was prepared from the corresponding acid by treatment with PFPTFA (1-1.2 eq) and pyridine (1-1.2 eq) in DMF. The precursor acid in turn was prepared from the corresponding alcohol by oxidation using TEMPO (0.2 eq) and BAIB in acetonitrile and water. The precursor alcohol was prepared from sugar intermediate 4 by reaction with 1,6-hexanediol (or 1,5-pentanediol or other diol for other n values) (2-4 eq) and TMSOTf using conditions described previously in example 47.
Example 55
Dose-Dependent Study of Oligonucleotides Comprising Either a 3′ or 5′-Conjugate Group (Comparison of GalNAc3-1, 3, 8 and 9) Targeting SRB-1 In Vivo
The oligonucleotides listed below were tested in a dose-dependent study for antisense inhibition of SRB-1 in mice. Unconjugated ISIS 353382 was included as a standard. Each of the various GalNAc3 conjugate groups was attached at either the 3′ or 5′ terminus of the respective oligonucleotide by a phosphodiester linked 2′-deoxyadenosine nucleoside (cleavable moiety).







TABLE 26 







Modified ASO targeting SRB-1















SEQ






ID


ASO
Sequence (5′ to 3′)
Motif
Conjugate
No.





ISIS 
GesmCesTesTesmCesAdsGds
5/10/5
none
28


353382
TdsmCdsAdsTdsGdsAdsmCds





(parent)
TdsTesmCesmCesTesTe





 


ISIS 
GesmCesTesTesmCesAdsGds
5/10/5
 
29


655861
TdsmCdsAdsTdsGdsAdsmCds






TdsTesmCesmCesTesTeo






 





 


ISIS 
GesmCesTesTesmCessAdsGds
5/10/5
 
29


664078
TdsmCdsAdsTdsGdsAdsmCds






TdsTesmCesmCesTesTe






 





 


ISIS 
 
5/10/5
 
30


661161
GesmCesTesTesmCesAdsGds






TdsmCdsAdsTdsGdsAdsmCds






TdsTesmCesmCesTesTe





 


ISIS 
 
5/10/5
 
30


665001
GesmCesTesTesmCesAdsGds






TdsmCdsAdsTdsGdsAdsmCds






TdsTesmCesmCesTesTe









Capital letters indicate the nucleobase for each nucleoside and mC indicates a 5-methyl cytosine. Subscripts: “e” indicates a 2′-MOE modified nucleoside; “d” indicates a β-D-2′-deoxyribonucleoside; “s” indicates a phosphorothioate internucleoside linkage (PS); “o” indicates a phosphodiester internucleoside linkage (PO); and “o′” indicates —O—P(═O)(OH)—. Conjugate groups are in bold.
The structure of GalNAc3-1a was shown previously in Example 9. The structure of GalNAc3-9 was shown previously in Example 52. The structure of GalNAc3-3 was shown previously in Example 39. The structure of GalNAc3-8 was shown previously in Example 47.
Treatment
Six week old male Balb/c mice (Jackson Laboratory, Bar Harbor, Me.) were injected subcutaneously once at the dosage shown below with ISIS 353382, 655861, 664078, 661161, 665001 or with saline. Each treatment group consisted of 4 animals. The mice were sacrificed 72 hours following the final administration to determine the liver SRB-1 mRNA levels using real-time PCR and RIBOGREEN® RNA quantification reagent (Molecular Probes, Inc. Eugene, Oreg.) according to standard protocols. The results below are presented as the average percent of SRB-1 mRNA levels for each treatment group, normalized to the saline control.
As illustrated in Table 27, treatment with antisense oligonucleotides lowered SRB-1 mRNA levels in a dose-dependent manner. Indeed, the antisense oligonucleotides comprising the phosphodiester linked GalNAc3-1 and GalNAc3-9 conjugates at the 3′ terminus (ISIS 655861 and ISIS 664078) and the GalNAc3-3 and GalNAc3-8 conjugates linked at the 5′ terminus (ISIS 661161 and ISIS 665001) showed substantial improvement in potency compared to the unconjugated antisense oligonucleotide (ISIS 353382). Furthermore, ISIS 664078, comprising a GalNAc3-9 conjugate at the 3′ terminus was essentially equipotent compared to ISIS 655861, which comprises a GalNAc3-1 conjugate at the 3′ terminus. The 5′ conjugated antisense oligonucleotides, ISIS 661161 and ISIS 665001, comprising a GalNAc3-3 or GalNAc3-9, respectively, had increased potency compared to the 3′ conjugated antisense oligonucleotides (ISIS 655861 and ISIS 664078).







TABLE 27







ASOs containing GalNAc3-1, 3, 8 or 9 targeting SRB-1











Dosage
SRB-1 mRNA



ISIS No.
(mg/kg)
(% Saline)
Conjugate













Saline
n/a
100



353382
3
88
none



10
68



30
36


655861
0.5
98
GalNac3-1 (3′)



1.5
76



5
31



15
20


664078
0.5
88
GalNac3-9 (3′)



1.5
85



5
46



15
20


661161
0.5
92
GalNac3-3 (5′)



1.5
59



5
19



15
11


665001
0.5
100
GalNac3-8 (5′)



1.5
73



5
29



15
13









Liver transaminase levels, alanine aminotransferase (ALT) and aspartate aminotransferase (AST), in serum were measured relative to saline injected mice using standard protocols. Total bilirubin and BUN were also evaluated. The change in body weights was evaluated with no significant change from the saline group. ALTs, ASTs, total bilirubin and BUN values are shown in the table below.













TABLE 28






Dosage


Total




ISIS No.
mg/kg
ALT
AST
Bilirubin
BUN
Conjugate





















Saline

24
59
0.1
37.52



353382
3
21
66
0.2
34.65
none



10
22
54
0.2
34.2



30
22
49
0.2
33.72


655861
0.5
25
62
0.2
30.65
GalNac3-1 (3′)



1.5
23
48
0.2
30.97



5
28
49
0.1
32.92



15
40
97
0.1
31.62


664078
0.5
40
74
0.1
35.3
GalNac3-9 (3′)



1.5
47
104
0.1
32.75



5
20
43
0.1
30.62



15
38
92
0.1
26.2


661161
0.5
101
162
0.1
34.17
GalNac3-3 (5′)



1.5 g
42
100
0.1
33.37



  5 g
23
99
0.1
34.97



15
53
83
0.1
34.8


665001
0.5
28
54
0.1
31.32
GalNac3-8 (5′)



1.5
42
75
0.1
32.32



5
24
42
0.1
31.85



15
32
67
0.1
31.









Example 56
Dose-Dependent Study of Oligonucleotides Comprising Either a 3′ or 5′-Conjugate Group (Comparison of GalNAc3-1, 2, 3, 5, 6, 7 and 10) Targeting SRB-1 In Vivo
The oligonucleotides listed below were tested in a dose-dependent study for antisense inhibition of SRB-1 in mice. Unconjugated ISIS 353382 was included as a standard. Each of the various GalNAc3 conjugate groups was attached at the 5′ terminus of the respective oligonucleotide by a phosphodiester linked 2′-deoxyadenosine nucleoside (cleavable moiety) except for ISIS 655861 which had the GalNAc3 conjugate group attached at the 3′ terminus.







TABLE 29 







Modified ASO targeting SRB-1















SEQ






ID


ASO
Sequence (5′ to 3′)
Motif
Conjugate
No.





ISIS
GesmCesTesTesmCesAdsGds
5/10/5
no
28


353382
TdsmCdsAdsTdsGdsAdsmCds

conjugate



(parent)
TdsTesmCesmCesTesTe





 


ISIS
GesmCesTesTesmCesAdsGds
5/10/5
 
29


655861
TdsmCdsAdsTdsGdsAdsmCds






TdsTesmCesmCesTesTeo






 





 


ISIS
 Gesm
5/10/5
 
30


664507
CesTesTesmCesAdsGdsTdsm






CdsAdsTdsGdsAdsCdsTds






TesCesCesTesTe





 


ISIS
 
5/10/5
 
30


661161
GesmCesTesTesmCesAdsGds






TdsmCdsAdsTdsGdsAdsmCds






TdsTesmCesmCesTesTe





 


ISIS 
 Gesm
5/10/5
 
30


666224
CesTesTesmCesAdsGds






TdsmCdsAdsTdsGdsAdsmCds






TdsTesmCesmCesTesTe





 


ISIS
 Gesm
5/10/5
 
30


666961
CesTesTesmCesAdsGds






TdsmCdsAdsTdsGdsAdsmCds






TdsTesmCesmCesTesTe





 


ISIS
 Gesm
5/10/5
 
30


666981
CesTesTesmCesAdsGds






TdsmCdsAdsTdsGdsAdsmCds






TdsTesmCesmCesTesTe





 


ISIS
 Gesm
5/10/5
 
30


666881
CesTesTesmCesAdsGds






TdsmCdsAdsTdsGdsAdsmCds






TdsTesmCesmCesTesTe









Capital letters indicate the nucleobase for each nucleoside and mC indicates a 5-methyl cytosine. Subscripts: “e” indicates a 2′-MOE modified nucleoside; “d” indicates a β-D-2′-deoxyribonucleoside; “s” indicates a phosphorothioate internucleoside linkage (PS); “o” indicates a phosphodiester internucleoside linkage (PO); and “o′” indicates —O—P(═O)(OH)—. Conjugate groups are in bold.
The structure of GalNAc3-1a was shown previously in Example 9. The structure of GalNAc3-2a was shown previously in Example 37. The structure of GalNAc3-3a was shown previously in Example 39. The structure of GalNAc3-5a was shown previously in Example 49. The structure of GalNAc3-6a was shown previously in Example 51. The structure of GalNAc3-7a was shown previously in Example 48. The structure of GalNAc3-10a was shown previously in Example 46.
Treatment
Six week old male Balb/c mice (Jackson Laboratory, Bar Harbor, Me.) were injected subcutaneously once at the dosage shown below with ISIS 353382, 655861, 664507, 661161, 666224, 666961, 666981, 666881 or with saline. Each treatment group consisted of 4 animals. The mice were sacrificed 72 hours following the final administration to determine the liver SRB-1 mRNA levels using real-time PCR and RIBOGREEN® RNA quantification reagent (Molecular Probes, Inc. Eugene, Oreg.) according to standard protocols. The results below are presented as the average percent of SRB-1 mRNA levels for each treatment group, normalized to the saline control.
As illustrated in Table 30, treatment with antisense oligonucleotides lowered SRB-1 mRNA levels in a dose-dependent manner Indeed, the conjugated antisense oligonucleotides showed substantial improvement in potency compared to the unconjugated antisense oligonucleotide (ISIS 353382). The 5′ conjugated antisense oligonucleotides showed a slight increase in potency compared to the 3′ conjugated antisense oligonucleotide.










TABLE 30






Dosage
SRB-1 mRNA



ISIS No.
(mg/kg)
(% Saline)
Conjugate


















Saline
n/a
100.0



353382
3
96.0
none



10
73.1



30
36.1


655861
0.5
99.4
GalNac3-1 (3′)



1.5
81.2



5
33.9



15
15.2


664507
0.5
102.0
GalNac3-2 (5′)



1.5
73.2



5
31.3



15
10.8


661161
0.5
90.7
GalNac3-3 (5′)



1.5
67.6



5
24.3



15
11.5


666224
0.5
96.1
GalNac3-5 (5′)



1.5
61.6



5
25.6



15
11.7


666961
0.5
85.5
GalNac3-6 (5′)



1.5
56.3



5
34.2



15
13.1


666981
0.5
84.7
GalNac3-7 (5′)



1.5
59.9



5
24.9



15
8.5


666881
0.5
100.0
GalNac3-10 (5′)



1.5
65.8



5
26.0



15
13.0









Liver transaminase levels, alanine aminotransferase (ALT) and aspartate aminotransferase (AST), in serum were measured relative to saline injected mice using standard protocols. Total bilirubin and BUN were also evaluated. The change in body weights was evaluated with no significant change from the saline group. ALTs, ASTs, total bilirubin and BUN values are shown in Table 31 below.













TABLE 31






Dosage


Total




ISIS No.
mg/kg
ALT
AST
Bilirubin
BUN
Conjugate





















Saline

26
57
0.2
27



353382
3
25
92
0.2
27
none



10
23
40
0.2
25



30
29
54
0.1
28


655861
0.5
25
71
0.2
34
GalNac3-1 (3′)



1.5
28
60
0.2
26



5
26
63
0.2
28



15
25
61
0.2
28


664507
0.5
25
62
0.2
25
GalNac3-2 (5′)



1.5
24
49
0.2
26



5
21
50
0.2
26



15
59
84
0.1
22


661161
0.5
20
42
0.2
29
GalNac3-3 (5′)



1.5 g
37
74
0.2
25



  5 g
28
61
0.2
29



15
21
41
0.2
25


666224
0.5
34
48
0.2
21
GalNac3-5 (5′)



1.5
23
46
0.2
26



5
24
47
0.2
23



15
32
49
0.1
26


666961
0.5
17
63
0.2
26
GalNac3-6 (5′)



1.5
23
68
0.2
26



5
25
66
0.2
26



15
29
107
0.2
28


666981
0.5
24
48
0.2
26
GalNac3-7 (5′)



1.5
30
55
0.2
24



5
46
74
0.1
24



15
29
58
0.1
26


666881
0.5
20
65
0.2
27
GalNac3-10 (5′)



1.5
23
59
0.2
24



5
45
70
0.2
26



15
21
57
0.2
24









Example 57
Duration of Action Study of Oligonucleotides Comprising a 3′-Conjugate Group Targeting ApoC III In Vivo
Mice were injected once with the doses indicated below and monitored over the course of 42 days for ApoC-III and plasma triglycerides (Plasma TG) levels. The study was performed using 3 transgenic mice that express human APOC-III in each group.







TABLE 32







Modified ASO targeting ApoC III












Link-
SEQ ID


ASO
Sequence (5′ to 3′)
ages
No.





ISIS
AesGesmCesTesTesmCdsTdsTdsGdsTds
PS
20


304801
mCdsmCdsAdsGdsmCdsTesTesTesAesTe




 


ISIS
AesGesmCesTesTesmCdsTdsTdsGdsTds
PS
21


647535
mCdsmCdsAdsGdsmCdsTesTesTesAesTeo





 




 


ISIS
AesGeomCeoTeoTeomCdsTdsTdsGdsTds
PO/PS
21


647536
mCdsmCdsAdsGdsmCdsTeoTeoTesAesTeo





 









Capital letters indicate the nucleobase for each nucleoside and mC indicates a 5-methyl cytosine. Subscripts: “e” indicates a 2′-MOE modified nucleoside; “d” indicates a β-D-2′-deoxyribonucleoside; “s” indicates a phosphorothioate internucleoside linkage (PS); “o” indicates a phosphodiester internucleoside linkage (PO); and “o′” indicates —O—P(═O)(OH)—. Conjugate groups are in bold.
The structure of GalNAc3-1a was shown previously in Example 9.







TABLE 33







ApoC III mRNA (% Saline on Day 1) and Plasma TG Levels (% Saline on Day 1)














ASO
Dose
Target
Day 3
Day 7
Day 14
Day 35
Day 42

















Saline
 0 mg/kg
ApoC-III
98
100
100
95
116


ISIS 304801
30 mg/kg
ApoC-III
28
30
41
65
74


ISIS 647535
10 mg/kg
ApoC-III
16
19
25
74
94


ISIS 647536
10 mg/kg
ApoC-III
18
16
17
35
51


Saline
 0 mg/kg
Plasma TG
121
130
123
105
109


ISIS 304801
30 mg/kg
Plasma TG
34
37
50
69
69


ISIS 647535
10 mg/kg
Plasma TG
18
14
24
18
71


ISIS 647536
10 mg/kg
Plasma TG
21
19
15
32
35









As can be seen in the table above the duration of action increased with addition of the 3′-conjugate group compared to the unconjugated oligonucleotide. There was a further increase in the duration of action for the conjugated mixed PO/PS oligonucleotide 647536 as compared to the conjugated full PS oligonucleotide 647535.
Example 58
Dose-Dependent Study of Oligonucleotides Comprising a 3′-Conjugate Group (Comparison of GalNAc3-1 and GalNAc4-11) Targeting SRB-1 In Vivo
The oligonucleotides listed below were tested in a dose-dependent study for antisense inhibition of SRB-1 in mice. Unconjugated ISIS 440762 was included as an unconjugated standard. Each of the conjugate groups were attached at the 3′ terminus of the respective oligonucleotide by a phosphodiester linked 2′-deoxyadenosine nucleoside cleavable moiety.
The structure of GalNAc3-1a was shown previously in Example 9. The structure of GalNAc3-11a was shown previously in Example 50.
Treatment
Six week old male Balb/c mice (Jackson Laboratory, Bar Harbor, Me.) were injected subcutaneously once at the dosage shown below with ISIS 440762, 651900, 663748 or with saline. Each treatment group consisted of 4 animals. The mice were sacrificed 72 hours following the final administration to determine the liver SRB-1 mRNA levels using real-time PCR and RIBOGREEN® RNA quantification reagent (Molecular Probes, Inc. Eugene, Oreg.) according to standard protocols. The results below are presented as the average percent of SRB-1 mRNA levels for each treatment group, normalized to the saline control.
As illustrated in Table 34, treatment with antisense oligonucleotides lowered SRB-1 mRNA levels in a dose-dependent manner. The antisense oligonucleotides comprising the phosphodiester linked GalNAc3-1 and GalNAc4-11 conjugates at the 3′ terminus (ISIS 651900 and ISIS 663748) showed substantial improvement in potency compared to the unconjugated antisense oligonucleotide (ISIS 440762). The two conjugated oligonucleotides, GalNAc3-1 and GalNAc4-11, were equipotent.







TABLE 34







Modified ASO targeting SRB-1












Sequence
Dose
% Saline
SEQ ID


ASO
(5′ to 3′)
mg/kg
control
No.














Saline


100



 


ISIS
TksmCksAdsGdsTdsmCdsAdsTdsGdsAds
0.6
73.45
22


440762
mCdsTdsTksmCk
2
59.66





6
23.50



 


ISIS
TksmCksAdsGdsTdsmCdsAdsTdsGdsAds
0.2
62.75
23


651900
mCdsTdsTksmCko 
0.6
29.14





2
8.61





6
5.62



 


ISIS
TksmCksAdsGdsTdsmCdsAdsTdsGdsAds
0.2
63.99
23


663748
mCdsTdsTksmCko 
0.6
33.53





2
7.58





6
5.52









Capital letters indicate the nucleobase for each nucleoside and mC indicates a 5-methyl cytosine. Subscripts: “e” indicates a 2′-MOE modified nucleoside; “k” indicates 6′-(S)—CH3 bicyclic nucleoside; “d” indicates a β-D-2′-deoxyribonucleoside; “s” indicates a phosphorothioate internucleoside linkage (PS); “o” indicates a phosphodiester internucleoside linkage (PO); and “o” indicates —O—P(═O)(OH)—. Conjugate groups are in bold.
Liver transaminase levels, alanine aminotransferase (ALT) and aspartate aminotransferase (AST), in serum were measured relative to saline injected mice using standard protocols. Total bilirubin and BUN were also evaluated. The change in body weights was evaluated with no significant change from the saline group. ALTs, ASTs, total bilirubin and BUN values are shown in Table 35 below.













TABLE 35






Dosage


Total




ISIS No.
mg/kg
ALT
AST
Bilirubin
BUN
Conjugate





















Saline

30
76
0.2
40



440762
0.60
32
70
0.1
35
none



2
26
57
0.1
35



6
31
48
0.1
39


651900
0.2
32
115
0.2
39
GalNac3-1 (3′)



0.6
33
61
0.1
35



2
30
50
0.1
37



6
34
52
0.1
36


663748
0.2
28
56
0.2
36
GalNac4-11 (3′)



0.6
34
60
0.1
35



2
44
62
0.1
36



6
38
71
0.1
33









Example 59
Effects of GalNAc3-1 Conjugated ASOs Targeting FXI In Vivo
The oligonucleotides listed below were tested in a multiple dose study for antisense inhibition of FXI in mice. ISIS 404071 was included as an unconjugated standard. Each of the conjugate groups was attached at the 3′ terminus of the respective oligonucleotide by a phosphodiester linked 2′-deoxyadenosine nucleoside cleavable moiety.







TABLE 36







Modified ASOs targeting FXI












Link-
SEQ ID


ASO
Sequence (5′ to 3′)
ages
No.





ISIS
TesGesGesTesAesAdsTdsmCdsmCdsAdsmCds
PS
31


404071
TdsTdsTdsmCdsAesGesAesGesGe




 


ISIS
TesGesGesTesAesAdsTdsmCdsmCdsAdsmCds
PS
32


656172
TdsTdsTdsmCdsAesGesAesGes





Ge 




 


ISIS
TesGeoGeoTeoAeoAdsTdsmCdsmCdsAdsmCds
PO/PS
32


656173
TdsTdsTdsmCdsAeoGeoAesGes





Ge 









Capital letters indicate the nucleobase for each nucleoside and mC indicates a 5-methyl cytosine.
Subscripts: “e” indicates a 2′-MOE modified nucleoside; “d” indicates a β-D-2′-deoxyribonucleoside; “s” indicates a phosphorothioate internucleoside linkage (PS); “o” indicates a phosphodiester internucleoside linkage (PO); and “o′” indicates —O—P(═O)(OH)—. Conjugate groups are in bold.
The structure of GalNAc3-1a was shown previously in Example 9.
Treatment
Six week old male Balb/c mice (Jackson Laboratory, Bar Harbor, Me.) were injected subcutaneously twice a week for 3 weeks at the dosage shown below with ISIS 404071, 656172, 656173 or with PBS treated control. Each treatment group consisted of 4 animals. The mice were sacrificed 72 hours following the final administration to determine the liver FXI mRNA levels using real-time PCR and RIBOGREEN® RNA quantification reagent (Molecular Probes, Inc. Eugene, Oreg.) according to standard protocols. Plasma FXI protein levels were also measured using ELISA. FXI mRNA levels were determined relative to total RNA (using RIBOGREEN®), prior to normalization to PBS-treated control. The results below are presented as the average percent of FXI mRNA levels for each treatment group. The data was normalized to PBS-treated control and is denoted as “% PBS”. The ED50s were measured using similar methods as described previously and are presented below.







TABLE 37







Factor XI mRNA (% Saline)












Dose





ASO
mg/kg
% Control
Conjugate
Linkages














Saline

100
none



ISIS
3
92
none
PS


404071
10
40



30
15


ISIS
0.7
74
GalNac3-1
PS


656172
2
33



6
9


ISIS
0.7
49
GalNac3-1
PO/PS


656173
2
22



6
1









As illustrated in Table 37, treatment with antisense oligonucleotides lowered FXI mRNA levels in a dose-dependent manner. The oligonucleotides comprising a 3′-GalNAc3-1 conjugate group showed substantial improvement in potency compared to the unconjugated antisense oligonucleotide (ISIS 404071). Between the two conjugated oligonucleotides an improvement in potency was further provided by substituting some of the PS linkages with PO (ISIS 656173).
As illustrated in Table 37a, treatment with antisense oligonucleotides lowered FXI protein levels in a dose-dependent manner. The oligonucleotides comprising a 3′-GalNAc3-1 conjugate group showed substantial improvement in potency compared to the unconjugated antisense oligonucleotide (ISIS 404071). Between the two conjugated oligonucleotides an improvement in potency was further provided by substituting some of the PS linkages with PO (ISIS 656173).







TABLE 37a







Factor XI protein (% Saline)












Dose
Protein (%




ASO
mg/kg
Control)
Conjugate
Linkages














Saline

100
none



ISIS
3
127
none
PS


404071
10
32



30
3


ISIS
0.7
70
GalNac3-1
PS


656172
2
23



6
1


ISIS
0.7
45
GalNac3-1
PO/PS


656173
2
6



6
0









Liver transaminase levels, alanine aminotransferase (ALT) and aspartate aminotransferase (AST), in serum were measured relative to saline injected mice using standard protocols. Total bilirubin, total albumin, CRE and BUN were also evaluated. The change in body weights was evaluated with no significant change from the saline group. ALTs, ASTs, total bilirubin and BUN values are shown in the table below.















TABLE 38






Dosage


Total
Total





ISIS No.
mg/kg
ALT
AST
Albumin
Bilirubin
CRE
BUN
Conjugate























Saline

71.8
84.0
3.1
0.2
0.2
22.9



404071
3
152.8
176.0
3.1
0.3
0.2
23.0
none



10
73.3
121.5
3.0
0.2
0.2
21.4



30
82.5
92.3
3.0
0.2
0.2
23.0


656172
0.7
62.5
111.5
3.1
0.2
0.2
23.8
GalNac3-1 (3′)



2
33.0
51.8
2.9
0.2
0.2
22.0



6
65.0
71.5
3.2
0.2
0.2
23.9


656173
0.7
54.8
90.5
3.0
0.2
0.2
24.9
GalNac3-1 (3′)



2
85.8
71.5
3.2
0.2
0.2
21.0



6
114.0
101.8
3.3
0.2
0.2
22.7









Example 60
Effects of Conjugated ASOs Targeting SRB-1 In Vitro
The oligonucleotides listed below were tested in a multiple dose study for antisense inhibition of SRB-1 in primary mouse hepatocytes. ISIS 353382 was included as an unconjugated standard. Each of the conjugate groups were attached at the 3′ or 5′ terminus of the respective oligonucleotide by a phosphodiester linked 2′-deoxyadenosine nucleoside cleavable moiety.







TABLE 39







Modified ASO targeting SRB-1















SEQ



Sequence


ID


ASO
(5′ to 3′)
Motif
Conjugate
No.





ISIS
GesmCesTesTesmCesAdsGds
5/10/5
none
28


353382
TdsmCdsAdsTdsGdsAdsmCds






TdsTesmCesmCesTesTe





 


ISIS
GesmCesTesTesmCesAdsGds
5/10/5
 
29


655861
TdsmCdsAdsTdsGdsAdsmCds






TdsTesmCesmCesTes






Te 





 


ISIS
GesmCeoTeoTeomCeoAdsGds
5/10/5
 
29


655862
TdsmCdsAdsTdsGdsAdsmCds






TdsTeomCeomCesTes






Te 





 


ISIS
 Ges
5/10/5
 
30


661161
mCesTesTesmCesAdsGds






TdsmCdsAdsTdsGdsAdsmCds






TdsTesmCesmCesTesTe





 


ISIS
 Ges
5/10/5
 
30


665001
mCesTesTesmCesAdsGdsTds






mCdsAdsTdsGdsAdsmCdsTds






TesmCesmCesTesTe





 


ISIS
GesmCesTesTesmCesAdsGds
5/10/5
 
29


664078
TdsmCdsAdsTdsGdsAdsmCds






TdsTesmCesmCesTes






Te 





 


ISIS
 Ges
5/10/5
 
30


666961
mCesTesTesmCesAdsGdsTds






mCdsAdsTdsGdsAdsmCdsTds






TesmCesmCesTesTe





 


ISIS
 Ges
5/10/5
 
30


664507
mCesTesTesmCesAdsGdsTds






mCdsAdsTdsGdsAdsmCdsTds






TesmCesmCesTesTe





 


ISIS
 Ges
5/10/5
 
30


666881
mCesTesTesmCesAdsGdsTds






mCdsAdsTdsGdsAdsmCdsTds






TesmCesmCesTesTe





 


ISIS
 Ges
5/10/5
 
30


666224
mCesTesTesmCesAdsGdsTds






mCdsAdsTdsGdsAdsmCdsTds






TesmCesmCesTesTe





 


ISIS
 Ges
5/10/5
 
30


666981
mCesTesTesmCesAdsGdsTds






mCdsAdsTdsGdsAdsmCdsTds






TesmCesmCesTesTe









Capital letters indicate the nucleobase for each nucleoside and mC indicates a 5-methyl cytosine. Subscripts: “e” indicates a 2′-MOE modified nucleoside; “d” indicates a β-D-2′-deoxyribonucleoside; “s” indicates a phosphorothioate internucleoside linkage (PS); “o” indicates a phosphodiester internucleoside linkage (PO); and “o′” indicates —O—P(═O)(OH)—. Conjugate groups are in bold.
The structure of GalNAc3-1a was shown previously in Example 9. The structure of GalNAc3-3a was shown previously in Example 39. The structure of GalNAc3-8a was shown previously in Example 47. The structure of GalNAc3-9a was shown previously in Example 52. The structure of GalNAc3-6a was shown previously in Example 51. The structure of GalNAc3-2a was shown previously in Example 37. The structure of GalNAc3-10a was shown previously in Example 46. The structure of GalNAc3-5a was shown previously in Example 49. The structure of GalNAc3-7a was shown previously in Example 48.
Treatment
The oligonucleotides listed above were tested in vitro in primary mouse hepatocyte cells plated at a density of 25,000 cells per well and treated with 0.03, 0.08, 0.24, 0.74, 2.22, 6.67 or 20 nM modified oligonucleotide. After a treatment period of approximately 16 hours, RNA was isolated from the cells and mRNA levels were measured by quantitative real-time PCR and the SRB-1 mRNA levels were adjusted according to total RNA content, as measured by RIBOGREEN®.
The IC50 was calculated using standard methods and the results are presented in Table 40. The results show that, under free uptake conditions in which no reagents or electroporation techniques are used to artificially promote entry of the oligonucleotides into cells, the oligonucleotides comprising a GalNAc conjugate were significantly more potent in hepatocytes than the parent oligonucleotide (ISIS 353382) that does not comprise a GalNAc conjugate.











TABLE 40







Internucleoside

SEQ ID


ASO
IC50 (nM)
linkages
Conjugate
No.







ISIS 353382
190a 
PS
none
28


ISIS 655861
 11a
PS
GalNac3-1
29


ISIS 655862
 3
PO/PS
GalNac3-1
29


ISIS 661161
 15a
PS
GalNac3-3
30


ISIS 665001
20
PS
GalNac3-8
30


ISIS 664078
55
PS
GalNac3-9
29


ISIS 666961
 22a
PS
GalNac3-6
30


ISIS 664507
30
PS
GalNac3-2
30


ISIS 666881
30
PS
GalNac3-10
30


ISIS 666224
 30a
PS
GalNac3-5
30


ISIS 666981
40
PS
GalNac3-7
30





aAverage of multiple runs.






Example 61
Preparation of Oligomeric Compound 175 Comprising GalNAc3-12













Compound 169 is commercially available. Compound 172 was prepared by addition of benzyl (perfluorophenyl) glutarate to compound 171. The benzyl (perfluorophenyl) glutarate was prepared by adding PFP-TFA and DIEA to 5-(benzyloxy)-5-oxopentanoic acid in DMF. Oligomeric compound 175, comprising a GalNAc3-12 conjugate group, was prepared from compound 174 using the general procedures illustrated in Example 46. The GalNAc3 cluster portion of the conjugate group GalNAc3-12 (GalNAc3-12a) can be combined with any cleavable moiety to provide a variety of conjugate groups. In a certain embodiments, the cleavable moiety is —P(═O)(OH)-Ad-P(═O)(OH)—. The structure of GalNAc3-12 (GalNAc3-12a-CM-) is shown below:




Example 62
Preparation of Oligomeric Compound 180 Comprising GalNAc3-13







Compound 176 was prepared using the general procedure shown in Example 2. Oligomeric compound 180, comprising a GalNAc3-13 conjugate group, was prepared from compound 177 using the general procedures illustrated in Example 49. The GalNAc3 cluster portion of the conjugate group GalNAc3-13 (GalNAc3-13a) can be combined with any cleavable moiety to provide a variety of conjugate groups. In a certain embodiments, the cleavable moiety is —P(═O)(OH)-Ad-P(═O)(OH)—. The structure of GalNAc3-13 (GalNAc3-13a-CM-) is shown below:




Example 63
Preparation of Oligomeric Compound 188 Comprising GalNAc3-14







Compounds 181 and 185 are commercially available. Oligomeric compound 188, comprising a GalNAc3-14 conjugate group, was prepared from compound 187 using the general procedures illustrated in Example 46. The GalNAc3 cluster portion of the conjugate group GalNAc3-14 (GalNAc3-14a) can be combined with any cleavable moiety to provide a variety of conjugate groups. In certain embodiments, the cleavable moiety is —P(═O)(OH)-Ad-P(═O)(OH)—. The structure of GalNAc3-14 (GalNAc3-14a-CM-) is shown below:




Example 64
Preparation of Oligomeric Compound 197 Comprising GalNAc3-15







Compound 189 is commercially available. Compound 195 was prepared using the general procedure shown in Example 31. Oligomeric compound 197, comprising a GalNAc3-15 conjugate group, was prepared from compounds 194 and 195 using standard oligonucleotide synthesis procedures. The GalNAc3 cluster portion of the conjugate group GalNAc3-15 (GalNAc3-15a) can be combined with any cleavable moiety to provide a variety of conjugate groups. In certain embodiments, the cleavable moiety is —P(═O)(OH)-Ad-P(═O)(OH)—. The structure of GalNAc3-15 (GalNAc3-15a-CM-) is shown below:




Example 65
Dose-Dependent Study of Oligonucleotides Comprising a 5′-Conjugate Group (Comparison of GalNAc3-3, 12, 13, 14, and 15) Targeting SRB-1 In Vivo
The oligonucleotides listed below were tested in a dose-dependent study for antisense inhibition of SRB-1 in mice. Unconjugated ISIS 353382 was included as a standard. Each of the GalNAc3 conjugate groups was attached at the 5′ terminus of the respective oligonucleotide by a phosphodiester linked 2′-deoxyadenosine nucleoside (cleavable moiety).







TABLE 41







Modified ASOs targeting SRB-1













SEQ


ISIS
Sequences

ID


No.
(5′ to 3′)
Conjugate
No.





353382
GesmCesTesTesmCesAdsGds
none
28



TdsmCdsAdsTdsGdsAdsmCds





TdsTesmCesmCesTesTe




 


661161
 Ges
GalNAc3-3
30



mCesTesTesmCesAdsGdsTds





mCdsAdsTdsGdsAdsmCdsTds





TesmCesmCesTesTe




 


671144
 Ges
GalNAc3-12
30



mCesTesTesmCesAdsGdsTds





mCdsAdsTdsGdsAdsmCdsTds





TesmCesmCesTesTe




 


670061
 Ges
GalNAc3-13
30



mCesTesTesmCesAdsGdsTds





mCdsAdsTdsGdsAdsmCdsTds





TesmCesmCesTesTe




 


671261
 Ges
GalNAc3-14
30



mCesTesTesmCesAdsGdsTds





mCdsAdsTdsGdsAdsmCdsTds





TesmCesmCesTesTe




 


671262
 Ges
GalNAc3-15
30



mCesTesTesmCesAdsGdsTds





mCdsAdsTdsGdsAdsmCdsTds





TesmCesmCesTesTe









Capital letters indicate the nucleobase for each nucleoside and mC indicates a 5-methyl cytosine. Subscripts: “e” indicates a 2′-MOE modified nucleoside; “d” indicates a β-D-2′-deoxyribonucleoside; “s” indicates a phosphorothioate internucleoside linkage (PS); “o” indicates a phosphodiester internucleoside linkage (PO); and “o′” indicates —O—P(═O)(OH)—. Conjugate groups are in bold.

The structure of GalNAc3-3a was shown previously in Example 39. The structure of GalNAc3-12a was shown previously in Example 61. The structure of GalNAc3-13a was shown previously in Example 62. The structure of GalNAc3-14a was shown previously in Example 63. The structure of GalNAc3-15a was shown previously in Example 64.
Treatment
Six to eight week old C57bl6 mice (Jackson Laboratory, Bar Harbor, Me.) were injected subcutaneously once or twice at the dosage shown below with ISIS 353382, 661161, 671144, 670061, 671261, 671262, or with saline. Mice that were dosed twice received the second dose three days after the first dose. Each treatment group consisted of 4 animals. The mice were sacrificed 72 hours following the final administration to determine the liver SRB-1 mRNA levels using real-time PCR and RIBOGREEN® RNA quantification reagent (Molecular Probes, Inc. Eugene, Oreg.) according to standard protocols. The results below are presented as the average percent of SRB-1 mRNA levels for each treatment group, normalized to the saline control.
As illustrated in Table 42, treatment with antisense oligonucleotides lowered SRB-1 mRNA levels in a dose-dependent manner. No significant differences in target knockdown were observed between animals that received a single dose and animals that received two doses (see ISIS 353382 dosages 30 and 2×15 mg/kg; and ISIS 661161 dosages 5 and 2×2.5 mg/kg). The antisense oligonucleotides comprising the phosphodiester linked GalNAc3-3, 12, 13, 14, and 15 conjugates showed substantial improvement in potency compared to the unconjugated antisense oligonucleotide (ISIS 335382).







TABLE 42







SRB-1 mRNA (% Saline)












Dosage
SRB-1 mRNA (%




ISIS No.
(mg/kg)
Saline)
ED50 (mg/kg)
Conjugate














Saline
n/a
100.0
n/a
n/a


353382
3
85.0
22.4
none



10
69.2



30
34.2



2 × 15 
36.0


661161
0.5
87.4
2.2
GalNAc3-3



1.5
59.0



5
25.6



2 × 2.5
27.5



15
17.4


671144
0.5
101.2
3.4
GalNAc3-12



1.5
76.1



5
32.0



15
17.6


670061
0.5
94.8
2.1
GalNAc3-13



1.5
57.8



5
20.7



15
13.3


671261
0.5
110.7
4.1
GalNAc3-14



1.5
81.9



5
39.8



15
14.1


671262
0.5
109.4
9.8
GalNAc3-15



1.5
99.5



5
69.2



15
36.1









Liver transaminase levels, alanine aminotransferase (ALT) and aspartate aminotransferase (AST), in serum were measured relative to saline injected mice using standard protocols. Total bilirubin and BUN were also evaluated. The changes in body weights were evaluated with no significant differences from the saline group (data not shown). ALTs, ASTs, total bilirubin and BUN values are shown in Table 43 below.













TABLE 43









Total





Dosage
ALT
AST
Bilirubin
BUN


ISIS No.
(mg/kg)
(U/L)
(U/L)
(mg/dL)
(mg/dL)
Conjugate





















Saline
n/a
28
60
0.1
39
n/a


353382
3
30
77
0.2
36
none



10
25
78
0.2
36



30
28
62
0.2
35



2 × 15 
22
59
0.2
33


661161
0.5
39
72
0.2
34
GalNac3-3



1.5
26
50
0.2
33



5
41
80
0.2
32



2 × 2.5
24
72
0.2
28



15
32
69
0.2
36


671144
0.5
25
39
0.2
34
GalNac3-12



1.5
26
55
0.2
28



5
48
82
0.2
34



15
23
46
0.2
32


670061
0.5
27
53
0.2
33
GalNac3-13



1.5
24
45
0.2
35



5
23
58
0.1
34



15
24
72
0.1
31


671261
0.5
69
99
0.1
33
GalNac3-14



1.5
34
62
0.1
33



5
43
73
0.1
32



15
32
53
0.2
30


671262
0.5
24
51
0.2
29
GalNac3-15



1.5
32
62
0.1
31



5
30
76
0.2
32



15
31
64
0.1
32









Example 66
Effect of Various Cleavable Moieties on Antisense Inhibition In Vivo by Oligonucleotides Targeting SRB-1 Comprising a 5′-GalNAc3 Cluster
The oligonucleotides listed below were tested in a dose-dependent study for antisense inhibition of SRB-1 in mice. Each of the GalNAc3 conjugate groups was attached at the 5′ terminus of the respective oligonucleotide by a phosphodiester linked nucleoside (cleavable moiety (CM)).







TABLE 44







Modified ASOs targeting SRB-1















SEQ


ISIS
Sequences
GalNAc3

ID


No.
(5′ to 3′)
Cluster
CM
No.





661161
 Ges
GalNAc3-3a
Ad
30



mCesTesTesmCesAdsGdsTds






mCdsAdsTdsGdsAdsmCdsTds






TesmCesmCesTesTe





 


670699
 Ges
GalNAc3-3a
Td
33



mCeoTeoTeomCeoAdsGdsTds






mCdsAdsTdsGdsAdsmCdsTds






TeomCeomCesTesTe





 


670700
 Ges
GalNAc3-3a
Ae
30



mCeoTeoTeomCeoAdsGdsTds






mCdsAdsTdsGdsAdsmCdsTds






TeomCeomCesTesTe





 


670701
 Ges
GalNac3-3a
Te
33



mCeoTeoTeomCeoAdsGdsTds






mCdsAdsTdsGdsAdsmCdsTds






TeomCeomCesTesTe





 


671165
 Ges
GalNAc3-13a
Ad
30



mCeoTeoTeomCeoAdsGdsTds





 
mCdsAdsTdsGdsAdsmCdsTds






TeomCeomCesTesTe





Capital letters indicate the nucleobase for each nucleoside and mC indicates a 5-methyl cytosine.


Subscripts:


“e” indicates a 2′-MOE modified nucleoside;


“d” indicates a β-D-2′-deoxyribonucleoside;


“s” indicates a phosphorothioate internucleoside linkage (PS);


“o” indicates a phosphodiester internucleoside linkage (PO);


and “o′” indicates -O-P(=O)(OH)-.


Conjugate groups are in bold.






The structure of GalNAc3-3a was shown previously in Example 39. The structure of GalNAc3-13a was shown previously in Example 62.
Treatment
Six to eight week old C57bl6 mice (Jackson Laboratory, Bar Harbor, Me.) were injected subcutaneously once at the dosage shown below with ISIS 661161, 670699, 670700, 670701, 671165, or with saline. Each treatment group consisted of 4 animals. The mice were sacrificed 72 hours following the final administration to determine the liver SRB-1 mRNA levels using real-time PCR and RIBOGREEN® RNA quantification reagent (Molecular Probes, Inc. Eugene, Oreg.) according to standard protocols. The results below are presented as the average percent of SRB-1 mRNA levels for each treatment group, normalized to the saline control.
As illustrated in Table 45, treatment with antisense oligonucleotides lowered SRB-1 mRNA levels in a dose-dependent manner. The antisense oligonucleotides comprising various cleavable moieties all showed similar potencies.







TABLE 45







SRB-1 mRNA (% Saline)













SRB-1 mRNA
GalNAc3



ISIS No.
Dosage (mg/kg)
(% Saline)
Cluster
CM














Saline
n/a
100.0
n/a
n/a


661161
0.5
87.8
GalNAc3-3a
Ad



1.5
61.3



5
33.8



15
14.0


670699
0.5
89.4
GalNAc3-3a
Td



1.5
59.4



5
31.3



15
17.1


670700
0.5
79.0
GalNAc3-3a
Ae



1.5
63.3



5
32.8



15
17.9


670701
0.5
79.1
GalNAc3-3a
Te



1.5
59.2



5
35.8



15
17.7


671165
0.5
76.4
GalNAc3-13a
Ad



1.5
43.2



5
22.6



15
10.0









Liver transaminase levels, alanine aminotransferase (ALT) and aspartate aminotransferase (AST), in serum were measured relative to saline injected mice using standard protocols. Total bilirubin and BUN were also evaluated. The changes in body weights were evaluated with no significant differences from the saline group (data not shown). ALTs, ASTs, total bilirubin and BUN values are shown in Table 46 below.














TABLE 46









Total






Dosage
ALT
AST
Bilirubin
BUN
GalNAc3


ISIS No.
(mg/kg)
(U/L)
(U/L)
(mg/dL)
(mg/dL)
Cluster
CM






















Saline
n/a
24
64
0.2
31
n/a
n/a


661161
0.5
25
64
0.2
31
GalNac3-3a
Ad



1.5
24
50
0.2
32



5
26
55
0.2
28



15
27
52
0.2
31


670699
0.5
42
83
0.2
31
GalNac3-3a
Td



1.5
33
58
0.2
32



5
26
70
0.2
29



15
25
67
0.2
29


670700
0.5
40
74
0.2
27
GalNac3-3a
Ae



1.5
23
62
0.2
27



5
24
49
0.2
29



15
25
87
0.1
25


670701
0.5
30
77
0.2
27
GalNac3-3a
Te



1.5
22
55
0.2
30



5
81
101
0.2
25



15
31
82
0.2
24


671165
0.5
44
84
0.2
26
GalNac3-13a
Ad



1.5
47
71
0.1
24



5
33
91
0.2
26



15
33
56
0.2
29









Example 67
Preparation of Oligomeric Compound 199 Comprising GalNAc3-16




Oligomeric compound 199, comprising a GalNAc3-16 conjugate group, is prepared using the general procedures illustrated in Examples 7 and 9. The GalNAc3 cluster portion of the conjugate group GalNAc3-16 (GalNAc3-16a) can be combined with any cleavable moiety to provide a variety of conjugate groups. In certain embodiments, the cleavable moiety is —P(═O)(OH)-Ad-P(═O)(OH)—. The structure of GalNAc3-16 (GalNAc3-16a-CM-) is shown below:




Example 68
Preparation of Oligomeric Compound 200 Comprising GalNAc3-17




Oligomeric compound 200, comprising a GalNAc3-17 conjugate group, was prepared using the general procedures illustrated in Example 46. The GalNAc3 cluster portion of the conjugate group GalNAc3-17 (GalNAc3-17a) can be combined with any cleavable moiety to provide a variety of conjugate groups. In certain embodiments, the cleavable moiety is —P(═O)(OH)-Ad-P(═O)(OH)—. The structure of GalNAc3-17 (GalNAc3-17a-CM-) is shown below:




Example 69
Preparation of Oligomeric Compound 201 Comprising GalNAc3-18




Oligomeric compound 201, comprising a GalNAc3-18 conjugate group, was prepared using the general procedures illustrated in Example 46. The GalNAc3 cluster portion of the conjugate group GalNAc3-18 (GalNAc3-18a) can be combined with any cleavable moiety to provide a variety of conjugate groups. In certain embodiments, the cleavable moiety is —P(═O)(OH)-Ad-P(═O)(OH)—. The structure of GalNAc3-18 (GalNAc3-18a-CM-) is shown below:




Example 70
Preparation of Oligomeric Compound 204 Comprising GalNAc3-19




Oligomeric compound 204, comprising a GalNAc3-19 conjugate group, was prepared from compound 64 using the general procedures illustrated in Example 52. The GalNAc3 cluster portion of the conjugate group GalNAc3-19 (GalNAc3-19a) can be combined with any cleavable moiety to provide a variety of conjugate groups. In certain embodiments, the cleavable moiety is —P(═O)(OH)-Ad-P(═O)(OH)—. The structure of GalNAc3-19 (GalNAc3-19a-CM-) is shown below:




Example 71
Preparation of Oligomeric Compound 210 Comprising GalNAc3-20







Compound 205 was prepared by adding PFP-TFA and DIEA to 6-(2,2,2-trifluoroacetamido)hexanoic acid in acetonitrile, which was prepared by adding triflic anhydride to 6-aminohexanoic acid. The reaction mixture was heated to 80° C., then lowered to rt. Oligomeric compound 210, comprising a GalNAc3-20 conjugate group, was prepared from compound 208 using the general procedures illustrated in Example 52. The GalNAc3 cluster portion of the conjugate group GalNAc3-20 (GalNAc3-20a) can be combined with any cleavable moiety to provide a variety of conjugate groups. In certain embodiments, the cleavable moiety is —P(═O)(OH)-Ad-P(═O)(OH)—. The structure of GalNAc3-20 (GalNAc3-20a-CM-) is shown below:




Example 72
Preparation of Oligomeric Compound 215 Comprising GalNAc3-21




Compound 211 is commercially available. Oligomeric compound 215, comprising a GalNAc3-21 conjugate group, was prepared from compound 213 using the general procedures illustrated in Example 52. The GalNAc3 cluster portion of the conjugate group GalNAc3-21 (GalNAc3-21a) can be combined with any cleavable moiety to provide a variety of conjugate groups. In certain embodiments, the cleavable moiety is —P(═O)(OH)-Ad-P(═O)(OH)—. The structure of GalNAc3-21 (GalNAc3-21a-CM-) is shown below:




Example 73
Preparation of Oligomeric Compound 221 Comprising GalNAc3-22







Compound 220 was prepared from compound 219 using diisopropylammonium tetrazolide. Oligomeric compound 221, comprising a GalNAc3-21 conjugate group, is prepared from compound 220 using the general procedure illustrated in Example 52. The GalNAc3 cluster portion of the conjugate group GalNAc3-22 (GalNAc3-22a) can be combined with any cleavable moiety to provide a variety of conjugate groups. In certain embodiments, the cleavable moiety is —P(═O)(OH)-Ad-P(═O)(OH)—. The structure of GalNAc3-22 (GalNAc3-22a-CM-) is shown below:




Example 74
Effect of Various Cleavable Moieties on Antisense Inhibition In Vivo by Oligonucleotides Targeting SRB-1 Comprising a 5′-GalNAc3 Conjugate
The oligonucleotides listed below were tested in a dose-dependent study for antisense inhibition of SRB-1 in mice. Each of the GalNAc3 conjugate groups was attached at the 5′ terminus of the respective oligonucleotide.







TABLE 47







Modified ASOs targeting SRB-1















SEQ


ISIS
Sequences
GalNAc3

ID


No.
(5′ to 3′)
Cluster
CM
No.





353382
GesmCesTesTesmCesAdsGds
n/a
n/a
28



TdsmCdsAdsTdsGdsAdsmCds






TdsTesmCesmCesTesTe





 


661161
 Ges
GalNAc3-3a
Ad
30



mCesTesTesmCesAdsGdsTds






mCdsAdsTdsGdsAdsmCdsTds






TesmCesmCesTesTe





 


666904
 GesmCes
GalNAc3-3a
PO
28



TesTesmCesAdsGdsTdsmCds






AdsTdsGdsAdsmCdsTdsTes






mCesmCesTesTe





 


675441
 
GalNAc3-17a
Ad
30



GesmCesTesTesmCesAdsGds






TdsmCdsAdsTdsGdsAdsmCds






TdsTesmCesmCesTesTe





 


675442
 
GalNAc3-18a
Ad
30



GesmCesTesTesmCesAdsGds






TdsmCdsAdsTdsGdsAdsmCds






TdsTesmCesmCesTesTe









In all tables, capital letters indicate the nucleobase for each nucleoside and mC indicates a 5-methyl cytosine. Subscripts: “e” indicates a 2′-MOE modified nucleoside; “d” indicates a β-D-2′-deoxyribonucleoside; “s” indicates a phosphorothioate internucleoside linkage (PS); “o” indicates a phosphodiester internucleoside linkage (PO); and “o′” indicates —O—P(═O)(OH)—. Conjugate groups are in bold.

The structure of GalNAc3-3a was shown previously in Example 39. The structure of GalNAc3-17a was shown previously in Example 68, and the structure of GalNAc3-18a was shown in Example 69.
Treatment
Six to eight week old C57BL/6 mice (Jackson Laboratory, Bar Harbor, Me.) were injected subcutaneously once at the dosage shown below with an oligonucleotide listed in Table 47 or with saline. Each treatment group consisted of 4 animals. The mice were sacrificed 72 hours following the final administration to determine the SRB-1 mRNA levels using real-time PCR and RIBOGREEN® RNA quantification reagent (Molecular Probes, Inc. Eugene, Oreg.) according to standard protocols. The results below are presented as the average percent of SRB-1 mRNA levels for each treatment group, normalized to the saline control.
As illustrated in Table 48, treatment with antisense oligonucleotides lowered SRB-1 mRNA levels in a dose-dependent manner. The antisense oligonucleotides comprising a GalNAc conjugate showed similar potencies and were significantly more potent than the parent oligonucleotide lacking a GalNAc conjugate.







TABLE 48







SRB-1 mRNA (% Saline)













SRB-1 mRNA
GalNAc3



ISIS No.
Dosage (mg/kg)
(% Saline)
Cluster
CM














Saline
n/a
100.0
n/a
n/a


353382
3
79.38
n/a
n/a



10
68.67



30
40.70


661161
0.5
79.18
GalNAc3-3a
Ad



1.5
75.96



5
30.53



15
12.52


666904
0.5
91.30
GalNAc3-3a
PO



1.5
57.88



5
21.22



15
16.49


675441
0.5
76.71
GalNAc3-17a
Ad



1.5
63.63



5
29.57



15
13.49


675442
0.5
95.03
GalNAc3-18a
Ad



1.5
60.06



5
31.04



15
19.40









Liver transaminase levels, alanine aminotransferase (ALT) and aspartate aminotransferase (AST), in serum were measured relative to saline injected mice using standard protocols. Total bilirubin and BUN were also evaluated. The change in body weights was evaluated with no significant change from the saline group (data not shown). ALTs, ASTs, total bilirubin and BUN values are shown in Table 49 below.














TABLE 49









Total






Dosage
ALT
AST
Bilirubin
BUN
GalNAc3


ISIS No.
(mg/kg)
(U/L)
(U/L)
(mg/dL)
(mg/dL)
Cluster
CM






















Saline
n/a
26
59
0.16
42
n/a
n/a


353382
3
23
58
0.18
39
n/a
n/a



10
28
58
0.16
43



30
20
48
0.12
34


661161
0.5
30
47
0.13
35
GalNac3-3a
Ad



1.5
23
53
0.14
37



5
26
48
0.15
39



15
32
57
0.15
42


666904
0.5
24
73
0.13
36
GalNac3-3a
PO



1.5
21
48
0.12
32



5
19
49
0.14
33



15
20
52
0.15
26


675441
0.5
42
148
0.21
36
GalNac3-17a
Ad



1.5
60
95
0.16
34



5
27
75
0.14
37



15
24
61
0.14
36


675442
0.5
26
65
0.15
37
GalNac3-18a
Ad



1.5
25
64
0.15
43



5
27
69
0.15
37



15
30
84
0.14
37









Example 75
Pharmacokinetic Analysis of Oligonucleotides Comprising a 5′-Conjugate Group
The PK of the ASOs in Tables 41, 44 and 47 above was evaluated using liver samples that were obtained following the treatment procedures described in Examples 65, 66, and 74. The liver samples were minced and extracted using standard protocols and analyzed by IP-HPLC-MS alongside an internal standard. The combined tissue level (μg/g) of all metabolites was measured by integrating the appropriate UV peaks, and the tissue level of the full-length ASO missing the conjugate (“parent,” which is Isis No. 353382 in this case) was measured using the appropriate extracted ion chromatograms (EIC).







TABLE 50







PK Analysis in Liver














Total
Parent






Tissue Level
ASO Tissue



Dosage
by UV
Level by
GalNAc3


ISIS No.
(mg/kg)
(μg/g)
EIC (μg/g)
Cluster
CM















353382
3
8.9
8.6
n/a
n/a



10
22.4
21.0



30
54.2
44.2


661161
5
32.4
20.7
GalNAc3-3a
Ad



15
63.2
44.1


671144
5
20.5
19.2
GalNAc3-12a
Ad



15
48.6
41.5


670061
5
31.6
28.0
GalNAc3-13a
Ad



15
67.6
55.5


671261
5
19.8
16.8
GalNAc3-14a
Ad



15
64.7
49.1


671262
5
18.5
7.4
GalNAc3-15a
Ad



15
52.3
24.2


670699
5
16.4
10.4
GalNAc3-3a
Td



15
31.5
22.5


670700
5
19.3
10.9
GalNAc3-3a
Ae



15
38.1
20.0


670701
5
21.8
8.8
GalNAc3-3a
Te



15
35.2
16.1


671165
5
27.1
26.5
GalNAc3-13a
Ad



15
48.3
44.3


666904
5
30.8
24.0
GalNAc3-3a
PO



15
52.6
37.6


675441
5
25.4
19.0
GalNAc3-17a
Ad



15
54.2
42.1


675442
5
22.2
20.7
GalNAc3-18a
Ad



15
39.6
29.0









The results in Table 50 above show that there were greater liver tissue levels of the oligonucleotides comprising a GalNAc3 conjugate group than of the parent oligonucleotide that does not comprise a GalNAc3 conjugate group (ISIS 353382) 72 hours following oligonucleotide administration, particularly when taking into consideration the differences in dosing between the oligonucleotides with and without a GalNAc3 conjugate group. Furthermore, by 72 hours, 40-98% of each oligonucleotide comprising a GalNAc3 conjugate group was metabolized to the parent compound, indicating that the GalNAc3 conjugate groups were cleaved from the oligonucleotides.
Example 76
Preparation of Oligomeric Compound 230 Comprising GalNAc3-23







Compound 222 is commercially available. 44.48 ml (0.33 mol) of compound 222 was treated with tosyl chloride (25.39 g, 0.13 mol) in pyridine (500 mL) for 16 hours. The reaction was then evaporated to an oil, dissolved in EtOAc and washed with water, sat. NaHCO3, brine, and dried over Na2SO4. The ethyl acetate was concentrated to dryness and purified by column chromatography, eluted with EtOAc/hexanes (1:1) followed by 10% methanol in CH2Cl2 to give compound 223 as a colorless oil. LCMS and NMR were consistent with the structure. 10 g (32.86 mmol) of 1-Tosyltriethylene glycol (compound 223) was treated with sodium azide (10.68 g, 164.28 mmol) in DMSO (100 mL) at room temperature for 17 hours. The reaction mixture was then poured onto water, and extracted with EtOAc. The organic layer was washed with water three times and dried over Na2SO4. The organic layer was concentrated to dryness to give 5.3 g of compound 224 (92%). LCMS and NMR were consistent with the structure. 1-Azidotriethylene glycol (compound 224, 5.53 g, 23.69 mmol) and compound 4 (6 g, 18.22 mmol) were treated with 4 A molecular sieves (5 g), and TMSOTf (1.65 ml, 9.11 mmol) in dichloromethane (100 mL) under an inert atmosphere. After 14 hours, the reaction was filtered to remove the sieves, and the organic layer was washed with sat. NaHCO3, water, brine, and dried over Na2SO4. The organic layer was concentrated to dryness and purified by column chromatography, eluted with a gradient of 2 to 4% methanol in dichloromethane to give compound 225. LCMS and NMR were consistent with the structure. Compound 225 (11.9 g, 23.59 mmol) was hydrogenated in EtOAc/Methanol (4:1, 250 mL) over Pearlman's catalyst. After 8 hours, the catalyst was removed by filtration and the solvents removed to dryness to give compound 226. LCMS and NMR were consistent with the structure.
In order to generate compound 227, a solution of nitromethanetrispropionic acid (4.17 g, 15.04 mmol) and Hunig's base (10.3 ml, 60.17 mmol) in DMF (100 mL) were treated dropwise with pentaflourotrifluoro acetate (9.05 ml, 52.65 mmol). After 30 minutes, the reaction was poured onto ice water and extracted with EtOAc. The organic layer was washed with water, brine, and dried over Na2SO4. The organic layer was concentrated to dryness and then recrystallized from heptane to give compound 227 as a white solid. LCMS and NMR were consistent with the structure. Compound 227 (1.5 g, 1.93 mmol) and compound 226 (3.7 g, 7.74 mmol) were stirred at room temperature in acetonitrile (15 mL) for 2 hours. The reaction was then evaporated to dryness and purified by column chromatography, eluting with a gradient of 2 to 10% methanol in dichloromethane to give compound 228. LCMS and NMR were consistent with the structure. Compound 228 (1.7 g, 1.02 mmol) was treated with Raney Nickel (about 2 g wet) in ethanol (100 mL) in an atmosphere of hydrogen. After 12 hours, the catalyst was removed by filtration and the organic layer was evaporated to a solid that was used directly in the next step. LCMS and NMR were consistent with the structure. This solid (0.87 g, 0.53 mmol) was treated with benzylglutaric acid (0.18 g, 0.8 mmol), HBTU (0.3 g, 0.8 mmol) and DIEA (273.7 μl, 1.6 mmol) in DMF (5 mL). After 16 hours, the DMF was removed under reduced pressure at 65° C. to an oil, and the oil was dissolved in dichloromethane. The organic layer was washed with sat. NaHCO3, brine, and dried over Na2SO4. After evaporation of the organic layer, the compound was purified by column chromatography and eluted with a gradient of 2 to 20% methanol in dichloromethane to give the coupled product. LCMS and NMR were consistent with the structure. The benzyl ester was deprotected with Pearlman's catalyst under a hydrogen atmosphere for 1 hour. The catalyst was them removed by filtration and the solvents removed to dryness to give the acid. LCMS and NMR were consistent with the structure. The acid (486 mg, 0.27 mmol) was dissolved in dry DMF (3 mL). Pyridine (53.61 μl, 0.66 mmol) was added and the reaction was purged with argon. Pentaflourotriflouro acetate (46.39 μl, 0.4 mmol) was slowly added to the reaction mixture. The color of the reaction changed from pale yellow to burgundy, and gave off a light smoke which was blown away with a stream of argon. The reaction was allowed to stir at room temperature for one hour (completion of reaction was confirmed by LCMS). The solvent was removed under reduced pressure (rotovap) at 70° C. The residue was diluted with DCM and washed with 1N NaHSO4, brine, saturated sodium bicarbonate and brine again. The organics were dried over Na2SO4, filtered, and were concentrated to dryness to give 225 mg of compound 229 as a brittle yellow foam. LCMS and NMR were consistent with the structure.
Oligomeric compound 230, comprising a GalNAc3-23 conjugate group, was prepared from compound 229 using the general procedure illustrated in Example 46. The GalNAc3 cluster portion of the GalNAc3-23 conjugate group (GalNAc3-23a) can be combined with any cleavable moiety to provide a variety of conjugate groups. The structure of GalNAc3-23 (GalNAc3-23a-CM) is shown below:




Example 77
Antisense Inhibition In Vivo by Oligonucleotides Targeting SRB-1 Comprising a GalNAc3 Conjugate
The oligonucleotides listed below were tested in a dose-dependent study for antisense inhibition of SRB-1 in mice.







TABLE 51







Modified ASOs targeting SRB-1















SEQ


ISIS
Sequences
GalNAc3

ID


No.
(5′ to 3′)
Cluster
CM
No.





661161
 
GalNAc3-3a 
Ad
30



GesmCesTesTesmCesAdsGds






TdsmCdsAdsTdsGdsAdsmCds






TdsTesmCesmCesTesTe





 


666904
 
GalNAc3-3a 
PO
28



GesmCesTesTesmCesAdsGds






TdsmCdsAdsTdsGdsAdsmCds






TdsTesmCesmCesTesTe





 


673502
 
GalNAc3-10a
Ad
30



GesmCeoTeoTeomCeoAdsGds






TdsmCdsAdsTdsGdsAdsmCds






TdsTeomCeomCesTesTe





 


677844
 
GalNAc3-9a
Ad
30



GesmCesTesTesmCesAdsGds






TdsmCdsAdsTdsGdsAdsmCds






TdsTesmCesmCesTesTe





 


677843
 
GalNAc3-23a
Ad
30



GesmCesTesTesmCesAdsGds






TdsmCdsAdsTdsGdsAdsmCds






TdsTesmCesmCesTesTe





 


655861
GesmCesTesTesmCesAdsGds
GalNAc3-1a 
Ad
29



TdsmCdsAdsTdsGdsAdsmCds






TdsTesmCesmCesTesTeo






 





 


677841
GesmCesTesTesmCesAdsGds
GalNAc3-19a
Ad
29



TdsmCdsAdsTdsGdsAdsmCds






TdsTesmCesmCesTesTeo






 





 


677842
GesmCesTesTesmCesAdsGds
GalNAc3-20a
Ad
29



TdsmCdsAdsTdsGdsAdsmCds






TdsTesmCesmCesTesTeo






 









The structure of GalNAc3-1a was shown previously in Example 9, GalNAc3-3a was shown in Example 39, GalNAc3-9a was shown in Example 52, GalNAc3-10a was shown in Example 46, GalNAc3-19a was shown in Example 70, GalNAc3-20a was shown in Example 71, and GalNAc3-23a was shown in Example 76.
Treatment
Six to eight week old C57BL/6 mice (Jackson Laboratory, Bar Harbor, Me.) were each injected subcutaneously once at a dosage shown below with an oligonucleotide listed in Table 51 or with saline. Each treatment group consisted of 4 animals. The mice were sacrificed 72 hours following the final administration to determine the SRB-1 mRNA levels using real-time PCR and RIBOGREEN® RNA quantification reagent (Molecular Probes, Inc. Eugene, Oreg.) according to standard protocols. The results below are presented as the average percent of SRB-1 mRNA levels for each treatment group, normalized to the saline control.
As illustrated in Table 52, treatment with antisense oligonucleotides lowered SRB-1 mRNA levels in a dose-dependent manner.







TABLE 52







SRB-1 mRNA (% Saline)













SRB-1 mRNA
GalNAc3



ISIS No.
Dosage (mg/kg)
(% Saline)
Cluster
CM














Saline
n/a
100.0
n/a
n/a


661161
0.5
89.18
GalNAc3-3a
Ad



1.5
77.02



5
29.10



15
12.64


666904
0.5
93.11
GalNAc3-3a
PO



1.5
55.85



5
21.29



15
13.43


673502
0.5
77.75
GalNAc3-10a
Ad



1.5
41.05



5
19.27



15
14.41


677844
0.5
87.65
GalNAc3-9a
Ad



1.5
93.04



5
40.77



15
16.95


677843
0.5
102.28
GalNAc3-23a
Ad



1.5
70.51



5
30.68



15
13.26


655861
0.5
79.72
GalNAc3-1a
Ad



1.5
55.48



5
26.99



15
17.58


677841
0.5
67.43
GalNAc3-19a
Ad



1.5
45.13



5
27.02



15
12.41


677842
0.5
64.13
GalNAc3-20a
Ad



1.5
53.56



5
20.47



15
10.23









Liver transaminase levels, alanine aminotransferase (ALT) and aspartate aminotransferase (AST), in serum were also measured using standard protocols. Total bilirubin and BUN were also evaluated. Changes in body weights were evaluated, with no significant change from the saline group (data not shown). ALTs, ASTs, total bilirubin and BUN values are shown in Table 53 below.














TABLE 53









Total






Dosage
ALT
AST
Bilirubin
BUN
GalNAc3


ISIS No.
(mg/kg)
(U/L)
(U/L)
(mg/dL)
(mg/dL)
Cluster
CM






















Saline
n/a
21
45
0.13
34
n/a
n/a


661161
0.5
28
51
0.14
39
GalNac3-3a
Ad



1.5
23
42
0.13
39



5
22
59
0.13
37



15
21
56
0.15
35


666904
0.5
24
56
0.14
37
GalNac3-3a
PO



1.5
26
68
0.15
35



5
23
77
0.14
34



15
24
60
0.13
35


673502
0.5
24
59
0.16
34
GalNac3-10a
Ad



1.5
20
46
0.17
32



5
24
45
0.12
31



15
24
47
0.13
34


677844
0.5
25
61
0.14
37
GalNac3-9a
Ad



1.5
23
64
0.17
33



5
25
58
0.13
35



15
22
65
0.14
34


677843
0.5
53
53
0.13
35
GalNac3-23a
Ad



1.5
25
54
0.13
34



5
21
60
0.15
34



15
22
43
0.12
38


655861
0.5
21
48
0.15
33
GalNac3-1a
Ad



1.5
28
54
0.12
35



5
22
60
0.13
36



15
21
55
0.17
30


677841
0.5
32
54
0.13
34
GalNac3-19a
Ad



1.5
24
56
0.14
34



5
23
92
0.18
31



15
24
58
0.15
31


677842
0.5
23
61
0.15
35
GalNac3-20a
Ad



1.5
24
57
0.14
34



5
41
62
0.15
35



15
24
37
0.14
32









Example 78
Antisense Inhibition In Vivo by Oligonucleotides Targeting Angiotensinogen Comprising a GalNAc3 Conjugate
The oligonucleotides listed below were tested in a dose-dependent study for antisense inhibition of Angiotensinogen (AGT) in normotensive Sprague Dawley rats.







TABLE 54







Modified ASOs targeting AGT















SEQ


ISIS
Sequences
GalNAc3

ID


No.
(5′ to 3′)
Cluster
CM
No.





552668
mCesAesmCesTesGesAdsTds
n/a
n/a
34



TdsTdsTdsTdsGdsmCdsmCds






mCdsAesGesGesAesTe





 


669509
mCesAesmCesTesGesAdsTds
GalNAc3-1a
Ad
35



TdsTdsTdsTdsGdsmCdsmCds






mCdsAesGesGesAesTeo






 









The structure of GalNAc3-1a was shown previously in Example 9.

Treatment

Six week old, male Sprague Dawley rats were each injected subcutaneously once per week at a dosage shown below, for a total of three doses, with an oligonucleotide listed in Table 54 or with PBS. Each treatment group consisted of 4 animals. The rats were sacrificed 72 hours following the final dose. AGT liver mRNA levels were measured using real-time PCR and RIBOGREEN® RNA quantification reagent (Molecular Probes, Inc. Eugene, Oreg.) according to standard protocols. AGT plasma protein levels were measured using the Total Angiotensinogen ELISA (Catalog #JP27412, IBL International, Toronto, ON) with plasma diluted 1:20,000. The results below are presented as the average percent of AGT mRNA levels in liver or AGT protein levels in plasma for each treatment group, normalized to the PBS control.
As illustrated in Table 55, treatment with antisense oligonucleotides lowered AGT liver mRNA and plasma protein levels in a dose-dependent manner, and the oligonucleotide comprising a GalNAc conjugate was significantly more potent than the parent oligonucleotide lacking a GalNAc conjugate.







TABLE 55







AGT liver mRNA and plasma protein levels














AGT liver
AGT plasma




ISIS
Dosage
mRNA
protein
GalNAc3


No.
(mg/kg)
(% PBS)
(% PBS)
Cluster
CM















PBS
n/a
100
100
n/a
n/a


552668
3
95
122
n/a
n/a



10
85
97



30
46
79



90
8
11


669509
0.3
95
70
GalNAc3-1a
Ad



1
95
129



3
62
97



10
9
23









Liver transaminase levels, alanine aminotransferase (ALT) and aspartate aminotransferase (AST), in plasma and body weights were also measured at time of sacrifice using standard protocols. The results are shown in Table 56 below.







TABLE 56







Liver transaminase levels and rat body weights

















Body





Dosage
ALT
AST
Weight (%
GalNAc3


ISIS No.
(mg/kg)
(U/L)
(U/L)
of baseline)
Cluster
CM





PBS
n/a
51
81
186
n/a
n/a


552668
3
54
93
183
n/a
n/a



10
51
93
194



30
59
99
182



90
56
78
170


669509
0.3
53
90
190
GalNAc3-1a
Ad



1
51
93
192



3
48
85
189



10
56
95
189









Example 79
Duration of Action In Vivo of Oligonucleotides Targeting APOC-III Comprising a GalNAc3 Conjugate
The oligonucleotides listed in Table 57 below were tested in a single dose study for duration of action in mice.







TABLE 57







Modified ASOs targeting APOC-III











ISIS
Sequences
GalNAc3

SEQ


No.
(5′ to 3′)
Cluster
CM
ID No.





304801
AesGesmCesTesTesmCdsTds
n/a
n/a
20



TdsGdsTdsmCdsmCdsAdsGds






mCdsTesTesTesAesTe





 


647535
AesGesmCesTesTesmCdsTds
GalNAc3-la
Ad
21



TdsGdsTdsmCdsmCdsAdsGds






mCdsTesTesTesAesTeo






 





 


663083
 
GalNAc3-3a
Ad
36



AesGesmCesTesTesmCdsTds






TdsGdsTdsmCdsmCdsAdsGds






mCdsTesTesTesAesTe





 


674449
 
GalNAc3-7a
Ad
36



AesGesmCesTesTesmCdsTds






TdsGdsTdsmCdsmCdsAdsGds






mCdsTesTesTesAesTe





 


674450
 
GalNAc3-10 a
Ad
36



AesGesmCesTesTesmCdsTds






TdsGdsTdsmCdsmCdsAdsGds






mCdsTesTesTesAesTe





 


674451
 
GalNAc3-13a
Ad
36



AesGesmCesTesTesmCdsTds






TdsGdsTdsmCdsmCdsAdsGds






mCdsTesTesTesAesTe









The structure of GalNAc3-1a was shown previously in Example 9, GalNAc3-3a was shown in Example 39, GalNAc3-7a was shown in Example 48, GalNAc3-10a was shown in Example 46, and GalNAc3-13a was shown in Example 62.

Treatment

Six to eight week old transgenic mice that express human APOC-III were each injected subcutaneously once with an oligonucleotide listed in Table 57 or with PBS. Each treatment group consisted of 3 animals. Blood was drawn before dosing to determine baseline and at 72 hours, 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, and 6 weeks following the dose. Plasma triglyceride and APOC-III protein levels were measured as described in Example 20. The results below are presented as the average percent of plasma triglyceride and APOC-III levels for each treatment group, normalized to baseline levels, showing that the oligonucleotides comprising a GalNAc conjugate group exhibited a longer duration of action than the parent oligonucleotide without a conjugate group (ISIS 304801) even though the dosage of the parent was three times the dosage of the oligonucleotides comprising a GalNAc conjugate group.







TABLE 58







Plasma triglyceride and APOC-III protein levels in transgenic mice















Time








point

APOC-III




(days

protein


ISIS
Dosage
post-
Triglycerides
(%
GalNAc3


No.
(mg/kg)
dose)
(% baseline)
baseline)
Cluster
CM
















PBS
n/a
3
97
102
n/a
n/a




7
101
98




14
108
98




21
107
107




28
94
91




35
88
90




42
91
105


304801
30
3
40
34
n/a
n/a




7
41
37




14
50
57




21
50
50




28
57
73




35
68
70




42
75
93


647535
10
3
36
37
GalNAc3-1a
Ad




7
39
47




14
40
45




21
41
41




28
42
62




35
69
69




42
85
102


663083
10
3
24
18
GalNAc3-3a
Ad




7
28
23




14
25
27




21
28
28




28
37
44




35
55
57




42
60
78


674449
10
3
29
26
GalNAc3-7a
Ad




7
32
31




14
38
41




21
44
44




28
53
63




35
69
77




42
78
99


674450
10
3
33
30
GalNAc3-
Ad




7
35
34
10a




14
31
34




21
44
44




28
56
61




35
68
70




42
83
95


674451
10
3
35
33
GalNAc3-
Ad




7
24
32
13a




14
40
34




21
48
48




28
54
67




35
65
75




42
74
97









Example 80
Antisense Inhibition In Vivo by Oligonucleotides Targeting Alpha-1 Antitrypsin (A1AT) Comprising a GalNAc3 Conjugate
The oligonucleotides listed in Table 59 below were tested in a study for dose-dependent inhibition of A1AT in mice.







TABLE 59







Modified ASOs targeting A1AT















SEQ


ISIS
Sequences
GalNAc3

ID


No.
(5′ to 3′)
Cluster
CM
No.





476366
AesmCesmCesmCesAesAdsTds
n/a
n/a
37



TdsmCdsAdsGdsAdsAdsGds






GdsAesAesGesGesAe





 


656326
AesmCesmCesmCesAesAdsTds
GalNAc3-1a
Ad
38



TdsmCdsAdsGdsAdsAdsGds






GdsAesAesGesGesAeo






 





 


678381
 Aes
GalNAc3-3a
Ad
39



mCesmCesmCesAesAdsTds






TdsmCdsAdsGdsAdsAds






GdsGdsAesAesGesGesAe





 


678382
 Aes
GalNAc3-7a
Ad
39



GesGesAemCesmCesmCes






AesAdsTdsTdsmCdsAdsGds






AdsAdsGdsGdsAesAes





 


678383
 
GalNAc3-10a
Ad
39



AesmCesmCesmCesAesAds






TdsTdsmCdsAdsGdsAdsAds






GdsGdsAesAesGesGesAe





 


678384
 
GalNAc3-13a
Ad
39



AesmCesmCesmCesAesAds






TdsTdsmCdsAdsGdsAdsAds






GdsGdsAesAes GesGesAe









The structure of GalNAc3-1a was shown previously in Example 9, GalNAc3-3a was shown in Example 39, GalNAc3-7a was shown in Example 48, GalNAc3-10a was shown in Example 46, and GalNAc3-13a was shown in Example 62.

Treatment

Six week old, male C57BL/6 mice (Jackson Laboratory, Bar Harbor, Me.) were each injected subcutaneously once per week at a dosage shown below, for a total of three doses, with an oligonucleotide listed in Table 59 or with PBS. Each treatment group consisted of 4 animals. The mice were sacrificed 72 hours following the final administration. A1AT liver mRNA levels were determined using real-time PCR and RIBOGREEN® RNA quantification reagent (Molecular Probes, Inc. Eugene, Oreg.) according to standard protocols. A1AT plasma protein levels were determined using the Mouse Alpha 1-Antitrypsin ELISA (catalog #41-A1AMS-E01, Alpco, Salem, N.H.). The results below are presented as the average percent of A1AT liver mRNA and plasma protein levels for each treatment group, normalized to the PBS control.
As illustrated in Table 60, treatment with antisense oligonucleotides lowered A1AT liver mRNA and A1AT plasma protein levels in a dose-dependent manner. The oligonucleotides comprising a GalNAc conjugate were significantly more potent than the parent (ISIS 476366).







TABLE 60







A1AT liver mRNA and plasma protein levels














A1AT liver
A1AT plasma




ISIS
Dosage
mRNA
protein
GalNAc3


No.
(mg/kg)
(% PBS)
(% PBS)
Cluster
CM















PBS
n/a
100
100
n/a
n/a


476366
5
86
78
n/a
n/a



15
73
61



45
30
38


656326
0.6
99
90
GalNAc3-1a
Ad



2
61
70



6
15
30



18
6
10


678381
0.6
105
90
GalNAc3-3a
Ad



2
53
60



6
16
20



18
7
13


678382
0.6
90
79
GalNAc3-7a
Ad



2
49
57



6
21
27



18
8
11


678383
0.6
94
84
GalNAc3-10a
Ad



2
44
53



6
13
24



18
6
10


678384
0.6
106
91
GalNAc3-13a
Ad



2
65
59



6
26
31



18
11
15









Liver transaminase and BUN levels in plasma were measured at time of sacrifice using standard protocols. Body weights and organ weights were also measured. The results are shown in Table 61 below. Body weight is shown as % relative to baseline. Organ weights are shown as % of body weight relative to the PBS control group.















TABLE 61










Body
Liver
Kidney
Spleen


ISIS
Dosage
ALT
AST
BUN
weight (%
weight (Rel
weight (Rel
weight (Rel


No.
(mg/kg)
(U/L)
(U/L)
(mg/dL)
baseline)
% BW)
% BW)
% BW)























PBS
n/a
25
51
37
119
100
100
100


476366
5
34
68
35
116
91
98
106



15
37
74
30
122
92
101
128



45
30
47
31
118
99
108
123


656326
0.6
29
57
40
123
100
103
119



2
36
75
39
114
98
111
106



6
32
67
39
125
99
97
122



18
46
77
36
116
102
109
101


678381
0.6
26
57
32
117
93
109
110



2
26
52
33
121
96
106
125



6
40
78
32
124
92
106
126



18
31
54
28
118
94
103
120


678382
0.6
26
42
35
114
100
103
103



2
25
50
31
117
91
104
117



6
30
79
29
117
89
102
107



18
65
112
31
120
89
104
113


678383
0.6
30
67
38
121
91
100
123



2
33
53
33
118
98
102
121



6
32
63
32
117
97
105
105



18
36
68
31
118
99
103
108


678384
0.6
36
63
31
118
98
103
98



2
32
61
32
119
93
102
114



6
34
69
34
122
100
100
96



18
28
54
30
117
98
101
104









Example 81
Duration of Action In Vivo of Oligonucleotides Targeting A1AT Comprising a GalNAc3 Cluster
The oligonucleotides listed in Table 59 were tested in a single dose study for duration of action in mice.
Treatment
Six week old, male C57BL/6 mice were each injected subcutaneously once with an oligonucleotide listed in Table 59 or with PBS. Each treatment group consisted of 4 animals. Blood was drawn the day before dosing to determine baseline and at 5, 12, 19, and 25 days following the dose. Plasma A1AT protein levels were measured via ELISA (see Example 80). The results below are presented as the average percent of plasma A1AT protein levels for each treatment group, normalized to baseline levels. The results show that the oligonucleotides comprising a GalNAc conjugate were more potent and had longer duration of action than the parent lacking a GalNAc conjugate (ISIS 476366). Furthermore, the oligonucleotides comprising a 5′-GalNAc conjugate (ISIS 678381, 678382, 678383, and 678384) were generally even more potent with even longer duration of action than the oligonucleotide comprising a 3′-GalNAc conjugate (ISIS 656326).







TABLE 62







Plasma A1AT protein levels in mice














Time point





ISIS
Dosage
(days post-
A1AT (%
GalNAc3


No.
(mg/kg)
dose)
baseline)
Cluster
CM















PBS
n/a
5
93
n/a
n/a




12
93




19
90




25
97


476366
100
5
38
n/a
n/a




12
46




19
62




25
77


656326
18
5
33
GalNAc3-1a
Ad




12
36




19
51




25
72


678381
18
5
21
GalNAc3-3a
Ad




12
21




19
35




25
48


678382
18
5
21
GalNAc3-7a
Ad




12
21




19
39




25
60


678383
18
5
24
GalNAc3-10a
Ad




12
21




19
45




25
73


678384
18
5
29
GalNAc3-13a
Ad




12
34




19
57




25
76









Example 82
Antisense Inhibition In Vitro by Oligonucleotides Targeting SRB-1 Comprising a GalNAc3 Conjugate
Primary mouse liver hepatocytes were seeded in 96 well plates at 15,000 cells/well 2 hours prior to treatment. The oligonucleotides listed in Table 63 were added at 2, 10, 50, or 250 nM in Williams E medium and cells were incubated overnight at 37° C. in 5% CO2. Cells were lysed 16 hours following oligonucleotide addition, and total RNA was purified using RNease 3000 BioRobot (Qiagen). SRB-1 mRNA levels were determined using real-time PCR and RIBOGREEN® RNA quantification reagent (Molecular Probes, Inc. Eugene, Oreg.) according to standard protocols. IC50 values were determined using Prism 4 software (GraphPad). The results show that oligonucleotides comprising a variety of different GalNAc conjugate groups and a variety of different cleavable moieties are significantly more potent in an in vitro free uptake experiment than the parent oligonucleotides lacking a GalNAc conjugate group (ISIS 353382 and 666841).







TABLE 63







Inhibition of SRB-1 expression in vitro













ISIS
Sequence
Link-
GalNAc

IC50
SEQ


No.
(5′ to 3′)
ages
cluster
CM
(nM)
ID No.
















353382
GesmCesTesTesmCesAdsGds
PS
n/a
n/a
250
28



TdsmCdsAdsTdsGdsAdsmCds








TdsTesmCesmCesTesTe







 


655861
GesmCesTesTesmCesAdsGds
PS
GalNAc3-1a 
Ad
40
29



TdsmCdsAdsTdsGdsAdsmCds








TdsTesmCesmCesTes








Te 







 


661161
 Ges
PS
GalNAc3-3a 
Ad
40
30



mCesTesTesmCesAdsGdsTds








mCdsAdsTdsGdsAdsmCdsTds








TesmCesmCesTesTe







 


661162
 Ges
PO/PS
GalNAc3-3a 
Ad
8
30



mCeoTeoTeomCeoAdsGdsTds








mCdsAdsTdsGdsAdsmCdsTds








TeomCeomCesTesTe







 


664078
GesmCesTesTesmCesAdsGds
PS
GalNAc3-9a 
Ad
20
29



TdsmCdsAdsTdsGdsAdsmCds








TdsTesmCesmCesTes








Te 







 


665001
 Ges
PS
GalNAc3-8a 
Ad
70
30



mCesTesTesmCesAdsGdsTds








mCdsAdsTdsGdsAdsmCdsTds








TesmCesmCesTesTe







 


666224
 Ges
PS
GalNAc3-5a 
Ad
80
30



mCesTesTesmCesAdsGdsTds








mCdsAdsTdsGdsAdsmCdsTds








TesmCesmCesTesTe







 


666841
GesmCeoTeoTeomCeoAdsGds
PO/PS
n/a
n/a
>250
28



TdsmCdsAdsTdsGdsAdsmCds








TdsTeomCeomCesTesTe







 


666881
 
PS
GalNAc3-10a
Ad
30
30



GesmCesTesTesmCesAdsGds








TdsmCdsAdsTdsGdsAdsmCds








TdsTesmCesmCesTesTe







 


666904
 GesmCes
PS
GalNAc3-3a 
PO
9
28



TesTesmCesAdsGdsTdsmCds








AdsTdsGdsAdsmCdsTdsTes








mCesmCesTesTe







 


666924
 Ges
PS
GalNAc3-3a 
Td
15
33



mCesTesTesmCesAdsGdsTds








mCdsAdsTdsGdsAdsmCdsTds








TesmCesmCesTesTe







 


666961
 Ges
PS
GalNAc3-6a 
Ad
150
30



mCesTesTesmCesAdsGdsTds








mCdsAdsTdsGdsAdsmCdsTds








TesmCesmCesTesTe







 


666981
 Ges
PS
GalNAc3-7a 
Ad
20
30



mCesTesTesmCesAdsGdsTds








mCdsAdsTdsGdsAdsmCdsTds








TesmCesmCesTesTe







 


670061
 
PS
GalNAc3-13a
Ad
30
30



GesmCesTesTesmCesAdsGds








TdsmCdsAdsTdsGdsAdsmCds








TdsTesmCesmCesTesTe







 


670699
 Ges
PO/PS
GalNAc3-3a 
Td
15
33



mCeoTeoTeomCeoAdsGdsTds








mCdsAdsTdsGdsAdsmCdsTds








TeomCeomCesTesTe







 


670700
 Ges
PO/PS
GalNAc3-3a 
Ae
30
30



mCeoTeoTeomCeoAdsGdsTds








mCdsAdsTdsGdsAdsmCdsTds








TeomCeomCesTesTe







 


670701
 Ges
PO/PS
GalNAc3-3a 
Te
25
33



mCeoTeoTeomCeoAdsGdsTds








mCdsAdsTdsGdsAdsmCdsTds








TeomCeomCesTesTe







 


671144
 
PS
GalNAc3-12a
Ad
40
30



GesmCesTesTesmCesAdsGds








TdsmCdsAdsTdsGdsAdsmCds








TdsTesmCesmCesTesTe







 


671165
 
PO/PS
GalNAc3-13a
Ad
8
30



GesmCeoTeoTeomCeoAdsGds








TdsmCdsAdsTdsGdsAdsmCds








TdsTeomCeomCesTesTe







 


671261
 
PS
GalNAc3-14a
Ad
>250
30



GesmCesTesTesmCesAdsGds








TdsmCdsAdsTdsGdsAdsmCds








TdsTesmCesmCesTesTe







 


671262
 
PS
GalNAc3-15a
Ad
>250
30



GesmCesTesTesmCesAdsGds








TdsmCdsAdsTdsGdsAdsmCds








TdsTesmCesmCesTesTe







 


673501
 Ges
PO/PS
GalNAc3-7a 
Ad
30
30



mCeoTeoTeomCeoAdsGdsTds








mCdsAdsTdsGdsAdsmCdsTds








TeomCeomCesTesTe







 


673502
 
PO/PS
GalNAc3-10a
Ad
8
30



GesmCeoTeoTeomCeoAdsGds








TdsmCdsAdsTdsGdsAdsmCds








TdsTeomCeomCesTesTe







 


675441
 
PS
GalNac3-17a
Ad
30
30



GesmCesTesTesmCesAdsGds








TdsmCdsAdsTdsGdsAdsmCds








TdsTesmCesmCesTesTe







 


675442
 
PS
GalNAc3-18a
Ad
20
30



GesmCesTesTesmCesAdsGds








TdsmCdsAdsTdsGdsAdsmCds








TdsTesmCesmCesTesTe







 


677841
GesmCesTesTesmCesAdsGds
PS
GalNAc3-19a
Ad
40
29



TdsmCdsAdsTdsGdsAdsmCds








TdsTesmCesmCesTes








Te 







 


677842
GesmCesTesTesmCesAdsGds
PS
GalNAc3-20a
Ad
30
29



TdsmCdsAdsTdsGdsAdsmCds








TdsTesmCesmCesTes








Te 







 


677843
 
PS
GalNAc3-23a
Ad
40
30



GesmCesTesTesmCesAdsGds








TdsmCdsAdsTdsGdsAdsmCds








TdsTesmCesmCesTesTe









The structure of GalNAc3-1a was shown previously in Example 9, GalNAc3-3a was shown in Example 39, GalNAc3-5a was shown in Example 49, GalNAc3-6a was shown in Example 51, GalNAc3-17a was shown in Example 48, GalNAc3-8a was shown in Example 47, GalNAc3-9a was shown in Example 52, GalNAc3-10a was shown in Example 46, GalNAc3-12a was shown in Example 61, GalNAc3-13a was shown in Example 62, GalNAc3-14a was shown in Example 63, GalNAc3-15a was shown in Example 64, GalNAc3-17a was shown in Example 68, GalNAc3-18a was shown in Example 69, GalNAc3-19a was shown in Example 70, GalNAc3-20a was shown in Example 71, and GalNAc3-23a was shown in Example 76.

Example 83
Antisense Inhibition In Vivo by Oligonucleotides Targeting Factor XI Comprising a GalNAc3 Cluster
The oligonucleotides listed in Table 64 below were tested in a study for dose-dependent inhibition of Factor XI in mice.







TABLE 64







Modified oligonucleotides


targeting Factor XI











ISIS
Sequence
GalNAc

SEQ


No.
(5′ to 3′)
cluster
CM
ID No.





404071
TesGesGesTesAesAdsTds
n/a
n/a
31



mCdsmCdsAdsmCdsTdsTds






TdsmCdsAesGesAesGesGe





 


656173
TesGeoGeoTeoAeoAdsTds
GalNAc3-1a
Ad
32



mCdsmCdsAdsmCdsTdsTds






TdsmCdsAeoGeoAesGes






Ge 





 


663086
 Tes
GalNAc3-3a
Ad
40



GeoGeoTeoAeoAdsTdsmCds






mCdsAdsmCdsTdsTdsTds






mCdsAeoGeoAesGesGe





 


678347
 Tes
GalNAc3-7a
Ad
40



GeoGeoTeoAeoAdsTdsmCds






mCdsAdsmCdsTdsTdsTds






mCdsAeoGeoAesGesGe





 


678348
 
GalNAc3-10a
Ad
40



TesGeoGeoTeoAeoAdsTds






mCdsmCdsAdsmCdsTdsTds






TdsmCdsAeoGeoAesGesGe





 


678349
 
GalNAc3-13a
Ad
40



TesGeoGeoTeoAeoAdsTds






mCdsmCdsAdsmCdsTdsTds






TdsmCdsAeoGeoAesGesGe









The structure of GalNAc3-1a was shown previously in Example 9, GalNAc3-3a was shown in Example 39, GalNAc3-7a was shown in Example 48, GalNAc3-10a was shown in Example 46, and GalNAc3-13a was shown in Example 62.

Treatment

Six to eight week old mice were each injected subcutaneously once per week at a dosage shown below, for a total of three doses, with an oligonucleotide listed below or with PBS. Each treatment group consisted of 4 animals. The mice were sacrificed 72 hours following the final dose. Factor XI liver mRNA levels were measured using real-time PCR and normalized to cyclophilin according to standard protocols. Liver transaminases, BUN, and bilirubin were also measured. The results below are presented as the average percent for each treatment group, normalized to the PBS control.
As illustrated in Table 65, treatment with antisense oligonucleotides lowered Factor XI liver mRNA in a dose-dependent manner. The results show that the oligonucleotides comprising a GalNAc conjugate were more potent than the parent lacking a GalNAc conjugate (ISIS 404071). Furthermore, the oligonucleotides comprising a 5′-GalNAc conjugate (ISIS 663086, 678347, 678348, and 678349) were even more potent than the oligonucleotide comprising a 3′-GalNAc conjugate (ISIS 656173).







TABLE 65







Factor XI liver mRNA, liver transaminase, BUN, and bilirubin levels















ISIS
Dosage
Factor XI
ALT
AST
BUN
Bilirubin
GalNAc3
SEQ


No.
(mg/kg)
mRNA (% PBS)
(U/L)
(U/L)
(mg/dL)
(mg/dL)
Cluster
ID No.


















PBS
n/a
100
63
70
21
0.18
n/a
n/a


404071
3
65
41
58
21
0.15
n/a
31



10
33
49
53
23
0.15



30
17
43
57
22
0.14


656173
0.7
43
90
89
21
0.16
GalNAc3-1a
32



2
9
36
58
26
0.17



6
3
50
63
25
0.15


663086
0.7
33
91
169
25
0.16
GalNAc3-3a
40



2
7
38
55
21
0.16



6
1
34
40
23
0.14


678347
0.7
35
28
49
20
0.14
GalNAc3-7a
40



2
10
180
149
21
0.18



6
1
44
76
19
0.15


678348
0.7
39
43
54
21
0.16
GalNAc3-10a
40



2
5
38
55
22
0.17



6
2
25
38
20
0.14


678349
0.7
34
39
46
20
0.16
GalNAc3-13a
40



2
8
43
63
21
0.14



6
2
28
41
20
0.14









Example 84
Duration of Action In Vivo of Oligonucleotides Targeting Factor XI Comprising a GalNAc3 Conjugate
The oligonucleotides listed in Table 64 were tested in a single dose study for duration of action in mice.
Treatment
Six to eight week old mice were each injected subcutaneously once with an oligonucleotide listed in Table 64 or with PBS. Each treatment group consisted of 4 animals. Blood was drawn by tail bleeds the day before dosing to determine baseline and at 3, 10, and 17 days following the dose. Plasma Factor XI protein levels were measured by ELISA using Factor XI capture and biotinylated detection antibodies from R & D Systems, Minneapolis, Minn. (catalog #AF2460 and #BAF2460, respectively) and the OptEIA Reagent Set B (Catalog #550534, BD Biosciences, San Jose, Calif.). The results below are presented as the average percent of plasma Factor XI protein levels for each treatment group, normalized to baseline levels. The results show that the oligonucleotides comprising a GalNAc conjugate were more potent with longer duration of action than the parent lacking a GalNAc conjugate (ISIS 404071). Furthermore, the oligonucleotides comprising a 5′-GalNAc conjugate (ISIS 663086, 678347, 678348, and 678349) were even more potent with an even longer duration of action than the oligonucleotide comprising a 3′-GalNAc conjugate (ISIS 656173).







TABLE 66







Plasma Factor XI protein levels in mice















Time








point
Factor


SEQ


ISIS
Dosage
(days
XI (%
GalNAc3

ID


No.
(mg/kg)
post-dose)
baseline)
Cluster
CM
No.
















PBS
n/a
3
123
n/a
n/a
n/a




10
56




17
100


404071
30
3
11
n/a
n/a
31




10
47




17
52


656173
6
3
1
GalNAc3-1a
Ad
32




10
3




17
21


663086
6
3
1
GalNAc3-3a
Ad
40




10
2




17
9


678347
6
3
1
GalNAc3-7a
Ad
40




10
1




17
8


678348
6
3
1
GalNAc3-10a
Ad
40




10
1




17
6


678349
6
3
1
GalNAc3-13a
Ad
40




10
1




17
5









Example 85
Antisense Inhibition In Vivo by Oligonucleotides Targeting SRB-1 Comprising a GalNAc3 Conjugate
Oligonucleotides listed in Table 63 were tested in a dose-dependent study for antisense inhibition of SRB-1 in mice.
Treatment
Six to eight week old C57BL/6 mice were each injected subcutaneously once per week at a dosage shown below, for a total of three doses, with an oligonucleotide listed in Table 63 or with saline. Each treatment group consisted of 4 animals. The mice were sacrificed 48 hours following the final administration to determine the SRB-1 mRNA levels using real-time PCR and RIBOGREEN® RNA quantification reagent (Molecular Probes, Inc. Eugene, Oreg.) according to standard protocols. The results below are presented as the average percent of liver SRB-1 mRNA levels for each treatment group, normalized to the saline control.
As illustrated in Tables 67 and 68, treatment with antisense oligonucleotides lowered SRB-1 mRNA levels in a dose-dependent manner







TABLE 67







SRB-1 mRNA in liver











ISIS 

SRB-1 mRNA (%




No.
Dosage (mg/kg)
Saline)
GalNAc3 Cluster
CM














Saline
n/a
100
n/a
n/a


655861
0.1
94
GalNAc3-1a
Ad



0.3
119



1
68



3
32


661161
0.1
120
GalNAc3-3a
Ad



0.3
107



1
68



3
26


666881
0.1
107
GalNAc3-10a
Ad



0.3
107



1
69



3
27


666981
0.1
120
GalNAc3-7a
Ad



0.3
103



1
54



3
21


670061
0.1
118
GalNAc3-13a
Ad



0.3
89



1
52



3
18


677842
0.1
119
GalNAc3-20a
Ad



0.3
96



1
65



3
23
















TABLE 68







SRB-1 mRNA in liver











ISIS

SRB-1 mRNA (%




No.
Dosage (mg/kg)
Saline)
GalNAc3 Cluster
CM














661161
0.1
107
GalNAc3-3a
Ad



0.3
95



1
53



3
18


677841
0.1
110
GalNAc3-19a
Ad



0.3
88



1
52



3
25









Liver transaminase levels, total bilirubin, BUN, and body weights were also measured using standard protocols. Average values for each treatment group are shown in Table 69 below.















TABLE 69





ISIS
Dosage
ALT
AST
Bilirubin
BUN
Body Weight
GalNAc3



No.
(mg/kg)
(U/L)
(U/L)
(mg/dL)
(mg/dL)
(% baseline)
Cluster
CM







Saline
n/a
19
39
0.17
26
118
n/a
n/a


655861
0.1
25
47
0.17
27
114
GalNAc3-1a
Ad



0.3
29
56
0.15
27
118



1
20
32
0.14
24
112



3
27
54
0.14
24
115


661161
0.1
35
83
0.13
24
113
GalNAc3-3a
Ad



0.3
42
61
0.15
23
117



1
34
60
0.18
22
116



3
29
52
0.13
25
117


666881
0.1
30
51
0.15
23
118
GalNAc3-10a
Ad



0.3
49
82
0.16
25
119



1
23
45
0.14
24
117



3
20
38
0.15
21
112


666981
0.1
21
41
0.14
22
113
GalNAc3-7a
Ad



0.3
29
49
0.16
24
112



1
19
34
0.15
22
111



3
77
78
0.18
25
115


670061
0.1
20
63
0.18
24
111
GalNAc3-13a
Ad



0.3
20
57
0.15
21
115



1
20
35
0.14
20
115



3
27
42
0.12
20
116


677842
0.1
20
38
0.17
24
114
GalNAc3-20a
Ad



0.3
31
46
0.17
21
117



1
22
34
0.15
21
119



3
41
57
0.14
23
118









Example 86
Antisense Inhibition In Vivo by Oligonucleotides Targeting TTR Comprising a GalNAc3 Cluster
Oligonucleotides listed in Table 70 below were tested in a dose-dependent study for antisense inhibition of human transthyretin (TTR) in transgenic mice that express the human TTR gene.
Treatment
Eight week old TTR transgenic mice were each injected subcutaneously once per week for three weeks, for a total of three doses, with an oligonucleotide and dosage listed in the tables below or with PBS. Each treatment group consisted of 4 animals. The mice were sacrificed 72 hours following the final administration. Tail bleeds were performed at various time points throughout the experiment, and plasma TTR protein, ALT, and AST levels were measured and reported in Tables 72-74. After the animals were sacrificed, plasma ALT, AST, and human TTR levels were measured, as were body weights, organ weights, and liver human TTR mRNA levels. TTR protein levels were measured using a clinical analyzer (AU480, Beckman Coulter, Calif.). Real-time PCR and RIBOGREEN® RNA quantification reagent (Molecular Probes, Inc. Eugene, Oreg.) were used according to standard protocols to determine liver human TTR mRNA levels. The results presented in Tables 71-74 are the average values for each treatment group. The mRNA levels are the average values relative to the average for the PBS group. Plasma protein levels are the average values relative to the average value for the PBS group at baseline. Body weights are the average percent weight change from baseline until sacrifice for each individual treatment group. Organ weights shown are normalized to the animal's body weight, and the average normalized organ weight for each treatment group is then presented relative to the average normalized organ weight for the PBS group.
In Tables 71-74, “BL” indicates baseline, measurements that were taken just prior to the first dose. As illustrated in Tables 71 and 72, treatment with antisense oligonucleotides lowered TTR expression levels in a dose-dependent manner. The oligonucleotides comprising a GalNAc conjugate were more potent than the parent lacking a GalNAc conjugate (ISIS 420915). Furthermore, the oligonucleotides comprising a GalNAc conjugate and mixed PS/PO internucleoside linkages were even more potent than the oligonucleotide comprising a GalNAc conjugate and full PS linkages.







TABLE 70







Oligonucleotides targeting human TTR












Isis

Link-
GalNAc

SEQ


No.
Sequence 5′ to 3′
ages
cluster
CM
ID No.





420915
TesmCesTesTesGesGdsTdsTdsAdsmCds
PS 
n/a
n/a
41



AdsTdsGdsAdsAdsAesTesmCesmCesmCe






 


660261
TesmCesTesTesGesGdsTdsTdsAdsmCds
PS 
GalNAc3-1a 
Ad
42



AdsTdsGdsAdsAdsAesTesmCesmCes







mCe 






 


682883
 TesmCeoTeoTeoGeo
PS/
GalNAc3-3a 
PO
74



GdsTdsTdsAdsmCdsAdsTdsGdsAdsAds
PO 






AeoTeomCesmCesmCe






 


682884
 TesmCeoTeoTeoGeo
PS/
GalNAc3-7a 
PO
41



GdsTdsTdsAdsmCdsAdsTdsGdsAdsAds
PO 






AeoTeomCesmCesmCe






 


682885
 TesmCeoTeoTeo
PS/
GalNAc3-10a
PO
41



GeoGdsTdsTdsAdsmCdsAdsTdsGdsAds
PO 






AdsAeoTeomCesmCesmCe






 


682886
 TesmCeoTeoTeo
PS/
GalNAc3-13a
PO
41



GeoGdsTdsTdsAdsmCdsAdsTdsGdsAds
PO 






AdsAeoTeomCesmCesmCe






 


684057
TesmCeoTeoTeoGeoGdsTdsTdsAds







mCdsAdsTdsGdsAdsAdsAeoTeomCes
PS/
GalNAc3-19a
Ad
42



mCesmCe 
PO 









The legend for Table 72 can be found in Example 74. The structure of GalNAc3-1 was shown in Example 9. The structure of GalNAc3-3a was shown in Example 39. The structure of GalNAc3-7a was shown in Example 48. The structure of GalNAc3-10a was shown in Example 46. The structure of GalNAc3-13a was shown in Example 62. The structure of GalNAc3-19a was shown in Example 70.








TABLE 71







Antisense inhibition of human TTR in vivo















TTR
Plasma


SEQ



Dosage
mRNA
TTR protein
GalNAc

ID


Isis No.
(mg/kg)
(% PBS)
(% PBS)
cluster
CM
No.
















PBS
n/a
100
100
n/a
n/a



420915
6
99
95
n/a
n/a
41



20
48
65



60
18
28


660261
0.6
113
87
GalNAc3-1a
Ad
42



2
40
56



6
20
27



20
9
11
















TABLE 72







Antisense inhibition of human TTR in vivo












TTR
Plasma TTR protein (% PBS at BL)

SEQ

















Dosage
mRNA



Day 17
GalNAc

ID


Isis No.
(mg/kg)
(% PBS)
BL
Day 3
Day 10
(After sac)
cluster
CM
No.



















PBS
n/a
100
100
96
90
114
n/a
n/a



420915
6
74
106
86
76
83
n/a
n/a
41



20
43
102
66
61
58



60
24
92
43
29
32


682883
0.6
60
88
73
63
68
GalNAc3-
PO
41



2
18
75
38
23
23
3a



6
10
80
35
11
9


682884
0.6
56
88
78
63
67
GalNAc3-
PO
41



2
19
76
44
25
23
7a



6
15
82
35
21
24


682885
0.6
60
92
77
68
76
GalNAc3-
PO
41



2
22
93
58
32
32
10a



6
17
85
37
25
20


682886
0.6
57
91
70
64
69
GalNAc3-
PO
41



2
21
89
50
31
30
13a



6
18
102
41
24
27


684057
0.6
53
80
69
56
62
GalNAc3-
Ad
42



2
21
92
55
34
30
19a



6
11
82
50
18
13
















TABLE 73







Transaminase levels, body weight changes, and relative organ weights















ALT (U/L)
AST (U/L)
Body
Liver
Spleen
Kidney
SEQ






















Dosage


Day
Day


Day
Day
(%
(%
(%
(%
ID


Isis No.
(mg/kg)
BL
Day 3
10
17
BL
Day 3
10
17
BL)
PBS)
PBS)
PBS)
No.
























PBS
n/a
33
34
33
24
58
62
67
52
105
100
100
100
n/a


420915
6
34
33
27
21
64
59
73
47
115
99
89
91
41



20
34
30
28
19
64
54
56
42
111
97
83
89



60
34
35
31
24
61
58
71
58
113
102
98
95


660261
0.6
33
38
28
26
70
71
63
59
111
96
99
92
42



2
29
32
31
34
61
60
68
61
118
100
92
90



6
29
29
28
34
58
59
70
90
114
99
97
95



20
33
32
28
33
64
54
68
95
114
101
106
92
















TABLE 74







Transaminase levels, body weight changes, and relative organ weights















ALT (U/L)
AST (U/L)
Body
Liver
Spleen
Kidney
SEQ






















Dosage


Day
Day


Day
Day
(%
(%
(%
(%
ID


Isis No.
(mg/kg)
BL
Day 3
10
17
BL
Day 3
10
17
BL)
PBS)
PBS)
PBS)
No.
























PBS
n/a
32
34
37
41
62
78
76
77
104
100
100
100
n/a


420915
6
32
30
34
34
61
71
72
66
102
103
102
105
41



20
41
34
37
33
80
76
63
54
106
107
135
101



60
36
30
32
34
58
81
57
60
106
105
104
99


682883
0.6
32
35
38
40
53
81
74
76
104
101
112
95
41



2
38
39
42
43
71
84
70
77
107
98
116
99



6
35
35
41
38
62
79
103
65
105
103
143
97


682884
0.6
33
32
35
34
70
74
75
67
101
100
130
99
41



2
31
32
38
38
63
77
66
55
104
103
122
100



6
38
32
36
34
65
85
80
62
99
105
129
95


682885
0.6
39
26
37
35
63
63
77
59
100
109
109
112
41



2
30
26
38
40
54
56
71
72
102
98
111
102



6
27
27
34
35
46
52
56
64
102
98
113
96


682886
0.6
30
40
34
36
58
87
54
61
104
99
120
101
41



2
27
26
34
36
51
55
55
69
103
91
105
92



6
40
28
34
37
107
54
61
69
109
100
102
99


684057
0.6
35
26
33
39
56
51
51
69
104
99
110
102
42



2
33
32
31
40
54
57
56
87
103
100
112
97



6
39
33
35
40
67
52
55
92
98
104
121
108









Example 87
Duration of Action In Vivo by Single Closes of Oligonucleotides Targeting TTR Comprising a GalNAc3 Cluster
ISIS numbers 420915 and 660261 (see Table 70) were tested in a single dose study for duration of action in mice. ISIS numbers 420915, 682883, and 682885 (see Table 70) were also tested in a single dose study for duration of action in mice.
Treatment
Eight week old, male transgenic mice that express human TTR were each injected subcutaneously once with 100 mg/kg ISIS No. 420915 or 13.5 mg/kg ISIS No. 660261. Each treatment group consisted of 4 animals. Tail bleeds were performed before dosing to determine baseline and at days 3, 7, 10, 17, 24, and 39 following the dose. Plasma TTR protein levels were measured as described in Example 86. The results below are presented as the average percent of plasma TTR levels for each treatment group, normalized to baseline levels.







TABLE 75







Plasma TTR protein levels















Time point



SEQ


ISIS
Dosage
(days
TTR (%
GalNAc3

ID


No.
(mg/kg)
post-dose)
baseline)
Cluster
CM
No.
















420915
100
3
30
n/a
n/a
41




7
23




10
35




17
53




24
75




39
100


660261
13.5
3
27
GalNAc3-1a
Ad
42




7
21




10
22




17
36




24
48




39
69









Treatment

Female transgenic mice that express human TTR were each injected subcutaneously once with 100 mg/kg ISIS No. 420915, 10.0 mg/kg ISIS No. 682883, or 10.0 mg/kg 682885. Each treatment group consisted of 4 animals. Tail bleeds were performed before dosing to determine baseline and at days 3, 7, 10, 17, 24, and 39 following the dose. Plasma TTR protein levels were measured as described in Example 86. The results below are presented as the average percent of plasma TTR levels for each treatment group, normalized to baseline levels.







TABLE 76







Plasma TTR protein levels















Time








point



SEQ


ISIS
Dosage
(days
TTR (%
GalNAc3

ID


No.
(mg/kg)
post-dose)
baseline)
Cluster
CM
No.
















420915
100
3
48
n/a
n/a
41




7
48




10
48




17
66




31
80


682883
10.0
3
45
GalNAc3-3a
PO
41




7
37




10
38




17
42




31
65


682885
10.0
3
40
GalNAc3-10a
PO
41




7
33




10
34




17
40




31
64









The results in Tables 75 and 76 show that the oligonucleotides comprising a GalNAc conjugate are more potent with a longer duration of action than the parent oligonucleotide lacking a conjugate (ISIS 420915).

Example 88
Splicing Modulation In Vivo by Oligonucleotides Targeting SMN Comprising a GalNAc3 Conjugate
The oligonucleotides listed in Table 77 were tested for splicing modulation of human survival of motor neuron (SMN) in mice.







TABLE 77







Modified ASOs targeting SMN











ISIS.

GalNAc3

SEQ


No.
Sequences (5′-3′)
Cluster
CM
ID No.





387954
AesTesTesmCesAesmCesTesTesTesmCesAesTesAesAes
n/a
n/a
43



TesGesmCesTesGesGe





 


699819
  AesTesTesmCesAesmCesTesTesTesm
GalNAc3-7a
PO
43



CesAesTesAesAesTesGesmCesTesGesGe





 


699821
  AesTeoTeomGeoAeomCeoTeoTeoTeom
GalNAc3-7a
PO
43



CeoAeoTeoAeoAeoTeoGeomCeoTesGesGe





 


700000
AesTesTesmCesAesmCesTesTesTesmCesAesTesAesAes
GalNAc3-1a
Ad
44



TesGesmCesTesGesGeo 





 


703421
X-ATTmCAmCTTTmCATAATGmCTGG
n/a
n/a
43


 


703422
 ATTmCAmCTTTmCATAATGmCTCG
GalNAc3-7b
n/a
43









The structure of GalNAc3-7a was shown previously in Example 48. “X” indicates a 5′ primary amine generated by Gene Tools (Philomath, Oreg.), and GalNAc3-7b indicates the structure of GalNAc3-7a lacking the —NH—C6—O portion of the linker as shown below:





ISIS numbers 703421 and 703422 are morpholino oligonucleotides, wherein each nucleotide of the two oligonucleotides is a morpholino nucleotide.

Treatment

Six week old transgenic mice that express human SMN were injected subcutaneously once with an oligonucleotide listed in Table 78 or with saline. Each treatment group consisted of 2 males and 2 females. The mice were sacrificed 3 days following the dose to determine the liver human SMN mRNA levels both with and without exon 7 using real-time PCR according to standard protocols. Total RNA was measured using Ribogreen reagent. The SMN mRNA levels were normalized to total mRNA, and further normalized to the averages for the saline treatment group. The resulting average ratios of SMN mRNA including exon 7 to SMN mRNA missing exon 7 are shown in Table 78. The results show that fully modified oligonucleotides that modulate splicing and comprise a GalNAc conjugate are significantly more potent in altering splicing in the liver than the parent oligonucleotides lacking a GlaNAc conjugate. Furthermore, this trend is maintained for multiple modification chemistries, including 2′-MOE and morpholino modified oligonucleotides.







TABLE 78







Effect of oligonucleotides targeting human SMN in vivo












ISIS
Dose

GalNAc3

SEQ


No.
(mg/kg)
+Exon 7/−Exon 7
Cluster
CM
ID No.





Saline
n/a
1.00
n/a
n/a
n/a


387954
32
1.65
n/a
n/a
43


387954
288
5.00
n/a
n/a
43


699819
32
7.84
GalNAc3-7a
PO
43


699821
32
7.22
GalNAc3-7a
PO
43


700000
32
6.91
GalNAc3-1a
Ad
44


703421
32
1.27
n/a
n/a
43


703422
32
4.12
GalNAc3-7b
n/a
43









Example 89
Antisense Inhibition In Vivo by Oligonucleotides Targeting Apolipoprotein A (Apo(a)) Comprising a GalNAc3 Conjugate
The oligonucleotides listed in Table 79 below were tested in a study for dose-dependent inhibition of Apo(a) in transgenic mice.







TABLE 79







Modified ASOs targeting Apo(a)











ISIS

GalNAc3

SEQ ID


No.
Sequences (5′ to 3′)
Cluster
CM
No.





494372
TesGesmCesTesmCesmCds
n/a
n/a
53



GdsTdsTdsGdsGdsTdsGds






mCdsTdsTesGesTesTesmCe





 


681257
 TesGeo
GalNAc3-7a
PO
53



mCeoTeomCeomCdsGdsTds






TdsGdsGdsTdsGdsmCdsTds






TeoGeoTesTesmCe





The structure of GalNAc3-7a was shown in Example 48.






Treatment

Eight week old, female C57BL/6 mice (Jackson Laboratory, Bar Harbor, Me.) were each injected subcutaneously once per week at a dosage shown below, for a total of six doses, with an oligonucleotide listed in Table 79 or with PBS. Each treatment group consisted of 3-4 animals. Tail bleeds were performed the day before the first dose and weekly following each dose to determine plasma Apo(a) protein levels. The mice were sacrificed two days following the final administration. Apo(a) liver mRNA levels were determined using real-time PCR and RIBOGREEN® RNA quantification reagent (Molecular Probes, Inc. Eugene, Oreg.) according to standard protocols. Apo(a) plasma protein levels were determined using ELISA, and liver transaminase levels were determined. The mRNA and plasma protein results in Table 80 are presented as the treatment group average percent relative to the PBS treated group. Plasma protein levels were further normalized to the baseline (BL) value for the PBS group. Average absolute transaminase levels and body weights (% relative to baseline averages) are reported in Table 81.
As illustrated in Table 80, treatment with the oligonucleotides lowered Apo(a) liver mRNA and plasma protein levels in a dose-dependent manner. Furthermore, the oligonucleotide comprising the GalNAc conjugate was significantly more potent with a longer duration of action than the parent oligonucleotide lacking a GalNAc conjugate. As illustrated in Table 81, transaminase levels and body weights were unaffected by the oligonucleotides, indicating that the oligonucleotides were well tolerated.







TABLE 80







Apo(a) liver mRNA and plasma protein levels










ISIS
Dosage
Apo(a) mRNA
Apo(a) plasma protein (% PBS)
















No.
(mg/kg)
(% PBS)
BL
Week 1
Week 2
Week 3
Week 4
Week 5
Week 6



















PBS
n/a
100
100
120
119
113
88
121
97


494372
3
80
84
89
91
98
87
87
79



10
30
87
72
76
71
57
59
46



30
5
92
54
28
10
7
9
7


681257
0.3
75
79
76
89
98
71
94
78



1
19
79
88
66
60
54
32
24



3
2
82
52
17
7
4
6
5



10
2
79
17
6
3
2
4
5




















TABLE 81









Body weight


ISIS No.
Dosage (mg/kg)
ALT (U/L)
AST (U/L)
(% baseline)







PBS
n/a
37
54
103


494372
3
28
68
106



10
22
55
102



30
19
48
103


681257
0.3
30
80
104



1
26
47
105



3
29
62
102



10
21
52
107









Example 90
Antisense Inhibition In Vivo by Oligonucleotides Targeting TTR Comprising a GalNAc3 Cluster
Oligonucleotides listed in Table 82 below were tested in a dose-dependent study for antisense inhibition of human transthyretin (TTR) in transgenic mice that express the human TTR gene.
Treatment
TTR transgenic mice were each injected subcutaneously once per week for three weeks, for a total of three doses, with an oligonucleotide and dosage listed in Table 83 or with PBS. Each treatment group consisted of 4 animals. Prior to the first dose, a tail bleed was performed to determine plasma TTR protein levels at baseline (BL). The mice were sacrificed 72 hours following the final administration. TTR protein levels were measured using a clinical analyzer (AU480, Beckman Coulter, Calif.). Real-time PCR and RIBOGREEN® RNA quantification reagent (Molecular Probes, Inc. Eugene, Oreg.) were used according to standard protocols to determine liver human TTR mRNA levels. The results presented in Table 83 are the average values for each treatment group. The mRNA levels are the average values relative to the average for the PBS group. Plasma protein levels are the average values relative to the average value for the PBS group at baseline. “BL” indicates baseline, measurements that were taken just prior to the first dose. As illustrated in Table 83, treatment with antisense oligonucleotides lowered TTR expression levels in a dose-dependent manner. The oligonucleotides comprising a GalNAc conjugate were more potent than the parent lacking a GalNAc conjugate (ISIS 420915), and oligonucleotides comprising a phosphodiester or deoxyadenosine cleavable moiety showed significant improvements in potency compared to the parent lacking a conjugate (see ISIS numbers 682883 and 666943 vs 420915 and see Examples 86 and 87).







TABLE 82







Oligonucleotides targeting human TTR















GalNAc

SEQ


Isis No.
Sequence 5′ to 3′
Linkages
cluster
CM
ID No.















420915
TesmCesTesTesGesGdsTdsTdsAdsmCdsAdsTdsGdsAdsAds
PS
n/a
n/a
41



AesTesmCesmCesmCe






 


682883
 TesmCeoTeoTeoGeoGdsTdsTdsAdsmCds
PS/PO
GalNAc3-3a
PO
41



AdsTdsGdsAdsAdsAeoTeomCesmCesmCe






 


666943
 TesmCeoTeoTeoGeoGdsTdsTdsAdsm
PS/PO
GalNAc3-3a
Ad
45



CdsAdsTdsGdsAdsAdsAeoTeomCesmCesmCe






 


682887
 TesmCeoTeoTeoGeoGdsTdsTdsAdsm
PS/PO
GalNAc3-7a
Ad
45



CdsAdsTdsGdsAdsAdsAeoTeomCesmCesmCe






 


682888
 TesmCeoTeoTeoGeoGdsTdsTdsAdsm
PS/PO
GalNAc3-10a
Ad
45



CdsAdsTdsGdsAdsAdsAeoTeomCesmCesmCe






 


682889
 TesmCeoTeoTeoGeoGdsTdsTdsAdsm
PS/PO
GalNAc3-13a
Ad
45



CdsAdsTdsGdsAdsAdsAeoTeomCesmCesmCe













The legend for Table 82 can be found in Example 74. The structure of GalNAc3-3a was shown in Example 39. The structure of GalNAc3-7a was shown in Example 48. The structure of GalNAc3-10a was shown in Example 46. The structure of GalNAc3-13a was shown in Example 62.








TABLE 83







Antisense inhibition of human TTR in vivo













Dosage
TTR mRNA
TTR protein
GalNAc



Isis No.
(mg/kg)
(% PBS)
(% BL)
cluster
CM















PBS
n/a
100
124
n/a
n/a


420915
6
69
114
n/a
n/a



20
71
86



60
21
36


682883
0.6
61
73
GalNAc3-3a
PO



2
23
36



6
18
23


666943
0.6
74
93
GalNAc3-3a
Ad



2
33
57



6
17
22


682887
0.6
60
97
GalNAc3-7a
Ad



2
36
49



6
12
19


682888
0.6
65
92
GalNAc3-10a
Ad



2
32
46



6
17
22


682889
0.6
72
74
GalNAc3-13a
Ad



2
38
45



6
16
18









Example 91
Antisense Inhibition In Vivo by Oligonucleotides Targeting Factor VII Comprising a GalNAc3 Conjugate in Non-Human Primates
Oligonucleotides listed in Table 84 below were tested in a non-terminal, dose escalation study for antisense inhibition of Factor VII in monkeys.
Treatment
Non-naïve monkeys were each injected subcutaneously on days 0, 15, and 29 with escalating doses of an oligonucleotide listed in Table 84 or with PBS. Each treatment group consisted of 4 males and 1 female. Prior to the first dose and at various time points thereafter, blood draws were performed to determine plasma Factor VII protein levels. Factor VII protein levels were measured by ELISA. The results presented in Table 85 are the average values for each treatment group relative to the average value for the PBS group at baseline (BL), the measurements taken just prior to the first dose. As illustrated in Table 85, treatment with antisense oligonucleotides lowered Factor VII expression levels in a dose-dependent manner, and the oligonucleotide comprising the GalNAc conjugate was significantly more potent in monkeys compared to the oligonucleotide lacking a GalNAc conjugate.







TABLE 84







Oligonucleotides targeting Factor VII















GalNAc

SEQ


Isis No.
Sequence 5′ to 3′
Linkages
cluster
CM
ID No.















407935
AesTesGesmCesAesTdsGdsGdsTdsGdsAdsTdsGdsmCdsTds
PS
n/a
n/a
46



TesmCesTesGesAe






 


686892
  AesTesGesmCesAesTdsGdsGdsTdsGds
PS
GalNAc3-10a
PO
46



AdsTdsGdsmCdsTdsTesmCesTesGesAe













The legend for Table 84 can be found in Example 74. The structure of GalNAc3-10a was shown in Example 46.








TABLE 85







Factor VII plasma protein levels












ISIS No.
Day
Dose (mg/kg)
Factor VII (% BL)
















407935
0
n/a
100




15
10
87




22
n/a
92




29
30
77




36
n/a
46




43
n/a
43



686892
0
 3
100




15
10
56




22
n/a
29




29
30
19




36
n/a
15




43
n/a
11










Example 92
Antisense Inhibition in Primary Hepatocytes by Antisense Oligonucleotides Targeting Apo-CIII Comprising a GalNAc3 Conjugate
Primary mouse hepatocytes were seeded in 96-well plates at 15,000 cells per well, and the oligonucleotides listed in Table 86, targeting mouse ApoC-III, were added at 0.46, 1.37, 4.12, or 12.35, 37.04, 111.11, or 333.33 nM or 1.00 μM. After incubation with the oligonucleotides for 24 hours, the cells were lysed and total RNA was purified using RNeasy (Qiagen). ApoC-III mRNA levels were determined using real-time PCR and RIBOGREEN® RNA quantification reagent (Molecular Probes, Inc.) according to standard protocols. IC50 values were determined using Prism 4 software (GraphPad). The results show that regardless of whether the cleavable moiety was a phosphodiester or a phosphodiester-linked deoxyadensoine, the oligonucleotides comprising a GalNAc conjugate were significantly more potent than the parent oligonucleotide lacking a conjugate.







TABLE 86







Inhibition of mouse APOC-III expression in mouse primary hepatocytes














IC50
SEQ


ISIS No.
Sequence (5′ to 3′)
CM
(nM)
ID No.














440670
mCesAesGesmCesTesTdsTdsAdsTdsTdsAdsGdsGdsGdsAdsmCesAesGesmCesAe
n/a
13.20
47


 


661180
mCesAesGesmCesTesTdsTdsAdsTdsTdsAdsGdsGdsGdsAdsmCesAesGesmCes
Ad
1.40
48



AesGesmCesAeo 





 


680771
  mCesAesGesmCesTesTdsTdsAdsTdsTdsAdsGdsGdsGds
PO
0.70
47



AdsmCesAesGesmCesAe





 


680772
  mCesAesGesmCesTesTdsTdsAdsTdsTdsAdsGdsGdsGds
PO
1.70
47



AdsmCesAesGesmCesAe





 


680773
  mCesAesGesmCesTesTdsTdsAdsTdsTdsAdsGdsGdsGds
PO
2.00
47



AdsmCesAesGesmCesAe





 


680774
  mCesAesGesmCesTesTdsTdsAdsTdsTdsAdsGdsGdsGds
PO
1.50
47



AdsmCesAesGesmCesAe





 


681272
  mCesAeoGeomCesTeoTdsTdsAdsTdsTdsAdsGdsGdsGds
PO
<0.46
47



AdsmCeoAeoGesmCesAe





 


681273
  mCesAesGesmCesTesTdsTdsAdsTdsTdsAdsGdsGdsGds
Ad
1.10
49



AdsmCesAesGesmCesAe





 


683733
mCesAesGesmCesTesTdsTdsAdsTdsTdsAdsGdsGdsGdsAdsmCesAesGesmCes
Ad
2.50
48



Aeo  












The structure of GalNAc3-1a was shown previously in Example 9, GalNAc3-3a was shown in Example 39, GalNAc3-7a was shown in Example 48, GalNAc3-10a was shown in Example 46, GalNAc3-13a was shown in Example 62, and GalNAc3-19a was shown in Example 70.

Example 93
Antisense Inhibition In Vivo by Oligonucleotides Targeting SRB-1 Comprising Mixed Wings and a 5′-GalNAc3 Conjugate
The oligonucleotides listed in Table 87 were tested in a dose-dependent study for antisense inhibition of SRB-1 in mice.







TABLE 87







Modified ASOs targeting SRB-1













GalNAc3

SEQ


ISIS No.
Sequences (5′ to 3′)
Cluster
CM
ID No.














449093
TksTksmCksAdsGdsTdsmCdsAdsTdsGdsAdsmCdsTdsTksmCksmCk
n/a
n/a
50


 


699806
 TksTksmCksAdsGdsTdsmCdsAdsTdsGdsAdsm
GalNAc3-3a
PO
50



CdsTdsTksmCksmCk





 


699807
 TksTksmCksAdsGdsTdsmCdsAdsTdsGdsAdsm
GalNAc3-7a
PO
50



CdsTdsTksmCksmCk





 


699809
 TksTksmCksAdsGdsTdsmCdsAdsTdsGdsAdsm
GalNAc3-7a
PO
50



CdsTdsTesmCesmCe





 


699811
 TesTesmCesAdsGdsTdsmCdsAdsTdsGdsAdsm
GalNAc3-7a
PO
50



CdsTdsTksmCksmCk





 


699813
 TksTdsmCksAdsGdsTdsmCdsAdsTdsGdsAdsm
GalNAc3-7a
PO
50



CdsTdsTksmCdsmCk





 


699815
 TesTksmCksAdsGdsTdsmCdsAdsTdsGdsAdsm
GalNAc3-7a
PO
50



CdsTdsTksmCksmCe












The structure of GalNAc3-3a was shown previously in Example 39, and the structure of GalNAc3-7a was shown previously in Example 48. Subscripts: “e” indicates 2′-MOE modified nucleoside; “d” indicates β-D-2′-deoxyribonucleoside; “k” indicates 6′-(S)—CH3 bicyclic nucleoside (cEt); “s” indicates phosphorothioate internucleoside linkages (PS); “o” indicates phosphodiester internucleoside linkages (PO). Supersript “m” indicates 5-methylcytosines.

Treatment

Six to eight week old C57BL/6 mice (Jackson Laboratory, Bar Harbor, Me.) were injected subcutaneously once at the dosage shown below with an oligonucleotide listed in Table 87 or with saline. Each treatment group consisted of 4 animals. The mice were sacrificed 72 hours following the final administration. Liver SRB-1 mRNA levels were measured using real-time PCR. SRB-1 mRNA levels were normalized to cyclophilin mRNA levels according to standard protocols. The results are presented as the average percent of SRB-1 mRNA levels for each treatment group relative to the saline control group. As illustrated in Table 88, treatment with antisense oligonucleotides lowered SRB-1 mRNA levels in a dose-dependent manner, and the gapmer oligonucleotides comprising a GalNAc conjugate and having wings that were either full cEt or mixed sugar modifications were significantly more potent than the parent oligonucleotide lacking a conjugate and comprising full cEt modified wings.
Body weights, liver transaminases, total bilirubin, and BUN were also measured, and the average values for each treatment group are shown in Table 88. Body weight is shown as the average percent body weight relative to the baseline body weight (% BL) measured just prior to the oligonucleotide dose.







TABLE 88







SRB-1 mRNA, ALT, AST, BUN, and total bilirubin levels and body


weights
















SRB-1







ISIS
Dosage
mRNA
ALT
AST


Body weight


No.
(mg/kg)
(% PBS)
(U/L)
(U/L)
Bil
BUN
(% BL)

















PBS
n/a
100
31
84
0.15
28
102


449093
1
111
18
48
0.17
31
104



3
94
20
43
0.15
26
103



10
36
19
50
0.12
29
104


699806
0.1
114
23
58
0.13
26
107



0.3
59
21
45
0.12
27
108



1
25
30
61
0.12
30
104


699807
0.1
121
19
41
0.14
25
100



0.3
73
23
56
0.13
26
105



1
24
22
69
0.14
25
102


699809
0.1
125
23
57
0.14
26
104



0.3
70
20
49
0.10
25
105



1
33
34
62
0.17
25
107


699811
0.1
123
48
77
0.14
24
106



0.3
94
20
45
0.13
25
101



1
66
57
104
0.14
24
107


699813
0.1
95
20
58
0.13
28
104



0.3
98
22
61
0.17
28
105



1
49
19
47
0.11
27
106


699815
0.1
93
30
79
0.17
25
105



0.3
64
30
61
0.12
26
105



1
24
18
41
0.14
25
106









Example 94
Antisense Inhibition In Vivo by Oligonucleotides Targeting SRB-1 Comprising 2′-Sugar Modifications and a 5′-GalNAc3 Conjugate
The oligonucleotides listed in Table 89 were tested in a dose-dependent study for antisense inhibition of SRB-1 in mice.







TABLE 89







Modified ASOs targeting SRB-1













GalNAc3

SEQ


ISIS No.
Sequences (5′ to 3′)
Cluster
CM
ID No.














353382
GesmCesTesTesmCesAdsGdsTdsmCdsAdsTdsGdsAdsmCdsTdsTesm
n/a
n/a
28



CesmCesTesTe





 


700989
GmsCmsUmsUmsCmsAdsGdsTdsmCdsAdsTdsGdsAdsmCdsTdsUmsCms
n/a
n/a
51



CmsUmsUm





 


666904
 GesmCesTesTesmCesAdsGdsTdsmCdsAdsTdsGds
GalNAc3-3a
PO
28



AdsmCdsTdsTesmCesmCesTesTe





 


700991
 GmsCmsUmsUmsCmsAdsGdsTdsmCdsAdsTdsGds
GalNAc3-7a
PO
51



AdsmCdsTdsUmsCmsCmsUmsUm












Subscript “m” indicates a 2′-O-methyl modified nucleoside. See Example 74 for complete table legend. The structure of GalNAc3-3a was shown previously in Example 39, and the structure of GalNAc3-7a was shown previously in Example 48.

Treatment

The study was completed using the protocol described in Example 93. Results are shown in Table 90 below and show that both the 2′-MOE and 2′-OMe modified oligonucleotides comprising a GalNAc conjugate were significantly more potent than the respective parent oligonucleotides lacking a conjugate. The results of the body weights, liver transaminases, total bilirubin, and BUN measurements indicated that the compounds were all well tolerated.







TABLE 90







SRB-1 mRNA











ISIS No.
Dosage (mg/kg)
SRB-1 mRNA (% PBS)















PBS
n/a
100



353382
5
116




15
58




45
27



700989
5
120




15
92




45
46



666904
1
98




3
45




10
17



700991
1
118




3
63




10
14










Example 95
Antisense Inhibition In Vivo by Oligonucleotides Targeting SRB-1 Comprising Bicyclic Nucleosides and a 5′-GalNAc3 Conjugate
The oligonucleotides listed in Table 91 were tested in a dose-dependent study for antisense inhibition of SRB-1 in mice.







TABLE 91







Modified ASOs targeting SRB-1













GalNAc3

SEQ


ISIS No.
Sequences (5′ to 3′)
Cluster
CM
ID No














440762
TksmCksAdsGdsTdsmCdsAdsTdsGdsAdsmCdsTdsTksmCk
n/a
n/a
22


 


666905
 TksmCksAdsGdsTdsmCdsAdsTdsGdsAdsmCdsTdsTksmCk
GalNAc3-3a
PO
22


 


699782
 TksmCksAdsGdsTdsmCdsAdsTdsGdsAdsmCdsTdsTksmCk
GalNAc3-7a
PO
22


 


699783
 TlsmClsAdsGdsTdsmCdsAdsTdsGdsAdsmCdsTdsTlsmCl
GalNAc3-3a
PO
22


 


653621
TlsClsAdsGdsTdsmCdsAdsTdsGdsAdsmCdsTdsTlsmClo 
GalNAc3-1a
Ad
23


 


439879
TgsmCgsAdsGdsTdsmCdsAdsTdGdsAdsmCdsTdsTgsmCg
n/a
n/a
22


 


699789
 TgsmCgsAdsGdsTdsmCdsAdsTdGdsAdsmCdsTdsTgsmCg
GalNAc3-3a
PO
22









Subscript “g” indicates a fluoro-HNA nucleoside, subscript “l” indicates a locked nucleoside comprising a 2′-O—CH2-4′ bridge. See the Example 74 table legend for other abbreviations. The structure of GalNAc3-1a was shown previously in Example 9, the structure of GalNAc3-3a was shown previously in Example 39, and the structure of GalNAc3-7a was shown previously in Example 48.

Treatment

The study was completed using the protocol described in Example 93. Results are shown in Table 92 below and show that oligonucleotides comprising a GalNAc conjugate and various bicyclic nucleoside modifications were significantly more potent than the parent oligonucleotide lacking a conjugate and comprising bicyclic nucleoside modifications. Furthermore, the oligonucleotide comprising a GalNAc conjugate and fluoro-HNA modifications was significantly more potent than the parent lacking a conjugate and comprising fluoro-HNA modifications. The results of the body weights, liver transaminases, total bilirubin, and BUN measurements indicated that the compounds were all well tolerated.







TABLE 92







SRB-1 mRNA, ALT, AST, BUN, and total bilirubin levels and body


weights











ISIS No.
Dosage (mg/kg)
SRB-1 mRNA (% PBS)















PBS
n/a
100



440762
1
104




3
65




10
35



666905
0.1
105




0.3
56




1
18



699782
0.1
93




0.3
63




1
15



699783
0.1
105




0.3
53




1
12



653621
0.1
109




0.3
82




1
27



439879
1
96




3
77




10
37



699789
0.1
82




0.3
69




1
26










Example 96
Plasma Protein Binding of Antisense Oligonucleotides Comprising a GalNAc3 Conjugate Group
Oligonucleotides listed in Table 57 targeting ApoC-III and oligonucleotides in Table 93 targeting Apo(a) were tested in an ultra-filtration assay in order to assess plasma protein binding.







TABLE 93







Modified oligonucleotides targeting Apo(a)













GalNAc3

SEQ


ISIS No.
Sequences (5′ to 3′)
Cluster
CM
ID No














494372
TesGesmCesTesmCesmCdsGdsTdsTdsGdsGdsTdsGdsmCdsTdsTesGesTes
n/a
n/a
53



TesmCe





 


693401
TesGeomCeoTeomCeomCdsGdsTdsTdsGdsGdsTdsGdsmCdsTdsTesGeoTes
n/a
n/a
53



TesmCe





 


681251
 TesGesmCesTesmCesmCdsGdsTdsTdsGdsGdsTdsGdsm
GalNAc3-7a
PO
53



CdsTdsTesGesTesTesmCe





 


681257
 TesGeomCeoTeomCeomCdsGdsTdsTdsGdsGdsTdsGdsm
GalNAc3-7a
PO
53



CdsTdsTeoGeoTesTesmCe












See the Example 74 for table legend. The structure of GalNAc3-7a was shown previously in Example 48.

Ultrafree-MC ultrafiltration units (30,000 NMWL, low-binding regenerated cellulose membrane, Millipore, Bedford, Mass.) were pre-conditioned with 300 μL of 0.5% Tween 80 and centrifuged at 2000 g for 10 minutes, then with 300 μL of a 300 μg/mL solution of a control oligonucleotide in H2O and centrifuged at 2000 g for 16 minutes. In order to assess non-specific binding to the filters of each test oligonucleotide from Tables 57 and 93 to be used in the studies, 300 μL of a 250 ng/mL solution of oligonucleotide in H2O at pH 7.4 was placed in the pre-conditioned filters and centrifuged at 2000 g for 16 minutes. The unfiltered and filtered samples were analyzed by an ELISA assay to determine the oligonucleotide concentrations. Three replicates were used to obtain an average concentration for each sample. The average concentration of the filtered sample relative to the unfiltered sample is used to determine the percent of oligonucleotide that is recovered through the filter in the absence of plasma (% recovery).
Frozen whole plasma samples collected in K3-EDTA from normal, drug-free human volunteers, cynomolgus monkeys, and CD-1 mice, were purchased from Bioreclamation LLC (Westbury, N.Y.). The test oligonucleotides were added to 1.2 mL aliquots of plasma at two concentrations (5 and 150 μg/mL). An aliquot (300 μL) of each spiked plasma sample was placed in a pre-conditioned filter unit and incubated at 37° C. for 30 minutes, immediately followed by centrifugation at 2000 g for 16 minutes. Aliquots of filtered and unfiltered spiked plasma samples were analyzed by an ELISA to determine the oligonucleotide concentration in each sample. Three replicates per concentration were used to determine the average percentage of bound and unbound oligonucleotide in each sample. The average concentration of the filtered sample relative to the concentration of the unfiltered sample is used to determine the percent of oligonucleotide in the plasma that is not bound to plasma proteins (% unbound). The final unbound oligonucleotide values are corrected for non-specific binding by dividing the % unbound by the % recovery for each oligonucleotide. The final % bound oligonucleotide values are determined by subtracting the final % unbound values from 100. The results are shown in Table 94 for the two concentrations of oligonucleotide tested (5 and 150 μg/mL) in each species of plasma. The results show that GalNAc conjugate groups do not have a significant impact on plasma protein binding. Furthermore, oligonucleotides with full PS internucleoside linkages and mixed PO/PS linkages both bind plasma proteins, and those with full PS linkages bind plasma proteins to a somewhat greater extent than those with mixed PO/PS linkages.







TABLE 94







Percent of modified oligonucleotide bound to plasma proteins










ISIS
Human plasma
Monkey plasma
Mouse plasma













No.
5 μg/mL
150 μg/mL
5 μg/mL
150 μg/mL
5 μg/mL
150 μg/mL





304801
99.2
98.0
99.8
99.5
98.1
97.2


663083
97.8
90.9
99.3
99.3
96.5
93.0


674450
96.2
97.0
98.6
94.4
94.6
89.3


494372
94.1
89.3
98.9
97.5
97.2
93.6


693401
93.6
89.9
96.7
92.0
94.6
90.2


681251
95.4
93.9
99.1
98.2
97.8
96.1


681257
93.4
90.5
97.6
93.7
95.6
92.7









Example 97
Modified Oligonucleotides Targeting TTR Comprising a GalNAc3 Conjugate Group
The oligonucleotides shown in Table 95 comprising a GalNAc conjugate were designed to target TTR.







TABLE 95







Modified oligonucleotides targeting TTR













GalNAc3

SEQ


ISIS No.
Sequences (5′ to 3′)
Cluster
CM
ID No














666941
 TesmCesTesTesGesGdsTdsTdsAdsmCdsAdsTds
GalNAc3-3
Ad
45



GdsAdsAdsAesTesmCesmCesmCe





 


666942
TesmCeoTeoTeoGeoGdsTdsTdsAdsmCdsAdsTdsGdsAdsAdsAeoTeomCesm
GalNAc3-1
Ad
42



CesmCeo 





 


682876
 TesmCesTesTesGesGdsTdsTdsAdsmCdsAdsTdsGds
GalNAc3-3
PO
41



AdsAdsAesTesmCesmCesmCe





 


682877
 TesmCesTesTesGesGdsTdsTdsAdsmCdsAdsTdsGds
GalNAc3-7
PO
41



AdsAdsAesTesmCesmCesmCe





 


682878
 TesmCesTesTesGesGdsTdsTdsAdsmCdsAdsTdsGds
GalNAc3-10
PO
41



AdsAdsAesTesmCesmCesmCe





 


682879
 TesmCesTesTesGesGdsTdsTdsAdsmCdsAdsTdsGds
GalNAc3-13
PO
41



AdsAdsAesTesmCesmCesmCe





 


682880
 TesmCesTesTesGesGdsTdsTdsAdsmCdsAdsTds
GalNAc3-7
Ad
45



GdsAdsAdsAesTesmCesmCesmCe





 


682881
 TesmCesTesTesGesGdsTdsTdsAdsmCdsAdsTds
GalNAc3-10
Ad
45



GdsAdsAdsAesTesmCesmCesmCe





 


682882
 TesmCesTesTesGesGdsTdsTdsAdsmCdsAdsTds
GalNAc3-13
Ad
45



GdsAdsAdsAesTesmCesmCesmCe





 


684056
TesmCesTesTesGesGdsTdsTdsAdsmCdsAdsTdsGdsAdsAdsAesTesmCesm
GalNAc3-19
Ad
42



CesmCeo 












The legend for Table 95 can be found in Example 74. The structure of GalNAc3-1 was shown in Example 9. The structure of GalNAc3-3a was shown in Example 39. The structure of GalNAc3-7a was shown in Example 48. The structure of GalNAc3-10a was shown in Example 46. The structure of GalNAc3-13a was shown in Example 62. The structure of GalNAc3-19a was shown in Example 70.

Example 98
Evaluation of Pro-Inflammatory Effects of Oligonucleotides Comprising a GalNAc Conjugate in hPMBC Assay
The oligonucleotides listed in Table 96 and were tested for pro-inflammatory effects in an hPMBC assay as described in Examples 23 and 24. (See Tables 17, 70, 82, and 95 for descriptions of the oligonucleotides.) ISIS 353512 is a high responder used as a positive control, and the other oligonucleotides are described in Tables 70, 82, and 95. The results shown in Table 96 were obtained using blood from one volunteer donor. The results show that the oligonucleotides comprising mixed PO/PS internucleoside linkages produced significantly lower pro-inflammatory responses compared to the same oligonucleotides having full PS linkages. Furthermore, the GalNAc conjugate group did not have a significant effect in this assay.











TABLE 96





ISIS No.
Emax/EC50
GalNAc3 cluster
Linkages
CM



















353512
3630
n/a
PS
n/a


420915
802
n/a
PS
n/a


682881
1311
GalNAc3-10
PS
Ad


682888
0.26
GalNAc3-10
PO/PS
Ad


684057
1.03
GalNAc3-19
PO/PS
Ad









Example 99
Binding Affinities of Oligonucleotides Comprising a GalNAc Conjugate for the Asialoglycoprotein Receptor
The binding affinities of the oligonucleotides listed in Table 97 (see Table 63 for descriptions of the oligonucleotides) for the asialoglycoprotein receptor were tested in a competitive receptor binding assay. The competitor ligand, α1-acid glycoprotein (AGP), was incubated in 50 mM sodium acetate buffer (pH 5) with 1 U neuraminidase-agarose for 16 hours at 37° C., and >90% desialylation was confirmed by either sialic acid assay or size exclusion chromatography (SEC). Iodine monochloride was used to iodinate the AGP according to the procedure by Atsma et al. (see J Lipid Res. 1991 January; 32(1):173-81.) In this method, desialylated α1-acid glycoprotein (de-AGP) was added to 10 mM iodine chloride, Na125I, and 1 M glycine in 0.25 M NaOH. After incubation for 10 minutes at room temperature, 125I-labeled de-AGP was separated from free 125I by concentrating the mixture twice utilizing a 3 KDMWCO spin column. The protein was tested for labeling efficiency and purity on a HPLC system equipped with an Agilent SEC-3 column (7.8×300 mm) and a β-RAM counter. Competition experiments utilizing 125I-labeled de-AGP and various GalNAc-cluster containing ASOs were performed as follows. Human HepG2 cells (106 cells/ml) were plated on 6-well plates in 2 ml of appropriate growth media. MEM media supplemented with 10% fetal bovine serum (FBS), 2 mM L-Glutamine and 10 mM HEPES was used. Cells were incubated 16-20 hours @ 37° C. with 5% and 10% CO2 respectively. Cells were washed with media without FBS prior to the experiment. Cells were incubated for 30 min @37° C. with 1 ml competition mix containing appropriate growth media with 2% FBS, 10−8 M 125I-labeled de-AGP and GalNAc-cluster containing ASOs at concentrations ranging from 10−11 to 10−5 M. Non-specific binding was determined in the presence of 10−2 M GalNAc sugar. Cells were washed twice with media without FBS to remove unbound 125I-labeled de-AGP and competitor GalNAc ASO. Cells were lysed using Qiagen's RLT buffer containing 1% β-mercaptoethanol. Lysates were transferred to round bottom assay tubes after a brief 10 min freeze/thaw cycle and assayed on a γ-counter. Non-specific binding was subtracted before dividing 125I protein counts by the value of the lowest GalNAc-ASO concentration counts. The inhibition curves were fitted according to a single site competition binding equation using a nonlinear regression algorithm to calculate the binding affinities (KD's).
The results in Table 97 were obtained from experiments performed on five different days. Results for oligonucleotides marked with superscript “a” are the average of experiments run on two different days. The results show that the oligonucleotides comprising a GalNAc conjugate group on the 5′-end bound the asialoglycoprotein receptor on human HepG2 cells with 1.5 to 16-fold greater affinity than the oligonucleotides comprising a GalNAc conjugate group on the 3′-end.







TABLE 97







Asialoglycoprotein receptor binding assay results












Oligonucleotide end to





which GalNAc conjugate


ISIS No.
GalNAc conjugate
is attached
KD (nM)













661161a
GalNAc3-3
5′
3.7


666881a
GalNAc3-10
5′
7.6


666981
GalNAc3-7
5′
6.0


670061
GalNAc3-13
5′
7.4


655861a
GalNAc3-1
3′
11.6


677841a
GalNAc3-19
3′
60.8









Example 100
Antisense Inhibition In Vivo by Oligonucleotides Comprising a GalNAc Conjugate Group Targeting Apo(a) In Vivo
The oligonucleotides listed in Table 98a below were tested in a single dose study for duration of action in mice.







TABLE 98a







Modified ASOs targeting APO(a)













GalNAc3

SEQ


ISIS No.
Sequences (5′ to 3′)
Cluster
CM
ID No.














681251
 TesGesmCesTesmCesmCdsGdsTdsTdsGdsGds
GalNAc3-7a
PO
53



TdsGdsmCdsTdsTesGesTesTesmCe





 


681257
 TesGeomCeoTeomCeomCdsGdsTdsTdsGdsGds
GalNAc3-7a
PO
53



TdsGdsmCdsTdsTeoGeoTesTesmCe












The structure of GalNAc3-7a was shown in Example 48.

Treatment

Female transgenic mice that express human Apo(a) were each injected subcutaneously once per week, for a total of 6 doses, with an oligonucleotide and dosage listed in Table 98b or with PBS. Each treatment group consisted of 3 animals. Blood was drawn the day before dosing to determine baseline levels of Apo(a) protein in plasma and at 72 hours, 1 week, and 2 weeks following the first dose. Additional blood draws will occur at 3 weeks, 4 weeks, 5 weeks, and 6 weeks following the first dose. Plasma Apo(a) protein levels were measured using an ELISA. The results in Table 98b are presented as the average percent of plasma Apo(a) protein levels for each treatment group, normalized to baseline levels (% BL), The results show that the oligonucleotides comprising a GalNAc conjugate group exhibited potent reduction in Apo(a) expression. This potent effect was observed for the oligonucleotide that comprises full PS internucleoside linkages and the oligonucleotide that comprises mixed PO and PS linkages.







TABLE 98b







Apo(a) plasma protein levels













Apo(a) at




ISIS
Dosage
72 hours
Apo(a) at 1 week
Apo(a) at 3 weeks


No.
(mg/kg)
(% BL)
(% BL)
(% BL)














PBS
n/a
116
104
107


681251
0.3
97
108
93



1.0
85
77
57



3.0
54
49
11



10.0
23
15
4


681257
0.3
114
138
104



1.0
91
98
54



3.0
69
40
6



10.0
30
21
4









Example 101
Antisense Inhibition by Oligonucleotides Comprising a GalNAc Cluster Linked Via a Stable Moiety
The oligonucleotides listed in Table 99 were tested for inhibition of mouse APOC-III expression in vivo. C57Bl/6 mice were each injected subcutaneously once with an oligonucleotide listed in Table 99 or with PBS. Each treatment group consisted of 4 animals. Each mouse treated with ISIS 440670 received a dose of 2, 6, 20, or 60 mg/kg. Each mouse treated with ISIS 680772 or 696847 received 0.6, 2, 6, or 20 mg/kg. The GalNAc conjugate group of ISIS 696847 is linked via a stable moiety, a phosphorothioate linkage instead of a readily cleavable phosphodiester containing linkage. The animals were sacrificed 72 hours after the dose. Liver APOC-III mRNA levels were measured using real-time PCR. APOC-III mRNA levels were normalized to cyclophilin mRNA levels according to standard protocols. The results are presented in Table 99 as the average percent of APOC-III mRNA levels for each treatment group relative to the saline control group. The results show that the oligonucleotides comprising a GalNAc conjugate group were significantly more potent than the oligonucleotide lacking a conjugate group. Furthermore, the oligonucleotide comprising a GalNAc conjugate group linked to the oligonucleotide via a cleavable moiety (ISIS 680772) was even more potent than the oligonucleotide comprising a GalNAc conjugate group linked to the oligonucleotide via a stable moiety (ISIS 696847).







TABLE 99







Modified oligonucleotides targeting mouse APOC-III
















APOC-III






Dosage
mRNA
SEQ


ISIS No.
Sequences (5′ to 3′)
CM
(mg/kg)
(% PBS)
ID No.















440670
mCesAesGesmCesTesTdsTdsAdsTdsAdsGdsGdsGdsAdsm
n/a
2
92
47



CesAesGesmCesAe

6
86






20
59






60
37



 


680772
 mCesAesGesmCesTesTdsTdsAdsTdsTds
PO
0.6
79
47



AdsGdsGdsGdsAdsmCesAesGesmCesAe

2
58






6
31






20
13



 


696847
 mCesAesGesmCesTesTdsTdsAdsTdsTds
n/a (PS)
0.6
83
47



AdsGdsGdsGdsAdsmCesAesGesmCesAe

2
73






6
40






20
28









The structure of GalNAc3-7a was shown in Example 48.

Example 102
Distribution in Liver of Antisense Oligonucleotides Comprising a GalNAc Conjugate
The liver distribution of ISIS 353382 (see Table 23) that does not comprise a GalNAc conjugate and ISIS 655861 (see Table 23) that does comprise a GalNAc conjugate was evaluated. Male balb/c mice were subcutaneously injected once with ISIS 353382 or 655861 at a dosage listed in Table 100. Each treatment group consisted of 3 animals except for the 18 mg/kg group for ISIS 655861, which consisted of 2 animals. The animals were sacrificed 48 hours following the dose to determine the liver distribution of the oligonucleotides. In order to measure the number of antisense oligonucleotide molecules per cell, a Ruthenium (II) tris-bipyridine tag (MSD TAG, Meso Scale Discovery) was conjugated to an oligonucleotide probe used to detect the antisense oligonucleotides. The results presented in Table 100 are the average concentrations of oligonucleotide for each treatment group in units of millions of oligonucleotide molecules per cell. The results show that at equivalent doses, the oligonucleotide comprising a GalNAc conjugate was present at higher concentrations in the total liver and in hepatocytes than the oligonucleotide that does not comprise a GalNAc conjugate. Furthermore, the oligonucleotide comprising a GalNAc conjugate was present at lower concentrations in non-parenchymal liver cells than the oligonucleotide that does not comprise a GalNAc conjugate. And while the concentrations of ISIS 655861 in hepatocytes and non-parenchymal liver cells were similar per cell, the liver is approximately 80% hepatocytes by volume. Thus, the majority of the ISIS 655861 oligonucleotide that was present in the liver was found in hepatocytes, whereas the majority of the ISIS 353382 oligonucleotide that was present in the liver was found in non-parenchymal liver cells.











TABLE 100









Concentration




Concentration
Concentration
in non-




in whole
in hepatocytes
parenchymal




liver
(molecules *
liver cells


ISIS
Dosage
(molecules *
10{circumflex over ( )}6 per
(molecules *


No.
(mg/kg)
10{circumflex over ( )}6 per cell)
cell)
10{circumflex over ( )}6 per cell)



















353382
3
9.7
1.2
37.2



10
17.3
4.5
34.0



20
23.6
6.6
65.6



30
29.1
11.7
80.0



60
73.4
14.8
98.0



90
89.6
18.5
119.9


655861
0.5
2.6
2.9
3.2



1
6.2
7.0
8.8



3
19.1
25.1
28.5



6
44.1
48.7
55.0



18
76.6
82.3
77.1









Example 103
Duration of Action In Vivo of Oligonucleotides Targeting APOC-III Comprising a GalNAc3 Conjugate
The oligonucleotides listed in Table 101 below were tested in a single dose study for duration of action in mice.







TABLE 101







Modified ASOs targeting APOC-III













GalNAc3

SEQ


ISIS No.
Sequences (5′ to 3′)
Cluster
CM
ID No.














304801
AesGesmCesTesTesmCdsTdsTdsGdsTdsmCdsmCdsAdsGdsmCdsTesTesTes
n/a
n/a
20



AesTe





 


663084
  AesGeomCeoTeoTeomCdsTdsTdsGdsTdsmCdsmCds
GalNAc3-3a
Ad
36



AdsGdsmCdsTeoTeoTesAesTe





 


679241
AesGeomCeoTeoTeomCdsTdsTdsGdsTdsmCdsmCdsAdsGdsmCdsTeoTeoTes
GalNAc3-19a
Ad
21



AesTeo 












The structure of GalNAc3-3a was shown in Example 39, and GalNAc3-19a was shown in Example 70.

Treatment

Female transgenic mice that express human APOC-III were each injected subcutaneously once with an oligonucleotide listed in Table 101 or with PBS. Each treatment group consisted of 3 animals. Blood was drawn before dosing to determine baseline and at 3, 7, 14, 21, 28, 35, and 42 days following the dose. Plasma triglyceride and APOC-III protein levels were measured as described in Example 20. The results in Table 102 are presented as the average percent of plasma triglyceride and APOC-III levels for each treatment group, normalized to baseline levels. A comparison of the results in Table 58 of example 79 with the results in Table 102 below show that oligonucleotides comprising a mixture of phosphodiester and phosphorothioate internucleoside linkages exhibited increased duration of action than equivalent oligonucleotides comprising only phosphorothioate internucleoside linkages.







TABLE 102







Plasma triglyceride and APOC-III protein levels in transgenic mice















Time








point




(days

APOC-III




ISIS
Dosage
post-
Triglycerides
protein (%
GalNAc3


No.
(mg/kg)
dose)
(% baseline)
baseline)
Cluster
CM
















PBS
n/a
3
96
101
n/a
n/a




7
88
98




14
91
103




21
69
92




28
83
81




35
65
86




42
72
88


304801
30
3
42
46
n/a
n/a




7
42
51




14
59
69




21
67
81




28
79
76




35
72
95




42
82
92


663084
10
3
35
28
GalNAc3-3a
Ad




7
23
24




14
23
26




21
23
29




28
30
22




35
32
36




42
37
47


679241
10
3
38
30
GalNAc3-
Ad




7
31
28
19a




14
30
22




21
36
34




28
48
34




35
50
45




42
72
64









Example 104
Synthesis of Oligonucleotides Comprising a 5′-GalNAc2 Conjugate







Compound 120 is commercially available, and the synthesis of compound 126 is described in Example 49. Compound 120 (1 g, 2.89 mmol), HBTU (0.39 g, 2.89 mmol), and HOBt (1.64 g, 4.33 mmol) were dissolved in DMF (10 mL, and N,N-diisopropylethylamine (1.75 mL, 10.1 mmol) were added. After about 5 min, aminohexanoic acid benzyl ester (1.36 g, 3.46 mmol) was added to the reaction. After 3 h, the reaction mixture was poured into 100 mL of 1 M NaHSO4 and extracted with 2×50 mL ethyl acetate. Organic layers were combined and washed with 3×40 mL sat NaHCO3 and 2× brine, dried with Na2SO4, filtered and concentrated. The product was purified by silica gel column chromatography (DCM:EA:Hex, 1:1:1) to yield compound 231. LCMS and NMR were consistent with the structure. Compounds 231 (1.34 g, 2.438 mmol) was dissolved in dichloromethane (10 mL) and trifluoracetic acid (10 mL) was added. After stirring at room temperature for 2 h, the reaction mixture was concentrated under reduced pressure and co-evaporated with toluene (3×10 mL). The residue was dried under reduced pressure to yield compound 232 as the trifluoracetate salt. The synthesis of compound 166 is described in Example 54. Compound 166 (3.39 g, 5.40 mmol) was dissolved in DMF (3 mL). A solution of compound 232 (1.3 g, 2.25 mmol) was dissolved in DMF (3 mL) and N,N-diisopropylethylamine (1.55 mL) was added. The reaction was stirred at room temperature for 30 minutes, then poured into water (80 mL) and the aqueous layer was extracted with EtOAc (2×100 mL). The organic phase was separated and washed with sat, aqueous NaHCO3 (3×80 mL), 1 M NaHSO4 (3×80 mL) and brine (2×80 mL), then dried (Na2SO4), filtered, and concentrated. The residue was purified by silica gel column chromatography to yield compound 233. LCMS and NMR were consistent with the structure. Compound 233 (0.59 g, 0.48 mmol) was dissolved in methanol (2.2 mL) and ethyl acetate (2.2 mL). Palladium on carbon (10 wt % Pd/C, wet, 0.07 g) was added, and the reaction mixture was stirred under hydrogen atmosphere for 3 h. The reaction mixture was filtered through a pad of Celite and concentrated to yield the carboxylic acid. The carboxylic acid (1.32 g, 1.15 mmol, cluster free acid) was dissolved in DMF (3.2 mL). To this N,N-diisopropylethylamine (0.3 mL, 1.73 mmol) and PFPTFA (0.30 mL, 1.73 mmol) were added. After 30 min stirring at room temperature the reaction mixture was poured into water (40 mL) and extracted with EtOAc (2×50 mL). A standard work-up was completed as described above to yield compound 234. LCMS and NMR were consistent with the structure. Oligonucleotide 235 was prepared using the general procedure described in Example 46. The GalNAc2 cluster portion (GalNAc2-24a) of the conjugate group GalNAc2-24 can be combined with any cleavable moiety present on the oligonucleotide to provide a variety of conjugate groups. The structure of GalNAc2-24 (GalNAc2-24a-CM) is shown below:




Example 105
Synthesis of Oligonucleotides Comprising a GalNAc1-25 Conjugate




The synthesis of compound 166 is described in Example 54. Oligonucleotide 236 was prepared using the general procedure described in Example 46.
Alternatively, oligonucleotide 236 was synthesized using the scheme shown below, and compound 238 was used to form the oligonucleotide 236 using procedures described in Example 10.




The GalNAc1 cluster portion (GalNAc1-25a) of the conjugate group GalNAc1-25 can be combined with any cleavable moiety present on the oligonucleotide to provide a variety of conjugate groups. The structure of GalNAc1-25 (GalNAc1-25a-CM) is shown below:





Example 106
Antisense Inhibition In Vivo by Oligonucleotides Targeting SRB-1 Comprising a 5′-GalNAc2 or a 5′-GalNAc3 Conjugate
Oligonucleotides listed in Tables 103 and 104 were tested in dose-dependent studies for antisense inhibition of SRB-1 in mice.
Treatment
Six to week old, male C57BL/6 mice (Jackson Laboratory, Bar Harbor, Me.) were injected subcutaneously once with 2, 7, or 20 mg/kg of ISIS No. 440762; or with 0.2, 0.6, 2, 6, or 20 mg/kg of ISIS No. 686221, 686222, or 708561; or with saline. Each treatment group consisted of 4 animals. The mice were sacrificed 72 hours following the final administration. Liver SRB-1 mRNA levels were measured using real-time PCR. SRB-1 mRNA levels were normalized to cyclophilin mRNA levels according to standard protocols. The antisense oligonucleotides lowered SRB-1 mRNA levels in a dose-dependent manner, and the ED50 results are presented in Tables 103 and 104. Although previous studies showed that trivalent
GalNAc-conjugated oligonucleotides were significantly more potent than divalent GalNAc-conjugated oligonucleotides, which were in turn significantly more potent than monovalent GalNAc conjugated oligonucleotides (see, e.g., Khorev et al., Bioorg. & Med. Chem., Vol. 16, 5216-5231 (2008)), treatment with antisense oligonucleotides comprising monovalent, divalent, and trivalent GalNAc clusters lowered SRB-1 mRNA levels with similar potencies as shown in Tables 103 and 104.







TABLE 103







Modified oligonucleotides targeting SRB-1













GalNAc3
ED50
SEQ


ISIS No.
Sequences (5′ to 3′)
Cluster
(mg/kg)
ID No














440762
TksmCksAdsGdsTdsmCdsAdsTdsGdsAdsmCdsTdsTksmCk
n/a
4.7
22


 


686221
 TksmCksAdsGdsTdsmCdsAdsTds
GalNAc2-24a
0.39
26



GdsAdsmCdsTdsTksmCk





 


686222
 TksmCksAdsGdsTdsmCdsAdsTds
GalNAc3-13a
0.41
26



GdsAdsmCdsTdsTksmCk












See Example 93 for table legend. The structure of GalNAc3-13a was shown in Example 62, and the structure of GalNAc2-24a was shown in Example 104.








TABLE 104







Modified oligonucleotides targeting SRB-1













GalNAc3
ED50
SEQ


ISIS No.
Sequences (5′ to 3′)
Cluster
(mg/kg)
ID No














440762
TksmCksAdsGdsTdsmCdsAdsTdsGdsAdsmCdsTdsTksmCk
n/a
5
22


 


708561
 TksmCksAdsGdsTdsmCdsAdsTdsGds
GalNAc1-25a
0.4
22



AdsmCdsTdsTksmCk












See Example 93 for table legend. The structure of GalNAc1-25a was shown in Example 105.

The concentrations of the oligonucleotides in Tables 103 and 104 in liver were also assessed, using procedures described in Example 75. The results shown in Tables 104a and 104b below are the average total antisense oligonucleotide tissues levels for each treatment group, as measured by UV in units of μg oligonucleotide per gram of liver tissue. The results show that the oligonucleotides comprising a GalNAc conjugate group accumulated in the liver at significantly higher levels than the same dose of the oligonucleotide lacking a GalNAc conjugate group. Furthermore, the antisense oligonucleotides comprising one, two, or three GalNAc ligands in their respective conjugate groups all accumulated in the liver at similar levels. This result is surprising in view of the Khorev et al. literature reference cited above and is consistent with the activity data shown in Tables 103 and 104 above.







TABLE 104a







Liver concentrations of oligonucleotides comprising a


GalNAc2 or GalNAc3 conjugate group












Dosage
[Antisense




ISIS No.
(mg/kg)
oligonucleotide] (μg/g)
GalNAc cluster
CM














440762
2
2.1
n/a
n/a



7
13.1



20
31.1


686221
0.2
0.9
GalNAc2-24a
Ad



0.6
2.7



2
12.0



6
26.5


686222
0.2
0.5
GalNAc3-13a
Ad



0.6
1.6



2
11.6



6
19.8
















TABLE 104b







Liver concentrations of oligonucleotides


comprising a GalNAc1 conjugate group












Dosage
[Antisense




ISIS No.
(mg/kg)
oligonucleotide] (μg/g)
GalNAc cluster
CM














440762
2
2.3
n/a
n/a



7
8.9



20
23.7


708561
0.2
0.4
GalNAc1-25a
PO



0.6
1.1



2
5.9



6
23.7



20
53.9









Example 107
Synthesis of Oligonucleotides Comprising a GalNAc1-26 or GalNAc1-27 Conjugate




Oligonucleotide 239 is synthesized via coupling of compound 47 (see Example 15) to acid 64 (see Example 32) using HBTU and DIEA in DMF. The resulting amide containing compound is phosphitylated, then added to the 5′-end of an oligonucleotide using procedures described in Example 10. The GalNAc1 cluster portion (GalNAc1-26a) of the conjugate group GalNAc1-26 can be combined with any cleavable moiety present on the oligonucleotide to provide a variety of conjugate groups. The structure of GalNAc1-26 (GalNAc1-26a-CM) is shown below:




In order to add the GalNAc1 conjugate group to the 3′-end of an oligonucleotide, the amide formed from the reaction of compounds 47 and 64 is added to a solid support using procedures described in Example 7. The oligonucleotide synthesis is then completed using procedures described in Example 9 in order to form oligonucleotide 240.




The GalNAc1 cluster portion (GalNAc1-27a) of the conjugate group GalNAc1-27 can be combined with any cleavable moiety present on the oligonucleotide to provide a variety of conjugate groups. The structure of GalNAc1-27 (GalNAc1-27a-CM) is shown below:





Example 108
Antisense Inhibition In Vivo by Oligonucleotides Comprising a GalNAc Conjugate Group Targeting Apo(a) In Vivo
The oligonucleotides listed in Table 105 below were tested in a single dose study in mice.







TABLE 105







Modified ASOs targeting APO(a)













GalNAc3

SEQ


ISIS No.
Sequences (5′ to 3′)
Cluster
CM
ID No.














494372
TesGesmCesTesmCesmCdsGdsTdsTdsGdsGdsTdsGdsmCdsTdsTesGesTesTesmCe
n/a
n/a
53


 


681251
 TesGesmCesTesmCesmCdsGdsTdsTdsGdsGdsTdsGdsmCds
GalNAc3-7a
PO
53



TdsTesGesTesTesmCe





 


681255
 TesGeomCeoTeomCeomCdsGdsTdsTdsGdsGdsTdsGdsmCds
GalNAc3-3a
PO
53



TdsTeoGeoTesTesmCe





 


681256
 TesGeomCeoTeomCeomCdsGdsTdsTdsGdsGdsTdsGdsmCds
GalNAc3-10a
PO
53



TdsTeoGeoTesTesmCe





 


681257
 TesGeomCeoTeomCeomCdsGdsTdsTdsGdsGdsTdsGdsmCds
GalNAc3-7a
PO
53



TdsTeoGeoTesTesmCe





 


681258
 TesGeomCeoTeomCeomCdsGdsTdsTdsGdsGdsTdsGdsmCds
GalNAc3-13a
PO
53



TdsTeoGeoTesTesmCe





 


681260
TesGeomCeoTeomCeomCdsGdsTdsTdsGdsGdsTdsGdsmCdsTdsTeoGeoTesTesm
GalNAc3-19a
Ad
52



Ceo 












The structure of GalNAc3-7a was shown in Example 48.

Treatment

Male transgenic mice that express human Apo(a) were each injected subcutaneously once with an oligonucleotide and dosage listed in Table 106 or with PBS. Each treatment group consisted of 4 animals. Blood was drawn the day before dosing to determine baseline levels of Apo(a) protein in plasma and at 1 week following the first dose. Additional blood draws will occur weekly for approximately 8 weeks. Plasma Apo(a) protein levels were measured using an ELISA. The results in Table 106 are presented as the average percent of plasma Apo(a) protein levels for each treatment group, normalized to baseline levels (% BL), The results show that the antisense oligonucleotides reduced Apo(a) protein expression. Furthermore, the oligonucleotides comprising a GalNAc conjugate group exhibited even more potent reduction in Apo(a) expression than the oligonucleotide that does not comprise a conjugate group.







TABLE 106







Apo(a) plasma protein levels











Apo(a) at 1 week


ISIS No.
Dosage (mg/kg)
(% BL)












PBS
n/a
143


494372
50
58


681251
10
15


681255
10
14


681256
10
17


681257
10
24


681258
10
22


681260
10
26









Example 109
Synthesis of Oligonucleotides Comprising a GalNAc1-28 or GalNAc1-29 Conjugate




Oligonucleotide 241 is synthesized using procedures similar to those described in Example 71 to form the phosphoramidite intermediate, followed by procedures described in Example 10 to synthesize the oligonucleotide. The GalNAc1 cluster portion (GalNAc1-28a) of the conjugate group GalNAc1-28 can be combined with any cleavable moiety present on the oligonucleotide to provide a variety of conjugate groups. The structure of GalNAc1-28 (GalNAc1-28a-CM) is shown below:




In order to add the GalNAc1 conjugate group to the 3′-end of an oligonucleotide, procedures similar to those described in Example 71 are used to form the hydroxyl intermediate, which is then added to the solid support using procedures described in Example 7. The oligonucleotide synthesis is then completed using procedures described in Example 9 in order to form oligonucleotide 242.




The GalNAc1 cluster portion (GalNAc1-29a) of the conjugate group GalNAc1-29 can be combined with any cleavable moiety present on the oligonucleotide to provide a variety of conjugate groups. The structure of GalNAc1-29 (GalNAc1-29a-CM) is shown below:





Example 110
Synthesis of Oligonucleotides Comprising a GalNAc1-30 Conjugate




Oligonucleotide 246 comprising a GalNAc1-30 conjugate group, wherein Y is selected from O, S, a substituted or unsubstituted C1-C10 alkyl, amino, substituted amino, azido, alkenyl or alkynyl, is synthesized as shown above. The GalNAc1 cluster portion (GalNAc1-30a) of the conjugate group GalNAc1-30 can be combined with any cleavable moiety to provide a variety of conjugate groups. In certain embodiments, Y is part of the cleavable moiety. In certain embodiments, Y is part of a stable moiety, and the cleavable moiety is present on the oligonucleotide. The structure of GalNAc1-30a is shown below:




Example 111
Synthesis of oligonucleotides comprising a GalNAc2-31 or GalNAc2-32 conjugate




Oligonucleotide 250 comprising a GalNAc2-31 conjugate group, wherein Y is selected from O, S, a substituted or unsubstituted C1-C10 alkyl, amino, substituted amino, azido, alkenyl or alkynyl, is synthesized as shown above. The GalNAc2 cluster portion (GalNAc2-31a) of the conjugate group GalNAc2-31 can be combined with any cleavable moiety to provide a variety of conjugate groups. In certain embodiments, the Y




-containing group directly adjacent to the 5′-end of the oligonucleotide is part of the cleavable moiety. In certain embodiments, the Y-containing group directly adjacent to the 5′-end of the oligonucleotide is part of a stable moiety, and the cleavable moiety is present on the oligonucleotide. The structure of GalNAc2-31a is shown below:

The synthesis of an oligonucleotide comprising a GalNAc2-32 conjugate is shown below.




Oligonucleotide 252 comprising a GalNAc2-32 conjugate group, wherein Y is selected from O, S, a substituted or unsubstituted C1-C10 alkyl, amino, substituted amino, azido, alkenyl or alkynyl, is synthesized as shown above. The GalNAc2 cluster portion (GalNAc2-32a) of the conjugate group GalNAc2-32 can be combined with any cleavable moiety to provide a variety of conjugate groups. In certain embodiments, the Y-containing group directly adjacent to the 5′-end of the oligonucleotide is part of the cleavable moiety. In certain embodiments, the Y-containing group directly adjacent to the 5′-end of the oligonucleotide is part of a stable moiety, and the cleavable moiety is present on the oligonucleotide. The structure of GalNAc2-32a is shown below:




Example 112
Modified Oligonucleotides Comprising a GalNAc1 Conjugate
The oligonucleotides in Table 107 targeting SRB-1 were synthesized with a GalNAc1 conjugate group in order to further test the potency of oligonucleotides comprising conjugate groups that contain one GalNAc ligand.











TABLE 107







GalNAc

SEQ


ISIS No.
Sequences (5′ to 3′)
cluster
CM
ID No



















711461
 GesmCesTesTesmCesAdsGdsTdsmCdsAdsTds
GalNAc1-25a
Ad
30



GdsAdsmCdsTdsTesmCesmCesTesTe





 


711462
 GesmCesTesTesmCesAdsGdsTdsmCdsAdsTdsGds
GalNAc1-25a
PO
28



AdsmCdsTdsTesmCesmCesTesTe





 


711463
 GesmCeoTeoTeomCeoAdsGdsTdsmCdsAdsTdsGdsAdsm
GalNAc1-25a
PO
28



CdsTdsTeomCeomCeoTesTe





 


711465
 GesmCesTesTesmCesAdsGdsTdsmCdsAdsTdsGds
GalNAc1-26a
Ad
30



AdsmCdsTdsTesmCesmCesTesTe





 


711466
 GesmCesTesTesmCesAdsGdsTdsmCdsAdsTdsGdsAdsm
GalNAc1-26a
PO
28



CdsTdsTesmCesmCesTesTe





 


711467
 GesmCeoTeoTeomCeoAdsGdsTdsmCdsAdsTdsGdsAdsm
GalNAc1-26a
PO
28



CdsTdsTesmCeomCesTesTe





 


711468
 GesmCesTesTesmCesAdsGdsTdsmCdsAdsTdsGds
GalNAc1-28a
Ad
30



AdsmCdsTdsTesmCesmCesTesTe





 


711469
 GesmCesTesTesmCesAdsGdsTdsmCdsAdsTdsGdsAdsm
GalNAc1-28a
PO
28



CdsTdsTesmCesmCesTesTe





 


711470
 GesmCeoTeoTeomCeoAdsGdsTdsmCdsAdsTdsGdsAdsm
GalNAc1-28a
PO
28



CdsTdsTe0mCeomCesTesTe





 


713844
GesmCesTesTesmCesAdsGdsTdsmCdsAdsTdsGdsAdsmCdsTdsTesmCesm
GalNAc1-27a
PO
28



CesTesTeo′- 





 


713845
GesmCeoTeoTeomCeoAdsGdsTdsmCdsAdsTdsGdsAdsmCdsTdsTeomCeom
GalNAc1-27a
PO
28



CesTesTeo′- 





 


713846
GesmCeoTeoTeomCeoAdsGdsTdsmCdsAdsTdsGdsAdsmCdsTdsTeomCeom
GalNAc1-27a
Ad
29



CesTesTeo 





 


713847
GesmCesTesTesmCesAdsGdsTdsmCdsAdsTdsGdsAdsmCdsTdsTesmCesm
GalNAc1-29a
PO
28



CesTesTeo′- 





 


713848
GesmCeoTeoTeomCeoAdsGdsTdsmCdsAdsTdsGdsAdsmCdsTdsTeomCeom
GalNAc1-29a
PO
28



CesTesTeo′- 





 


713849
GesmCesTesTesmCesAdsGdsTdsmCdsAdsTdsGdsAdsmCdsTdsTesmCesm
GalNAc1-29a
Ad
29



CesTesTeo 





 


713850
GesmCeoTeoTeomCeoAdsGdsTdsmCdsAdsTdsGdsAdsmCdsTdsTeomCeom
GalNAc1-29a
Ad
29



CesTesTeo

## Claims

1. A compound comprising a modified oligonucleotide and a conjugate group, wherein the modified oligonucleotide is 10-30 linked nucleosides in length and consists of the nucleobase sequence of SEQ ID NO: 81, wherein the conjugate group comprises:




and wherein the conjugate group is linked to the modified oligonucleotide at the 5′ end of the modified oligonucleotide.

2. The compound of claim 1, wherein the modified oligonucleotide comprises at least one modified sugar.

3. The compound of claim 2, wherein the modified sugar is a bicyclic sugar.

4. The compound of claim 3, wherein the bicyclic sugar is selected from the group consisting of: 4′-(CH2)—O-2′ (LNA); 4′-(CH2)2—O-2′ (ENA); and 4′-CH(CH3)—O-2′ (cEt).

5. The compound of claim 2, wherein the modified sugar is 2′-O-methoxyethyl.

6. The compound of claim 1, wherein the modified oligonucleotide comprises at least one modified nucleobase.

7. The compound of claim 6, wherein the modified nucleobase is a 5-methylcytosine.

8. The compound of claim 1, wherein the compound is single-stranded.

9. The compound of claim 1, wherein the compound is double-stranded.

10. The compound of claim 1, wherein the modified oligonucleotide comprises at least one modified internucleoside linkage.

11. The compound of claim 10, wherein the modified internucleoside linkage is a phosphorothioate internucleoside linkage.

12. The compound of claim 10, wherein the modified oligonucleotide comprises at least one phosphodiester internucleoside linkage.

13. A composition comprising the compound of claim 1 or salt thereof and at least one of a pharmaceutically acceptable carrier or diluent.

14. A prodrug comprising the compound of claim 1.

15. A method comprising administering to an animal the compound or composition of claim 1.

16. The method of claim 15, wherein the animal is a human.

17. The method of claim 15, comprising co-administering the compound or composition and a second agent.