WO2025104709A1 - Microrna-378a-3p antisense oligonucleotides and uses thereof - Google Patents
Microrna-378a-3p antisense oligonucleotides and uses thereof Download PDFInfo
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- C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
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- C12N2310/34—Spatial arrangement of the modifications
- C12N2310/341—Gapmers, i.e. of the type ===---===
Definitions
- the present disclosure provides an oligonucleotide targeting miRNA 378a-3p, which can be used to treat a disease or condition affecting the liver.
- miRNA 378a-3p is known to be associated with Burkitt lymphoma cell growth (Niu F. et al., Cancers (Basel). 2020 Nov 27;12(12):3546. doi: 10.3390/cancersl2123546), promotes differentiation and inhibits proliferation of myoblasts by targeting HDAC4 in skeletal muscle development (Wei X., et al., RNA Biol. 2016; 13(12): 1300-1309. doi:
- MAFLD Metabolic dysfunction-associated fatty liver disease
- MASH metabolic dysfunction-associated steatohepatitis
- MAFLD is one of the most common chronic liver diseases and can cause hepatocyte injury, inflammation of the liver, and fibrosis of the liver (Pouwels, et al., BMC Endocr Disord 22:63 (2022)).
- MASH is a severe, progressive form of MAFLD which can cause cirrhosis of the liver, hepatocellular cancer, and death (Raza, et al., Front Biosci (Landmark Ed). 26:206 (2021)).
- MASH is the leading cause of liver transplants in the world, and, as of 2022, MAFLD was responsible for $103 billion in annual medical costs in the United States (Witkowski, et al. Pharmacoeconomics 40:751 (2022)).
- MAFLD was responsible for $103 billion in annual medical costs in the United States (Witkowski, et al. Pharmacoeconomics 40:751 (2022)).
- There are currently no FDA approved treatments for MAFLD or MASH (Attia, et al., Clin Transl Sci. 14: 11 (2021).
- the FDA raised concerns over a pending MASH therapy, finding that it increased the risk of diabetes and liver injury; this drug was previously expected to become the first FDA approved MASH therapy.
- the present disclosure is directed to oligonucleotides comprising a miR-378a-3p inhibitor.
- the oligonucleotide comprises siRNA, shRNA, antisense oligonucleotide, microRNA, IncRNA, mRNA, or any combination thereof. In some aspects, the oligonucleotide targets a miRNA, a gene encoding a protein, a gene encoding a transcription factor, a regulatory element, or any combination thereof.
- the oligonucleotide has from about 10 nucleotides and up to about 20, about 30, about 40, about 50, about 60, about 70, about 80, about 90, about 100, about 150, about 200, about 300, about 400, about 500, about 600, about 700, about 800, about 900, about 1000, about 1100, about 1200, about 1300, about 1400, about 1500, about 1600, about 1700, about 1800, about 1900, or about 2000 nucleotides.
- the oligonucleotide comprises a miRNA inhibitor.
- the miRNA is miR-378a-3p.
- the miR-378a-3p comprises 5'- ACUGGACUUGGAGUCAGAAGGC-3' (SEQ ID NO: 1).
- the miRNA inhibitor comprises a nucleotide sequence comprising 5'-AGUCCAG-3' and wherein the miRNA inhibitor comprises about 6 to about 30 nucleotides in length.
- the miRNA inhibitor comprises at least 1 nucleotide, at least 2 nucleotides, at least 3 nucleotides, at least 4 nucleotides, at least 5 nucleotides, at least 6 nucleotides, at least 7 nucleotides, at least 8 nucleotides, at least 9 nucleotides, at least 10 nucleotides, at least 11 nucleotides, at least 12 nucleotides, at least 13 nucleotides, at least 14 nucleotides, at least 15 nucleotides, at least 16 nucleotides, at least 17 nucleotides, at least 18 nucleotides, at least 19 nucleotides, or at least 20 nucleotides at the 5' of the nucleotide sequence.
- the miRNA inhibitor comprises at least 1 nucleotide, at least 2 nucleotides, at least 3 nucleotides, at least 4 nucleotides, at least 5 nucleotides, at least 6 nucleotides, at least 7 nucleotides, at least 8 nucleotides, at least 9 nucleotides, at least 10 nucleotides, at least 11 nucleotides, at least 12 nucleotides, at least 13 nucleotides, at least 14 nucleotides, at least 15 nucleotides, at least 16 nucleotides, at least 17 nucleotides, at least 18 nucleotides, at least 19 nucleotides, or at least 20 nucleotides at the 3' of the nucleotide sequence.
- the miRNA inhibitor has a sequence selected from the group consisting of: 5'-AGUCCAG-3', 5'-AAGUCCAG-3', 5'-CAAGUCCAG-3', 5'-CCAAGUCCAG-3' (SEQ ID NO: 2), 5'-UCCAAGUCCAG-3' (SEQ ID NO: 3), 5'-CUCCAAGUCCAG-3' (SEQ ID NO: 4), 5'- ACUCCAAGUCCAG-3' (SEQ ID NO: 5), 5'-GACUCCAAGUCCAG-3' (SEQ ID NO: 6), 5'- UGACUCCAAGUCCAG-3' (SEQ ID NO: 7), 5'-CUGACUCCAAGUCCAG-3' (SEQ ID NO: 8), 5'- UCUGACUCCAAGUCCAG-3' (SEQ ID NO: 9), 5'- UUCUGACUCCAAGUCCAG-3' (SEQ ID NO: 10), 5'-CUUCUGACUCCAAGUCCAG-3' (SEQ ID NO: 10), 5
- the miRNA inhibitor has a sequence selected from the group consisting of: 5'-AGTCCAG-3', 5'-AAGTCCAG-3', 5'-CAAGTCCAG -3', 5'-CCAAGTCCAG-3' (SEQ ID NO: 26), 5'-TCCAAGTCCAG-3' (SEQ ID NO: 27), 5'-CTCCAAGTCCAG-3' (SEQ ID NO: 28), 5'-ACTCCAAGTCCAG-3' (SEQ ID NO: 29), 5'-GACTCCAAGTCCAG-3' (SEQ ID NO: 30), 5'- TGACTCCAAGTCCAG-3' (SEQ ID NO: 31), 5'-CTGACTCCAAGTCCAG-3' (SEQ ID NO: 32), 5'- TCTGACTCCAAGTCCAG-3' (SEQ ID NO: 33), 5'-TTCTGACTCCAAGTCCAG-3' (SEQ ID NO: 34), 5'-CTTCTGACTCCAAGTCCAG-3' (SEQ ID NO: 26), 5'-
- the sequence of the miRNA inhibitor is at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% sequence identity to 5'- GCCUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 25) or 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49).
- the miRNA inhibitor has a sequence that has at least 90% similarity to 5'-GCCUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 25) or 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49).
- the miRNA inhibitor comprises the nucleotide sequence 5'-GCCUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 25) or 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49) with one substitution or two substitutions.
- the miRNA inhibitor comprises the nucleotide sequence 5'- GCCUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 25) or 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49). In some aspects, the miRNA inhibitor comprises the nucleotide sequence 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49).
- the miRNA inhibitor comprises at least one modified nucleotide.
- the modified nucleotide is a locked nucleic acid (LNA), an unlocked nucleic acid (UNA), an arabino nucleic acid (ABA), a bridged nucleic acid (BNA), and/or a peptide nucleic acid (PNA).
- the modified nucleotide comprises 2'-O-alkyl-RNA; 2'-amino-DNA; 2'-fluoro-DNA; arabino nucleic acid (ANA); 2'-fluoro-ANA, hexitol nucleic acid (HNA), intercalating nucleic acid (INA), constrained ethyl nucleoside (cEt), 2'-O-methyl nucleic acid (2 - OMe), 2'-O-methoxyethyl nucleic acid (2'-M0E), 5'-methyl pyrimidine nucleobase, or any combination thereof.
- the oligonucleotide comprises a nucleotide sequence having 5 to 30 nucleotides in length.
- the oligonucleotide is 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26 nucleotides in length. In some aspects, the oligonucleotide is a gapmer, a mixmer, a totalmer, or any combination thereof. In some aspects, the oligonucleotide comprises a backbone modification. In some aspects, the backbone modification is a phosphodiester linkage, a phosphotriester linkage, a methylphosphonate linkage, a phosphoramidate linkage, a phosphorothioate linkage, a phosphorodiamidate morpholino oligomer (PMO), or any combination thereof.
- PMO phosphorodiamidate morpholino oligomer
- the miRNA inhibitor has a nucleotide sequence comprising 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49) and a backbone modification comprising one or more phosphorothioate linkages (SEQ ID NO: 55).
- the disclosure provides an oligonucleotide comprising, consisting essentially of, or consisting of the nucleotide sequence as set forth in 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein each of nucleotide residues 1, 2, 3, and 22 is a LNA; and each of nucleotide residues 4-21 is a DNA (SEQ ID NO: 57).
- each of nucleotide residues 2 and 3 comprise a 5'-methyl pyrimidine nucleobase modification (SEQ ID NO: 56).
- the nucleotide sequence comprises one or more phosphorothioate linkages (SEQ ID NO: 58).
- an oligonucleotide comprising, consisting essentially of, or consisting of the nucleotide sequence as set forth in 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49); wherein: the nucleotide sequence comprises a fully phosphorothioate modified backbone structure; each of nucleotide residues 1, 2,
- each of nucleotide residues 4-21 is a DNA; and each of nucleotide residues 2 and 3 comprises a 5'-methyl pyrimidine nucleobase modification (SEQ ID NO: 50).
- the disclosure provides an oligonucleotide comprising, consisting essentially of, or consisting of the nucleotide sequence as set forth in 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein each of nucleotide residues 1, 2, 3, and 22 is a LNA; and each of nucleotide residues 4-21 is a DNA (SEQ ID NO: 57) and each of nucleotide residues 2, 3, 6, 10, 12, 13, 18, and 19 comprise a 5'-methyl pyrimidine nucleobase modification (SEQ ID NO: 72).
- the nucleotide sequence comprises one or more phosphorothioate linkages (SEQ ID NO: 73).
- the disclosure provides an oligonucleotide comprising, consisting essentially of, or consisting of the nucleotide sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49); wherein: the nucleotide sequence comprises a fully phosphorothioate modified backbone structure; each of nucleotide residues 1, 2, 3, and 22 is a LNA; each of nucleotide residues 4-21 is a DNA; and each of nucleotide residues 2, 3, 6, 10, 12, 13, 18, and 19 comprises a 5'-methyl pyrimidine nucleobase modification (SEQ ID NO: 67).
- the disclosure provides an oligonucleotide comprising, consisting essentially of, or consisting of the nucleotide sequence as set forth in 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein each of nucleotide residues 1, 2, 3,
- each of nucleotide residues 6-17 is a DNA (SEQ ID NO: 74).
- each of nucleotide residues 2, 3, 6, 10, 12, 13, 18, and 19 comprises a 5'-methyl pyrimidine nucleobase modification (SEQ ID NO: 75).
- the nucleotide sequence comprises one or more phosphorothioate linkages (SEQ ID NO: 76).
- the disclosure provides an oligonucleotide comprising, consisting essentially of, or consisting of the nucleotide sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49); wherein: the nucleotide sequence comprises a fully phosphorothioate modified backbone structure; each of nucleotide residues 1, 2, 3, 4, 5, 18, 19, 20, 21, and 22 is aLNA; each of nucleotide residues 6-17 is aDNA; and each of nucleotide residues 2, 3, 6, 10, 12, 13, 18, and 19 comprises a 5'-methyl pyrimidine nucleobase modification (SEQ ID NO: 70).
- an optional targeting moiety is conjugated or linked to the oligonucleotide to form a conjugate.
- the targeting moiety is capable of targeting a tissue.
- the tissue is liver, brain, kidney, lung, ovary, pancreas, thyroid, breast, stomach, or any combination thereof.
- the tissue is liver.
- the targeting moiety is capable of being transported by glycose transporter type 1 (GLUT1).
- the targeting moiety is an amino acid.
- the targeting moiety comprises a branched-chain or aromatic amino acid.
- the targeting moiety is phenylalanine, valine, leucine, and/or isoleucine.
- the amino acid is phenylalanine.
- the targeting moiety is linked to the oligonucleotide by a linker.
- the linker is a non-cleavable linker.
- the linker is a cleavable linker.
- the cleavable linker is cleavable by a protease.
- the linker is a bioreducible linker, an acid cleavable linker, a click-to-release linker, a pyrophosphatase cleavable linker, a beta-glucuronidase cleavable linker, or any combination thereof.
- the present disclosure provides a pharmaceutical composition
- a pharmaceutical composition comprising the oligonucleotide or conjugate disclosed herein and a pharmaceutically acceptable carrier.
- the present disclosure provides a method of preparing the conjugate disclosed herein or the pharmaceutical composition disclosed herein comprising linking the oligonucleotide to the targeting moiety, through the optional linker. In some aspects, the method further comprises purifying the conjugate.
- the present disclosure provides a method of treating a disease or condition in a subject in need thereof comprising administering the oligonucleotide or conjugate disclosed herein or the pharmaceutical composition disclosed herein to the subject.
- the disease or conition is cirrhosis, type 2 diabetes mellitus, hepatitis, fibrosis, fibrosis of the liver, obesity (e.g., abdominal obesity), dyslipidemia (hypercholesterolemia, hypertriglyceridemia), atherosclerosis, type 2 diabetes (T2D), hepatocellular carcinoma (HCC), hypertension, polycystic ovary syndrome (PCOS), chronic kidney disease (CKD), or cardiovascular disease (CVD).
- obesity e.g., abdominal obesity
- dyslipidemia hyperherosesterolemia, hypertriglyceridemia
- HCC hepatocellular carcinoma
- PCOS polycystic ovary syndrome
- CKD chronic kidney disease
- CVD cardiovascular disease
- the disease or condition is obesity (e.g., abdominal obesity). In some aspects, the obesity comprises an abdominal obesity. In some aspects the disease or condition is a liver disease or condition. In some aspect the liver disease or condition is metabolic dysfunction-associated fatty liver disease (MAFLD) or metabolic dysfunction-associated steatohepatitis (MASH). In some aspects, the oligonucleotide useful for the method exhibits a longer half-life than a corresponding oligonucleotide not linked to the targeting moiety. In some aspects, the subject for the method is a mammal.
- MASH metabolic dysfunction-associated fatty liver disease
- FIG. 1A and IB show the effect of ASO Ml (Ml) administration on the miR-378a- 3p expression and deposition of lipid droplets in Oleic Acid (OA)/Palmitic Acid (PA)-administered HepG2 cells.
- FIG. 2A-2C show miR-378a-3p expression in high fat diet (HFD)-fed mice.
- FIG. 2A shows a schedule for the experiments on the HFD-fed mouse model.
- a quantitative summary comparing the different groups is presented under the chart. All data are mean ⁇ SEM. *P ⁇ 0.05 and ***P ⁇ 0.001 compared to the SD-fed mice. Significance was determined using a Student’s unpaired t-test.
- FIG. 3A-3G show the effects of ASO Ml administration in the HFD-induced metabolic dysfunction-associated fatty liver disease and LPS-induced metabolic dysfunction- associated steatohepatitis mouse models.
- FIG. 3A shows the schedule of the experiments for the HFD-induced metabolic dysfunction-associated fatty liver disease and LPS-induced metabolic dysfunction-associated steatohepatitis mouse models.
- FIG. 3E shows morphological analysis of liver sections from each group carried out via H&E staining (first and third row) and also shows lipid droplets in the tissue sections from each group analyzed via oil red O staining (second and fourth row). Images from the induced MAFLD (top two rows) and MASH (bottom two rows) groups are shown.
- FIGs. 4A-4C show a schematic diagram of the naked Homo sapiens-sm ⁇ Q stranded-microRNA-378a-3p (FIG. 4A), an antisense oligonucleotide (ASO) Ml which possesses various nucleotide modifications (e.g., backbone modification, nucleobase modification), specifically 100% of the backbone linkages are phosphorothioate linkages, nucleotide residues 1, 2, 3, and 22 are a LNA, nucleotide residues 4-21 are a DNA, and nucleotide residues 2 and 3 comprise a 5'-methyl pyrimidine nucleobase modification (FIG.
- ASO antisense oligonucleotide
- nucleotide residues 1, 2, 3, and 22 are a 2 ’-MOE
- nucleotide residues 4-21 are a DNA
- nucleotide residues 2 and 3 comprise a 5'-methyl pyrimidine nucleobase modification (FIG. 4C).
- the Nucelotide Sequence, Complement to the Nucleotide Sequence, Length, GC (guanine-cytosine) content, Melting Temperature, Seed Sequence, and Molecular Weight for each are also shown.
- FIGs. 5A-5D show the analysis of miR-378a-3p expression level after naked
- FIG. 5A shows the IC50, % at KD Max, and % expression of miR-378a-3p in HepG2 cells for naked ASO, modified ASO #1, and modified ASO #2 from 0 nM to 1000 nM.
- FIG. 5A shows the IC50, % at KD Max, and % expression of miR-378a-3p in HepG2 cells for naked ASO, modified ASO #1, and modified ASO #2 from 0 nM to 1000 nM.
- FIG. 5B shows % inhibition of miR-378a-3p in HepG2 cells for naked ASO, modified ASO #1, and modified ASO #2 at concentrations of 15.625, 31.25, 61.25, 125, 250, 500 nM.
- FIG. 5C shows the IC50, % at KD Max, and % expression of miR-378a-3p in BV-2 cells for naked ASO, modified ASO #1, and modified ASO #2 from 0 nM to 1000 nM.
- FIG. 5D shows % inhibition of miR- 378a-3p in BV-2 cells for naked ASO, modified ASO #1, and modified ASO #2 at concentrations of 15.625, 31.25, 61.25, 125, 250, 500 nM.
- FIGs. 6A-6C show a comparison of anti-inflammatory effect 24 hours after transfection of Naked ASO, Modified ASO #1, and Modified ASO #2 in BV-2 cells.
- FIG. 6B and 6C show ELISA of IL-1 (FIG.
- FIGs. 7A-7G show the comparison of the reduction effects of semaglutide, tirzepatide, and ASO Ml on body weight and cumulative food intake in HFD mice.
- FIG. 7A shows the schedule of the experiments for the HFD mouse models. After 1 week of acclimation, mice were fed with high-fat diet for 12 weeks. HFD mice were dosed once daily for 14 days with vehicle, semaglutide (500 pg/kg), tirzepatide (500 pg/kg) or ASO-M1 (500 pg/kg
- FIG. 7B shows the body weight change % for the control, semaglutide, tirzepatide and ASO Ml administered HFD mice from days 1 to 14.
- FIG. 7C shows the cumulative food intake (measure of appetite) for the control, semaglutide, tirzepatide and ASO Ml administered HFD mice from days 1 to 14.
- FIG. 7D shows quantification of mass (g) changes of fat mass and lean mass after daily injection of control, semaglutide, tirzepatide or ASO Ml for 14 days.
- FIGs. 7E-7G show the Epididymal (eWAT; visceral fat) (FIG. 7E), inguinal WAT (iWAT; Subcutaneous fat) (FIG. 7F) and interscapular BAT (iBAT) (FIG.
- FIGs. 7E-7G Tissue weight (left panel) and Ratio of tissue weight to body weight (right panel) are shown for FIGs. 7E-7G. All data are mean ⁇ SD. *P ⁇ 0.05, **P ⁇ 0.01, ***p ⁇ 0.001 and ****p ⁇ 0.0001 compared to the high-fat diet (Vehicle) group. # P ⁇ 0.05, ##P ⁇ 0.01, ###P ⁇ 0.001 and ####P ⁇ 0.0001 for the indicated comparisons. Significance was determined using a one-way ANOVA and post-hoc tukey’s test.
- FIGs. 8A-8G show the comparison of the reduction effects of ASO Ml at 2 different administration schedules on body weight and cumulative food intake in HFD mice.
- FIG. 8B shows changes in body weight of HFD mice after 3-day interval injection of ASO Ml (1.5 mg/kg), weekly injection of ASO Ml (5 mg/kg), or control.
- FIG. 8C shows the cumulative food intake (measure of appetite) for the control, 3-day interval injection of ASO Ml (1.5 mg/kg), and weekly injection of ASO Ml (5 mg/kg) administered HFD mice for 3 weeks.
- FIG. 8D shows quantification of mass (g) changes of fat mass and lean mass after control injection, 3-day interval injection of ASO Ml (1.5 mg/kg), or weekly injection of ASO Ml (5 mg/kg) in HFD mice for 3 weeks.
- FIGs. 8E-8G show the Epididymal (eWAT; visceral fat) (FIG.
- FIG. 8E inguinal WAT (iWAT; Subcutaneous fat) (FIG. 8F) and interscapular BAT (iBAT) (FIG. 8G) after control injection, 3-day interval injection of ASO Ml (1.5 mg/kg), or weekly injection of ASO Ml (5 mg/kg) in HFD mice for 3 weeks.
- Tissue weight (left panel) and Ratio of tissue weight to body weight (right panel) are shown for FIGs. 8E- 8G. All data are mean ⁇ SD. **P ⁇ 0.01, ***p ⁇ 0.001 and ****p ⁇ 0.0001 compared to the high- fat diet (Vehicle) group. # P ⁇ 0.05, and ##P ⁇ 0.01, for the indicated comparisons. Significance was determined using a one-way ANOVA and post-hoc tukey’s test.
- FIG. 9B shows changes in body weight of HFD mice after injection of control, weekly injection of ASO Ml (10 mg/kg) starting at week 8, and single injection of ASO-M1 (30 mg/kg) at week 10, across 12 weeks.
- FIGs 9C-9G show analysis of miRNA and mRNA expression levels in liver obtained from standard diet (SD), HFD and HFD+ASO-M1 mice (under both weekly injection of ASO Ml (10 mg/kg), and single injection of ASO-M1 (30 mg/kg) conditions).
- miR-378a-3p levels (FIG. 9C) were quantified by qRT-PCR and normalized to U6B.
- Atg2a (FIG. 9D), Glp2r (FIG. 9E), Igflr (FIG. 9F) and Igfl (FIG. 9G) mRNA levels were normalized to Actb. All data are mean ⁇ SEM.
- lOA and lOB mice were injected 2 times per week with lO mpk ASO-M1 and terminated on 10th week (top row), 4 times with lOmpk and terminated on 12th week (middle row), or injected once with 30mpk on 10th week then terminated 2 weeks later (bottom row). All images were obtained under lOOx magnification.
- FIG. 11A-11F show clinical chemistry analysis of lipid profiles in SD, HFD and HFD+ASO-M1 mice (at both 10 and 30mg/kg dosing schedules). Specifically the lipid profiles of low-density lipoprotein cholesterol (LDL) (FIG. 11 A), high density lipoprotein cholesterol (HDL) (FIG. 11B), triglyceride (TG) (FIG. 11C), total cholesterol (TC) (FIG. 11D), alanine transaminase (ALT) (FIG. HE) and aspartate transaminase (AST) (FIG. HF). All data are mean ⁇ SEM. ****p ⁇ 0.0001 compared to the Standard diet (SD) group. ###P ⁇ 0.001 and ####P ⁇ 0.0001 compared to the High-fat diet (HFD) group. Significance was determined using a one-way ANOVA and post- hoc tukey’s test.
- LDL low-density lipoprotein
- FIGs. 12A-12I show a schematic diagram of the naked Homo sapiens-sm ⁇ Q stranded-microRNA-378a-3p (FIG. 12A), and modified antisense oligonucleotides (ASO) Ml (FIG. 12B), ML (FIG. 12C), M2 (FIG. 12D), M4 (FIG. 12E), M5 (FIG. 12F), M6 (FIG. 12G), M7 (FIG. 12H), and M8 (FIG. 121).
- ASO antisense oligonucleotides
- FIGs. 13A and 13B show the inhibitory activity of modified miR-378a-3p ASOs with RNAiMAX in HepG2 and Hep3B cells.
- FIGs. 14A and 14B show the inhibitory activity of modified miR-378a-3p ASOs in Hep3B cells without co-administration with a transfection reagent.
- FIG. 14A shows miR- 378a-3p expression level after administration of ASO #M1, #ME, #M4, #M5, #M6, #M7 and #M8 (1000 nM).
- FIGs. 15A and 15B show a comparison of miR-378a-3p expression levels of ASO #M1 and #M7 with/without transfection reagent in Hep3B cells.
- FIG. 15A shows miR-378a-3p expression level after transfection of ASO #M1 or #M7 in Hep3B cells, with RNAiMAX, in a dose-dependent manner (0.937, 3.75, 15, 60 and 240 nM) for 24 h.
- FIG. 16 shows in vivo activity of modified miR-378a-3p ASOs in C57BL/6 strain rodents.
- FIG. 17 shows the stability of modified miR-378a-3p ASO in mouse plasma. Stability is shown by measuring absorbance for ASO #M1, #M2, #M4, #M5, #M6, #M7 and #M8 at 0 minutes, 30 minutes, 1 hour, 1 day, 3 days, 7 days, 15 days, and 30 days. All data are mean ⁇ SEM.
- the present disclosure is directed to oligonucleotides comprising a miR-378a-3p inhibitor.
- Non-limiting examples of various aspects are shown in the present disclosure.
- a or “an” entity refers to one or more of that entity; for example, "a nucleotide sequence,” is understood to represent one or more nucleotide sequences.
- the terms “a” (or “an”), “one or more,” and “at least one” can be used interchangeably herein.
- the claims can be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as “solely,” “only” and the like in connection with the recitation of claim elements, or use of a negative limitation.
- MASH is interchangeable with the term NASH (nonalcoholic steatohepatitis).
- MAFLD is interchangeable with the term NAFLD (non-alcoholic fatty liver disease).
- ranges recited are understood to be shorthand for all of the values within the range, inclusive of the recited endpoints.
- a range of 1 to 10 is understood to include any number, combination of numbers, or sub-range from the group consisting of 1, 2, 3, 4, 5, 6, 7, 8, 9, and 10.
- Nucleotides are referred to by their commonly accepted single-letter codes. Unless otherwise indicated, nucleotide sequences are written left to right in 5' to 3' orientation. Specific nucleotides (nucleotide residues) in a sequence may be referred to by their numeric position in the sequence with nucleotide 1 (nucleotide residue 1) being the first residue on the 5’ end, nucleotide 2 (nucleotide residue 2) being the second residue on the 5’ end, and so forth, until reaching the 3’ end. Nucleotides are referred to herein by their commonly known one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Accordingly, ‘a’ represents adenine, ‘c’ represents cytosine, ‘g’ represents guanine, ‘f represents thymine, and ‘u’ represents uracil.
- Amino acid sequences are written left to right in amino to carboxy orientation. Amino acids are referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission.
- administration refers to introducing a composition, such as an oligonucleotide or conjugate of the present disclosure, into a subject via a pharmaceutically acceptable route.
- the introduction of a composition, such as an oligonucleotide or conjugate of the present disclosure, into a subject is by any suitable route, including intratumorally, orally, pulmonarily, intranasally, parenterally (intravenously, intraarterially, intramuscularly, intraperitoneally, or subcutaneously), rectally, intralymphatically, intrathecally, periocularly or topically.
- Administration includes self-administration and the administration by another.
- a suitable route of administration allows the composition or the agent to perform its intended function. For example, if a suitable route is intravenous, the composition is administered by introducing the composition or agent into a vein of the subject.
- the term “approximately,” as applied to one or more values of interest, refers to a value that is similar to a stated reference value. In certain aspects, the term “approximately” refers to a range of values that fall within 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, or less in either direction (greater than or less than) of the stated reference value unless otherwise stated or otherwise evident from the context (except where such number would exceed 100% of a possible value).
- Nucleotides or amino acids that are relatively conserved are those that are conserved amongst more related sequences than nucleotides or amino acids appearing elsewhere in the sequences.
- two or more sequences are said to be “completely conserved” or “identical” if they are 100% identical to one another.
- two or more sequences are said to be “highly conserved” if they are at least 70% identical, at least 80% identical, at least 90% identical, or at least 95% identical to one another.
- two or more sequences are said to be “highly conserved” if they are about 70% identical, about 80% identical, about 90% identical, about 95% identical, about 98% identical, or about 99% identical to one another.
- two or more sequences are said to be "conserved” if they are at least 30% identical, at least 40% identical, at least 50% identical, at least 60% identical, at least 70% identical, at least 80% identical, at least 90% identical, or at least 95% identical to one another. In some aspects, two or more sequences are said to be “conserved” if they are about 30% identical, about 40% identical, about 50% identical, about 60% identical, about 70% identical, about 80% identical, about 90% identical, about 95% identical, about 98% identical, or about 99% identical to one another. Conservation of sequence may apply to the entire length of a polynucleotide or polypeptide or may apply to a portion, region or feature thereof.
- derived from refers to a component that is isolated from or made using a specified molecule or organism, or information (e.g., amino acid or nucleic acid sequence) from the specified molecule or organism.
- a nucleic acid sequence that is derived from a second nucleic acid sequence can include a nucleotide sequence that is identical or substantially similar to the nucleotide sequence of the second nucleic acid sequence.
- the derived species can be obtained by, for example, naturally occurring mutagenesis, artificial directed mutagenesis or artificial random mutagenesis.
- the mutagenesis used to derive nucleotides or polypeptides can be intentionally directed or intentionally random, or a mixture of each.
- the mutagenesis of a nucleotide or polypeptide to create a different nucleotide or polypeptide derived from the first can be a random event (e.g., caused by polymerase infidelity) and the identification of the derived nucleotide or polypeptide can be made by appropriate screening methods, e.g., as discussed herein.
- Mutagenesis of a polypeptide typically entails manipulation of the polynucleotide that encodes the polypeptide.
- complementary and complementarity refer to two or more oligomers (i.e., each comprising a nucleobase sequence), or between an oligomer and a target gene, that are related with one another by Watson-Crick base-pairing rules.
- nucleobase sequence “T-G-A (5’->3’) is complementary to the nucleobase sequence “A-C-T (3’-> 5’).
- Complementarity may be "partial,” in which less than all of the nucleobases of a given nucleobase sequence are matched to the other nucleobase sequence according to base pairing rules.
- complementarity between a given nucleobase sequence and the other nucleobase sequence may be about 70%, about 75%, about 80%, about 85%, about 90% or about 95%. Or, there may be "complete” or “perfect” (100%) complementarity between a given nucleobase sequence and the other nucleobase sequence to continue the example.
- the degree of complementarity between nucleobase sequences has significant effects on the efficiency and strength of hybridization between the sequences.
- downstream refers to a nucleotide sequence that is located 3’ to a reference nucleotide sequence.
- downstream nucleotide sequences relate to sequences that follow the starting point of transcription. For example, the translation initiation codon of a gene is located downstream of the start site of transcription.
- excipient and “carrier” are used interchangeably and refer to an inert substance added to a pharmaceutical composition to further facilitate administration of a compound.
- homology refers to the overall relatedness between polymeric molecules, e.g. between nucleic acid molecules (e.g. DNA molecules and/or RNA molecules) and/or between polypeptide molecules.
- nucleic acid molecules e.g. DNA molecules and/or RNA molecules
- homology implies an evolutionary relationship between two molecules. Thus, two molecules that are homologous will have a common evolutionary ancestor.
- homology encompasses both to identity and similarity.
- identity refers to the overall monomer conservation between polymeric molecules, e.g, between polypeptide molecules or polynucleotide molecules (e.g. DNA molecules and/or RNA molecules).
- polypeptide molecules or polynucleotide molecules e.g. DNA molecules and/or RNA molecules.
- identity without any additional qualifiers, e.g., protein A is identical to protein B, implies the sequences are 100% identical (100% sequence identity). Describing two sequences as, e.g., "70% identical,” is equivalent to describing them as having, e.g., "70% sequence identity.”
- Calculation of the percent identity of two polypeptide or polynucleotide sequences can be performed by aligning the two sequences for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second polypeptide or polynucleotide sequences for optimal alignment and non-identical sequences can be disregarded for comparison purposes).
- the length of a sequence aligned for comparison purposes is at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95%, or about 100% of the length of the reference sequence.
- the amino acids at corresponding amino acid positions, or bases in the case of nucleic acid sequences, are then compared.
- Suitable software programs are available from various sources, and for alignment of both protein and nucleotide sequences.
- One suitable program to determine percent sequence identity is bl2seq, part of the BLAST suite of program available from the U.S. government's National Center for Biotechnology Information BLAST web site (blast.ncbi.nlm.nih.gov).
- B12seq performs a comparison between two sequences using either the BLASTN or BLASTP algorithm.
- BLASTN is used to compare nucleic acid sequences
- BLASTP is used to compare amino acid sequences.
- Sequence alignments can be conducted using methods known in the art such as MAFFT, Clustal (ClustalW, Clustal X or Clustal Omega), MUSCLE, etc.
- Different regions within a single polynucleotide or polypeptide target sequence that aligns with a polynucleotide or polypeptide reference sequence can each have their own percent sequence identity. It is noted that the percent sequence identity value is rounded to the nearest tenth. For example, 80.11, 80.12, 80.13, and 80.14 are rounded down to 80.1, while 80.15, 80.16, 80.17, 80.18, and 80.19 are rounded up to 80.2. It also is noted that the length value will always be an integer.
- sequence alignments can be generated by integrating sequence data with data from heterogeneous sources such as structural data (e.g., crystallographic protein structures), functional data (e.g., location of mutations), or phylogenetic data.
- a suitable program that integrates heterogeneous data to generate a multiple sequence alignment is T-Coffee, available at www.tcoffee.org, and alternatively available, e.g, from the EBI. It will also be appreciated that the final alignment used to calculate percent sequence identity can be curated either automatically or manually.
- isolating or purifying as used herein is the process of removing, partially removing (e.g., a fraction) of a composition of the present disclosure from a sample containing contaminants.
- an isolated composition has no detectable undesired activity or, alternatively, the level or amount of the undesired activity is at or below an acceptable level or amount.
- an isolated composition has an amount and/or concentration of desired composition of the present disclosure, at or above an acceptable amount and/or concentration and/or activity.
- the isolated composition is enriched as compared to the starting material from which the composition is obtained. This enrichment can be by at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, or greater than 99.9999% as compared to the starting material.
- isolated preparations are substantially free of residual biological products.
- the isolated preparations are 100% free, at least about 99% free, at least about 98% free, at least about 97% free, at least about 96% free, at least about 95% free, at least about 94% free, at least about 93% free, at least about 92% free, at least about 91% free, or at least about 90% free of any contaminating biological matter.
- Residual biological products can include abiotic materials (including chemicals) or unwanted nucleic acids, proteins, lipids, or metabolites.
- the term "linked” as used herein refers to a first amino acid sequence or polynucleotide sequence covalently or non-covalently joined to a second amino acid sequence or polynucleotide sequence, respectively.
- the first amino acid or polynucleotide sequence can be directly joined or juxtaposed to the second amino acid or polynucleotide sequence or alternatively an intervening sequence can covalently join the first sequence to the second sequence.
- the term "linked” means not only a fusion of a first polynucleotide sequence to a second polynucleotide sequence at the 5’-end or the 3’-end, but also includes insertion of the whole first polynucleotide sequence (or the second polynucleotide sequence) into any two nucleotides in the second polynucleotide sequence (or the first polynucleotide sequence, respectively).
- the first polynucleotide sequence can be linked to a second polynucleotide sequence by a phosphodiester bond or a linker.
- the linker can be, e.g., a polynucleotide.
- miRNA or “miR” or “microRNA” are used interchangeably and refer to a microRNA molecule found in eukaryotes that is involved in RNA-based gene regulation. Accordingly, the terms “miR-378-3p” and “miRNA 387a-3p” refer to microRNA 387a-3p molecule. Exemplary sequences for miR-378-3p and a miR-378a-3p inhibitor are provided in Table 1. The term will be used to refer to the single-stranded RNA molecule processed from a precursor. Names of miRNAs and their sequences related to the present disclosure are provided herein.
- MicroRNAs recognize and bind to target mRNAs through imperfect base pairing leading to destabilization or translational inhibition of the target mRNA and thereby downregulate target gene expression. Conversely, targeting miRNAs via molecules comprising a miRNA binding site (generally a molecule comprising a sequence complementary to the seed region of the miRNA) can reduce or inhibit the miRNA-induced translational inhibition leading to an upregulation of the target gene.
- a miRNA binding site generally a molecule comprising a sequence complementary to the seed region of the miRNA
- miRNA 387a-3p inhibitor refers to a compound that can decrease, alter, and/or modulate miRNA 387a-3p expression, function, and/or activity.
- the miRNA 387a-3p inhibitor can be a polynucleotide sequence that is at least partially complementary to the target miRNA 387a-3p nucleic acid sequence, such that the miRNA 387a-3p inhibitor hybridizes to the target miRNA sequence.
- a miRNA 387a-3p inhibitor of the present disclosure comprises a nucleotide sequence encoding a nucleotide molecule that is at least partially complementary to the target miRNA 387a-3p nucleic acid sequence, such that the miRNA 387a-3p inhibitor hybridizes to the miRNA 387a-3p sequence.
- the hybridization of the miRNA 387a-3p inhibitor to the miRNA 387a-3p sequence decreases, alters, and/or modulates the expression, function, and/or activity of miRNA 387a-3p.
- mismatch refers to one or more nucleobases (whether contiguous or separate) in an oligomer nucleobase sequence that are not matched to a target pre- mRNA according to base pairing rules. While perfect complementarity is often desired, some aspects can include one or more but preferably 6, 5, 4, 3, 2, or 1 mismatches with respect to the target pre-mRNA. Variations at any location within the oligomer are included. In certain aspects, antisense oligomers of the disclosure include variations in nucleobase sequence near the termini, variations in the interior, and if present are typically within about 6, 5, 4, 3, 2, or 1 subunits of the 5' and/or 3' terminus. In certain aspects, one, two, or three nucleobases can be removed and still provide on-target binding.
- the terms “modulate,” “modify,” and grammatical variants thereof, generally refer when applied to a specific concentration, level, expression, function or behavior, to the ability to alter, by increasing or decreasing, e.g., directly or indirectly promoting/stimulating/up-regulating or interfering with/inhibiting/down-regulating the specific concentration, level, expression, function or behavior, such as, e.g., to act as an antagonist or agonist.
- a modulator can increase and/or decrease a certain concentration, level, activity or function relative to a control, or relative to the average level of activity that would generally be expected or relative to a control level of activity.
- Nucleic acid refers to the phosphate ester polymeric form of ribonucleosides (adenosine, guanosine, uridine or cytidine; "RNA molecules”) or deoxyribonucleosides (deoxyadenosine, deoxyguanosine, deoxythymidine, or deoxycytidine; "DNA molecules”), or any phosphoester analogs thereof, such as phosphorothioates and thioesters, in either single stranded form, or a double-stranded helix.
- RNA molecules phosphate ester polymeric form of ribonucleosides
- deoxyribonucleosides deoxyadenosine, deoxyguanosine, deoxythymidine, or deoxycytidine
- DNA molecules or any phosphoester analogs thereof, such as phosphorothioates and thioesters, in either single stranded form, or a double-stranded
- Single stranded nucleic acid sequences refer to single-stranded DNA (ssDNA) or single-stranded RNA (ssRNA). Double stranded DNA- DNA, DNA-RNA and RNA-RNA helices are possible.
- nucleic acid molecule and in particular DNA or RNA molecule, refers only to the primary and secondary structure of the molecule, and does not limit it to any particular tertiary forms. Thus, this term includes doublestranded DNA found, inter alia, in linear or circular DNA molecules (e.g., restriction fragments), plasmids, supercoiled DNA and chromosomes.
- a "recombinant DNA molecule” is a DNA molecule that has undergone a molecular biological manipulation.
- DNA includes, but is not limited to, cDNA, genomic DNA, plasmid DNA, synthetic DNA, and semi -synthetic DNA.
- a "nucleic acid composition" of the disclosure comprises one or more nucleic acids as described herein.
- parenteral administration and “administered parenterally” as used herein means modes of administration other than enteral and topical administration, usually by injection, and includes, without limitation, intravenous, intramuscular, intraarterial, intrathecal, intracapsular, intraorbital, intracardiac, intradermal, intraperitoneal, transtracheal, subcutaneous, subcuticular, intraarticular, subcapsular, subarachnoid, intraspinal and intrastemal injection and infusion.
- pharmaceutically-acceptable carrier encompass any of the agents approved by a regulatory agency of the U.S. Federal government or listed in the U.S. Pharmacopeia for use in animals, including humans, as well as any carrier or diluent that does not cause the production of undesirable physiological effects to a degree that prohibits administration of the composition to a subject and does not abrogate the biological activity and properties of the administered compound. Included are excipients and carriers that are useful in preparing a pharmaceutical composition and are generally safe, non-toxic, and desirable.
- the term "pharmaceutical composition” refers to one or more of the compounds described herein, such as, e.g., an oligonucleotide of the present disclosure, mixed or intermingled with, or suspended in one or more other chemical components, such as pharmaceutically-acceptable carriers and excipients.
- a pharmaceutical composition is to facilitate administration of preparations of oligonucleotides to a subject.
- polynucleotide refers to polymers of nucleotides of any length, including ribonucleotides, deoxyribonucleotides, analogs thereof, or mixtures thereof. This term refers to the primary structure of the molecule. Thus, the term includes triple-, double- and single-stranded deoxyribonucleic acid ("DNA”), as well as triple-, double- and single-stranded ribonucleic acid (“RNA”). It also includes modified, for example by alkylation, and/or by capping, and unmodified forms of the polynucleotide.
- DNA triple-, double- and single-stranded deoxyribonucleic acid
- RNA triple-, double- and single-stranded ribonucleic acid
- polynucleotide includes polydeoxyribonucleotides (containing 2-deoxy-D-ribose), polyribonucleotides (containing D-ribose), including tRNA, rRNA, hRNA, siRNA and mRNA, whether spliced or unspliced, any other type of polynucleotide which is an N- or C-glycoside of a purine or pyrimidine base, and other polymers containing normucleotidic backbones, for example, polyamide (e.g., peptide nucleic acids "PNAs”) and polymorpholino polymers, and other synthetic sequence-specific nucleic acid polymers providing that the polymers contain nucleobases in a configuration which allows for base pairing and base stacking, such as is found in DNA and RNA.
- PNAs peptide nucleic acids
- a polynucleotide can be, e.g., an oligonucleotide, such as an antisense oligonucleotide.
- the oligonucleotide is an RNA.
- the RNA is a synthetic RNA.
- the synthetic RNA comprises at least one unnatural nucleobase.
- all nucleobases of a certain class have been replaced with unnatural nucleobases (e.g., all uridines in a polynucleotide disclosed herein can be replaced with an unnatural nucleobase, e.g., 5-methoxyuridine).
- polypeptide polypeptide
- peptide protein
- protein polymers of amino acids of any length.
- the polymer can comprise modified amino acids.
- the terms also encompass an amino acid polymer that has been modified naturally or by intervention; for example, disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation or modification, such as conjugation with a labeling component.
- polypeptides containing one or more analogs of an amino acid including, for example, unnatural amino acids such as homocysteine, ornithine, p-acetylphenylalanine, D-amino acids, and creatine
- polypeptide refers to proteins, polypeptides, and peptides of any size, structure, or function. Polypeptides include gene products, naturally occurring polypeptides, synthetic polypeptides, homologs, orthologs, paralogs, fragments and other equivalents, variants, and analogs of the foregoing.
- a polypeptide can be a single polypeptide or can be a multi -molecular complex such as a dimer, trimer or tetramer. They can also comprise single chain or multichain polypeptides. Most commonly, disulfide linkages are found in multichain polypeptides.
- the term polypeptide can also apply to amino acid polymers in which one or more amino acid residues are an artificial chemical analogue of a corresponding naturally occurring amino acid.
- a "peptide" can be less than or equal to 50 amino acids long, e.g., about 5, 10, 15, 20, 25, 30, 35, 40, 45, or 50 amino acids long.
- prevent refers partially or completely delaying onset of an disease, disorder and/or condition; partially or completely delaying onset of one or more symptoms, features, or clinical manifestations of a particular disease, disorder, and/or condition; partially or completely delaying onset of one or more symptoms, features, or manifestations of a particular disease, disorder, and/or condition; partially or completely delaying progression from a particular disease, disorder and/or condition; and/or decreasing the risk of developing pathology associated with the disease, disorder, and/or condition. In some aspects, preventing an outcome is achieved through prophylactic treatment.
- prophylactic refers to a therapeutic or course of action used to prevent the onset of a disease or condition, or to prevent or delay a symptom associated with a disease or condition.
- a “prophylaxis” refers to a measure taken to maintain health and prevent or delay the onset of a bleeding episode, or to prevent or delay symptoms associated with a disease or condition.
- similarity refers to the overall relatedness between polymeric molecules, e.g. between polynucleotide molecules (e.g. DNA molecules and/or RNA molecules) and/or between polypeptide molecules. Calculation of percent similarity of polymeric molecules to one another can be performed in the same manner as a calculation of percent identity, except that calculation of percent similarity takes into account conservative substitutions as is understood in the art. It is understood that percentage of similarity is contingent on the comparison scale used, i.e., whether the amino acids are compared, e.g, according to their evolutionary proximity, charge, volume, flexibility, polarity, hydrophobicity, aromaticity, isoelectric point, antigenicity, or combinations thereof.
- subject refers to any mammalian subject, including without limitation, humans, domestic animals (e.g., dogs, cats and the like), farm animals (e.g., cows, sheep, pigs, horses and the like), and laboratory animals (e.g., monkey, rats, mice, rabbits, guinea pigs and the like) for whom diagnosis, treatment, or therapy is desired, particularly humans.
- domestic animals e.g., dogs, cats and the like
- farm animals e.g., cows, sheep, pigs, horses and the like
- laboratory animals e.g., monkey, rats, mice, rabbits, guinea pigs and the like for whom diagnosis, treatment, or therapy is desired, particularly humans.
- laboratory animals e.g., monkey, rats, mice, rabbits, guinea pigs and the like
- the phrase "subject in need thereof includes subjects, such as mammalian subjects, that would benefit from administration of an oligonucleotide of the disclosure, e.g., to improve homeostasis.
- systemic administration means the administration of a compound, drug or other material other than directly into the central nervous system, such that it enters the patient's system and, thus, is subject to metabolism and other like processes, for example, subcutaneous administration.
- terapéuticaally effective amount is the amount of reagent or pharmaceutical compound comprising an oligonucleotide of the present disclosure that is sufficient to a produce a desired therapeutic effect, pharmacologic and/or physiologic effect on a subject in need thereof.
- a therapeutically effective amount can be a "prophylactically effective amount” as prophylaxis can be considered therapy.
- treat refers to, e.g., the reduction in severity of a disease or condition; the reduction in the duration of a disease course; the amelioration or elimination of one or more symptoms associated with a disease or condition; the provision of beneficial effects to a subject with a disease or condition, without necessarily curing the disease or condition.
- the term also include prophylaxis or prevention of a disease or condition or its symptoms thereof.
- treating or “treatment” means inducing an immune response in a subject against an antigen.
- upstream refers to a nucleotide sequence that is located 5’ to a reference nucleotide sequence.
- oligonucleotides comprising a miRNA 387a-3p inhibitor.
- the terms “oligonucleotide” and “miRNA 387a-3p inhibitor” (and variants thereof) are used interchangeably herein.
- the oligonucleotide comprises a contiguous nucleotide sequence having 10-30 nucleotides in length, for example from 14-25 nucleotides in length.
- the oligonucleotide has a contiguous nucleotide sequence with a length of 16-30 nucleotides, 18-25 nucleotides, particularly 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides.
- the oligonucleotide comprises a contiguous nucleotide sequence having less than 200 nucleotides in length. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence having less than about 150, about 140, about 130, about 120, about 110, about 100, about 90, about 80, about 70, about 60, about 50, about 40, about 30, about 25, about 24, about 23, about 22, about 21, about 20, about 19, about 18, about 17, about 16, about 15, about 14, about 13, about 12, about 11, or about 10 nucleotides in length.
- the oligonucleotide comprises a contiguous nucleotide sequence having from about 30 to about 10, from about 25 to about 11, from about 30 to about 15, from about 25 to about 15, from about 24 to about 15, or from about 23 to about 15 nucleotides in length. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence having about 30, about 29, about 28, about 27, about 26, about 25, about 24, about 23, about 22, about 21, about 20, about 19, about 18, about 17, about 16, about 15, about 14, or about 13 nucleotides in length. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence having about 22 nucleotides in length.
- the contiguous nucleotide sequence is about 21 nucleotides in length. In some aspects, the contiguous nucleotide sequence is about 20 nucleotides in length. In some aspects, the contiguous nucleotide sequence is about 23 nucleotides in length. In some aspects, the contiguous nucleotide sequence is about 24 nucleotides in length.
- the oligonucleotides are phosphodiester antisense oligonucleotides, and any oligonucleotides where the sugar-phosphate "backbone” has been derivatized or replaced with "backbone analogues” such as with phosphorothioate, phosphorodithioate, phosphoroamidate, alkyl phosphotriester, or methylphosphonate linkages.
- the oligonucleotide are antisense oligonucleotides, and any oligonucleotides or oligodeoxynucleotides with non-phosphorous backbone analogues such as sulfamate, 3'- thioformacetal, methylene(methylimino) (MMI), 3'-N-carbamate, or morpholino carbamate.
- non-phosphorous backbone analogues such as sulfamate, 3'- thioformacetal, methylene(methylimino) (MMI), 3'-N-carbamate, or morpholino carbamate.
- the oligonucleotide is an antimir.
- antimir refers to molecules (e.g., synthetically generated molecules) that are used to neutralize microRNA (miRNA) function in cells for desired responses. miRNA are complementary sequences (approx. 20-22bp) to mRNA that are involved in the cleavage of RNA or the suppression of the translation.
- antimirs also called anti-miRNA oligonucleotides, AMOs, or antagomirs
- AMOs anti-miRNA oligonucleotides
- antagomirs can be used as further regulation as well as for therapeutic for certain cellular disorders. This regulation can occur through a steric blocking mechanism as well as hybridization to miRNA.
- oligonucleotides can be manipulated to affect the binding affinity and potency of the oligonucleotides.
- the 2’ -sugar of the oligonucleotides can be modified to be substituted with fluorine and various methyl groups, almost all with an increase in binding affinity.
- some of these modified 2’ -sugar oligonucleotides lead to negative effects on cell growth.
- Modifying the 5'-3' phosphodiester backbone linkage to a phosphorothioate (P-S) backbone linkage is also known to have an effect on target affinity.
- oligonucleotide Using the P-S mutation was shown to decrease the T m (melting temperature) of the oligonucleotides, which leads to a lower target affinity.
- T m melting temperature
- a final requirement for oligonucleotides is mismatch specificity and length restrictions. Due to miRNAs in the same families sharing "seed" (shared) sequences and differ by only a couple of additional nucleotides; one oligonucleotide can potentially target multiple miRNA sequences.
- An example of an oligonucleotide or miRNA sequence is shown in the following table.
- the oligonucleotide comprises a contiguous nucleotide sequence having 5 to 30 nucleotides in length.
- the polynucleotide has 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length.
- the contiguous nucleotide sequence has 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26 nucleotides in length.
- the contiguous nucleotide sequence has less than about 30, about 25, about 24, about 23, about 22, about 21, about 20, about 19, about 18, about 17, about 16, about 15, about 14, about 13, about 12, about 11, or about 10 nucleotides in length.
- the contiguous nucleotide sequence has from about 30 to about 10, from about 25 to about 11, from about 30 to about 15, from about 25 to about 15, from about 24 to about 15, or from about 23 to about 15 nucleotides in length. In some aspects, the contiguous nucleotide sequence having about 30, about 29, about 28, about 27, about 26, about 25, about 24, about 23, about 22, about 21, about 20, about 19, about 18, about 17, about 16, about 15, about 14, or about 13 nucleotides in length.
- the oligonucleotide is a contiguous nucleotide sequence targeting hsa-miR-378a, e.g., hsa-miR-378a-3p.
- the hsa-miR-378a-3p has the sequence ACUGGACUUGGAGUCAGAAGGC (SEQ ID NO: 1).
- the oligonucleotide comprises a contiguous nucleotide sequence comprising, consisting essentially of, or consisting of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein U can be optionally T.
- the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein U can be optionally T. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence consisting essentially of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein U can be optionally T. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence consisting of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein U can be optionally T.
- the oligonucleotide comprises a contiguous nucleotide sequence comprising, consisting essentially of, or consisting of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has one mismatch, two mismatches, three mismatches, or four mismatches.
- the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has one mismatch, two mismatches, three mismatches, or four mismatches.
- the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has one mismatch. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has two mismatches.
- the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has three mismatches. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has four mismatches.
- the oligonucleotide comprises a contiguous nucleotide sequence consisting essentially of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has one mismatch, two mismatches, three mismatches, or four mismatches. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence consisting essentially of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has one mismatch.
- the oligonucleotide comprises a contiguous nucleotide sequence consisting essentially of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has two mismatches. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence consisting essentially of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has three mismatches.
- the oligonucleotide comprises a contiguous nucleotide sequence consisting essentially of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has four mismatches. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence consisting of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has one mismatch, two mismatches, three mismatches, or four mismatches.
- the oligonucleotide comprises a contiguous nucleotide sequence consisting of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has one mismatch. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence consisting of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has two mismatches.
- the oligonucleotide comprises a contiguous nucleotide sequence consisting of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has three mismatches. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence consisting of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has four mismatches.
- the oligonucleotide comprises a contiguous nucleotide sequence comprising, consisting essentially of, or consisting of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has one or two mismatches. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has one or two mismatches.
- the oligonucleotide comprises a contiguous nucleotide sequence consisting essentially of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has one or two mismatches. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence consisting of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has one or two mismatches.
- the oligonucleotide comprises a contiguous nucleotide sequence targeting the seed sequence of hsa-miR-378a-3p (z.e., CUGGACU).
- the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence AGUCCAG, wherein U can be optionally T (complement of the seed), wherein the contiguous nucleotide sequence is about 10 nucleotides to about 30 nucleotides (e.g., 10 to 25, 10 to 24, 10 to 23, 10 to 22, 10 to 21, 10 to 20, 10 to 19, or 10 to 18) in length.
- the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence AGUCCAG , wherein U can be optionally T (complement of the seed), wherein the contiguous nucleotide sequence comprises one, two, three, four, five, six, seven, eight, nine, ten, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleic acids at the 5' terminus of the complement of the seed sequence and/or one, two, three, four, five, six, seven, eight, nine, ten, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleic acids at the 3' terminus of the complement of the seed sequence.
- the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence AGUCCAG, wherein U can be optionally T (complement of the seed), wherein the contiguous nucleotide sequence comprises one, two, three, four, five, six, seven, eight, nine, ten, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleic acids at the 5' terminus of the complement of the seed sequence.
- the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence AGUCCAG, wherein U can be optionally T (complement of the seed), wherein the contiguous nucleotide sequence comprises one, two, three, four, five, six, seven, eight, nine, ten, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleic acids at the 3 ' terminus of the complement of the seed sequence.
- the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence AGUCCAG, wherein U can be optionally T (complement of the seed), wherein the contiguous nucleotide sequence comprises one, two, three, four, five, six, seven, eight, nine, ten, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleic acids both at the 5' terminus and the 3' terminus of the complement of the seed sequence.
- the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence set forth in 5'-AGUCCAG-3', 5'-AAGUCCAG-3', 5'-CAAGUCCAG-3', 5'- CCAAGUCCAG-3' (SEQ ID NO: 2), 5'-UCCAAGUCCAG-3' (SEQ ID NO: 3), 5'-CUCCAAGUCCAG- 3' (SEQ ID NO: 4), 5'-ACUCCAAGUCCAG-3' (SEQ ID NO: 5), 5'-GACUCCAAGUCCAG-3' (SEQ ID NO: 6), 5'-UGACUCCAAGUCCAG-3' (SEQ ID NO: 7), 5'-CUGACUCCAAGUCCAG-3' (SEQ ID NO: 8), 5'-UCUGACUCCAAGUCCAG-3' (SEQ ID NO: 9), 5'- UUCUGACUCCAAGUCCAG-3' (SEQ ID NO: 10), 5'-
- the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-AGUCCAG-3'. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-AAGUCCAG-3'. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-CAAGUCCAG-3'. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'- CCAAGUCCAG-3' (SEQ ID NO: 2).
- the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-UCCAAGUCCAG-3' (SEQ ID NO: 3). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-CUCCAAGUCCAG-3' (SEQ ID NO: 4). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'- ACUCCAAGUCCAG-3' (SEQ ID NO: 5).
- the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-GACUCCAAGUCCAG-3' (SEQ ID NO: 6). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-UGACUCCAAGUCCAG-3' (SEQ ID NO: 7). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'- CUGACUCCAAGUCCAG-3' (SEQ ID NO: 8).
- the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-UCUGACUCCAAGUCCAG-3' (SEQ ID NO: 9). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'- UUCUGACUCCAAGUCCAG-3' (SEQ ID NO: 10). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-CUUCUGACUCCAAGUCCAG-3' (SEQ ID NO: 11).
- the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'- CCUUCUGACUCCAAGUCCAG-3' (SEQ ID NO: 12). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-AGUCCAGU-3'. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-AAGUCCAGU-3'. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-CAAGUCCAGU-3' (SEQ ID NO: 13).
- the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'- CCAAGUCCAGU-3' (SEQ ID NO: 14). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'- UCCAAGUCCAGU-3' (SEQ ID NO: 15). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-CUCCAAGUCCAGU-3' (SEQ ID NO: 16).
- the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-ACUCCAAGUCCAGU-3' (SEQ ID NO: 17). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'- GACUCCAAGUCCAGU-3' (SEQ ID NO: 18). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-UGACUCCAAGUCCAGU-3' (SEQ ID NO: 19).
- the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-CUGACUCCAAGUCCAGU-3' (SEQ ID NO: 20). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-UCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 21). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'- UUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 22).
- the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'- CUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 23). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-
- the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-
- the oligonucleotide comprises a contiguous nucleotide sequence which consists essentially of the sequence 5'- GCCUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 25). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which consists of the sequence 5'- GCCUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 25).
- the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence as set forth in 5'-AGTCCAG-3', 5'-AAGTCCAG-3', 5'-CAAGTCCAG -3', 5'- CCAAGTCCAG-3' (SEQ ID NO: 26), 5'-TCCAAGTCCAG-3' (SEQ ID NO: 27), 5'- CTCCAAGTCCAG-3' (SEQ ID NO: 28), 5'-ACTCCAAGTCCAG-3' (SEQ ID NO: 29), 5'- GACTCCAAGTCCAG-3' (SEQ ID NO: 30), 5'-TGACTCCAAGTCCAG-3' (SEQ ID NO: 31), 5'- CTGACTCCAAGTCCAG-3' (SEQ ID NO: 32), 5'-TCTGACTCCAAGTCCAG-3' (SEQ ID NO: 33), 5'- TTCTGACTCCAAGTCCAG-3' (SEQ ID NO: 34), 5'- CTTCTG
- the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'- AGTCCAG-3'. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-AAGTCCAG-3'. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-CAAGTCCAG-3'. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'- CCAAGTCCAG-3' (SEQ ID NO: 26).
- the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-TCCAAGTCCAG-3' (SEQ ID NO: 27). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-CTCCAAGTCCAG-3' (SEQ ID NO: 28). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-ACTCCAAGTCCAG-3' (SEQ ID NO: 29).
- the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'- GACTCCAAGTCCAG-3' (SEQ ID NO: 30). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-TGACTCCAAGTCCAG-3' (SEQ ID NO: 31). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-CTGACTCCAAGTCCAG-3' (SEQ ID NO: 32).
- the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-TCTGACTCCAAGTCCAG-3' (SEQ ID NO: 33). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'- TTCTGACTCCAAGTCCAG-3' (SEQ ID NO: 34). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-
- the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-
- the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-AGTCCAGT-3'. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-AAGTCCAGT-3'. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-CAAGTCCAGT-3' (SEQ ID NO: 37).
- the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'- CCAAGTCCAGT-3' (SEQ ID NO: 38). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-TCCAAGTCCAGT-3' (SEQ ID NO: 39). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-CTCCAAGTCCAGT-3' (SEQ ID NO: 40).
- the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'- ACTCCAAGTCCAGT- 3' (SEQ ID NO: 41). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-GACTCCAAGTCCAGT-3' (SEQ ID NO: 42). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-TGACTCCAAGTCCAGT-3' (SEQ ID NO: 43).
- the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-CTGACTCCAAGTCCAGT-3' (SEQ ID NO: 44). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-TCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 45). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-TTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 46).
- the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'- CTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 47). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-
- the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-
- the oligonucleotide comprises a contiguous nucleotide sequence consisting essentially of the sequence 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence consisting of the sequence 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49).
- the oligonucleotide comprises a contiguous nucleotide sequence that is at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% identical to the sequence 5'-GCCUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 25) or 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49).
- the oligonucleotide comprises a contiguous nucleotide sequence that has at least 90% similarity to the sequence 5'-GCCUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 25) or 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49).
- IL A.2. Chemically Modified Oligonucleotides
- oligonucleotides of the present disclosure comprises at least one chemically modified nucleoside and/or nucleotide.
- the nucleic acids can be referred to as "modified nucleic acids.”
- modified ASO refers to an antisense oligonucleotide that has been chemically modified.
- Oligonucleotides that have not been chemically modified are referred to herein as "naked” oligonucleotides (e.g., naked ASO).
- nucleoside refers to a compound containing a sugar molecule (e.g., a pentose or ribose) or a derivative thereof in combination with an organic base (e.g., a purine or pyrimidine) or a derivative thereof (also referred to herein as "nucleobase").
- an organic base e.g., a purine or pyrimidine
- nucleobase also referred to herein as “nucleobase”
- nucleotide refers to a nucleoside including a phosphate group.
- Modified nucleotides can be synthesized by any useful method, such as, for example, chemically, enzymatically, or recombinantly, to include one or more modified or non-natural nucleosides.
- Nucleic acids can comprise a region or regions of linked nucleosides. Such regions can have variable backbone linkages.
- the linkages can be standard phosphodiester linkages, in which case the nucleic acids would comprise regions of nucleotides.
- modified nucleic acids disclosed herein can comprise various distinct modifications.
- the modified nucleic acids contain one, two, or more (optionally different) nucleoside or nucleotide modifications.
- a modified polynucleotide can exhibit one or more desirable properties, e.g., improved thermal or chemical stability, reduced immunogenicity, reduced degradation, increased binding to the target microRNA, reduced nonspecific binding to non-target microRNA or other molecules, as compared to an unmodified polynucleotide.
- one or more nucleic acids in the oligonucleotide of the present disclosure are chemically modified.
- chemical modification or, as appropriate, “chemically modified” refer to modification with respect to adenosine (A), guanosine (G), uridine (U), thymidine (T) or cytidine (C) ribo- or deoxyribonucleosides in one or more of their position, pattern, percent or population, including, but not limited to, its nucleobase, sugar, backbone, or any combination thereof.
- an oligonucleotide of the present disclosure can have a uniform chemical modification of all or any of the same nucleoside type or a population of modifications produced by downward titration of the same starting modification in all or any of the same nucleoside type, or a measured percent of a chemical modification of all any of the same nucleoside type but with random incorporation.
- the oligonucleotide of the present disclosure can have a uniform chemical modification of two, three, or four of the same nucleoside type throughout the entire polynucleotide (such as all uridines and/or all cytidines, etc. are modified in the same way).
- Modified nucleotide base pairing encompasses not only the standard adeninethymine, adenine-uracil, or guanine-cytosine base pairs, but also base pairs formed between nucleotides and/or modified nucleotides comprising non-standard or modified bases, wherein the arrangement of hydrogen bond donors and hydrogen bond acceptors permits hydrogen bonding between a non-standard base and a standard base or between two complementary non-standard base structures.
- non-standard base pairing is the base pairing between the modified nucleobase inosine and adenine, cytosine, or uracil. Any combination of base/sugar or linker can be incorporated into nucleic acids of the present disclosure.
- TD polynucleotide sequences set forth in the instant application will recite “T”s in a representative DNA sequence but where the sequence represents RNA, the "T”s would be substituted for "U”s.
- TD polynucleotide sequences set forth in the instant application will recite “T”s in a representative DNA sequence but where the sequence represents RNA, the "T”s would be substituted for "U”s.
- TD’s of the present disclosure can be administered as RNAs, as DNAs, or as hybrid molecules comprising both RNA and DNA units.
- the oligonucleotide of the disclosure includes a combination of at least two (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more) modified nucleobases.
- the oligonucleotide has two modified nucleobases.
- the oligonucleotide has three modified nucleobases.
- the oligonucleotide has four modified nucleobases.
- the oligonucleotide has five modified nucleobases.
- the oligonucleotide has six modified nucleobases.
- the oligonucleotide has seven modified nucleobases. In some aspects, the oligonucleotide has eight modified nucleobases. In some aspects, the oligonucleotide has nine modified nucleobases. In some aspects, the oligonucleotide has 10 modified nucleobases. In some aspects, the oligonucleotide has 11 modified nucleobases. In some aspects, the oligonucleotide has 12 modified nucleobases. In some aspects, the oligonucleotide has 13 modified nucleobases. In some aspects, the oligonucleotide has 14 modified nucleobases.
- the oligonucleotide has 15 modified nucleobases. In some aspects, the oligonucleotide has 16 modified nucleobases. In some aspects, the oligonucleotide has 17 modified nucleobases. In some aspects, the oligonucleotide has 18 modified nucleobases. In some aspects, the oligonucleotide has 19 modified nucleobases. In some aspects, the oligonucleotide has 20 modified nucleobases. In some aspects, the oligonucleotide has more than 20 modified nucleobases.
- the nucleobases, sugars, backbone linkages, or any combination thereof in an oligonucleotide are modified by at least about 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% or 100%.
- the chemical modification is at nucleobases in an oligonucleotide of the present disclosure.
- the chemically modified nucleoside is a modified uridine (e.g., pseudouridine (y), 2-thiouridine (s2U), 1-methyl-pseudouridine (mly), 1-ethyl- pseudouridine (ely), or 5-methoxy-uridine (mo5U)), a modified cytosine (e.g., 5-methyl-cytidine (m5C)) a modified adenosine (e.g, 1-methyl-adenosine (ml A), N6-methyl-adenosine (m6A), or 2- methyl-adenine (m2A)), a modified guanosine e.g., 7-methyl-guanosine (m7G) or 1-methyl- guanosine (mlG)), a 5'-methyl pyrimidine e.g.,
- the oligonucleotide of the present disclosure is uniformly modified (e.g., fully modified, modified throughout the entire sequence) for a particular modification.
- an oligonucleotide can be uniformly modified with the same type of base modification, e.g., 5-methyl-cytidine (m5C), meaning that all cytidine residues in the oligonucleotide sequence are replaced with 5-methyl-cytidine (m5C).
- an oligonucleotide can be uniformly modified for any type of nucleoside residue present in the sequence by replacement with a modified nucleoside, such as any of those set forth above.
- the oligonucleotide of the present disclosure e.g., an antimir, e.g., a miR378a antimir
- an antimir e.g., a miR378a antimir
- the oligonucleotide of the present disclosure includes a combination of at least two (e.g., 2, 3, 4 or more) modified nucleobases. In some aspects, at least about 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about
- nucleobases 96%, at least about 97%, at least about 98%, at least about 99% or 100% of a type of nucleobase in an oligonucleotide of the present disclosure e.g., an antimir, e.g., a miR378a inhibitor) are modified nucleobases.
- an antimir e.g., a miR378a inhibitor
- the "oligonucleotide of the present disclosure” (for example an antimir, e.g., a miR378a inhibitor), comprises any useful modification to the linkages between the nucleosides.
- linkages, including backbone modifications, that are useful in the oligonucleotide of the present disclosure include, but are not limited to the following: 3'-alkylene phosphonates, 3 '-amino phosphoramidate, alkene containing backbones, aminoalkylphosphoramidates, aminoalkylphosphotriesters, boranophosphates, -CH2-O-N(CH 3 )- CH 2 -, -CH 2 -N(CH 3 )-N(CH 3 )-CH 2 -, -CH2-NH-CH2-, chiral phosphonates, chiral phosphorothioates, formacetyl and thioformacetyl backbones, methylene (methylimino), methylene forma
- the presence of a backbone linkage disclosed above increase the stability (e.g., thermal stability) and/or resistance to degradation (e.g., enzyme degradation) of an oligonucleotide of the present disclosure (e.g., an antimir, e.g., a miR378a inhibitor).
- the stability and/or resistance to degradation increases by at least about 10%, at least about
- 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21 backbone linkages in an oligonucleotide of the present disclosure are modified (e.g., phosphorothioate).
- the backbone comprises linkages selected from the group consisting of phosphodiester linkage, phosphotriesters linkage, methylphosphonate linkage, phosphoramidate linkage, phosphorothioate linkage, and combinations thereof.
- modified nucleosides and nucleotides which can be incorporated into an oligonucleotide of the present disclosure can be modified on the sugar of the nucleic acid.
- the oligonucleotide comprises a nucleic acid, wherein the nucleic acid comprises at least one nucleoside analog (e.g., a nucleoside with a sugar modification).
- the sugar modification increases the affinity of the binding of the oligonucleotide to its target miRNA.
- Incorporating affinity-enhancing nucleotide analogues in the oligonucleotide, such as LNA or 2 ’-substituted sugar can allow the length of oligonucleotide to be reduced, and also may reduce the upper limit of the size an oligonucleotide can be before nonspecific or aberrant binding takes place.
- At least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100% of the nucleotides in an oligonucleotide of the present disclosure e.g., an antimir, e.g., a miR378a inhibitor
- sugar modifications e.g., LNA
- nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA).
- one of the nucleotide units in an oligonucleotide of the present disclosure is sugar modified (e.g., LNA).
- two of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA).
- three of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA). In some aspects, four of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA). In some aspects, five of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA). In some aspects, six of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA).
- seven of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA). In some aspects, eight of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA). In some aspects, nine of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA). In some aspects, 10 of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA).
- 11 of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA).
- 12 of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA).
- 13 of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA).
- 14 of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA).
- 15 of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA).
- 16 of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA).
- 17 of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA).
- 18 of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA).
- 19 of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA).
- 20 of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA).
- more than 20 of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA).
- RNA includes the sugar group ribose, which is a 5-membered ring having an oxygen.
- modified nucleotides include replacement of the oxygen in ribose (e.g., with S, Se, or alkylene, such as methylene or ethylene); addition of a double bond (e.g., to replace ribose with cyclopentenyl or cyclohexenyl); ring contraction of ribose (e.g., to form a 4-membered ring of cyclobutane or oxetane); ring expansion of ribose (e.g., to form a 6- or 7-membered ring having an additional carbon or heteroatom, such as for anhydrohexitol, altritol, mannitol, cyclohexanyl, cyclohexenyl, and morpholino that also has a phosphoramidate backbone); multicyclic
- the sugar group can also contain one or more carbons that possess the opposite stereochemical configuration than that of the corresponding carbon in ribose.
- an oligonucleotide molecule can include nucleotides containing, e.g., arabinose, as the sugar.
- the 2' hydroxyl group (OH) of ribose can be modified or replaced with a number of different substituents.
- Exemplary substitutions at the 2'-position include, but are not limited to, H, halo, optionally substituted Ci-6 alkyl; optionally substituted Ci-6 alkoxy; optionally substituted Ce-io aryloxy; optionally substituted C3-8 cycloalkyl; optionally substituted C3-8 cycloalkoxy; optionally substituted Ce-io aryloxy; optionally substituted Ce-io aryl-Ci-6 alkoxy; optionally substituted C1-12 (heterocyclyl)oxy; a sugar (e.g., ribose, pentose, or any described herein); a polyethyleneglycol (PEG), -O(CH2CH2O)nCH2CH2OR, where R is H or optionally substituted alkyl, and n is an integer from 0 to 20 (e.g., from hal
- nucleoside analogues present in an oligonucleotide of the present disclosure comprise, e.g., 2’-O-alkyl-RNA units, 2’- OMe-RNA units, 2’-O-alkyl-SNA units, 2’-amino-DNA units, 2’-fluoro-DNA units, LNA units, arabino nucleic acid (ANA) units, 2’ -fluoro- ANA units, HNA units, INA (intercalating nucleic acid) units, 2’MOE units, or any combination thereof.
- an antimir e.g., a miR378a inhibitor
- nucleoside analogues present in an oligonucleotide of the present disclosure comprise, e.g., 2’-O-alkyl-RNA units, 2’- OMe-RNA units, 2’-O-alkyl-SNA units, 2’-amino-DNA units, 2’-fluoro-DNA units, LNA units, arab
- the LNA is, e.g., oxy-LNA (such as beta-D-oxy-LNA, or alpha-L-oxy-LNA), amino-LNA (such as beta-D-amino-LNA or alpha-L-amino-LNA), thio-LNA (such as beta-D-thio-LNA or alpha-L-thio-LNA), ENA (such a beta-D-ENA or alpha-L-ENA), or any combination thereof.
- oxy-LNA such as beta-D-oxy-LNA, or alpha-L-oxy-LNA
- amino-LNA such as beta-D-amino-LNA or alpha-L-amino-LNA
- thio-LNA such as beta-D-thio-LNA or alpha-L-thio-LNA
- ENA such a beta-D-ENA or alpha-L-ENA
- nucleoside analogs present in an oligonucleotide of the present disclosure comprise Locked Nucleic Acid (LNA), 2'-O-alkyl-RNA, 2'-amino-DNA, 2'-fluoro- DNA, arabino nucleic acid (ANA), 2'-fluoro-ANA, hexitol nucleic acid (HNA), intercalating nucleic acid (INA), constrained ethyl nucleoside (cEt), 2'-O-methyl nucleic acid (2'-0Me), 2'-O- methoxyethyl nucleic acid (2'-M0E), or any combination thereof.
- LNA Locked Nucleic Acid
- 2'-O-alkyl-RNA 2'-amino-DNA
- 2'-fluoro- DNA arabino nucleic acid
- ANA arabino nucleic acid
- 2'-fluoro-ANA hexitol nucleic acid
- INA intercalating nucle
- an oligonucleotide of the present disclosure can comprise both modified RNA nucleotide analogues (e.g., LNA) and DNA units.
- an oligonucleotide of the present disclosure is a gapmer. See, e.g., U.S. Pat. Nos. 8,404,649; 8,580,756; 8,163,708; 9,034,837; all of which are herein incorporated by reference in their entireties.
- an oligonucleotide of the present disclosure is a micromir. See U.S. Pat. Appl. Publ. No. US20180201928, which is herein incorporated by reference in its entirety.
- an oligonucleotide of the present disclosure comprises a miRNA inhibitor.
- the miRNA inhibitor of the present disclosure has a nucleotide sequence comprising the sequence 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49) and a backbone modification comprising one or more phosphorothioate linkages (SEQ ID NO: 55).
- the miRNA inhibitor of the present disclosure comprises the ASO sequence and design of ASO Ml as shown in FIG. 12B.
- the miRNA inhibitor of the present disclosure comprises a nucleotide sequence comprising the sequence 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein (from 5'- end) nucleotide residues 1, 2, 3, and 22 are a LNA, and nucleotide residues 4-21 are a DNA (SEQ ID NO: 57).
- the miRNA inhibitor of the present disclosure has a nucleotide sequence comprising the sequence 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49) and a backbone modification comprising one or more phosphorothioate linkages, wherein (from 5'- end) nucleotide residues 1, 2, 3, and 22 are a LNA, and nucleotide residues 4-21 are a DNA (SEQ ID NO: 58).
- the disclosure comprises an oligonucleotide comprising a contiguous nucleotide sequence of 10 to 30 nucleic acids in length that are complementary to a nucleic acid sequence within miRNA 378a-3p, wherein the contiguous nucleotide sequence comprises the sequence 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein the first, second, and third nucleotides from the 5’ to 3’ are LNAs (SEQ ID NO: 63).
- the oligonucleotide comprises a contiguous nucleotide sequence of 10 to 30 nucleic acids in length that are complementary to a nucleic acid sequence within miRNA 378a-3p, wherein the contiguous nucleotide sequence comprises the sequence 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein the first, second, third, and 22 nd nucleotides from the 5’ to 3’ are LNAs (SEQ ID NO: 57).
- the 4 th , 5 th , 6 th , 7 th , 8 th , 9 th , 10 th , 11 th , 12 th , 13 th , 14 th , 15 th , 16 th , 17 th , 18 th , 19 th , 20 th , or 21 st nucleotides from the 5’ to 3’ are DNAs.
- the base of the 2 nd and 3 rd nucleotides from 5’ to 3’ are 5-methyl- pyrimidine (SEQ ID NO: 64).
- the disclosure comprises an oligonucleotide comprising a contiguous nucleotide sequence of 10 to 30 nucleic acids in length that are complementary to a nucleic acid sequence within miRNA 378a-3p, wherein the contiguous nucleotide sequence comprises the sequence 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein the first, second, third, and 22 nd nucleotides from the 5’ to 3’ are LNAs, wherein the 4 th , 5 th , 6 th , 7 th , 8 th , 9 th , 10 th , 11 th , 12 th , 13 th , 14 th , 15 th , 16 th , 17 th , 18 th , 19 th , 20 th , or 21 st nucleotides from the 5’ to 3’ are DNAs, and the base of the 2 nd and 3 rd nucleotides from the 5
- each of the nucleotides is linked by a phosphothioate bond (SEQ ID NO: 50).
- a miRNA 387a-3p inhibitor comprises a contiguous nucleotide sequence comprising the sequence 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein (from the 5'- end) the 1 st , 2 nd , 3 rd , and 22 nd nucleotides are LNA, wherein the 4 th - 21 st nucleotides are DNA, and the base of the 2 nd and 3 rd nucleotides are 5-methyl-pyrimidine, and wherein each of the nucleotides is linked by a phosphothioate bond (SEQ ID NO: 50).
- the miRNA inhibitor of the present disclosure has a nucleotide sequence comprising 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49) and a backbone modification comprising one or more phosphorothioate linkages wherein (from the 5'- end) nucleotide residues 1, 2, 3, and 22 are a LNA, nucleotide residues 4-21 are a DNA, and nucleotide residues 2 and 3 comprise a 5-methyl-pyrimidine nucleobase modification (SEQ ID NO: 56).
- the miRNA inhibitor of the present disclosure has a nucleotide sequence comprising 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), a backbone modification wherein 100% of the backbone linkages are phosphorothioate linkages, and wherein (from 5'- end) nucleotide residues 1, 2, 3, and 22 are a LNA, nucleotide residues 4-21 are a DNA, and nucleotide residues 2 and 3 comprise a 5-methyl-pyrimidine nucleobase modification (e.g., ASO Ml provided herein (the phrase “ASO Ml” is used interchangeably with “ASO #1”, “Modified ASO #1”, and “Ml”)) (SEQ ID NO: 50).
- ASO Ml provided herein (the phrase “ASO Ml” is used interchangeably with “ASO #1”, “Modified ASO #1”, and “Ml”)
- the ASO Ml induces an increased suppression of miR378a-3p in a cell, e.g., HepG2 or HepG3 cells, compared to a reference ASO (e.g., M2, Ml’, M5, M6, or M8).
- a reference ASO e.g., M2, Ml’, M5, M6, or M8.
- the structures of ASOs M2, Ml’, M5, M6, and M8 are provided in FIGs. 12D, 12C, 12F, 12G, and 121 respectively.
- the induced suppression level is at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 100%, as compared to the reference ASO.
- the ASO Ml induces loss of body fat mass at a higher percentage than lean muscle mass compared to a reference ASO (e.g., M2, Ml’, M5, M6, or M8). In some aspects, the ASO Ml induces loss of body fat mass at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least aout 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or about 100% more than lean muscle mass compared to a reference ASO (e.g., M2, Ml’, M5, M6, or M8).
- a reference ASO e.g., M2, Ml’, M5, M6, or M8.
- the subject that received ASO Ml loses body fat mass more efficiently than a corresponding subject that received a control, e.g., a GLP-1 agonist, e.g., semaglutide or tirzepatide, or a reference ASO (e.g., M2, Ml’, M5, M6, or M8).
- a control e.g., a GLP-1 agonist, e.g., semaglutide or tirzepatide
- a reference ASO e.g., M2, Ml’, M5, M6, or M8.
- the ASO Ml is stable in mouse plasma when administered up to (from the administration to) about 1 day, about 2 days, about 3 days, about 4 days, about 5 days, about 6 days, or about 7 days.
- the miRNA inhibitor comprises the ASO sequence and design of ASO M7 as shown in FIG. 12H.
- the miRNA inhibitor of the present disclosure comprises a nucleotide sequence comprising 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein (from 5'- end) each of nucleotide residues 1, 2, 3, 4, 5, 18, 19, 20, 21, and 22 is a LNA, and each of nucleotide residues 6-17 is a DNA (SEQ ID NO: 74).
- the miRNA inhibitor of the present disclosure has a nucleotide sequence comprising 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49) and a backbone modification comprising one or more phosphorothioate linkages wherein (from 5'- end) each of nucleotide residues 1, 2, 3, 4, 5, 18, 19, 20, 21, and 22 is a LNA, and each of nucleotide residues 6-17 is a DNA (SEQ ID NO: 77).
- the miRNA inhibitor of the present disclosure has a nucleotide sequence comprising 5'-GCC C GAC CCAAG CCAG -3' (SEQ ID NO: 49), wherein the backbone of the nucleotide sequence comprises phosphorothioate linkages and wherein (from 5'- end) each of nucleotide residues 1, 2, 3, 4, 5, 18, 19, 20, 21, and 22 is a LNA, and each of nucleotide residues 6-17 is a DNA (SEQ ID NO: 78).
- the disclosure comprises an oligonucleotide comprising a contiguous nucleotide sequence of 10 to 30 nucleic acids in length that are complementary to a nucleic acid sequence within miRNA 378a-3p, wherein the contiguous nucleotide sequence comprises the sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein each of the first, second, third, fourth, fifth, 18, 19, 20, 21, and 22 nucleotides from the 5’ to 3’ is a nucleic acid comprising a LNA (SEQ ID NO: 74).
- the oligonucleotide comprising a contiguous nucleotide sequence of 10 to 30 nucleic acids in length that are complementary to a nucleic acid sequence within miRNA 378a-3p, wherein the contiguous nucleotide sequence comprises the sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein each of the first, second, third, fourth, fifth, 18 th , 19 th , 20 th , 21 st , and 22 nd nucleotides from the 5’ to 3’ is a LNA (SEQ ID NO: 74).
- each of the 6 th , 7 th , 8 th , 9 th , 10 th , 11 th , 12 th , 13 th , 14 th , 15 th , 16 th , and 17 th , nucleotides from the 5’ to 3’ is a DNA.
- each of the base of the 2 nd , 3 rd , 6 th , 10 th , 12 th , 13 th , 18 th , and 19 th nucleotides from 5’ to 3’ is a nucleic acid comprising 5-methyl-pyrimidine (SEQ ID NO: 75).
- the disclosure comprises an oligonucleotide comprising a contiguous nucleotide sequence of 10 to 30 nucleic acids in length that are complementary to a nucleic acid sequence within miRNA 378a-3p, wherein the contiguous nucleotide sequence comprises the sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein each of the first, second, third, fourth, fifth, 18 th , 19 th , 20 th , 21 st , and 22 nd nucleotides from the 5’ to 3’ is a nucleic acid comprising LNAs, wherein each of the 6 th , 7 th , 8 th , 9 th , 10 th , 11 th , 12 th , 13 th , 14 th , 15 th , 16 th , and 17 th nucleotides from the 5’ to 3’ is a DNA, and each of
- each of the nucleotides is linked by a phosphothioate bond (SEQ ID NO: 70).
- a miRNA 387a-3p inhibitor comprises a contiguous nucleotide sequence comprising the sequence 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein each of the l st -5 th and 18 th -22 nd nucleotides is a LNA, wherein each of the 6 th - 17 th nucleotides is a DNA, and each of the base of the 2 nd , 3 rd , 6 th , 10 th , 12 th , 13 th , 18 th , and 19 th nucleotides comprises a 5-methyl-pyrimidine.
- each of the nucleotides is linked by a phosphothioate bond (SEQ ID NO: 70).
- the miRNA inhibitor of the present disclosure has a nucleotide sequence comprising 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49) and a backbone modification comprising one or more phosphorothioate linkages wherein (from the 5'- end) each of nucleotide residues 1, 2, 3, 4, 5, 18, 19, 20, 21, and 22 is a nucleic acid comprising a LNA, each of nucleotide residues 6-17 is a DNA, and each of nucleotide residues 2, 3, 6, 10, 12, 13, 18, and 19 comprises a nucleic acid comprising a 5-methyl-pyrimidine (SEQ ID NO: 76).
- the miRNA inhibitor of the present disclosure has a nucleotide sequence comprising 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), a backbone modification wherein 100% of the backbone linkages are phosphorothioate linkages, and wherein each of nucleotide residues 1, 2, 3, 4, 5, 18, 19, 20, 21, and 22 is a nucleic acid comprising a LNA, each of nucleotide residues 6-17 is a DNA, and each of nucleotide residues 2, 3, 6, 10, 12, 13, 18, and 19 comprises a nucleic acid comprising a 5-methyl-pyrimidine (ASO M7 (the phrase “ASO M7” is used interchangeably with “ASO #7”, “Modified ASO #7” and “M7”)) (SEQ ID NO: 70).
- ASO M7 the phrase “ASO M7” is used interchangeably with “ASO #7”, “Modified ASO #7” and “M7”
- the ASO M7 induces an increased suppression of miR378a-3p in a cell, e.g., HepG2 or HepG3 cells, compared to a reference ASO (e.g., M2, ME, M5, M6, or M8).
- the induced suppression level is at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 100%.
- the ASO M7 induces loss of body fat mass at a higher percentage than lean muscle mass compared to a reference ASO (e.g., M2, Ml’, M5, M6, or M8).
- the ASO-M1 induces loss of body fat mass at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least aout 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or about 100% more than lean muscle mass compared to a reference ASO (e.g., M2, Ml’, M5, M6, or M8).
- a reference ASO e.g., M2, Ml’, M5, M6, or M8.
- the subject loses body fat mass more efficiently than a corresponding subject that received a control, e.g., a GLP-1 agonist, e.g., semaglutide or tirzepatide, or a reference ASO (e.g., M2, Ml’, M5, M6, or M8).
- a control e.g., a GLP-1 agonist, e.g., semaglutide or tirzepatide
- a reference ASO e.g., M2, Ml’, M5, M6, or M8.
- the miRNA inhibitor of the present disclosure comprises the ASO sequence and design of ASO M4 as shown in FIG. 12E.
- the oligonucleotide comprising a contiguous nucleotide sequence of 10 to 30 nucleic acids in length that are complementary to a nucleic acid sequence within miRNA 378a-3p, wherein the contiguous nucleotide sequence comprises the sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein the first, second, third, and 22 nd nucleotides from the 5’ to 3’ are LNAs (SEQ ID NO: 57), wherein the 4 th , 5 th , 6 th , 7 th , 8 th , 9 th , 10 th , 11 th , 12 th , 13 th , 14 th , 15 th , 16 th , 17 th , 18 th , 19 th
- each of the nucleotides is linked by a phosphothioate bond (SEQ ID NO: 79).
- a miRNA 387a-3p inhibitor comprises a contiguous nucleotide sequence comprising the sequence 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein (from the 5'- end) the 1 st , 2 nd , 3 rd , and 22 nd nucleotides are LNA, wherein the 4 th -21 st nucleotides are DNA, wherein the based of the 2 nd , 3 rd , 6 th , 10 th , 12 th , 13 th , 18 th , and 19 th nucleotides are 5-methyl-pyrimidine, and wherein each of the nucleotides is linked by a phosphothioate bond (SEQ ID NO: 67).
- the miRNA inhibitor of the present disclosure has a nucleotide sequence comprising 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49) and a backbone modification comprising one or more phosphorothioate linkages wherein (from the 5'- end) nucleotide residues 1, 2, 3, and 22 are a LNA, nucleotide residues 4-21 are a DNA, and nucleotide residues 2, 3, 6, 10, 12, 13, 18, and 19 comprise a 5-methyl-pyrimidine nucleobase modification (SEQ ID NO: 73).
- the miRNA inhibitor of the present disclosure has a nucleotide sequence comprising 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), a backbone modification wherein 100% of the backbone linkages are phosphorothioate linkages, and wherein (from the 5'- end) nucleotide residues 1, 2, 3, and 22 are a LNA, nucleotide residues 4-21 are a DNA, and nucleotide residues 2, 3, 6, 10, 12, 13, 18, and 19 comprise a 5-methyl-pyrimidine nucleobase modification (ASO M4 (the phrase “ASO M4” is used interchangeably with “ASO #4”, “Modified ASO #4”, and “M4”)) (SEQ ID NO: 67).
- ASO M4 the phrase “ASO M4” is used interchangeably with “ASO #4”, “Modified ASO #4”, and “M4”
- the ASO M4 induces an increased suppression of miR378a-3p in a cell, e.g., HepG2 or HepG3 cells, compared to a reference ASO (e.g., M2, Ml’, M5, M6, or M8).
- a reference ASO e.g., M2, Ml’, M5, M6, or M8.
- the induced suppression level is at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 100%, as compared to that observed with the reference ASO.
- the ASO M4 induces loss of body fat mass at a higher percentage than lean muscle mass compared to a reference ASO (e.g., M2, Ml’, M5, M6, or M8).
- the ASO-M1 induces loss of body fat mass at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least aout 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or about 100% more than lean muscle mass compared to a reference ASO (e.g., M2, Ml’, M5, M6, or M8).
- a reference ASO e.g., M2, Ml’, M5, M6, or M8.
- the subject loses body fat mass more efficiently than a corresponding subject that received a control, e.g., a GLP-1 agonist, e.g., semaglutide or tirzepatide, or a reference ASO (e.g., M2, Ml’, M5, M6, or M8).
- a control e.g., a GLP-1 agonist, e.g., semaglutide or tirzepatide
- a reference ASO e.g., M2, Ml’, M5, M6, or M8.
- the ASO M4 is stable in mouse plasma when administered up to (from the administration to) about 1 day, about 2 days, about 3 days, about 4 days, about 5 days, about 6 days, or about 7 days.
- a miRNA inhibitor comprises ASO M2.
- a miRNA inhibitor comprises a nucleotide sequence comprising 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein (from 5'- end) each of nucleotide residues 1, 2, 3, and 22 is a nucleic acid comprising a 2’-M0E, and each of nucleotide residues 4- 21 is a DNA (SEQ ID NO: 59).
- a miRNA inhibitor has a nucleotide sequence comprising 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49) and a backbone modification comprising one or more phosphorothioate linkages wherein (from 5'-end) each of nucleotide residues 1, 2, 3, and 22 is a 2’-M0E, and each of nucleotide residues 4-21 is a DNA (SEQ ID NO: 60).
- a miRNA inhibitor of the present disclosure has a nucleotide sequence comprising 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein the backbone of the nucleotide sequence comprises phosphorothioate linkages and wherein (from 5'- end) each of nucleotide residues 1, 2, 3, and 22 is a nucleic acid comprising a 2’-M0E, and each of nucleotide residues 4- 21 is a DNA (SEQ ID NO: 60).
- an oligonucleotide comprising a contiguous nucleotide sequence of 10 to 30 nucleic acids in length that are complementary to a nucleic acid sequence within miRNA 378a-3p, wherein the contiguous nucleotide sequence comprises the sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein (from 5'- end) each of the first, second, and third nucleotides from the 5’ to 3’ is a nucleic acid comprising a 2’-M0E (SEQ ID NO: 65).
- an oligonucleotide comprising a contiguous nucleotide sequence of 10 to 30 nucleic acids in length that are complementary to a nucleic acid sequence within miRNA 378a-3p, wherein the contiguous nucleotide sequence comprises the sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein (from 5'- end) each of the first, second, third, and 22 nd nucleotides is a nucleic acid comprising a 2’ -MOE (SEQ ID NO: 59).
- each of the 4 th , 5 th , 6 th , 7 th , 8 th , 9 th , 10 th , 11 th , 12 th , 13 th , 14 th , 15 th , 16 th , 17 th , 18 th , 19 th , 20 th , or 21 st nucleotides from the 5’ to 3’ is a DNA.
- each of the base of the 2 nd and 3 rd nucleotides from 5’ to 3’ is a nucleic acid comprising 5-methyl- pyrimidine (SEQ ID NO: 66).
- an oligonucleotide comprising a contiguous nucleotide sequence of 10 to 30 nucleic acids in length that are complementary to a nucleic acid sequence within miRNA 378a-3p, wherein the contiguous nucleotide sequence comprises the sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein (from the 5'- end) each of the first, second, third, and 22 nd nucleotides is a nucleic acid comprising 2’- MOEs, wherein each of the 4 th , 5 th , 6 th , 7 th , 8 th , 9 th , 10 th , 11 th , 12 th , 13 th , 14 th , 15 th , 16 th , 17 th , 18 th , 19 th , 20 th , or 21 st nucleotides from the 5’
- a miRNA inhibitor has a nucleotide sequence comprising 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49) and a backbone modification comprising one or more phosphorothioate linkages wherein (from the 5'- end) each of nucleotide residues 1, 2, 3, and 22 is a nucleic acid comprising a 2’ -MOE, each of nucleotide residues 4-21 is a DNA, and each of nucleotide residues 2 and 3 comprises a nucleic acid comprising a 5-methyl-pyrimidine (SEQ ID NO: 61).
- a miRNA inhibitor has a nucleotide sequence comprising 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), a backbone modification wherein 100% of the backbone linkages are phosphorothioate linkages, and wherein (from the 5'- end) each of nucleotide residues 1, 2, 3, and 22 is a nucleic acid comprising a 2’-M0E, each of nucleotide residues 4-21 is a DNA, and each of nucleotide residues 2 and 3 comprises a nucleic acid comprising a 5-methyl-pyrimidine (ASO M2 (the phrase “ASO M2” is used interchangeably with “ASO #2”, “Modified ASO #2” and “M2”)) (SEQ ID NO: 62).
- ASO M2 is a reference ASO as used herein compared to ASO Ml, ASO M4, and/or ASO M7.
- a miRNA inhibitor comprise ASO ME.
- the miRNA inhibitor comprises a nucleotide sequence comprising 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), a backbone modification wherein 100% of the backbone linkages are phosphorothioate linkages, and wherein (from 5'- end) nucleotide residues 1, 2, 3, and 22 are a LNA, nucleotide residues 4-21 are a DNA, nucleotide residues 2 and 3 comprise a 5-methyl-pyrimidine nucleobase modification, and a cholesteryl moiety is attached to the 3 ’ end of the nucleotide sequence (ASO Ml’ (the phrase “ASO Ml’” is used interchangeably with “ASO #1’”, “Modified ASO #1’”, and “Ml ’”)) (SEQ ID NO: 50).
- ASO Ml’ is a reference ASO compared to ASO Ml, ASO
- a miRNA inhibitor comprises ASO M6.
- the miRNA inhibitor comprises a nucleotide sequence comprising 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), a backbone modification wherein 100% of the backbone linkages are phosphorothioate linkages, and wherein (from 5'- end) each of nucleotide residues 1, 2, 3, 4, 5, 18, 19, 20, 21, and 22 is a nucleic acid comprising a 2’-M0E, each of nucleotide residues 6-17 is a DNA, and each of nucleotide residues 2, 3, 6, 10, 12, 13, 18, and 19 comprises a nucleic acid comprising a 5-methyl-pyrimidine (ASO M6 (the phrase “ASO M6” is used interchangeably with “ASO #6”, “Modified ASO #6” and “M6”)) (SEQ ID NO: 69).
- ASO M6 is a reference ASO compared to ASO
- the conjugate comprises a targeting moiety, which is linked to the oligonucleotide, optionally via a linker.
- targeting moiety refers to a biorecognition molecule that binds to a specific biological substance or site.
- the targeting moiety is specific for a certain target molecule (e.g., a ligand targeting a receptor, or an antibody targeting a surface protein) or tissue (e.g., a molecule that would preferentially carry the conjugate to a specific organ or tissue, e.g., liver, brain, or endothelium), or facilitates transport through a physiological barrier (e.g., a peptide or other molecule that may facilitate transport across the brain blood barrier or plasma membrane).
- a certain target molecule e.g., a ligand targeting a receptor, or an antibody targeting a surface protein
- tissue e.g., a molecule that would preferentially carry the conjugate to a specific organ or tissue, e.g., liver, brain, or endothelium
- a physiological barrier e.g., a peptide or other molecule that may facilitate transport across the brain blood barrier or plasma membrane.
- a targeting moiety can be coupled to the payload, either directly or indirectly through a linker.
- the targeting moiety is capable of targeting the conjugate of the present disclosure to a tissue.
- the tissue is liver, brain, kidney, lung, ovary, pancreas, thyroid, breast, stomach, or any combination thereof.
- the tissue is cancer tissue, e.g., liver cancer, brain cancer, kidney cancer, lung cancer, ovary cancer, pancreas cancer, thyroid cancer, breast cancer, stomach cancer, or any combination thereof.
- the tissue is liver.
- the targeting moiety targeting liver is cholesterol.
- the targeting moiety targeting liver is a ligand that binds an asialoglycoprotein receptor targeting moiety.
- a targeting moiety comprises glucose, e.g., D-glucose, which can bind to Glucose transporter 1 (or GLUT1).
- GLUT1 also known as solute carrier family 2, facilitated glucose transporter member 1 (SLC2A1), is a uniporter protein that, in humans, is encoded by the SLC2A1 gene.
- SLC2A1 facilitated glucose transporter member 1
- a targeting moiety comprises galactose, e.g., D-galactose, which can bind to GLUT1.
- a targeting moiety comprises glutamic acid, which can bind to acetylcholinesterase inhibitor (AChEI) and/or EAATs inhibitors.
- Acetylcholinesterase is the enzyme that is the primary member of the cholinesterase enzyme family.
- An acetylcholinesterase inhibitor (AChEI) is the inhibitor that inhibits acetylcholinesterase from breaking down acetylcholine into choline and acetate.
- Acetylcholinesterase inhibitors are one of two types of cholinesterase inhibitors; the other being butyryl-cholinesterase inhibitors.
- a targeting moiety is GABA, which can bind to GABA receptors.
- GABA receptors are a class of receptors that respond to the neurotransmitter gamma- aminobutyric acid (GABA), the chief inhibitory compound in the mature vertebrate central nervous system.
- GABAA and GAB AB There are two classes of GABA receptors: GABAA and GAB AB.
- GABAA receptors are ligand-gated ion channels (also known as ionotropic receptors); whereas GAB AB receptors are G protein-coupled receptors, also called metabotropic receptors.
- a targeting moiety comprises tyrosine. In some aspects, a targeting moiety comprises lysine. In some aspects, a targeting moiety comprises glutamine. In some aspects, a targeting moiety comprises phenylalanine, which can bind to GABA receptors, CNS reverse transcriptase inhibitors, and/or dopamine (DA) receptors.
- Dopamine receptors are a class of G protein-coupled receptors that are prominent in the vertebrate central nervous system (CNS). Dopamine receptors activate different effectors through not only G-protein coupling, but also signaling through different protein (dopamine receptor-interacting proteins) interactions. The neurotransmitter dopamine is the primary endogenous ligand for dopamine receptors.
- a targeting moiety comprises valine, which can bind to CNS reverse transcriptase inhibitors.
- a targeting moiety comprises tryptophan, which can bind to GABA receptors and/or CNS reverse transcriptase inhibitors.
- a targeting moiety comprises leucine, which can bind to GABA receptors and/or CNS reverse transcriptase inhibitors.
- a targeting moiety comprises methionine, which can bind to GABA receptors and/or CNS reverse transcriptase inhibitors.
- a targeting moiety comprises histidine, which can bind to GABA receptors.
- a ligand functions as a type of targeting moiety defined as a selectively bindable material that has a selective (or specific), affinity for another substance.
- the ligand is recognized and bound by a usually, but not necessarily, larger specific binding body or "binding partner,” or "receptor.”
- binding partner or "receptor.”
- ligands suitable for targeting are antigens, haptens, biotin, biotin derivatives, lectins, galactosamine and fucosylamine moieties, receptors, substrates, coenzymes and cofactors among others.
- the ligand When applied to the oligonucleotides of the present disclosure that is conjugated to a ligand, the ligand includes an antigen or hapten that is capable of being bound by, or to, its corresponding antibody or fraction thereof. Also included are viral antigens or hemagglutinins and neuraminidases and nucleocapsids including those from any DNA and RNA viruses, AIDS, HIV and hepatitis viruses, adenoviruses, alphaviruses, arenaviruses, coronaviruses, flaviviruses, herpesviruses, myxoviruses, oncornaviruses, papovaviruses, paramyxoviruses, parvoviruses, picornaviruses, poxviruses, reoviruses, rhabdoviruses, rhinoviruses, togaviruses and viroids; any bacterial antigens including those of gram-negative and gram-
- Bacteroides Clostridium, Chlamydia, enterobacteria, Haemophilus, Lactobacillus, Neisseria, Staphyloccus, or Streptoccocus,' any fungal antigens including those of Aspergillus, Candida, Coccidiodes, mycoses, phycomycetes, and yeasts; any mycoplasma antigens; any rickettsial antigens; any protozoan antigens; any parasite antigens; any human antigens including those of blood cells, virus infected cells, genetic markers, heart diseases, oncoproteins, plasma proteins, complement factors, rheumatoid factors.
- cancer and tumor antigens such as alpha-fetoproteins, prostate specific antigen (PSA) and CEA, cancer markers and oncoproteins, among others.
- PSA prostate specific antigen
- CEA cancer markers and oncoproteins, among others.
- Other substances that can function as ligands for targeting an oligonucleotide of the present disclosure are certain vitamins (i.e. folic acid, B12), steroids, prostaglandins, carbohydrates, lipids, antibiotics, drugs, digoxins, pesticides, narcotics, neuro-transmitters, and substances used or modified such that they function as ligands.
- the targeting moiety comprises a protein or protein fragment (e.g., hormones, toxins), and synthetic or natural polypeptides with cell affinity.
- Ligands also include various substances with selective affinity for ligators that are produced through recombinant DNA, genetic and molecular engineering. Except when stated otherwise, ligands of the instant disclosure also include ligands as defined in U.S. Pat. No. 3,817,837, which is herein incorporated by reference in its entirety.
- a ligator functions as a type of targeting moiety defined for this disclosure as a specific binding body or "partner" or “receptor,” that is usually, but not necessarily, larger than the ligand it can bind to. For the purposes of this disclosure, it can be a specific substance or material or chemical or “reactant” that is capable of selective affinity binding with a specific ligand.
- a ligator can be a protein such as an antibody, a nonprotein binding body, or a "specific reactor.”
- a ligator includes an antibody, which is defined to include all classes of antibodies, monoclonal antibodies, chimeric antibodies, Fab fractions, fragments and derivatives thereof.
- antibody encompasses an immunoglobulin whether natural or partly or wholly synthetically produced, and fragments thereof. The term also covers any protein having a binding domain that is homologous to an immunoglobulin binding domain. “Antibody” further includes a polypeptide comprising a framework region from an immunoglobulin gene or fragments thereof that specifically binds and recognizes an antigen.
- antibody is meant to include whole antibodies, polyclonal, monoclonal and recombinant antibodies, fragments thereof, and further includes single-chain antibodies, humanized antibodies, murine antibodies, chimeric, mouse-human, mouse-primate, primate-human monoclonal antibodies, anti-idiotype antibodies, antibody fragments, such as, e.g., scFv, scFab, (scFab)2, (SCFV)2, Fab, Fab', and F(ab')2, F(abl)2, Fv, dAb, and Fd fragments, diabodies, and antibody-related polypeptides.
- Antibody includes bispecific antibodies and multispecific antibodies so long as they exhibit the desired biological activity or function.
- the targeting moiety is an antibody or a molecule comprising an antigen binding fragment thereof.
- the antibody is a nanobody.
- the antibody is an ADC.
- antibody-drug conjugate and “ADC” are used interchangeably and refer to an antibody linked, e.g., covalently, to a therapeutic agent (sometimes referred to herein as agent, drug, or active pharmaceutical ingredient) or agents.
- the targeting moiety is an antibody-drug conjugate.
- ligators suitable for targeting include naturally occurring receptors, any hemagglutinins and cell membrane and nuclear derivatives that bind specifically to hormones, vitamins, drugs, antibiotics, cancer markers, genetic markers, viruses, and histocompatibility markers.
- Another group of ligators includes any RNA and DNA binding substances such as polyethylenimine (PEI) and polypeptides or proteins such as histones and protamines.
- ligators also include enzymes, especially cell surface enzymes such as neuraminidases, plasma proteins, avidins, streptavidins, chalones, cavitands, thyroglobulin, intrinsic factor, globulins, chelators, surfactants, organometallic substances, staphylococcal protein A, protein G, ribosomes, bacteriophages, cytochromes, lectins, certain resins, and organic polymers.
- enzymes especially cell surface enzymes such as neuraminidases, plasma proteins, avidins, streptavidins, chalones, cavitands, thyroglobulin, intrinsic factor, globulins, chelators, surfactants, organometallic substances, staphylococcal protein A, protein G, ribosomes, bacteriophages, cytochromes, lectins, certain resins, and organic polymers.
- Targeting moieties also include various substances such as any proteins, protein fragments or polypeptides with affinity for the surface of any cells, tissues or microorganisms that are produced through recombinant DNA, genetic and molecular engineering.
- the targeting moiety directs a conjugate of the present disclosure to a specific tissue (i.e., liver tissue or brain tissue), to a specific type of cell (e.g., a certain type of cancer cells), or to a physiological compartment or physiological barrier (e.g., the plasma membrane).
- an oligonucleotide disclosed herein is optionally conjugated to a targeting moiety via one or more linkers.
- linker refers to a peptide or polypeptide sequence (e.g., a synthetic peptide or polypeptide sequence), or a non-peptide linker for which its main function is to connect two moieties with an oligonucleotide disclosed herein.
- oligonucleotides conjugated to a targeting moiety can comprise at least one linker connecting thetissue-specific targeting moiety (TM) with the oligonucleotide.
- linkers provide flexibility to the oligonucleotide and targeting moiety conjugate.
- Linkers are not typically cleaved; however, in certain aspects, such cleavage can be desirable.
- a linker can comprise one or more protease-cleavable sites, which can be located within the sequence of the linker or flanking the linker at either end of the linker sequence.
- the cleavable linker is cleavable by a protease.
- the linker is a bioreducible linker, an acid cleavable linker, a click-to-release linker, a pyrophosphatase cleavable linker, a beta-glucuronidase cleavable linker, or any combination thereof.
- the linker is a peptide linker.
- the linker comprises a non-peptide linker.
- the linker consists of a non-peptide linker.
- the non-peptide linker can be, e.g., maleimido caproyl (MC), maleimido propanoyl (MP), methoxyl polyethyleneglycol (MPEG), succinimidyl 4-(N-maleimidomethyl)-cyclohexane-l -carboxylate (SMCC), m-maleimidobenzoyl- N-hydroxysuccinimide ester (MBS), succinimidyl 4-(p-maleimidophenyl)butyrate (SMPB), N- succinimidyl(4-iodoacetyl)aminobenzonate (SIAB), succinimidyl 6-[3-(2-pyridyldithio)- propionami de] hexanoate (LC-SPDP), 4-succinimidyl
- MC maleimido caproyl
- linkers include, but are not limited to:
- the present disclosure also provides pharmaceutical compositions comprising the oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates of the present disclosure that are suitable for administration to a subject.
- oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates of the present disclosure can be homogeneous (i.e., all oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates comprises the same type of oligonucleotide with the same targeting moiety).
- the oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates can comprise multiple targeting moieties, multiple payloads, etc.
- compositions generally comprise an oligonucleotide (e.g., ASO Ml, M7, and/or M4) or a conjugate of the present disclosure and a pharmaceutically-acceptable excipient or carrier in a form suitable for administration to a subject.
- oligonucleotide e.g., ASO Ml, M7, and/or M4
- a pharmaceutically-acceptable excipient or carrier in a form suitable for administration to a subject.
- Pharmaceutically acceptable excipients or carriers are determined in part by the particular composition being administered, as well as by the particular method used to administer the composition.
- oligonucleotides e.g., ASO Ml, M7, and/or M4
- conjugates of the present disclosure See, e.g., Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa. 18th ed. (1990)).
- the pharmaceutical compositions are generally formulated sterile and in full compliance with all Good Manufacturing Practice (GMP) regulations of the U.S. Food and Drug Administration.
- the pharmaceutical composition comprises one or more oligonucleotides or conjugates described herein.
- the oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates described herein are co-administered with one or more additional therapeutic agents, in a pharmaceutically acceptable carrier.
- the pharmaceutical composition comprising the oligonucleotides or conjugates described herein is administered prior to administration of the additional therapeutic agent(s).
- the pharmaceutical composition comprising the oligonucleotides or conjugates described herein is administered after the administration of the additional therapeutic agent(s).
- the pharmaceutical composition comprising the oligonucleotides or conjugates described herein is administered concurrently with the additional therapeutic agent(s).
- Acceptable carriers, excipients, or stabilizers are nontoxic to recipients (e.g., animals or humans) at the dosages and concentrations employed, and include buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid and methionine; preservatives (such as octadecyldimethylbenzyl ammonium chloride; hexamethonium chloride; benzalkonium chloride, benzethonium chloride; phenol, butyl or benzyl alcohol; alkyl parabens such as methyl or propyl paraben; catechol; resorcinol; cyclohexanol; 3-pentanol; and m-cresol); low molecular weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine,
- Examples of carriers or diluents include, but are not limited to: water, saline, Ringer's solutions, dextrose solution, and 5% human serum albumin.
- the use of such media and compounds for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or compound is incompatible with the oligonucleotides or conjugates disclosed herein, use thereof in the compositions is contemplated.
- Supplementary therapeutic agents can also be incorporated into the compositions of the present disclosure. Typically, a pharmaceutical composition is formulated to be compatible with its intended route of administration.
- Solutions or suspensions can include the following components: a sterile diluent such as water, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial compounds such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating compounds such as ethylenediaminetetraacetic acid (EDTA); buffers such as acetates, citrates or phosphates, and compounds for the adjustment of tonicity such as sodium chloride or dextrose.
- the pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide.
- the preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.
- compositions suitable for injectable use include sterile aqueous solutions (if water soluble) or dispersions and sterile powders.
- suitable carriers include physiological saline, bacteriostatic water, Cremophor ELTM (BASF, Parsippany, N.J.) or phosphate buffered saline (PBS).
- the composition is generally sterile and fluid to the extent that easy syringeability exists.
- the carrier can be a solvent or dispersion medium containing, e.g., water, ethanol, polyol (e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like), and suitable mixtures thereof.
- the proper fluidity can be maintained, e.g., by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants.
- a coating such as lecithin
- surfactants Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal compounds, e.g., parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like.
- isotonic compounds e.g., sugars, polyalcohols such as mannitol, sorbitol, and sodium chloride can be added to the composition.
- Prolonged absorption of the injectable compositions can be brought about by including in the composition a compound which delays absorption, e.g., aluminum monostearate and gelatin.
- Pharmaceutical compositions of the present disclosure can be sterilized by conventional, well known sterilization techniques. Aqueous solutions can be packaged for use or filtered under aseptic conditions and lyophilized, the lyophilized preparation being combined with a sterile aqueous solution prior to administration.
- Sterile injectable solutions can be prepared by incorporating the oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates described herein in an effective amount and in an appropriate solvent with one or a combination of ingredients enumerated herein, as desired.
- dispersions are prepared by incorporating the oligonucleotides or conjugates described herein into a sterile vehicle that contains a basic dispersion medium and any desired other ingredients.
- methods of preparation are vacuum drying and freeze-drying that yields a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
- oligonucleotides e.g., ASO Ml, M7, and/or M4
- conjugates described herein can be administered in the form of a depot injection or implant preparation which can be formulated in such a manner to permit a sustained or pulsatile release of the oligonucleotides or conjugates described herein.
- compositions comprising oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates described herein can also be by transmucosal means.
- penetrants appropriate to the barrier to be permeated are used in the formulation.
- penetrants are generally known in the art, and include, e.g., for transmucosal administration, detergents, bile salts, and fusidic acid derivatives.
- Transmucosal administration can be accomplished through the use of, e.g., nasal sprays.
- the pharmaceutical composition comprising oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates described herein is administered intravenously into a subject that would benefit from the pharmaceutical composition.
- the composition is administered to the lymphatic system, e.g., by intralymphatic injection or by intranodal injection (see e.g., Senti et al., PNAS 105(46): 17908 (2008)), or by intramuscular injection, by subcutaneous administration, by intratumoral injection, by direct injection into the thymus, or into the liver.
- the pharmaceutical composition comprising oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates described herein is administered as a liquid suspension.
- the pharmaceutical composition is administered as a formulation that is capable of forming a depot following administration.
- the depot slowly releases the conjugates described herein into circulation, or remains in depot form.
- compositions are highly purified to be free of contaminants, are biocompatible and not toxic, and are suited to administration to a subject. If water is a constituent of the carrier, the water is highly purified and processed to be free of contaminants, e.g., endotoxins.
- the pharmaceutically-acceptable carrier can be lactose, dextrose, sucrose, sorbitol, mannitol, starch, gum acacia, calcium phosphate, alginates, gelatin, calcium silicate, microcrystalline cellulose, polyvinylpyrrolidone, cellulose, water, syrup, methyl cellulose, methylhydroxy benzoate, propylhydroxy benzoate, talc, magnesium stearate, and/or mineral oil, but is not limited thereto.
- the pharmaceutical composition can further include a lubricant, a wetting agent, a sweetener, a flavor enhancer, an emulsifying agent, a suspension agent, and/or a preservative.
- compositions described herein comprise the oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates described herein and optionally a pharmaceutically active or therapeutic agent.
- the therapeutic agent can be a biological agent, a small molecule agent, or a nucleic acid agent.
- Dosage forms are provided that comprise oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates described herein.
- the dosage form is formulated as a liquid suspension for intravenous injection.
- the oligonucleotides e.g., ASO Ml, M7, and/or M4 or conjugates disclosed herein or pharmaceutical composition comprising the oligonucleotides or conjugates may be used concurrently with other drugs.
- the oligonucleotides e.g., ASO Ml, M7, and/or M4
- conjugates or pharmaceutical compositions of the present disclosure may be used together with medicaments such as hormonal therapeutic agents, chemotherapeutic agents, immunotherapeutic agents, medicaments inhibiting the action of cell growth factors or cell growth factor receptors and the like.
- the present disclosure also provides methods of making an oligonucleotide (e.g., ASO Ml, M7, and/or M4) or a conjugate of the present disclosure.
- the present disclosure provides a method of preparing an oligonucleotide (e.g., ASO Ml, M7, and/or M4) or a conjugate of the present disclosure comprising synthesizing the oligonucleotide (e.g., ASO Ml, M7, and/or M4) or conjugate as described, e.g., in the Examples section.
- the term "synthesizing” refers the assembling the oligonucleotide (e.g., ASO Ml, M7, and/or M4) or conjugate using methods known in the art.
- each one of the components of the oligonucleotide (e.g., ASO Ml, M7, and/or M4) or conjugate can be prepared using methods known in the art, e.g., recombinant protein production, solid phase peptide or nucleic acid synthesis, chemical synthesis, enzymatic synthesis, or any combination thereof, and the resulting component can be conjugated using chemical and/or enzymatic methods known in the art.
- the oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates of the present disclosure can be purified to remove contaminants.
- the oligonucleotide (e.g., ASO Ml, M7, and/or M4) or conjugate composition comprises a uniform population of oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates.
- the oligonucleotide (e.g., ASO Ml, M7, and/or M4) or conjugate composition can comprise multiple species (e.g., some of them comprising a targeting moiety, and some comprising the remaining moieties but without a targeting moiety).
- the manufacture of the oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates of the present disclosure comprise lyophilization or any other form of dry storage suitable for reconstitution.
- the oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates of the present disclosure can be purified, e.g., to remove contaminants and/or to generate a uniform population of oligonucleotides or conjugates (e.g., oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates having the same size, or conjugates having the same payload or the same targeting moiety).
- the present disclosure also provides methods of treating a disease or condition in a subject in need thereof comprising administering an oligonucleotide or a conjugate of the present disclosure or a combination thereof (e.g., ASO Ml, M7, and/or M4) to the subject, e.g., a mammal, such as human subject.
- an oligonucleotide or a conjugate of the present disclosure or a combination thereof e.g., ASO Ml, M7, and/or M4
- the disease or disorder is cirrhosis, type 2 diabetes mellitus, hepatitis, fibrosis, fibrosis of the liver, obesity (e.g., abdominal obesity), dyslipidemia (hypercholesterolemia, hypertriglyceridemia), atherosclerosis, type 2 diabetes (T2D), hepatocellular carcinoma (HCC), hypertension, polycystic ovary syndrome (PCOS), chronic kidney disease (CKD), or cardiovascular disease (CVD).
- obesity e.g., abdominal obesity
- dyslipidemia hypercholesterolemia, hypertriglyceridemia
- atherosclerosis e.g., type 2 diabetes (T2D)
- HCC hepatocellular carcinoma
- PCOS polycystic ovary syndrome
- CKD chronic kidney disease
- CVD cardiovascular disease
- the present disclosure provides a method of treating a liver disease or disorder in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of an oligonucleotide or a conjugate of the present disclosure (e.g., ASO Ml, M7, and/or M4), or a pharmaceutical composition of the present disclosure.
- a therapeutically effective amount of an oligonucleotide or a conjugate of the present disclosure e.g., ASO Ml, M7, and/or M4
- the liver disease or disorder is metabolic dysfunction-associated fatty liver disease (MAFLD) or metabolic dysfunction-associated steatohepatitis (MASH).
- MAFLD metabolic dysfunction-associated fatty liver disease
- MASH metabolic dysfunction-associated steatohepatitis
- the present disclosure provides a method of treating obesity (e.g., abdominal obesity) in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of an oligonucleotide or a conjugate of the present disclosure (e.g., ASO Ml, M7, and/or M4), or a pharmaceutical composition of the present disclosure.
- a therapeutically effective amount of an oligonucleotide or a conjugate of the present disclosure e.g., ASO Ml, M7, and/or M4
- the oligonucleotides or conjugates of the present disclosure can administered via intravenous, intramuscular, intraarterial, intrathecal, intracapsular, intraorbital, intracardiac, intradermal, intraperitoneal, transtracheal, subcutaneous, subcuticular, intraarticular, subcapsular, subarachnoid, intraspinal and intrasternal injection and infusion.
- the oligonucleotides or conjugates of the present disclosure can administered via subcutaneous or intravenous injection.
- the oligonucleotides or conjugates of the present disclosure can be used concurrently with other medicaments or treatment suitable for the treatment of the diseases and conditions disclosed herein.
- the oligonucleotides or conjugates of the present disclosure can be used to target liver cells and tissue, e.g., to deliver therapeutic molecules (e.g., an oligonucleotide or antimir).
- the oligonucleotides or conjugates of the present disclosure e.g., ASO Ml, M7, and/or M4 can be used to treat MASH and/or MAFLD.
- oligonucleotides or conjugates of the present disclosure can target a marker specific for MASH and/or MAFLD (e.g.
- miR-378a-3p may additionally carry as payload a therapeutic molecule (e.g., a therapeutic polynucleotide, a peptide, an antimir, an oligonucleotide, or a small molecule).
- a therapeutic molecule e.g., a therapeutic polynucleotide, a peptide, an antimir, an oligonucleotide, or a small molecule.
- the oligonucleotides or conjugates of the present disclosure can be used to target adipose tissue, e.g., to deliver therapeutic molecules (e.g., an oligonucleotide or antimir).
- the oligonucleotides or conjugates of the present disclosure e.g., ASO Ml, M7, and/or M4 can be used to treat obesity (e.g., abdominal obesity).
- oligonucleotides or conjugates of the present disclosure can target a marker specific for obesity (e.g., abdominal obesity), and may additionally carry as payload a therapeutic molecule (e.g., a therapeutic polynucleotide, a peptide, an antimir, an oligonucleotide, or a small molecule).
- a therapeutic molecule e.g., a therapeutic polynucleotide, a peptide, an antimir, an oligonucleotide, or a small molecule.
- the oligonucleotides or conjugates of the present disclosure treats obesity e.g., abdominal obesity).
- the oligonucleotides or conjugates of the present disclosure are capable of reducing a body weight or inducing a weight loss in a subject in need thereof comprising administering the oligonucleotides or conjugates described herein (e.g., ASO Ml, M7, and/or M4) to the subject.
- the disclosure provides a method of reducing a body weight or inducing a weight loss in a subject in need thereof comprising administering the oligonucleotides or conjugates described herein (e.g., ASO Ml, M7, and/or M4) to the subject.
- the subject loses body fat mass at a higher percentage than lean muscle mass. In some aspects, the subject loses body fat mass at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least aout 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or about 100% more than lean muscle mass.
- the subject loses body fat mass more efficiently than a corresponding subject that received a control, e.g., a GLP-1 agonist, e.g., semaglutide or tirzepatide or a reference ASO, e.g., ASO Ml’, ASO M2, ASO M5, ASO M6, or ASO M8.
- a control e.g., a GLP-1 agonist, e.g., semaglutide or tirzepatide
- a reference ASO e.g., ASO Ml’, ASO M2, ASO M5, ASO M6, or ASO M8.
- the subject after administration of the oligonucleotide (e.g., ASO Ml, M7, and/or M4) or conjugate of the present disclosure reduces body fat mass without changing lean muscle mass. Loss of muscle mass is indeed a major side effect of GLP-1 agonists.
- the STEP 1 and SUSTAIN 8 of semaglutide trials found 39-40% of weight lost on the GLP-1 drugs was lean mass. Often, twenty-five percent or more of the weight loss on these drugs is muscle.
- the oligonucleotides (e.g., ASO Ml, M7, and/or M4) and conjugates of the present disclosure are capable of maintaining the lean muscle mass in a subject administered with the oligonucleotides.
- the subject after administration of the oligonucleotide disclosure (e.g., ASO Ml, M7, and/or M4) or conjugate of the present disclosure reduces white adipose tissue (WAT). In mammals, white adipose tissue (WAT) stores and releases lipids, whereas brown adipose tissue (BAT) oxidizes lipids to fuel thermogenesis.
- WAT white adipose tissue
- BAT brown adipose tissue
- the oligonucleotides disclosure e.g., ASO Ml, M7, and/or M4
- conjugates of the present surprisingly reduces WAT, without affecting the BAT.
- the subject after administration of the oligonucleotide (e.g., ASO Ml, M7, and/or M4) or conjugate of the present disclosure does not significantly lose brown adipose tissue.
- visceral fat also known as toxic fat, is hidden inside your body on and around your vital organs.
- Visceral fat can cause health issues such as high blood pressure, heart disease, diabetes and some cancers. Visceral fat is caused by eating more calories than you burn and not moving enough.
- the oligonucleotides e.g., ASO Ml, M7, and/or M4 or conjugate of the present disclosure reduces visceral fat.
- the subject after administration of the oligonucleotide (e.g., ASO Ml, M7, and/or M4) or conjugate of the present disclosure reduces hepatic steatosis and/or lipid accumulation.
- the oligonucleotide e.g., ASO Ml, M7, and/or M4
- conjugate of the present disclosure reduces hepatic steatosis and/or lipid accumulation.
- kits, or products of manufacture comprising an oligonucleotide (e.g., ASO Ml, M7, and/or M4), a conjugate, or a pharmaceutical composition of the present disclosure and optionally instructions for use.
- the kit or product of manufacture comprises an oligonucleotide (e.g., ASO Ml, M7, and/or M4), a conjugate, or a pharmaceutical composition of the present disclosure in one or more containers.
- the kit or product of manufacture comprises an oligonucleotide (e.g., ASO Ml, M7, and/or M4), a conjugate, or a pharmaceutical composition of the present disclosure and a brochure.
- the kit or product of manufacture comprises an oligonucleotide (e.g., ASO Ml, M7, and/or M4), a conjugate, or a pharmaceutical composition of the present disclosure and instructions for use.
- an oligonucleotide e.g., ASO Ml , M7, and/or M4
- a conjugate, or a pharmaceutical composition of the present disclosure, or combinations thereof can be readily incorporated into one of the established kit formats which are well known in the art.
- the kit or product of manufacture comprises an oligonucleotide (e.g., ASO Ml, M7, and/or M4) or a conjugate of the present disclosure in dry form in a container (e.g., a glass vial), and optionally a vial with a solvent suitable to hydrate the oligonucleotide (e.g., ASO Ml, M7, and/or M4) or conjugate, and optionally instructions for the hydration of the oligonucleotide (e.g., ASO Ml, M7, and/or M4) or conjugate.
- a container e.g., a glass vial
- a vial with a solvent suitable to hydrate the oligonucleotide (e.g., ASO Ml, M7, and/or M4) or conjugate e.g., ASO Ml, M7, and/or M4 or conjugate.
- the kit or product of manufacture comprises an oligonucleotide (e.g., ASO Ml, M7, and/or M4) or a conjugate of the present disclosure in a dry form.
- the kit or product of manufacture comprises an oligonucleotide (e.g., ASO Ml, M7, and/or M4) or a conjugate of the present disclosure in solution.
- the kit or product of manufacture comprises an oligonucleotide (e.g., ASO Ml, M7, and/or M4) or a conjugate of the present disclosure in solution, and instructions for use.
- the kit or product of manufacture comprises an oligonucleotide (e.g., ASO Ml, M7, and/or M4) or a conjugate of the present disclosure in dry form, and instructions for use (e.g., instructions for reconstitution and administration).
- an oligonucleotide e.g., ASO Ml, M7, and/or M4
- instructions for use e.g., instructions for reconstitution and administration
- FIG. 1A The results from the in vitro efficacy test of ASO Ml is shown in FIG. 1A.
- HepG2 cells were obtained from the Korean Cell Line Bank (KCLB®, Seoul, South Korea) and cultured in suspension at 37°C with a 5% CO2 atmosphere. The cells were grown in Dulbecco's Modified Eagle Medium (DMEM; Welgene, LM001-05) supplemented with 10% fetal bovine serum (FBS; HyClone, Sh30919.03) and a penicillin-streptomycin mix (Gibco, 15140-122). HepG2 cells were seeded at a density of 40,000 cells/well in a 12-well plate and incubated overnight.
- DMEM Dulbecco's Modified Eagle Medium
- FBS HyClone, Sh30919.03
- Gibco penicillin-streptomycin mix
- the cells were then administered a combination of .22
- OA JM oleic acid
- PA .11
- Qiagen Qiagen, 79306
- miScript RT II Kit Qiagen, 218161
- the primer sequences (5'— >3 ') used in this study were as follows: miR- 378a-3p forward: 5’-ACTGGACTTGGAGTCAGAAGGCAA-3’ (SEQ ID NO: 51), RNU6 forward (reference/normalized): 5’-GCTTCGGCAGCACATATACTAAAAT-3’ (SEQ ID NO: 52), Reverse primer: 5’-GAATCGAGCACCAGTTACG-3’ (SEQ ID NO: 53), probe: FAM-
- CGAGGTCGACTTCCTAGA SEQ ID NO: 54.
- the RT-qPCR was carried out for 40 cycles under the following conditions: pre-denaturation at 95°C for 15 minutes, denaturation at 95°C for 10 seconds, annealing at 60°C for 1 minute, and extension at 72°C for 10 seconds. Relative miRNA levels were determined using the 2 -AACt method.
- FIG. 1A shows that ASO Ml reduced the expression of miR-378a-3p in cells induced by oleic acid/palmitic acid.
- the overexpressed levels of miR-378a-3p were down-regulated when samples were additionally transfected with ASO Ml (500nM) at all three time points (6, 12, and 24 hours).
- miR-378a-3p overexpression in the OA/PA group compared to the control group was +84% ⁇ 7.6 at the 6 hour time point, +53% ⁇ 5.9 at the 12 hour time point, and +63% ⁇ 5.2 at the 24 hour time point (the difference between the two groups was statistically significant at all 3 time points).
- Oil red O staining in HepG2 is shown in FIG. IB.
- To stain HepG2 cells first wash the cells three times with PBS to remove any unbound stain. Then, fix the cells with 4% PFA in PB (Biosesang, Cat No: PC2205- 100-74) for 30 minutes. Afterward, remove the PFA and wash the cells twice using distilled water. Add 60% isopropanol to the cells and let them incubate for 5 minutes. Next, discard the isopropanol and incubate the cells with Oil Red O solution (Sigma- Aldrich, Cat No: O1391-250ML) at room temperature for 15 minutes.
- Oil Red O solution Sigma- Aldrich, Cat No: O1391-250ML
- FIG. IB shows that ASO Ml reduced the deposition of lipid droplets in cells induced by oleic acid/palmitic acid.
- the left column representing the control group, shows very few lipid droplet deposits (indicated by red staining) at the 6, 12, and 24 hour time points.
- the middle column representing the OA/PA administered group, shows many lipid droplet deposits, with the amount of deposits increasing across the 6, 12, and 24 hour time points.
- the right column, representing the OA/PA + ASO Ml administered group shows some lipid droplet deposits, with the amount of deposits increasing across the 6, 12, and 24 hour time points. This indicates that ASO Ml is able to partially counteract the deposition of lipid droplets induced by the OA/PA administration, and return the cells to a state more similar to the control group.
- Each group, n 3.
- FIG. 2A The experimental schedule for the in vivo expression of miR-378a-3p in HFD-fed mice experiment is shown in FIG. 2A.
- Seven-week-old wild-type male C57BL/6N mice (koatech) were maintained on either a standard diet (SD; felako, S-01010) or a high-fat diet (HFD; Open Source, DI 2492) for 5 weeks. Mice were not subjected to fasting and re-feeding. Mice were sacrificed after 5 weeks elapsed. After such time, the brain, liver, heart, lung, kidney, and spleen were collected for gene expression analysis, protein analysis, and histological analysis. All procedures involving mice were approved by the institutional animal care committee at Biorchestra.
- Qiagen Qiagen, 79306
- miScript RT II Kit Qiagen, 218161
- the primer sequences (5'— >3') used in this study were as follows: miR- 378a-3p forward: 5’-ACTGGACTTGGAGTCAGAAGGCAA-3’ (SEQ ID NO: 51), RNU6 forward (reference/normalized): 5’-GCTTCGGCAGCACATATACTAAAAT-3’ (SEQ ID NO: 52), Reverse primer: 5’-GAATCGAGCACCAGTTACG-3’ (SEQ ID NO: 53), probe: FAM-
- CGAGGTCGACTTCCTAGA SEQ ID NO: 54.
- the RT-qPCR was carried out for 40 cycles under the following conditions: pre-denaturation at 95°C for 15 minutes, denaturation at 95°C for 10 seconds, annealing at 60°C for 1 minute, and extension at 72°C for 10 seconds. Relative miRNA levels were determined using the 2 -AACt method.
- liver miR-378a-3p expression in HFD-fed mice is shown in FIG 2B.
- miR-378a-3p was robustly induced in HFD-fed mice, especially in the in fatty liver of HFD-fed mice.
- FIG 2C Brain, heart, lung, spleen, and kidney miR-378a-3p expression in HFD-fed mice is shown in FIG 2C.
- miR-378a-3p expression in HFD-fed mice compared to the SD-fed mice was - 13.3% ⁇ 4.6 for the brain, +108.7% ⁇ 114.0 for the heart, +67.8% ⁇ 22.8 for the lungs, +19.56% ⁇ 11.1 in the spleen, and -9.6% ⁇ 34.3 in the kidneys.
- the differences in the miR-378a-3p expression in the heart and lungs were statistically significant (each group, n 5).
- FIG. 3A The experimental schedule for the in vivo efficacy of ASO Ml in induced MAFLD and MASH mice experiment is shown in FIG. 3A.
- the mice were maintained on either a standard diet (SD; aparako, S-01010) or a high-fat diet (HFD; Open Source, D12492) for 5 weeks.
- mice received a dose of 2.5mg/kg ASO Ml (Ml) complexed with in vivo-jetPEI (Polyplus Transfection, 1010000030), which was adminsiterd via intraperitoneal injection 3 times (every 5 days starting at week 3) before sacrifice.
- LPS Long Term Evolution
- HFD+LPS Long Term Evolution
- HFD+ASO Ml+LPS groups 5mg/kg LPS (Siga-Aldrich, L2630-10MG) was administered via intraperitoneal injection 24h before sacrifice. Mice were not subjected to fasting and re-feeding. Mice were sacrificed after 5 weeks elapsed.
- MAFLD was induced in the mice by feeding the mice a HFD.
- MASH was induced in the mice by feeding the mice a HFD and additionally injecting the mice with LPS. All procedures involving mice were approved by the institutional animal care committee at Biorchestra.
- FIG. 3B The morphology of the bodies and livers of the mice for the SD, HFD, and HFD + ASO Ml groups are shown in FIG. 3B.
- the body and organs, notably the liver, were smaller and lighter in HFD +ASO Ml mice when compared to the HFD- induced MAFLD mice (each group, n 4). This indicates that ASO Ml is able to partially counteract the change in morphology caused by the MAFLD induced by the HFD, and return the mice to a state more similar to the control group.
- FIG. 3C shows that body weight was significantly reduced in HFD-fed+ASO Ml mice compared to the HFD-fed mice. It should be noted that the body weight reduction in the HFD-fed+ASO Ml mice only began after injections with ASO Ml began 3 weeks into the experiment., before that the HFD-fed+ASO Ml mice and the HFD-fed mice were at essentially the same body weight. Following the ASO Ml
- 3D shows that body weight and liver weight was significantly reduced, and body temperature remained the same, in HFD-fed+ASO Ml mice compared to the HFD-fed mice.
- the increase in body weight of the HFD-fed mice was statistically significant when compared to both the SD and HFD-fed+ASO Ml mice.
- the increase in liver weight of the HFD-fed mice was statistically significant when compared to both the SD and HFD-fed+ASO Ml mice.
- H&E staining and Oil red O staining of mouse liver samples for both induced MAFLD and MASH mice are shown in FIG. 3E.
- the liver samples were fixed in 4% PFA in PB (Biosesang, PC2205- 100-74), then embedded in OCT compound (SAKURA Tissue-Tek, 4583).
- OCT compound SAKURA Tissue-Tek, 4583.
- H&E staining OCT-embedded liver tissues were coronally sectioned into 25pm slices using a cryostat microtome (Leica Biosystems, CM1860). OCT-embedded sections were stained using an H&E staining kit according to the manufacturer’s instructions (abeam, ab245880).
- liver tissues embedded in OCT compound were sectioned (10pm), mounted on slides, and allowed to dry for 1-2 hours. After drying, the sections were rinsed with distilled water 3 times. The slides were then placed in 60% isopropanol for 30 sec, and stained in Oil Red O solution in isopropanol for 10 min. The slides were transferred to a 60% isopropanol solution for 10 sec, rinsed in distilled water 3 times, stained in hematoxylin for 2min, and then rinsed in distilled water 3 times. Then, slides were mounted onto glass slides, air-dried, and coverslipped with an aqueous mounting medium. Stained slides were observed under a digital microscope (Leica Biosystems, DM500). All images were obtained under lOOx magnification.
- FIG. 3E shows that ASO Ml ameliorated liver histopathologies of mice with induced MAFLD.
- H&E staining revealed that hepatic steatosis (fatty liver disease) was increased in the HFD-fed group compared to the SD-fed group, whereas hepatic steatosis decreased in the HFD+ASO Ml group compared to the HFD-fed group.
- FIG. 3E shows that ASO Ml ameliorated liver histopathology of mice with induced
- H&E staining revealed that hepatic steatosiswas increased in the HFD+LPS-fed group compared to the SD+LPS-fed group, whereas hepatic steatosis decreased in the HFD+LPS+ASO Ml group compared to the HFD+LPS-fed group.
- Qiagen Qiagen, 79306
- miScript RT II Kit Qiagen, 218161
- the primer sequences (5'— >3') used in this study were as follows: miR-378a-3p forward: 5’-ACTGGACTTGGAGTCAGAAGGCAA-3’ (SEQ ID NO: 51), RNU6 forward (reference/normalized): 5’-GCTTCGGCAGCACATATACTAAAAT-3’ (SEQ ID NO: 52), Reverse primer: 5’-GAATCGAGCACCAGTTACG-3’ (SEQ ID NO: 53), probe: FAM- CGAGGTCGACTTCCTAGA (SEQ ID NO: 54).
- the RT-qPCR was carried out for 40 cycles under the following conditions: pre-denaturation at 95°C for 15 minutes, denaturation at 95°C for 10 seconds, annealing at 60°C for 1 minute, and extension at 72°C for 10 seconds. Relative miRNA levels were determined using the 2 -AACt method. Data generated is shown in FIG. 3F.
- FIG. 3F shows that ASO Ml has an effect on miR-378a-3p expression in the liver of induced MAFLD and MASH mice.
- miR-378a-3p expression in the liver was significantly higher in the HFD and HFD+LPS groups compared to the SD and SD+LPS control groups respectively.
- RT for 20 min for coagulation before centrifugation at 13000 rpm for 15 min at 4°C.
- the supernatant (serum) was collected.
- ELISA kits for mouse TNF-a (TNF-a; R&D systems) were used to measure cytokines in the serum according to the manufacturer’s instruction.
- the level of TNF-a was evaluated by comparison with the regression curve for its cytokine standard. Cytokine concentration is reported as pg of cytokine per milliliter of serum. Data generated is shown in FIG.
- FIG. 3G shows that ASO Ml has an anti-inflammatory effect in the induced MAFLD and MASH mice, as evidenced by the concentration of TNF-a in serum.
- TNF- a in serum was significantly higher in the HFD and HFD+LPS groups compared to the SD and SD+LPS control groups respectively.
- Example 4 in vitro Knockdown Efficacy of miR-378a-3p after Transfection of Naked ASO, Modified ASO Ml, and Modified ASO M2 in HepG2 and BV-2 Cells
- miR-378a-3p in vitro knockdown efficacy of miR-378a-3p was investigated.
- miR-378a-3p mimics were transfected for 2 hours. The media was replaced after 2 hours and an ASOs in vitro efficacy test was conducted. ASOs were transfected with 2-fold dilution at each step (15.625, 31.25, 61.25, 125, 250, 500 nM) in HepG2 and BV-2 cells.
- Modified ASO #1 reduced target miR-378a-3p mRNA 25.87% more than naked ASO and 40.73% more than modified ASO #2 in HepG2 cells (human liver cell line).
- the chemical modifications of Modified ASO #1 can result in improved therapeutic effects in a liver disease model compared to a naked ASO and Modified ASO #2 as Modified ASO #1 targets miR-378a-3p better than the naked ASO and Modified ASO #2.
- Modified ASO #1 reduced the miR-378a-3p mRNA by 38.46% more than the naked ASO and 29.04% more than modified ASO #2 in BV-2 cells (Mouse brain microglia cell line).
- the chemical modifications of Modified ASO #1 can result in improved therapeutic effects in a brain disease model as Modified ASO #1 targets miR-378a-3p better than the naked ASO and Modified ASO #2.
- Modified ASO #1 reduced the expression of miR-378a-3p more effectively than the naked ASO and Modified ASO #2.
- Example 5 in vitro Anti-Inflammatory Effect after Transfection of Naked ASO, Modified ASO Ml, and Modified ASO M2 in BV-2 Cells
- mice whole blood was collected from the mice that are administered with Modified ASO #1, the naked ASO, or Modified ASO #2 via cardiac puncture, and left at room temperature (RT) for 20 min for coagulation before centrifugation at 13000 rpm for 15 min at 4°C.
- the supernatant (serum) of BV-2 cells were collected.
- ELISA kits for mouse TNF-a, IL-ip, and IL-18 were used to measure cytokines in the serum according to the manufacturer’s instruction.
- Modified ASO #1 administered groups had significantly lower concentrations of TNF-a, IL-ip, and IL-18 than the naked ASO and Modified ASO #2.
- Modified ASO #1 reduced the pro-inflammatory cytokines more effectively than the naked ASO and Modified ASO #2.
- Modified ASO #1 effectively reduced excessive TNF-a induced by LPS, and NLRP3 inflammasome activation induced by LPS+ATP. Therefore, based on the antiinflammatory effects, Modified ASO #1 can be expected to have superior therapeutic effects for MAFLD and MASH by effectively reducing inflammation.
- Example 6 Comparative Evaluation of the Therapeutic Efficacy of Various Weight Loss Methods in MAFLD Model
- mice were individually housed in a temperature-controlled ( ⁇ 24 °C) facility with 12h/12h light/dark cycle. Animal protocols were approved by Biorchestra and Co. IACUC (Institutional Animal Care and Use Committee). All studies were conducted in obese male mice (C57/BL6J). The body weight of all mice was measured daily at a consistent time. Animals were maintained on a high-fat diet (consisting of 60% fat, D12492; Research Diets) for 16-weeks, with free access to food and water before randomization by weight. Mice in the HFD group were fed for 8 to 12 weeks before injection.
- mice were injected subcutaneously (SC) with vehicle, semaglutide (910463-68-2; Coldspring), tizepatide (2023788-19-2; Coldspring) or ASO-M1 (Example 6 only). Semaglutide and Tirzepatide were administered daily via SC injection for a duration of two weeks, with one injection each day (Example 6 only).
- the injection schedule for ASO-M1 varied according to the experimental conditions. ASO Ml was injected without transfection reagent (Gymnotic delivery). For the repeat injection conditions, injections were administered every three days, every seven days, or daily. In the case of a single injection, there was a schedule where the subject was sacrificed two weeks after the injection.
- mice were not subjected to fasting and re-feeding. After such time, the brain, liver, heart, lung, kidney, spleen, and whole blood were collected for gene expression analysis, protein analysis, clinical chemistry analysis and histological analysis.
- mice were deeply anaesthetized with isoflurane, and the organs were immediately isolated from the mice bodies. Inguinal WAT (iWAT), interscapular WAT (isWAT), perigonadal WAT (pWAT), mesenteric WAT (mW AT), liver, quad muscle, kidney, spleen and heart were isloared.
- FIG. 7A shows the schedule of the administration.
- FIGs 7B-7G show the results of the Therapeutic Efficacy of Various Weight Loss Methods in MAFLD Model test.
- daily ASO-M1 administration resulted in about 25% weight loss, outperforming semaglutide (19%) and closely maching tirzepatide efficacy (29%) (compared to control).
- FIG. 7C semaglutide and tirzepatide reduced body weight by reducing food intake, but ASO-M1 caused only moderate reduction of food intake.
- FIG. 7D ASO-M1 induced efficient weight loss by specifically reducing fat mass without changing lean muscle mass. As shown in FIGs.
- ASO-M1 administration revealed overall benefits, compared with semaglutide and tizepatide, in reducing hepatic steatosis and lipid accumulation, specifically reducing white adipose tissue (WAT) and visceral fat (FIGs. 7E and 7F) without negatively impacting on brown adipose tissue (BAT) (FIG. 7G).
- WAT white adipose tissue
- BAT brown adipose tissue
- Example 7 Comparative Evaluation of the Therapeutic Efficacy of Various Schedules of ASO Ml in MAFLD Model
- a MAFLD Model test was conducted to show the results of the therapeutic efficacy of various schedules of ASO ML This test shows that the weight loss effect by ASO-M1 is due to reducing fat mass (e.g., visceral fat), and not due to reducing food intake (FIGs. 8B-8D).
- Doses of 1.5 mg/kg ASO-M1 were administered three times a week, and 5 mg/kg ASO-M1 were administered once a week. See FIG. 8A.
- the administrations of ASO-M1 resulted in significantly better and comparable weight loss compared to the daily injection of Semaglutide and Tirzepatide, respectively (FIGs 8B-8G). As shown in FIG.
- FIG. 8B doses of 1.5 mg/kg ASO-M1 three times a week, and 5 mg/kg ASO-M1 once a week resulted in about 34% and about 21% weight loss respectively compared to the control.
- FIG. 8C shows that doses of 1.5 mg/kg ASO-M1 three times a week, and 5 mg/kg ASO-M1 once a week resulted in about 27% and about 15% reduction in food intake respectively.
- FIG. 8D shows that ASO-M1 at both dosing schedules induced efficient weight loss by specifically reducing fat mass without changing lean muscle mass. Doses of 1.5 mg/kg AS0-M1 three times a week outperformed 5 mg/kg AS0-M1 once a week in reducing fat mass. As shown in FIGs.
- AS0-M1 at both dosing schedules revealed overall benefits, in reducing hepatic steatosis and lipid accumulation, specifically reducing white adipose tissue (WAT) and visceral fat (FIGs. 8E and 8F) without negatively impacting brown adipose tissue (BAT) (FIG. 8G).
- WAT white adipose tissue
- BAT brown adipose tissue
- Example 8 Comparative Evaluation of the Expression of miRNA and mRNA for Various Schedules of ASO Ml in MAFLD Model
- FIG. 9A shows the schedule of the ASO Ml administration.
- FIGs 9B-9G show that ASO Ml maintains a continuous therapeutic effect for up to two weeks after a single injection by regulating the genes related to lipid clearance and metabolism.
- doses of ASO Ml (10 mg/kg) weekly for 4 weeks (weeks 8-11) and a dose of ASO Ml (30 mg/kg) once (week 10) resulted in about 32% and about 24% weight loss respectively compared to control.
- FIG. 9C the HFD significantly elevated miR-378 levels in the liver.
- ASO Ml at both dosing schedules restored the miR-378 level back to substantially the normal level.
- ASO-M1 administration at both dosing schedules restored altered (lowered) expression of ATG2a, IGF-1, and IGF-1R, which are potential targets of miR-378, to the substantially normal level in the liver.
- FIG. 9E ASO-M1 administration at both dosing schedules significantly up-regulated GLP-2Rcompared to control. Down-regulation of GLP-2R is strongly associated with hepatic inflammation and steatosis.
- Example 9 Evaluation of MAFLD Progression in a HFD Mouse MAFLD Model via H&E and Oil Red O Staining
- H&E staining and Oil red O staining of mouse liver samples for both induced MAFLD and MASH mice are shown in FIG. 10A and 10B.
- the liver samples were fixed in 4% PFA in PB (Biosesang, PC2205-100-74), then embedded in OCT compound (SAKURA Tissue- Tek, 4583).
- OCT compound SAKURA Tissue- Tek, 4583.
- H&E staining OCT-embedded liver tissues were coronally sectioned into 25pm slices using a cryostat microtome (Leica Biosystems, CM1860). OCT- embedded sections were stained using an H&E staining kit according to the manufacturer’s instructions (abeam, ab245880).
- liver tissues embedded in OCT compound were sectioned (10pm), mounted on slides, and allowed to dry for 1-2 hours. After drying, the sections were rinsed with distilled water 3 times. The slides were then placed in 60% isopropanol for 30 sec, and stained in Oil Red O solution in isopropanol for 10 min. The slides were transferred to a 60% isopropanol solution for 10 sec, rinsed in distilled water 3 times, stained in hematoxylin for 2min, and then rinsed in distilled water 3 times. Then, slides were mounted onto glass slides, air-dried, and coverslipped with an aqueous mounting medium. Stained slides were observed under a digital microscope (Leica Biosystems, DM500). All images were obtained under lOOx magnification.
- FIGs. 10A and 10B show the results of the evaluation of MAFLD Progression via H&E and Oil Red O Staining test. The results show that ASO-M1 reduces the lipid droplet, fat accumulation and ballooned hepatocytes in the livers of the mice in the HFD mouse MAFLD model.
- the arrows indicate lipid droplets.
- FIG. 10A shows that the amount of lipid droplets was significantly increased in all HFD conditions compared to all HFD+ASO-M1 conditions which mirrors the control condition.
- FIG. 10B the ballooned hepatocytes and the areas of fat accumulation were circled.
- FIG. 10B shows that the amount of ballooned hepatocytes and the areas of fat accumulation were significantly increased in all HFD conditions compared to all HFD+ASO-M1 conditions which mirrors the control condition.
- FIG. 11A-11F ASO-M1 administration at both dosing schedules reversed abnormal lipid profiles induced by the HFD, such as high Low-density lipoprotein (LDL) (FIG. HA), high triglyceride (TG) (FIG. 11C), and high total cholesterol (TC) levels (FIG. HD).
- LDL Low-density lipoprotein
- TG high triglyceride
- TC total cholesterol
- FIG. HD high total cholesterol
- ASO-M1 administration at both dosing schedules also normalized the increased levels of Alanine transaminase (ALT) (FIG. HE) and Aspartate transaminase (AST) (FIG. HF) activities, both of which are markers for liver damage.
- ALT Alanine transaminase
- AST Aspartate transaminase
- ASO-M1 administration at both dosing schedules was able to reverse elevated levels of malign lipids and maintain stable levels of benign lipids, which is predicted to improve liver health and prevent liver damage.
- HepG2 and Hep3B cells were obtained from the Korean Cell Line Bank (KCLB®, Seoul, South Korea) and cultured in suspension at 37°C with a 5% C02 atmosphere.
- the cells were grown in Dulbecco's Modified Eagle Medium (DMEM; Welgene, LM001-05) supplemented with 10% fetal bovine serum (FBS; HyClone, Sh30919.03) and a penicillin-streptomycin mix (Gibco, 15140-122).
- DMEM Dulbecco's Modified Eagle Medium
- FBS HyClone, Sh30919.03
- Gibco penicillin-streptomycin mix
- RNAiMAX InvitrogenTM, 13778450
- Qiagen Qiagen, 79306
- miScript RT II Kit Qiagen, 218161
- the primer sequences (5'— >3') used in this study were as follows: miR-378a-3p forward: 5’- ACTGGACTTGGAGTCAGAAGGCAA-3’ (SEQ ID NO: 51), RNU6 forward (reference): 5’- GCTTCGGCAGCACATATACTAAAAT-3’ (SEQ ID NO: 52), Reverse: 5’-
- FIGs. 13A and 13B show that modified ASO #1 (Ml), #4 (M4) and #7 (M7) were most effective in reducing miR-378a-3p expression levels in both HepG2 and Hep3B cell lines compared to the control.
- FIGs. 14A and 14B show that in the absence of a transfection reagent (gymnotic) modified ASO #1 (Ml), #4 (M4) and #7 (M7) were most effective in reducing miR- 378a-3p expression levels in the Hep3B cell line compared to the control. It also shows that greater dose concentration increased the effectiveness of the reduction in expression.
- FIG. 16 shows that in the absence of a transfection reagent modified ASO #1 (Ml), #4 (M4) and #7 (M7) were most effective in reducing miR-378a-3p expression levels in C57BL/6 mice compared to the control.
- modified miR-378a-3p ASO #1 (Ml), #2 (M2), #4 (M4), #5 (M5), #6 (M6), #7 (M7), and #8 (M8) in mouse plasma 500 pL of mouse plasma was mixed with 500 pL of modified miR-378a-3p ASO (200 pM) in a 1 : 1 ratio.
- the ASO in the mixed plasma was incubated at 37°C, and samples were collected at 0 minutes, 30 minutes, 1 hour, 1 day, 3 days, 7 days, 15 days, and 30 days.
- FIG. 17 shows that miR-378a-3p ASO #7 maintains stability in mouse plasma from 0 minutes to at least 15 days post injection and that ASO #1 maintains stability in mouse plasma from 0 minutes to at least 7 days post injection.
- ASO #2, #5, #6, and #8 were also stable from 0 minutes to at least 7 days post injection, with ASO #8 remaining stable up to at least 30 days post injection.
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Abstract
The present disclosure includes an oligonucleotide comprising a miR-378a-3p inhibitor. The disclosure also includes pharmaceutical compositions comprising the oligonucleotide, and also methods of treating diseases or conditions (i.e., liver diseases or conditions) in a subject in need thereof comprising administering the oligonucleotide to the subject.
Description
MICRORNA-378A-3P ANTISENSE OLIGONUCLEOTIDES AND USES THEREOF
CROSS REFERENCE TO EARLIER FILED APPLICATIONS
[0001] This Application claims the priority benefit of U.S. Provisional Application No. 63/600,279, filed on November 17, 2023, and U.S. Provisional Application No. 63/574,745, filed on April 4, 2024. The entire disclosure of the above-referenced applications are incorporated herein by reference in their entireties.
REFERENCE TO ELECTRONICALLY FILED SEQUENCE LISTING [0002] The content of the electronically submitted sequence listing (Name: 4366_078PC02_SequenceListing_ST26.xml; Size: 104,676 bytes; and Date of Creation: November 15, 2024) is herein incorporated by reference in its entirety.
FIELD
[0003] The present disclosure provides an oligonucleotide targeting miRNA 378a-3p, which can be used to treat a disease or condition affecting the liver.
BACKGROUND
[0004] miRNA 378a-3p is known to be associated with Burkitt lymphoma cell growth (Niu F. et al., Cancers (Basel). 2020 Nov 27;12(12):3546. doi: 10.3390/cancersl2123546), promotes differentiation and inhibits proliferation of myoblasts by targeting HDAC4 in skeletal muscle development (Wei X., et al., RNA Biol. 2016; 13(12): 1300-1309. doi:
10.1080/15476286.2016.1239008), or acts as a tumor suppressor in colorectal cancer stem-like cells and affects the expression of MALAT1 and NEAT' IncRNAs (Castellani G., et al., Front. Oncol., (12), 24 June 2022. Sec. Gastrointestinal Cancers: Colorectal Cancer. doi.org/10.3389/fonc.2022.867886).
[0005] Metabolic dysfunction-associated fatty liver disease (MAFLD) and metabolic dysfunction-associated steatohepatitis (MASH) are diseases that negatively impact the liver. MAFLD is one of the most common chronic liver diseases and can cause hepatocyte injury, inflammation of the liver, and fibrosis of the liver (Pouwels, et al., BMC Endocr Disord 22:63 (2022)). MASH is a severe, progressive form of MAFLD which can cause cirrhosis of the liver, hepatocellular cancer, and death (Raza, et al., Front Biosci (Landmark Ed). 26:206 (2021)). MASH
is the leading cause of liver transplants in the world, and, as of 2022, MAFLD was responsible for $103 billion in annual medical costs in the United States (Witkowski, et al. Pharmacoeconomics 40:751 (2022)). There are currently no FDA approved treatments for MAFLD or MASH (Attia, et al., Clin Transl Sci. 14: 11 (2021). In May of 2023 the FDA raised concerns over a pending MASH therapy, finding that it increased the risk of diabetes and liver injury; this drug was previously expected to become the first FDA approved MASH therapy. There is a current need for safe and effective treatments for MASH and MAFLD.
BRIEF SUMMARY
[0006] The present disclosure is directed to oligonucleotides comprising a miR-378a-3p inhibitor.
[0007] In some aspects, the oligonucleotide comprises siRNA, shRNA, antisense oligonucleotide, microRNA, IncRNA, mRNA, or any combination thereof. In some aspects, the oligonucleotide targets a miRNA, a gene encoding a protein, a gene encoding a transcription factor, a regulatory element, or any combination thereof. In some aspects, the oligonucleotide has from about 10 nucleotides and up to about 20, about 30, about 40, about 50, about 60, about 70, about 80, about 90, about 100, about 150, about 200, about 300, about 400, about 500, about 600, about 700, about 800, about 900, about 1000, about 1100, about 1200, about 1300, about 1400, about 1500, about 1600, about 1700, about 1800, about 1900, or about 2000 nucleotides.
[0008] In some aspects, the oligonucleotide comprises a miRNA inhibitor. In some aspects, the miRNA is miR-378a-3p. In some aspects, the miR-378a-3p comprises 5'- ACUGGACUUGGAGUCAGAAGGC-3' (SEQ ID NO: 1). In some aspects, the miRNA inhibitor comprises a nucleotide sequence comprising 5'-AGUCCAG-3' and wherein the miRNA inhibitor comprises about 6 to about 30 nucleotides in length.
[0009] In some aspects, the miRNA inhibitor comprises at least 1 nucleotide, at least 2 nucleotides, at least 3 nucleotides, at least 4 nucleotides, at least 5 nucleotides, at least 6 nucleotides, at least 7 nucleotides, at least 8 nucleotides, at least 9 nucleotides, at least 10 nucleotides, at least 11 nucleotides, at least 12 nucleotides, at least 13 nucleotides, at least 14 nucleotides, at least 15 nucleotides, at least 16 nucleotides, at least 17 nucleotides, at least 18 nucleotides, at least 19 nucleotides, or at least 20 nucleotides at the 5' of the nucleotide sequence. [0010] In some aspects, the miRNA inhibitor comprises at least 1 nucleotide, at least 2 nucleotides, at least 3 nucleotides, at least 4 nucleotides, at least 5 nucleotides, at least 6
nucleotides, at least 7 nucleotides, at least 8 nucleotides, at least 9 nucleotides, at least 10 nucleotides, at least 11 nucleotides, at least 12 nucleotides, at least 13 nucleotides, at least 14 nucleotides, at least 15 nucleotides, at least 16 nucleotides, at least 17 nucleotides, at least 18 nucleotides, at least 19 nucleotides, or at least 20 nucleotides at the 3' of the nucleotide sequence.
[0011] In some aspects, the miRNA inhibitor has a sequence selected from the group consisting of: 5'-AGUCCAG-3', 5'-AAGUCCAG-3', 5'-CAAGUCCAG-3', 5'-CCAAGUCCAG-3' (SEQ ID NO: 2), 5'-UCCAAGUCCAG-3' (SEQ ID NO: 3), 5'-CUCCAAGUCCAG-3' (SEQ ID NO: 4), 5'- ACUCCAAGUCCAG-3' (SEQ ID NO: 5), 5'-GACUCCAAGUCCAG-3' (SEQ ID NO: 6), 5'- UGACUCCAAGUCCAG-3' (SEQ ID NO: 7), 5'-CUGACUCCAAGUCCAG-3' (SEQ ID NO: 8), 5'- UCUGACUCCAAGUCCAG-3' (SEQ ID NO: 9), 5'- UUCUGACUCCAAGUCCAG-3' (SEQ ID NO: 10), 5'-CUUCUGACUCCAAGUCCAG-3' (SEQ ID NO: 11), 5'-CCUUCUGACUCCAAGUCCAG-3' (SEQ ID NO: 12); 5'-AGUCCAGU-3', 5'-AAGUCCAGU-3', 5'-CAAGUCCAGU-3' (SEQ ID NO: 13), 5'- CCAAGUCCAGU-3' (SEQ ID NO: 14), 5'-UCCAAGUCCAGU-3' (SEQ ID NO: 15), 5'- CUCCAAGUCCAGU-3' (SEQ ID NO: 16), 5'-ACUCCAAGUCCAGU-3' (SEQ ID NO: 17), 5'- GACUCCAAGUCCAGU-3' (SEQ ID NO: 18), 5'-UGACUCCAAGUCCAGU-3' (SEQ ID NO: 19), 5'- CUGACUCCAAGUCCAGU-3' (SEQ ID NO: 20), 5'-UCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 21), 5'-UUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 22), 5'-CUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 23), 5'-CCUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 24), and 5'- GCCUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 25).
[0012] In some aspects, the miRNA inhibitor has a sequence selected from the group consisting of: 5'-AGTCCAG-3', 5'-AAGTCCAG-3', 5'-CAAGTCCAG -3', 5'-CCAAGTCCAG-3' (SEQ ID NO: 26), 5'-TCCAAGTCCAG-3' (SEQ ID NO: 27), 5'-CTCCAAGTCCAG-3' (SEQ ID NO: 28), 5'-ACTCCAAGTCCAG-3' (SEQ ID NO: 29), 5'-GACTCCAAGTCCAG-3' (SEQ ID NO: 30), 5'- TGACTCCAAGTCCAG-3' (SEQ ID NO: 31), 5'-CTGACTCCAAGTCCAG-3' (SEQ ID NO: 32), 5'- TCTGACTCCAAGTCCAG-3' (SEQ ID NO: 33), 5'-TTCTGACTCCAAGTCCAG-3' (SEQ ID NO: 34), 5'-CTTCTGACTCCAAGTCCAG-3' (SEQ ID NO: 35), 5'-CCTTCTGACTCCAAGTCCAG-3' (SEQ ID NO: 36); 5'-AGTCCAGT-3', 5'-AAGTCCAGT-3', 5'-CAAGTCCAGT-3' (SEQ ID NO: 37), 5'- CCAAGTCCAGT-3' (SEQ ID NO: 38), 5'-TCCAAGTCCAGT-3' (SEQ ID NO: 39), 5'- CTCCAAGTCCAGT-3' (SEQ ID NO: 40), 5'-ACTCCAAGTCCAGT-3' (SEQ ID NO: 41), 5'- GACTCCAAGTCCAGT-3' (SEQ ID NO: 42), 5'-TGACTCCAAGTCCAGT-3' (SEQ ID NO: 43), 5'- CTGACTCCAAGTCCAGT-3' (SEQ ID NO: 44), 5'-TCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 45),
5'-TTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 46), 5'-CTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 47), 5'-CCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 48), and 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49).
[0013] In some aspects, the sequence of the miRNA inhibitor is at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% sequence identity to 5'- GCCUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 25) or 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49). In some aspects, the miRNA inhibitor has a sequence that has at least 90% similarity to 5'-GCCUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 25) or 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49). In some aspects, the miRNA inhibitor comprises the nucleotide sequence 5'-GCCUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 25) or 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49) with one substitution or two substitutions. In some aspects, the miRNA inhibitor comprises the nucleotide sequence 5'- GCCUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 25) or 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49). In some aspects, the miRNA inhibitor comprises the nucleotide sequence 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49).
[0014] In some aspects, the miRNA inhibitor comprises at least one modified nucleotide. In some aspects, the modified nucleotide is a locked nucleic acid (LNA), an unlocked nucleic acid (UNA), an arabino nucleic acid (ABA), a bridged nucleic acid (BNA), and/or a peptide nucleic acid (PNA). In some aspects, the modified nucleotide comprises 2'-O-alkyl-RNA; 2'-amino-DNA; 2'-fluoro-DNA; arabino nucleic acid (ANA); 2'-fluoro-ANA, hexitol nucleic acid (HNA), intercalating nucleic acid (INA), constrained ethyl nucleoside (cEt), 2'-O-methyl nucleic acid (2 - OMe), 2'-O-methoxyethyl nucleic acid (2'-M0E), 5'-methyl pyrimidine nucleobase, or any combination thereof. In some aspects, the oligonucleotide comprises a nucleotide sequence having 5 to 30 nucleotides in length. In some aspects, the oligonucleotide is 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26 nucleotides in length. In some aspects, the oligonucleotide is a gapmer, a mixmer, a totalmer, or any combination thereof. In some aspects, the oligonucleotide comprises a backbone modification. In some aspects, the backbone modification is a phosphodiester linkage, a phosphotriester linkage, a methylphosphonate linkage, a phosphoramidate linkage, a phosphorothioate linkage, a phosphorodiamidate morpholino oligomer (PMO), or any combination thereof.
[0015] In some aspects, the miRNA inhibitor has a nucleotide sequence comprising 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49) and a backbone modification comprising one or more phosphorothioate linkages (SEQ ID NO: 55).
[0016] In some aspects, the disclosure provides an oligonucleotide comprising, consisting essentially of, or consisting of the nucleotide sequence as set forth in 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein each of nucleotide residues 1, 2, 3, and 22 is a LNA; and each of nucleotide residues 4-21 is a DNA (SEQ ID NO: 57). In some aspects, each of nucleotide residues 2 and 3 comprise a 5'-methyl pyrimidine nucleobase modification (SEQ ID NO: 56). In some aspects, the nucleotide sequence comprises one or more phosphorothioate linkages (SEQ ID NO: 58). In some aspects, provided herein is an oligonucleotide comprising, consisting essentially of, or consisting of the nucleotide sequence as set forth in 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49); wherein: the nucleotide sequence comprises a fully phosphorothioate modified backbone structure; each of nucleotide residues 1, 2,
3, and 22 is a LNA; each of nucleotide residues 4-21 is a DNA; and each of nucleotide residues 2 and 3 comprises a 5'-methyl pyrimidine nucleobase modification (SEQ ID NO: 50).
[0017] In some aspects, the disclosure provides an oligonucleotide comprising, consisting essentially of, or consisting of the nucleotide sequence as set forth in 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein each of nucleotide residues 1, 2, 3, and 22 is a LNA; and each of nucleotide residues 4-21 is a DNA (SEQ ID NO: 57) and each of nucleotide residues 2, 3, 6, 10, 12, 13, 18, and 19 comprise a 5'-methyl pyrimidine nucleobase modification (SEQ ID NO: 72). In some aspects, the nucleotide sequence comprises one or more phosphorothioate linkages (SEQ ID NO: 73). In some aspects, the disclosure provides an oligonucleotide comprising, consisting essentially of, or consisting of the nucleotide sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49); wherein: the nucleotide sequence comprises a fully phosphorothioate modified backbone structure; each of nucleotide residues 1, 2, 3, and 22 is a LNA; each of nucleotide residues 4-21 is a DNA; and each of nucleotide residues 2, 3, 6, 10, 12, 13, 18, and 19 comprises a 5'-methyl pyrimidine nucleobase modification (SEQ ID NO: 67).
[0018] In some aspects, the disclosure provides an oligonucleotide comprising, consisting essentially of, or consisting of the nucleotide sequence as set forth in 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein each of nucleotide residues 1, 2, 3,
4, 5, 18, 19, 20, 21, and 22 is a LNA; each of nucleotide residues 6-17 is a DNA (SEQ ID NO: 74).
In some aspects, each of nucleotide residues 2, 3, 6, 10, 12, 13, 18, and 19 comprises a 5'-methyl pyrimidine nucleobase modification (SEQ ID NO: 75). In some aspects, the nucleotide sequence comprises one or more phosphorothioate linkages (SEQ ID NO: 76). In some aspects, the disclosure provides an oligonucleotide comprising, consisting essentially of, or consisting of the nucleotide sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49); wherein: the nucleotide sequence comprises a fully phosphorothioate modified backbone structure; each of nucleotide residues 1, 2, 3, 4, 5, 18, 19, 20, 21, and 22 is aLNA; each of nucleotide residues 6-17 is aDNA; and each of nucleotide residues 2, 3, 6, 10, 12, 13, 18, and 19 comprises a 5'-methyl pyrimidine nucleobase modification (SEQ ID NO: 70).
[0019] In some aspects, an optional targeting moiety is conjugated or linked to the oligonucleotide to form a conjugate. In some aspects, the targeting moiety is capable of targeting a tissue. In some aspects, the tissue is liver, brain, kidney, lung, ovary, pancreas, thyroid, breast, stomach, or any combination thereof. In some aspects, the tissue is liver. In some aspects, the targeting moiety is capable of being transported by glycose transporter type 1 (GLUT1). In some aspects, the targeting moiety is an amino acid. In some aspects, the targeting moiety comprises a branched-chain or aromatic amino acid. In some aspects, the targeting moiety is phenylalanine, valine, leucine, and/or isoleucine. In some aspects, the amino acid is phenylalanine.
[0020] In some aspects, the targeting moiety is linked to the oligonucleotide by a linker. In some aspects, the linker is a non-cleavable linker. In some aspects, the linker is a cleavable linker. In some aspects, the cleavable linker is cleavable by a protease. In some aspects, the linker is a bioreducible linker, an acid cleavable linker, a click-to-release linker, a pyrophosphatase cleavable linker, a beta-glucuronidase cleavable linker, or any combination thereof.
[0021] In some aspects, the present disclosure provides a pharmaceutical composition comprising the oligonucleotide or conjugate disclosed herein and a pharmaceutically acceptable carrier.
[0022] In some aspects, the present disclosure provides a method of preparing the conjugate disclosed herein or the pharmaceutical composition disclosed herein comprising linking the oligonucleotide to the targeting moiety, through the optional linker. In some aspects, the method further comprises purifying the conjugate.
[0023] In some aspects, the present disclosure provides a method of treating a disease or condition in a subject in need thereof comprising administering the oligonucleotide or conjugate disclosed herein or the pharmaceutical composition disclosed herein to the subject. In some aspects
the disease or conition is cirrhosis, type 2 diabetes mellitus, hepatitis, fibrosis, fibrosis of the liver, obesity (e.g., abdominal obesity), dyslipidemia (hypercholesterolemia, hypertriglyceridemia), atherosclerosis, type 2 diabetes (T2D), hepatocellular carcinoma (HCC), hypertension, polycystic ovary syndrome (PCOS), chronic kidney disease (CKD), or cardiovascular disease (CVD). In some aspects the disease or condition is obesity (e.g., abdominal obesity). In some aspects, the obesity comprises an abdominal obesity. In some aspects the disease or condition is a liver disease or condition. In some aspect the liver disease or condition is metabolic dysfunction-associated fatty liver disease (MAFLD) or metabolic dysfunction-associated steatohepatitis (MASH). In some aspects, the oligonucleotide useful for the method exhibits a longer half-life than a corresponding oligonucleotide not linked to the targeting moiety. In some aspects, the subject for the method is a mammal.
BRIEF DESCRIPTION OF THE DRAWINGS
[0024] FIG. 1A and IB show the effect of ASO Ml (Ml) administration on the miR-378a- 3p expression and deposition of lipid droplets in Oleic Acid (OA)/Palmitic Acid (PA)-administered HepG2 cells. FIG. 1A shows relative miR-378a-3p expression of HepG2 cells administered OA/PA (0.22pM/0.1 IpM) (middle column), OA/PA+ASO Ml (500nM) (right column) and unadministered control (left column) (each group, n=3). Results are shown at 6 hours (left chart), 12 hours (middle chart), and 24 hours (right chart). A quantitative summary comparing the different groups at the 6, 12, and 24 hour time points is presented below the charts. All data are mean ± SEM. **P < 0.01, and ***P < 0.001 when compared to the unadministered control (Con). ###P < 0.001 and ####P < 0.0001 when compared to the OA/PA administered group (OA/PA). Significance was determined using a Student’s unpaired t-test. FIG. IB shows oil red O staining of HepG2 cells administered OA/PA (0.22pM/0.11pM) (middle column), OA/PA+ASO Ml (500nM) (right column) and unadministered control (left column). Results are shown at 6 hours (top row), 12 hours (middle row), and 24 hours (bottom row) (each group, n=3). All images were obtained under lOOx magnification.
[0025] FIG. 2A-2C show miR-378a-3p expression in high fat diet (HFD)-fed mice. FIG. 2A shows a schedule for the experiments on the HFD-fed mouse model. FIG. 2B shows the levels of miR-378a-3p in the livers of HFD-fed (right column) mice compared to standard diet (SD)-fed mice (left column) (each group, n=4). A quantitative summary comparing the different groups is presented to the right of the chart. FIG. 2C shows levels of miR-378a-3p in the brain (left group),
heart (second-from-left group), lung (middle group), spleen (second-from-right group), and kidney (right group) of HFD-fed mice (right column) compared to SD-fed mice (left column) (each group, n=8). A quantitative summary comparing the different groups is presented under the chart. All data are mean ± SEM. *P < 0.05 and ***P < 0.001 compared to the SD-fed mice. Significance was determined using a Student’s unpaired t-test.
[0026] FIG. 3A-3G show the effects of ASO Ml administration in the HFD-induced metabolic dysfunction-associated fatty liver disease and LPS-induced metabolic dysfunction- associated steatohepatitis mouse models. FIG. 3A shows the schedule of the experiments for the HFD-induced metabolic dysfunction-associated fatty liver disease and LPS-induced metabolic dysfunction-associated steatohepatitis mouse models. FIG. 3B shows a representative image of body (top) and liver (bottom) aspects for SD (left), HFD (middle), and HFD + ASO Ml (right) (each group, n=4). FIG. 3C shows a line graph of body weight change (each group, n=4). Data is reported for 36 days. SD data is indicated by circles, HFD data is indicated by triangles, and HFD + ASO Ml is indicated by diamonds. FIG. 3D shows final body weight (left chart), liver weight (middle chart), and body temperature (right chart) for SD (left bar), HFD (middle bar), and HFD + ASO Ml (right bar) (each group, n=4). FIG. 3E shows morphological analysis of liver sections from each group carried out via H&E staining (first and third row) and also shows lipid droplets in the tissue sections from each group analyzed via oil red O staining (second and fourth row). Images from the induced MAFLD (top two rows) and MASH (bottom two rows) groups are shown. SD (left column), HFD (middle column), and HFD + ASO Ml (right column) images are shown for the induced MAFLD groups. SD+LPS (left column), HFD+LPS (middle column), and (HFD+LPS) + ASO Ml (right column) images are shown for the induced MASH groups. All images were obtained under lOOx magnification (each group, n=4). FIG.3F shows a comparison of the relative miRNA expression levels of miR-378a-3p in liver tissue from mice in various experimental groups (each group, n=4). Data from the induced MAFLD (left chart) and MASH (right chart) groups are shown. SD (left column), HFD (middle column), and HFD + ASO Ml (right column) data is shown for the induced MAFLD group. SD+LPS (left column), HFD+LPS (middle column), and (HFD+LPS) + ASO Ml (right column) data is shown for the induced MASH group. All data are mean ± SEM. *P < 0.05 and **P < 0.01. #P < 0.05 and ###P < 0.001. Significance was determined using a Student’s unpaired t-test. FIG. 3G shows a comparison of the relative TNF-a secretion levels in serum from mice in various experimental groups analyzed via ELISA (each group, n=4). Data from the induced MAFLD (left chart) and MASH (right chart) groups are shown. SD (left column), HFD (middle column), and HFD + ASO Ml (right column)
data is shown for the induced MAFLD group. SD+LPS (left column), HFD+LPS (middle column), and (HFD+LPS) + ASO Ml (right column) data is shown for the induced MASH group. All data are mean ± SEM. **P < 0.01 and ****p < 0.0001. #P < 0.05 and ##P < 0.01. Significance was determined using a Student’ s unpaired t-test.
[0027] FIGs. 4A-4C show a schematic diagram of the naked Homo sapiens-sm^Q stranded-microRNA-378a-3p (FIG. 4A), an antisense oligonucleotide (ASO) Ml which possesses various nucleotide modifications (e.g., backbone modification, nucleobase modification), specifically 100% of the backbone linkages are phosphorothioate linkages, nucleotide residues 1, 2, 3, and 22 are a LNA, nucleotide residues 4-21 are a DNA, and nucleotide residues 2 and 3 comprise a 5'-methyl pyrimidine nucleobase modification (FIG. 4B) and an antisense oligonucleotide (ASO) M2 which possesses various nucleotide modifications (e.g., backbone modification, nucleobase modification), specifically specifically 100% of the the backbone linkages are phosphorothioate linkages, nucleotide residues 1, 2, 3, and 22 are a 2 ’-MOE, nucleotide residues 4-21 are a DNA, and nucleotide residues 2 and 3 comprise a 5'-methyl pyrimidine nucleobase modification (FIG. 4C). The Nucelotide Sequence, Complement to the Nucleotide Sequence, Length, GC (guanine-cytosine) content, Melting Temperature, Seed Sequence, and Molecular Weight for each are also shown.
[0028] FIGs. 5A-5D show the analysis of miR-378a-3p expression level after naked
ASO, modified ASO #1 (ASO Ml), and modified ASO #2 (ASO M2) transfection for 12 hours in miR-378a-3p overexpressed HepG2 (FIGs. 5A and 5B) and BV-2 cells (FIG. 5C and 5D) (each group, n=3). FIG. 5A shows the IC50, % at KD Max, and % expression of miR-378a-3p in HepG2 cells for naked ASO, modified ASO #1, and modified ASO #2 from 0 nM to 1000 nM. FIG. 5B shows % inhibition of miR-378a-3p in HepG2 cells for naked ASO, modified ASO #1, and modified ASO #2 at concentrations of 15.625, 31.25, 61.25, 125, 250, 500 nM. FIG. 5C shows the IC50, % at KD Max, and % expression of miR-378a-3p in BV-2 cells for naked ASO, modified ASO #1, and modified ASO #2 from 0 nM to 1000 nM. FIG. 5D shows % inhibition of miR- 378a-3p in BV-2 cells for naked ASO, modified ASO #1, and modified ASO #2 at concentrations of 15.625, 31.25, 61.25, 125, 250, 500 nM.
[0029] FIGs. 6A-6C show a comparison of anti-inflammatory effect 24 hours after transfection of Naked ASO, Modified ASO #1, and Modified ASO #2 in BV-2 cells. FIG. 6A shows an ELISA of TNF-a in the supernatants of BV-2 cells after administration of control (first colomn), LPS (100 ng/ml) (second colomn), LPS (100 ng/ml) + naked ASO (third colomn), modified ASO #1 (fourth colomn), or modified ASO #2 (fifth colomn) (100 nM) for 24 h (each
group, n=3). FIG. 6B and 6C show ELISA of IL-1 (FIG. 6B) and IL-18 (FIG. 6C) in the supernatants of BV-2 cells after administration of control (first colomn), LPS (100 ng/ml) + ATP (2.5 mM) (second colomn), LPS (100 ng/ml) + ATP (2.5 mM) + naked ASO (third colomn), modified ASO #1 (fourth colomn), or modified ASO #2 (fifth colomn) (100 nM) for 24 h (each group, n=3). LPS+ATP administered BV-2 cells were transfected with ASOs upon LPS administration. All data are mean ± SEM***P < 0.0001 compared to the control (Con). #P < 0.05, ##P < 0.01 and ####P < 0.0001 compared to the control, ffp < 0.01 for indicated comparisons. Significance was determined using a one-way ANOVA and post-hoc tukey’s test.
[0030] FIGs. 7A-7G show the comparison of the reduction effects of semaglutide, tirzepatide, and ASO Ml on body weight and cumulative food intake in HFD mice. FIG. 7A shows the schedule of the experiments for the HFD mouse models. After 1 week of acclimation, mice were fed with high-fat diet for 12 weeks. HFD mice were dosed once daily for 14 days with vehicle, semaglutide (500 pg/kg), tirzepatide (500 pg/kg) or ASO-M1 (500 pg/kg) (each group, n=6) then sacrificed. Blood and tissue was collected, and MRI and lipid tests were performed. FIG. 7B shows the body weight change % for the control, semaglutide, tirzepatide and ASO Ml administered HFD mice from days 1 to 14. FIG. 7C shows the cumulative food intake (measure of appetite) for the control, semaglutide, tirzepatide and ASO Ml administered HFD mice from days 1 to 14. FIG. 7D shows quantification of mass (g) changes of fat mass and lean mass after daily injection of control, semaglutide, tirzepatide or ASO Ml for 14 days. FIGs. 7E-7G show the Epididymal (eWAT; visceral fat) (FIG. 7E), inguinal WAT (iWAT; Subcutaneous fat) (FIG. 7F) and interscapular BAT (iBAT) (FIG. 7G) after daily injection of control, semaglutide, tirzepatide or ASO Ml for 14 days. Tissue weight (left panel) and Ratio of tissue weight to body weight (right panel) are shown for FIGs. 7E-7G. All data are mean ± SD. *P < 0.05, **P < 0.01, ***p < 0.001 and ****p < 0.0001 compared to the high-fat diet (Vehicle) group. # P< 0.05, ##P < 0.01, ###P < 0.001 and ####P < 0.0001 for the indicated comparisons. Significance was determined using a one-way ANOVA and post-hoc tukey’s test.
[0031] FIGs. 8A-8G show the comparison of the reduction effects of ASO Ml at 2 different administration schedules on body weight and cumulative food intake in HFD mice. FIG. 8A shows the schedule of the experiments for the HFD mouse models. After 1 week of acclimation these mice were fed with high-fat diet for 11 weeks. In two experimental group, HFD mice were dosed vehicle or ASO-M1 (1.5 mg/kg) dosing once every 3 days for 3 weeks (each group, n=5). In another two experimental group, HFD mice were dosed vehicle or ASO-M1 (5 mg/kg) dosing weekly for 3 weeks (each group, n=5). FIG. 8B shows changes in body weight of HFD mice after
3-day interval injection of ASO Ml (1.5 mg/kg), weekly injection of ASO Ml (5 mg/kg), or control. FIG. 8C shows the cumulative food intake (measure of appetite) for the control, 3-day interval injection of ASO Ml (1.5 mg/kg), and weekly injection of ASO Ml (5 mg/kg) administered HFD mice for 3 weeks. FIG. 8D shows quantification of mass (g) changes of fat mass and lean mass after control injection, 3-day interval injection of ASO Ml (1.5 mg/kg), or weekly injection of ASO Ml (5 mg/kg) in HFD mice for 3 weeks. FIGs. 8E-8G show the Epididymal (eWAT; visceral fat) (FIG. 8E), inguinal WAT (iWAT; Subcutaneous fat) (FIG. 8F) and interscapular BAT (iBAT) (FIG. 8G) after control injection, 3-day interval injection of ASO Ml (1.5 mg/kg), or weekly injection of ASO Ml (5 mg/kg) in HFD mice for 3 weeks. Tissue weight (left panel) and Ratio of tissue weight to body weight (right panel) are shown for FIGs. 8E- 8G. All data are mean ± SD. **P < 0.01, ***p < 0.001 and ****p < 0.0001 compared to the high- fat diet (Vehicle) group. # P< 0.05, and ##P < 0.01, for the indicated comparisons. Significance was determined using a one-way ANOVA and post-hoc tukey’s test.
[0032] FIG. 9A shows the schedule of the experiments for the HFD mouse models. After 1 week of acclimation, mice were fed with high-fat diet for 8 weeks. In two experimental group, HFD mice were dosed vehicle or ASO Ml (10 mg/kg) dosing weekly for 4 weeks (each group, n=6). In another two experimental group, HFD mice were administered of vehicle or ASO Ml (30 mg/kg) once 2 weeks before the end of the experiment (each group, n=6). FIG. 9B, shows changes in body weight of HFD mice after injection of control, weekly injection of ASO Ml (10 mg/kg) starting at week 8, and single injection of ASO-M1 (30 mg/kg) at week 10, across 12 weeks. FIGs 9C-9G, show analysis of miRNA and mRNA expression levels in liver obtained from standard diet (SD), HFD and HFD+ASO-M1 mice (under both weekly injection of ASO Ml (10 mg/kg), and single injection of ASO-M1 (30 mg/kg) conditions). miR-378a-3p levels (FIG. 9C) were quantified by qRT-PCR and normalized to U6B. Atg2a (FIG. 9D), Glp2r (FIG. 9E), Igflr (FIG. 9F) and Igfl (FIG. 9G) mRNA levels were normalized to Actb. All data are mean ± SEM. **P < 0.01, ***p < 0.001 and ****p < 0.0001 compared to the Standard diet (SD) group. ##P< 0.01, ###P< 0.001 and ####P< 0.0001 compared to the High-fat diet (HFD) group. Significance was determined using a one-way ANOVA and post-hoc tukey’s test.
[0033] FIG. 10A shows lipid droplets in liver cross-sections from control, HFD, and HFD+ASO-M1 groups analyzed by oil red O staining (each group, n=5-6). FIG. 10B shows morphological analysis (lipid accumulation and ballooned hepatocytes, etc.) of liver cross-sections from control, HFD, and HFD+ASO-M1 groups carried out by H&E staining (each group, n=5-6). For FIGs. lOA and lOB mice were injected 2 times per week with lO mpk ASO-M1 and terminated
on 10th week (top row), 4 times with lOmpk and terminated on 12th week (middle row), or injected once with 30mpk on 10th week then terminated 2 weeks later (bottom row). All images were obtained under lOOx magnification.
[0034] FIG. 11A-11F show clinical chemistry analysis of lipid profiles in SD, HFD and HFD+ASO-M1 mice (at both 10 and 30mg/kg dosing schedules). Specifically the lipid profiles of low-density lipoprotein cholesterol (LDL) (FIG. 11 A), high density lipoprotein cholesterol (HDL) (FIG. 11B), triglyceride (TG) (FIG. 11C), total cholesterol (TC) (FIG. 11D), alanine transaminase (ALT) (FIG. HE) and aspartate transaminase (AST) (FIG. HF). All data are mean ± SEM. ****p < 0.0001 compared to the Standard diet (SD) group. ###P< 0.001 and ####P< 0.0001 compared to the High-fat diet (HFD) group. Significance was determined using a one-way ANOVA and post- hoc tukey’s test.
[0035] FIGs. 12A-12I show a schematic diagram of the naked Homo sapiens-sm^Q stranded-microRNA-378a-3p (FIG. 12A), and modified antisense oligonucleotides (ASO) Ml (FIG. 12B), ML (FIG. 12C), M2 (FIG. 12D), M4 (FIG. 12E), M5 (FIG. 12F), M6 (FIG. 12G), M7 (FIG. 12H), and M8 (FIG. 121).
[0036] FIGs. 13A and 13B show the inhibitory activity of modified miR-378a-3p ASOs with RNAiMAX in HepG2 and Hep3B cells. FIG. 13A shows miR-378a-3p expression level after transfection of ASO #M1, #ML, #M4, #M5, #M6, #M7 and #M8 (100 nM) with RNAiMAX for 24 h in HepG2 cells (each group, n=3). FIG. 13B shows miR-378a-3p expression level after transfection of ASO #M1, #ML, #M4, #M5, #M6, #M7 and #M8 (100 nM) with RNAiMAX for 24 h in Hep3B cells (each group, n=3). All data is mean ± SEM. ****p < 0.0001, compared to the control (Con; RNAiMAX only); significance was determined with a one-way ANOVA.
[0037] FIGs. 14A and 14B show the inhibitory activity of modified miR-378a-3p ASOs in Hep3B cells without co-administration with a transfection reagent. FIG. 14A shows miR- 378a-3p expression level after administration of ASO #M1, #ME, #M4, #M5, #M6, #M7 and #M8 (1000 nM). FIG. 14B shows miR-378a-3p expression level after administration of ASO #M1, #ME, #M4, #M5, #M6, #M7 and #M8 in a dose-dependent manner (10, 100, and 500 nM) for 24 h in Hep3B cells (each group, n=3). All data is mean ± SEM. ns (no significance), **P < 0.01, and ****p < 0.0001, compared to the control (Con; RNAiMAX only); significance was determined with a one-way ANOVA.
[0038] FIGs. 15A and 15B show a comparison of miR-378a-3p expression levels of ASO #M1 and #M7 with/without transfection reagent in Hep3B cells. FIG. 15A shows miR-378a-3p
expression level after transfection of ASO #M1 or #M7 in Hep3B cells, with RNAiMAX, in a dose-dependent manner (0.937, 3.75, 15, 60 and 240 nM) for 24 h. FIG. 15B shows miR-378a- 3p expression level after transfection of ASO #M1 or #M7, without RNAiMAX, in a dosedependent manner (0.937, 3.75, 15, 60 and 240 nM) for 24 h (each group, n=3). All data is mean ± SEM. *P < 0.05, **P < 0.01, and ****p < 0.0001, compared to the control (Con; RNAiMAX only); significance was determined with a one-way ANOVA.
[0039] FIG. 16 shows in vivo activity of modified miR-378a-3p ASOs in C57BL/6 strain rodents. miR-378a-3p expression level are shown after intraperitoneal injection of ASO #M1, #M1’, #M4, #M5 and #M7 (5 mg/kg), without co-administration with a transfection reagent, for 7 days in C57BL/6 strain rodents (each group, n=4). All data are mean ± SEM. ns (no significance), ****p < 0.0001, compared to the control (Con; PBS-administration); significance was determined with a one-way ANOVA.
[0040] FIG. 17 shows the stability of modified miR-378a-3p ASO in mouse plasma. Stability is shown by measuring absorbance for ASO #M1, #M2, #M4, #M5, #M6, #M7 and #M8 at 0 minutes, 30 minutes, 1 hour, 1 day, 3 days, 7 days, 15 days, and 30 days. All data are mean ± SEM.
DETAILED DESCRIPTION
[0041] The present disclosure is directed to oligonucleotides comprising a miR-378a-3p inhibitor. Non-limiting examples of various aspects are shown in the present disclosure.
[0042] It is to be understood that this disclosure is not limited to the particular compositions or process steps described, which can vary. As will be apparent to those of skill in the art upon reading this disclosure, each of the individual aspects described and illustrated herein have discrete components and features which can be readily separated from or combined with the features of any of the other several aspects without departing from the scope or spirit of the present disclosure. Any recited method can be carried out in the order of events recited or in any other order which is logically possible.
[0043] The headings provided herein are not limitations of the various aspects of the disclosure, which can be defined by reference to the specification as a whole. It is also to be understood that the terminology used herein is for the purpose of describing particular aspects only, and is not intended to be limiting, since the scope of the present disclosure will be limited only by the appended claims.
[0044] Accordingly, the terms defined immediately below are more fully defined by reference to the specification in its entirety.
I. Definitions
[0045] In order for the present description to be more readily understood, certain terms are first defined immediately below. Additional definitions are set forth throughout the detailed description.
[0046] It is to be noted that the term "a" or "an" entity refers to one or more of that entity; for example, "a nucleotide sequence," is understood to represent one or more nucleotide sequences. As such, the terms "a" (or "an"), "one or more," and "at least one" can be used interchangeably herein. It is further noted that the claims can be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as "solely," "only" and the like in connection with the recitation of claim elements, or use of a negative limitation.
[0047] Furthermore, "and/or" where used herein is to be taken as specific disclosure of each of the two specified features or components with or without the other. Thus, the term "and/or" as used in a phrase such as "A and/or B" herein is intended to include "A and B," "A or B," "A" (alone), and "B" (alone). Likewise, the term "and/or" as used in a phrase such as "A, B, and/or C" is intended to encompass each of the following aspects: A, B, and C; A, B, or C; A or C; A or B; B or C; A and C; A and B; B and C; A (alone); B (alone); and C (alone).
[0048] It is understood that wherever aspects are described herein with the language "comprising," otherwise analogous aspects described in terms of "consisting of' and/or "consisting essentially of are also provided.
[0049] It is to be noted that the term MASH is interchangeable with the term NASH (nonalcoholic steatohepatitis). It is to be noted that the term MAFLD is interchangeable with the term NAFLD (non-alcoholic fatty liver disease).
[0050] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure is related. For example, the Concise Dictionary of Biomedicine and Molecular Biology, Juo, Pei- Show, 2nd ed., 2002, CRC Press; The Dictionary of Cell and Molecular Biology, 3rd ed., 1999, Academic Press; and the Oxford Dictionary Of Biochemistry And Molecular Biology, Revised, 2000, Oxford University Press, provide one of skill with a general dictionary of many of the terms used in this disclosure.
[0051] Units, prefixes, and symbols are denoted in their Systeme International de Unites (SI) accepted form. Numeric ranges are inclusive of the numbers defining the range. Where a range of values is recited, it is to be understood that each intervening integer value, and each fraction thereof, between the recited upper and lower limits of that range is also specifically disclosed, along with each subrange between such values. The upper and lower limits of any range can independently be included in or excluded from the range, and each range where either, neither or both limits are included is also encompassed within the disclosure. Thus, ranges recited herein are understood to be shorthand for all of the values within the range, inclusive of the recited endpoints. For example, a range of 1 to 10 is understood to include any number, combination of numbers, or sub-range from the group consisting of 1, 2, 3, 4, 5, 6, 7, 8, 9, and 10.
[0052] Where a value is explicitly recited, it is to be understood that values which are about the same quantity or amount as the recited value are also within the scope of the disclosure. Where a combination is disclosed, each subcombination of the elements of that combination is also specifically disclosed and is within the scope of the disclosure. Conversely, where different elements or groups of elements are individually disclosed, combinations thereof are also disclosed. Where any element of a disclosure is disclosed as having a plurality of alternatives, examples of that disclosure in which each alternative is excluded singly or in any combination with the other alternatives are also hereby disclosed; more than one element of a disclosure can have such exclusions, and all combinations of elements having such exclusions are hereby disclosed.
[0053] Nucleotides are referred to by their commonly accepted single-letter codes. Unless otherwise indicated, nucleotide sequences are written left to right in 5' to 3' orientation. Specific nucleotides (nucleotide residues) in a sequence may be referred to by their numeric position in the sequence with nucleotide 1 (nucleotide residue 1) being the first residue on the 5’ end, nucleotide 2 (nucleotide residue 2) being the second residue on the 5’ end, and so forth, until reaching the 3’ end. Nucleotides are referred to herein by their commonly known one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Accordingly, ‘a’ represents adenine, ‘c’ represents cytosine, ‘g’ represents guanine, ‘f represents thymine, and ‘u’ represents uracil.
[0054] Amino acid sequences are written left to right in amino to carboxy orientation. Amino acids are referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission.
[0055] The term "about" is used herein to mean approximately, roughly, around, or in the regions of. When the term "about" is used in conjunction with a numerical range, it modifies that range by extending the boundaries above and below the numerical values set forth. In general, the
term "about" can modify a numerical value above and below the stated value by a variance of, e.g., 10 percent, up or down (higher or lower).
[0056] The terms "administration," "administering," and grammatical variants thereof refer to introducing a composition, such as an oligonucleotide or conjugate of the present disclosure, into a subject via a pharmaceutically acceptable route. The introduction of a composition, such as an oligonucleotide or conjugate of the present disclosure, into a subject is by any suitable route, including intratumorally, orally, pulmonarily, intranasally, parenterally (intravenously, intraarterially, intramuscularly, intraperitoneally, or subcutaneously), rectally, intralymphatically, intrathecally, periocularly or topically. Administration includes self-administration and the administration by another. A suitable route of administration allows the composition or the agent to perform its intended function. For example, if a suitable route is intravenous, the composition is administered by introducing the composition or agent into a vein of the subject.
[0057] As used herein, the term "approximately," as applied to one or more values of interest, refers to a value that is similar to a stated reference value. In certain aspects, the term "approximately" refers to a range of values that fall within 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, or less in either direction (greater than or less than) of the stated reference value unless otherwise stated or otherwise evident from the context (except where such number would exceed 100% of a possible value).
[0058] As used herein, the term "conserved" refers to nucleotides or amino acid residues of a polynucleotide sequence or polypeptide sequence, respectively, that are those that occur unaltered in the same position of two or more sequences being compared. Nucleotides or amino acids that are relatively conserved are those that are conserved amongst more related sequences than nucleotides or amino acids appearing elsewhere in the sequences.
[0059] In some aspects, two or more sequences are said to be "completely conserved" or "identical" if they are 100% identical to one another. In some aspects, two or more sequences are said to be "highly conserved" if they are at least 70% identical, at least 80% identical, at least 90% identical, or at least 95% identical to one another. In some aspects, two or more sequences are said to be "highly conserved" if they are about 70% identical, about 80% identical, about 90% identical, about 95% identical, about 98% identical, or about 99% identical to one another. In some aspects, two or more sequences are said to be "conserved" if they are at least 30% identical, at least 40% identical, at least 50% identical, at least 60% identical, at least 70% identical, at least 80% identical, at least 90% identical, or at least 95% identical to one another. In some aspects, two or more sequences are said to be "conserved" if they are about 30% identical, about 40% identical, about
50% identical, about 60% identical, about 70% identical, about 80% identical, about 90% identical, about 95% identical, about 98% identical, or about 99% identical to one another. Conservation of sequence may apply to the entire length of a polynucleotide or polypeptide or may apply to a portion, region or feature thereof.
[0060] The term "derived from," as used herein, refers to a component that is isolated from or made using a specified molecule or organism, or information (e.g., amino acid or nucleic acid sequence) from the specified molecule or organism. For example, a nucleic acid sequence that is derived from a second nucleic acid sequence can include a nucleotide sequence that is identical or substantially similar to the nucleotide sequence of the second nucleic acid sequence. In the case of nucleotides or polypeptides, the derived species can be obtained by, for example, naturally occurring mutagenesis, artificial directed mutagenesis or artificial random mutagenesis. The mutagenesis used to derive nucleotides or polypeptides can be intentionally directed or intentionally random, or a mixture of each. The mutagenesis of a nucleotide or polypeptide to create a different nucleotide or polypeptide derived from the first can be a random event (e.g., caused by polymerase infidelity) and the identification of the derived nucleotide or polypeptide can be made by appropriate screening methods, e.g., as discussed herein. Mutagenesis of a polypeptide typically entails manipulation of the polynucleotide that encodes the polypeptide. In some aspects, a nucleotide or amino acid sequence that is derived from a second nucleotide or amino acid sequence has a sequence identity of at least about 50%, at least about 51%, at least about 52%, at least about 53%, at least about 54%, at least about 55%, at least about 56%, at least about 57%, at least about 58%, at least about 59%, at least about 60%, at least about 61%, at least about 62%, at least about 63%, at least about 64%, at least about 65%, at least about 66%, at least about 67%, at least about 68%, at least about 69%, at least about 70%, at least about 71%, at least about 72%, at least about 73%, at least about 74%, at least about 75%, at least about 76%, at least about 77%, at least about 78%, at least about 79%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or about 100% to the second nucleotide or amino acid sequence, respectively, wherein the first nucleotide or amino acid sequence retains the biological activity of the second nucleotide or amino acid sequence.
[0061] The terms "complementary" and "complementarity" refer to two or more oligomers (i.e., each comprising a nucleobase sequence), or between an oligomer and a target gene, that are
related with one another by Watson-Crick base-pairing rules. For example, the nucleobase sequence "T-G-A (5’->3’)," is complementary to the nucleobase sequence "A-C-T (3’-> 5’)." Complementarity may be "partial," in which less than all of the nucleobases of a given nucleobase sequence are matched to the other nucleobase sequence according to base pairing rules. For example, in some aspects, complementarity between a given nucleobase sequence and the other nucleobase sequence may be about 70%, about 75%, about 80%, about 85%, about 90% or about 95%. Or, there may be "complete" or "perfect" (100%) complementarity between a given nucleobase sequence and the other nucleobase sequence to continue the example. The degree of complementarity between nucleobase sequences has significant effects on the efficiency and strength of hybridization between the sequences.
[0062] The term "downstream" refers to a nucleotide sequence that is located 3’ to a reference nucleotide sequence. In certain aspects, downstream nucleotide sequences relate to sequences that follow the starting point of transcription. For example, the translation initiation codon of a gene is located downstream of the start site of transcription.
[0063] The terms "excipient" and "carrier" are used interchangeably and refer to an inert substance added to a pharmaceutical composition to further facilitate administration of a compound.
[0064] As used herein, the term "homology" refers to the overall relatedness between polymeric molecules, e.g. between nucleic acid molecules (e.g. DNA molecules and/or RNA molecules) and/or between polypeptide molecules. Generally, the term "homology" implies an evolutionary relationship between two molecules. Thus, two molecules that are homologous will have a common evolutionary ancestor. In the context of the present disclosure, the term homology encompasses both to identity and similarity.
[0065] As used herein, the term "identity" refers to the overall monomer conservation between polymeric molecules, e.g, between polypeptide molecules or polynucleotide molecules (e.g. DNA molecules and/or RNA molecules). The term "identical" without any additional qualifiers, e.g., protein A is identical to protein B, implies the sequences are 100% identical (100% sequence identity). Describing two sequences as, e.g., "70% identical," is equivalent to describing them as having, e.g., "70% sequence identity."
[0066] Calculation of the percent identity of two polypeptide or polynucleotide sequences, for example, can be performed by aligning the two sequences for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second polypeptide or polynucleotide sequences for optimal alignment and non-identical sequences can be disregarded for comparison
purposes). In certain aspects, the length of a sequence aligned for comparison purposes is at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95%, or about 100% of the length of the reference sequence. The amino acids at corresponding amino acid positions, or bases in the case of nucleic acid sequences, are then compared.
[0067] When a position in the first sequence is occupied by the same amino acid as the corresponding position in the second sequence, then the molecules are identical at that position. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which needs to be introduced for optimal alignment of the two sequences. The comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm.
[0068] Suitable software programs are available from various sources, and for alignment of both protein and nucleotide sequences. One suitable program to determine percent sequence identity is bl2seq, part of the BLAST suite of program available from the U.S. government's National Center for Biotechnology Information BLAST web site (blast.ncbi.nlm.nih.gov). B12seq performs a comparison between two sequences using either the BLASTN or BLASTP algorithm. BLASTN is used to compare nucleic acid sequences, while BLASTP is used to compare amino acid sequences. Other suitable programs are, e.g., Needle, Stretcher, Water, or Matcher, part of the EMBOSS suite of bioinformatics programs and also available from the European Bioinformatics Institute (EBI) at www.ebi.ac.uk/Tools/psa.
[0069] Sequence alignments can be conducted using methods known in the art such as MAFFT, Clustal (ClustalW, Clustal X or Clustal Omega), MUSCLE, etc.
[0070] Different regions within a single polynucleotide or polypeptide target sequence that aligns with a polynucleotide or polypeptide reference sequence can each have their own percent sequence identity. It is noted that the percent sequence identity value is rounded to the nearest tenth. For example, 80.11, 80.12, 80.13, and 80.14 are rounded down to 80.1, while 80.15, 80.16, 80.17, 80.18, and 80.19 are rounded up to 80.2. It also is noted that the length value will always be an integer.
[0071] In certain aspects, the percentage identity (%ID) of a first amino acid sequence (or nucleic acid sequence) to a second amino acid sequence (or nucleic acid sequence) is calculated as %ID = 100 x (Y/Z), where Y is the number of amino acid residues (or nucleobases) scored as identical matches in the alignment of the first and second sequences (as aligned by visual inspection
or a particular sequence alignment program) and Z is the total number of residues in the second sequence. If the length of a first sequence is longer than the second sequence, the percent identity of the first sequence to the second sequence will be higher than the percent identity of the second sequence to the first sequence.
[0072] One skilled in the art will appreciate that the generation of a sequence alignment for the calculation of a percent sequence identity is not limited to binary sequence-sequence comparisons exclusively driven by primary sequence data. It will also be appreciated that sequence alignments can be generated by integrating sequence data with data from heterogeneous sources such as structural data (e.g., crystallographic protein structures), functional data (e.g., location of mutations), or phylogenetic data. A suitable program that integrates heterogeneous data to generate a multiple sequence alignment is T-Coffee, available at www.tcoffee.org, and alternatively available, e.g, from the EBI. It will also be appreciated that the final alignment used to calculate percent sequence identity can be curated either automatically or manually.
[0073] As used herein, the terms "isolated," "purified," "extracted," and grammatical variants thereof are used interchangeably and refer to the state of a preparation of desired composition of the present disclosure, that has undergone one or more processes of purification. In some aspects, isolating or purifying as used herein is the process of removing, partially removing (e.g., a fraction) of a composition of the present disclosure from a sample containing contaminants. In some aspects, an isolated composition has no detectable undesired activity or, alternatively, the level or amount of the undesired activity is at or below an acceptable level or amount. In other aspects, an isolated composition has an amount and/or concentration of desired composition of the present disclosure, at or above an acceptable amount and/or concentration and/or activity. In other aspects, the isolated composition is enriched as compared to the starting material from which the composition is obtained. This enrichment can be by at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.9%, at least about 99.99%, at least about 99.999%, at least about 99.9999%, or greater than 99.9999% as compared to the starting material. In some aspects, isolated preparations are substantially free of residual biological products. In some aspects, the isolated preparations are 100% free, at least about 99% free, at least about 98% free, at least about 97% free, at least about 96% free, at least about 95% free, at least about 94% free, at least about 93% free, at least about 92% free, at least about 91% free, or at least about 90% free of any
contaminating biological matter. Residual biological products can include abiotic materials (including chemicals) or unwanted nucleic acids, proteins, lipids, or metabolites.
[0074] The term "linked" as used herein refers to a first amino acid sequence or polynucleotide sequence covalently or non-covalently joined to a second amino acid sequence or polynucleotide sequence, respectively. The first amino acid or polynucleotide sequence can be directly joined or juxtaposed to the second amino acid or polynucleotide sequence or alternatively an intervening sequence can covalently join the first sequence to the second sequence. The term "linked" means not only a fusion of a first polynucleotide sequence to a second polynucleotide sequence at the 5’-end or the 3’-end, but also includes insertion of the whole first polynucleotide sequence (or the second polynucleotide sequence) into any two nucleotides in the second polynucleotide sequence (or the first polynucleotide sequence, respectively). The first polynucleotide sequence can be linked to a second polynucleotide sequence by a phosphodiester bond or a linker. The linker can be, e.g., a polynucleotide.
[0075] The terms "miRNA" or "miR" or "microRNA" are used interchangeably and refer to a microRNA molecule found in eukaryotes that is involved in RNA-based gene regulation. Accordingly, the terms "miR-378-3p" and "miRNA 387a-3p" refer to microRNA 387a-3p molecule. Exemplary sequences for miR-378-3p and a miR-378a-3p inhibitor are provided in Table 1. The term will be used to refer to the single-stranded RNA molecule processed from a precursor. Names of miRNAs and their sequences related to the present disclosure are provided herein. MicroRNAs recognize and bind to target mRNAs through imperfect base pairing leading to destabilization or translational inhibition of the target mRNA and thereby downregulate target gene expression. Conversely, targeting miRNAs via molecules comprising a miRNA binding site (generally a molecule comprising a sequence complementary to the seed region of the miRNA) can reduce or inhibit the miRNA-induced translational inhibition leading to an upregulation of the target gene.
[0076] The terms "miR-378a-3p inhibitor," "miRNA 387a-3p inhibitor," "miR378a inhibitor," and "miRNA inhibitor" are used interchangeably herein and refer to a compound that can decrease, alter, and/or modulate miRNA 387a-3p expression, function, and/or activity. The miRNA 387a-3p inhibitor can be a polynucleotide sequence that is at least partially complementary to the target miRNA 387a-3p nucleic acid sequence, such that the miRNA 387a-3p inhibitor hybridizes to the target miRNA sequence. For instance, in some aspects, a miRNA 387a-3p inhibitor of the present disclosure comprises a nucleotide sequence encoding a nucleotide molecule that is at least partially complementary to the target miRNA 387a-3p nucleic acid sequence, such
that the miRNA 387a-3p inhibitor hybridizes to the miRNA 387a-3p sequence. In some aspects, the hybridization of the miRNA 387a-3p inhibitor to the miRNA 387a-3p sequence decreases, alters, and/or modulates the expression, function, and/or activity of miRNA 387a-3p.
[0077] The terms "mismatch" or "mismatches" refer to one or more nucleobases (whether contiguous or separate) in an oligomer nucleobase sequence that are not matched to a target pre- mRNA according to base pairing rules. While perfect complementarity is often desired, some aspects can include one or more but preferably 6, 5, 4, 3, 2, or 1 mismatches with respect to the target pre-mRNA. Variations at any location within the oligomer are included. In certain aspects, antisense oligomers of the disclosure include variations in nucleobase sequence near the termini, variations in the interior, and if present are typically within about 6, 5, 4, 3, 2, or 1 subunits of the 5' and/or 3' terminus. In certain aspects, one, two, or three nucleobases can be removed and still provide on-target binding.
[0078] As used herein, the terms "modulate," "modify," and grammatical variants thereof, generally refer when applied to a specific concentration, level, expression, function or behavior, to the ability to alter, by increasing or decreasing, e.g., directly or indirectly promoting/stimulating/up-regulating or interfering with/inhibiting/down-regulating the specific concentration, level, expression, function or behavior, such as, e.g., to act as an antagonist or agonist. In some instances, a modulator can increase and/or decrease a certain concentration, level, activity or function relative to a control, or relative to the average level of activity that would generally be expected or relative to a control level of activity.
[0079] "Nucleic acid," "nucleic acid molecule," "nucleotide sequence," "polynucleotide," and grammatical variants thereof are used interchangeably and refer to the phosphate ester polymeric form of ribonucleosides (adenosine, guanosine, uridine or cytidine; "RNA molecules") or deoxyribonucleosides (deoxyadenosine, deoxyguanosine, deoxythymidine, or deoxycytidine; "DNA molecules"), or any phosphoester analogs thereof, such as phosphorothioates and thioesters, in either single stranded form, or a double-stranded helix. Single stranded nucleic acid sequences refer to single-stranded DNA (ssDNA) or single-stranded RNA (ssRNA). Double stranded DNA- DNA, DNA-RNA and RNA-RNA helices are possible. The term nucleic acid molecule, and in particular DNA or RNA molecule, refers only to the primary and secondary structure of the molecule, and does not limit it to any particular tertiary forms. Thus, this term includes doublestranded DNA found, inter alia, in linear or circular DNA molecules (e.g., restriction fragments), plasmids, supercoiled DNA and chromosomes. In discussing the structure of particular doublestranded DNA molecules, sequences can be described herein according to the normal convention
of giving only the sequence in the 5’ to 3’ direction along the non-transcribed strand of DNA (i.e., the strand having a sequence homologous to the mRNA). A "recombinant DNA molecule" is a DNA molecule that has undergone a molecular biological manipulation. DNA includes, but is not limited to, cDNA, genomic DNA, plasmid DNA, synthetic DNA, and semi -synthetic DNA. A "nucleic acid composition" of the disclosure comprises one or more nucleic acids as described herein.
[0080] The phrases "parenteral administration" and "administered parenterally" as used herein means modes of administration other than enteral and topical administration, usually by injection, and includes, without limitation, intravenous, intramuscular, intraarterial, intrathecal, intracapsular, intraorbital, intracardiac, intradermal, intraperitoneal, transtracheal, subcutaneous, subcuticular, intraarticular, subcapsular, subarachnoid, intraspinal and intrastemal injection and infusion.
[0081] The terms "pharmaceutically-acceptable carrier," "pharmaceutically-acceptable excipient," and grammatical variations thereof, encompass any of the agents approved by a regulatory agency of the U.S. Federal government or listed in the U.S. Pharmacopeia for use in animals, including humans, as well as any carrier or diluent that does not cause the production of undesirable physiological effects to a degree that prohibits administration of the composition to a subject and does not abrogate the biological activity and properties of the administered compound. Included are excipients and carriers that are useful in preparing a pharmaceutical composition and are generally safe, non-toxic, and desirable.
[0082] As used herein, the term "pharmaceutical composition" refers to one or more of the compounds described herein, such as, e.g., an oligonucleotide of the present disclosure, mixed or intermingled with, or suspended in one or more other chemical components, such as pharmaceutically-acceptable carriers and excipients. One purpose of a pharmaceutical composition is to facilitate administration of preparations of oligonucleotides to a subject.
[0083] The term "polynucleotide" as used herein refers to polymers of nucleotides of any length, including ribonucleotides, deoxyribonucleotides, analogs thereof, or mixtures thereof. This term refers to the primary structure of the molecule. Thus, the term includes triple-, double- and single-stranded deoxyribonucleic acid ("DNA"), as well as triple-, double- and single-stranded ribonucleic acid ("RNA"). It also includes modified, for example by alkylation, and/or by capping, and unmodified forms of the polynucleotide.
[0084] More particularly, the term "polynucleotide" includes polydeoxyribonucleotides (containing 2-deoxy-D-ribose), polyribonucleotides (containing D-ribose), including tRNA,
rRNA, hRNA, siRNA and mRNA, whether spliced or unspliced, any other type of polynucleotide which is an N- or C-glycoside of a purine or pyrimidine base, and other polymers containing normucleotidic backbones, for example, polyamide (e.g., peptide nucleic acids "PNAs") and polymorpholino polymers, and other synthetic sequence-specific nucleic acid polymers providing that the polymers contain nucleobases in a configuration which allows for base pairing and base stacking, such as is found in DNA and RNA.
[0085] In some aspects of the present disclosure a polynucleotide can be, e.g., an oligonucleotide, such as an antisense oligonucleotide. In some aspects, the oligonucleotide is an RNA. In some aspects, the RNA is a synthetic RNA. In some aspects, the synthetic RNA comprises at least one unnatural nucleobase. In some aspects, all nucleobases of a certain class have been replaced with unnatural nucleobases (e.g., all uridines in a polynucleotide disclosed herein can be replaced with an unnatural nucleobase, e.g., 5-methoxyuridine).
[0086] The terms "polypeptide," "peptide," and "protein" are used interchangeably herein to refer to polymers of amino acids of any length. The polymer can comprise modified amino acids. The terms also encompass an amino acid polymer that has been modified naturally or by intervention; for example, disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation or modification, such as conjugation with a labeling component. Also included within the definition are, for example, polypeptides containing one or more analogs of an amino acid (including, for example, unnatural amino acids such as homocysteine, ornithine, p-acetylphenylalanine, D-amino acids, and creatine), as well as other modifications known in the art. The term "polypeptide," as used herein, refers to proteins, polypeptides, and peptides of any size, structure, or function. Polypeptides include gene products, naturally occurring polypeptides, synthetic polypeptides, homologs, orthologs, paralogs, fragments and other equivalents, variants, and analogs of the foregoing. A polypeptide can be a single polypeptide or can be a multi -molecular complex such as a dimer, trimer or tetramer. They can also comprise single chain or multichain polypeptides. Most commonly, disulfide linkages are found in multichain polypeptides. The term polypeptide can also apply to amino acid polymers in which one or more amino acid residues are an artificial chemical analogue of a corresponding naturally occurring amino acid. In some aspects, a "peptide" can be less than or equal to 50 amino acids long, e.g., about 5, 10, 15, 20, 25, 30, 35, 40, 45, or 50 amino acids long.
[0087] The terms "prevent," "preventing," and variants thereof as used herein, refer partially or completely delaying onset of an disease, disorder and/or condition; partially or completely delaying onset of one or more symptoms, features, or clinical manifestations of a
particular disease, disorder, and/or condition; partially or completely delaying onset of one or more symptoms, features, or manifestations of a particular disease, disorder, and/or condition; partially or completely delaying progression from a particular disease, disorder and/or condition; and/or decreasing the risk of developing pathology associated with the disease, disorder, and/or condition. In some aspects, preventing an outcome is achieved through prophylactic treatment.
[0088] As used herein, "prophylactic" refers to a therapeutic or course of action used to prevent the onset of a disease or condition, or to prevent or delay a symptom associated with a disease or condition.
[0089] As used herein, a "prophylaxis" refers to a measure taken to maintain health and prevent or delay the onset of a bleeding episode, or to prevent or delay symptoms associated with a disease or condition.
[0090] As used herein, the term "similarity" refers to the overall relatedness between polymeric molecules, e.g. between polynucleotide molecules (e.g. DNA molecules and/or RNA molecules) and/or between polypeptide molecules. Calculation of percent similarity of polymeric molecules to one another can be performed in the same manner as a calculation of percent identity, except that calculation of percent similarity takes into account conservative substitutions as is understood in the art. It is understood that percentage of similarity is contingent on the comparison scale used, i.e., whether the amino acids are compared, e.g, according to their evolutionary proximity, charge, volume, flexibility, polarity, hydrophobicity, aromaticity, isoelectric point, antigenicity, or combinations thereof.
[0091] The terms "subject," "patient," "individual," and "host," and variants thereof are used interchangeably herein and refer to any mammalian subject, including without limitation, humans, domestic animals (e.g., dogs, cats and the like), farm animals (e.g., cows, sheep, pigs, horses and the like), and laboratory animals (e.g., monkey, rats, mice, rabbits, guinea pigs and the like) for whom diagnosis, treatment, or therapy is desired, particularly humans. The methods described herein are applicable to both human therapy and veterinary applications.
[0092] As used herein, the phrase "subject in need thereof includes subjects, such as mammalian subjects, that would benefit from administration of an oligonucleotide of the disclosure, e.g., to improve homeostasis.
[0093] The phrases "systemic administration," "administered systemically," "peripheral administration" and "administered peripherally" as used herein mean the administration of a compound, drug or other material other than directly into the central nervous system, such that it
enters the patient's system and, thus, is subject to metabolism and other like processes, for example, subcutaneous administration.
[0094] As used herein the term "therapeutically effective amount" is the amount of reagent or pharmaceutical compound comprising an oligonucleotide of the present disclosure that is sufficient to a produce a desired therapeutic effect, pharmacologic and/or physiologic effect on a subject in need thereof. A therapeutically effective amount can be a "prophylactically effective amount" as prophylaxis can be considered therapy.
[0095] The terms "treat," "treatment," or "treating," as used herein refers to, e.g., the reduction in severity of a disease or condition; the reduction in the duration of a disease course; the amelioration or elimination of one or more symptoms associated with a disease or condition; the provision of beneficial effects to a subject with a disease or condition, without necessarily curing the disease or condition. The term also include prophylaxis or prevention of a disease or condition or its symptoms thereof. In one aspect, the term "treating" or "treatment" means inducing an immune response in a subject against an antigen.
[0096] The term "upstream" refers to a nucleotide sequence that is located 5’ to a reference nucleotide sequence.
II. Oligonucleotides
[0097] The present disclosure provides oligonucleotides comprising a miRNA 387a-3p inhibitor. Unless indicated otherwise, the terms "oligonucleotide" and "miRNA 387a-3p inhibitor" (and variants thereof) are used interchangeably herein. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence having 10-30 nucleotides in length, for example from 14-25 nucleotides in length. In some aspects, the oligonucleotide has a contiguous nucleotide sequence with a length of 16-30 nucleotides, 18-25 nucleotides, particularly 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence having less than 200 nucleotides in length. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence having less than about 150, about 140, about 130, about 120, about 110, about 100, about 90, about 80, about 70, about 60, about 50, about 40, about 30, about 25, about 24, about 23, about 22, about 21, about 20, about 19, about 18, about 17, about 16, about 15, about 14, about 13, about 12, about 11, or about 10 nucleotides in length. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence having from about 30 to about 10, from about 25 to about 11, from about 30 to about 15, from about 25 to about 15, from about 24 to about 15, or from about 23 to about 15 nucleotides in length. In some aspects, the
oligonucleotide comprises a contiguous nucleotide sequence having about 30, about 29, about 28, about 27, about 26, about 25, about 24, about 23, about 22, about 21, about 20, about 19, about 18, about 17, about 16, about 15, about 14, or about 13 nucleotides in length. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence having about 22 nucleotides in length. In some aspects, the contiguous nucleotide sequence is about 21 nucleotides in length. In some aspects, the contiguous nucleotide sequence is about 20 nucleotides in length. In some aspects, the contiguous nucleotide sequence is about 23 nucleotides in length. In some aspects, the contiguous nucleotide sequence is about 24 nucleotides in length.
[0098] In some aspects, the oligonucleotides are phosphodiester antisense oligonucleotides, and any oligonucleotides where the sugar-phosphate "backbone" has been derivatized or replaced with "backbone analogues" such as with phosphorothioate, phosphorodithioate, phosphoroamidate, alkyl phosphotriester, or methylphosphonate linkages. In some aspects, the oligonucleotide are antisense oligonucleotides, and any oligonucleotides or oligodeoxynucleotides with non-phosphorous backbone analogues such as sulfamate, 3'- thioformacetal, methylene(methylimino) (MMI), 3'-N-carbamate, or morpholino carbamate.
[0099] In some aspects, the oligonucleotide is an antimir. As used herein, the terms "antimir," "anti microRNA," "anti miRNA," and variants thereof refer to molecules (e.g., synthetically generated molecules) that are used to neutralize microRNA (miRNA) function in cells for desired responses. miRNA are complementary sequences (approx. 20-22bp) to mRNA that are involved in the cleavage of RNA or the suppression of the translation. By controlling the miRNA that regulate mRNAs in cells, antimirs (also called anti-miRNA oligonucleotides, AMOs, or antagomirs) can be used as further regulation as well as for therapeutic for certain cellular disorders. This regulation can occur through a steric blocking mechanism as well as hybridization to miRNA.
[0100] Various components of oligonucleotides can be manipulated to affect the binding affinity and potency of the oligonucleotides. The 2’ -sugar of the oligonucleotides can be modified to be substituted with fluorine and various methyl groups, almost all with an increase in binding affinity. However, some of these modified 2’ -sugar oligonucleotides lead to negative effects on cell growth. Modifying the 5'-3' phosphodiester backbone linkage to a phosphorothioate (P-S) backbone linkage is also known to have an effect on target affinity. Using the P-S mutation was shown to decrease the Tm (melting temperature) of the oligonucleotides, which leads to a lower target affinity. A final requirement for oligonucleotides is mismatch specificity and length restrictions. Due to miRNAs in the same families sharing "seed" (shared) sequences and differ by
only a couple of additional nucleotides; one oligonucleotide can potentially target multiple miRNA sequences. An example of an oligonucleotide or miRNA sequence is shown in the following table.
[0101] In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence having 5 to 30 nucleotides in length. In some aspects, the polynucleotide has 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length. In some aspects, the contiguous nucleotide sequence has 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26 nucleotides in length. In some aspects, the contiguous nucleotide sequence has less than about 30, about 25, about 24, about 23, about 22, about 21, about 20, about 19, about 18, about 17, about 16, about 15, about 14, about 13, about 12, about 11, or about 10 nucleotides in length. In some aspects, the contiguous nucleotide sequence has from about 30 to about 10, from about 25 to about 11, from about 30 to about 15, from about 25 to about 15, from about 24 to about 15, or from about 23 to about 15 nucleotides in length. In some aspects, the contiguous nucleotide sequence having about 30, about 29, about 28, about 27, about 26, about 25, about 24, about 23, about 22, about 21, about 20, about 19, about 18, about 17, about 16, about 15, about 14, or about 13 nucleotides in length.
[0102] In some aspects, the oligonucleotide is a contiguous nucleotide sequence targeting hsa-miR-378a, e.g., hsa-miR-378a-3p. In some aspects, the hsa-miR-378a-3p has the sequence ACUGGACUUGGAGUCAGAAGGC (SEQ ID NO: 1). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising, consisting essentially of, or consisting of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein U can be optionally T. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein U can be optionally T. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence consisting essentially of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein U can be optionally T. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence consisting of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25),
wherein U can be optionally T. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising, consisting essentially of, or consisting of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has one mismatch, two mismatches, three mismatches, or four mismatches. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has one mismatch, two mismatches, three mismatches, or four mismatches. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has one mismatch. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has two mismatches. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has three mismatches. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has four mismatches. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence consisting essentially of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has one mismatch, two mismatches, three mismatches, or four mismatches. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence consisting essentially of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has one mismatch. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence consisting essentially of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has two mismatches. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence consisting essentially of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has three mismatches. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence consisting essentially of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has four mismatches. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence consisting of the sequence GCCUUCUGACUCCAAGUCCAGU
(SEQ ID NO: 25), wherein the contiguous nucleotide sequence has one mismatch, two mismatches, three mismatches, or four mismatches. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence consisting of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has one mismatch. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence consisting of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has two mismatches. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence consisting of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has three mismatches. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence consisting of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has four mismatches. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising, consisting essentially of, or consisting of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has one or two mismatches. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has one or two mismatches. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence consisting essentially of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has one or two mismatches. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence consisting of the sequence GCCUUCUGACUCCAAGUCCAGU (SEQ ID NO: 25), wherein the contiguous nucleotide sequence has one or two mismatches.
[0103] In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence targeting the seed sequence of hsa-miR-378a-3p (z.e., CUGGACU). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence AGUCCAG, wherein U can be optionally T (complement of the seed), wherein the contiguous nucleotide sequence is about 10 nucleotides to about 30 nucleotides (e.g., 10 to 25, 10 to 24, 10 to 23, 10 to 22, 10 to 21, 10 to 20, 10 to 19, or 10 to 18) in length. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence AGUCCAG , wherein U can be optionally T (complement of the seed), wherein the contiguous nucleotide sequence comprises one, two, three, four, five, six, seven, eight, nine, ten, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleic acids at the 5' terminus of the complement of the seed sequence and/or one, two, three,
four, five, six, seven, eight, nine, ten, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleic acids at the 3' terminus of the complement of the seed sequence. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence AGUCCAG, wherein U can be optionally T (complement of the seed), wherein the contiguous nucleotide sequence comprises one, two, three, four, five, six, seven, eight, nine, ten, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleic acids at the 5' terminus of the complement of the seed sequence. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence AGUCCAG, wherein U can be optionally T (complement of the seed), wherein the contiguous nucleotide sequence comprises one, two, three, four, five, six, seven, eight, nine, ten, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleic acids at the 3 ' terminus of the complement of the seed sequence. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence AGUCCAG, wherein U can be optionally T (complement of the seed), wherein the contiguous nucleotide sequence comprises one, two, three, four, five, six, seven, eight, nine, ten, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleic acids both at the 5' terminus and the 3' terminus of the complement of the seed sequence.
[0104] In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence set forth in 5'-AGUCCAG-3', 5'-AAGUCCAG-3', 5'-CAAGUCCAG-3', 5'- CCAAGUCCAG-3' (SEQ ID NO: 2), 5'-UCCAAGUCCAG-3' (SEQ ID NO: 3), 5'-CUCCAAGUCCAG- 3' (SEQ ID NO: 4), 5'-ACUCCAAGUCCAG-3' (SEQ ID NO: 5), 5'-GACUCCAAGUCCAG-3' (SEQ ID NO: 6), 5'-UGACUCCAAGUCCAG-3' (SEQ ID NO: 7), 5'-CUGACUCCAAGUCCAG-3' (SEQ ID NO: 8), 5'-UCUGACUCCAAGUCCAG-3' (SEQ ID NO: 9), 5'- UUCUGACUCCAAGUCCAG-3' (SEQ ID NO: 10), 5'-CUUCUGACUCCAAGUCCAG-3' (SEQ ID NO: 11), 5'-CCUUCUGACUCCAAGUCCAG-3' (SEQ ID NO: 12), 5'-AGUCCAGU-3', 5'-AAGUCCAGU-3', 5'-CAAGUCCAGU-3' (SEQ ID NO: 13), 5'- CCAAGUCCAGU-3' (SEQ ID NO: 14), 5'-UCCAAGUCCAGU-3' (SEQ ID NO: 15), 5'- CUCCAAGUCCAGU-3' (SEQ ID NO: 16), 5'-ACUCCAAGUCCAGU-3' (SEQ ID NO: 17), 5'- GACUCCAAGUCCAGU-3' (SEQ ID NO: 18), 5'-UGACUCCAAGUCCAGU-3' (SEQ ID NO: 19), 5'- CUGACUCCAAGUCCAGU-3' (SEQ ID NO: 20), 5'-UCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 21), 5'-UUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 22), 5'-CUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 23), 5'-CCUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 24), or 5'- GCCUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 25). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-AGUCCAG-3'. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises
the sequence 5'-AAGUCCAG-3'. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-CAAGUCCAG-3'. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'- CCAAGUCCAG-3' (SEQ ID NO: 2). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-UCCAAGUCCAG-3' (SEQ ID NO: 3). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-CUCCAAGUCCAG-3' (SEQ ID NO: 4). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'- ACUCCAAGUCCAG-3' (SEQ ID NO: 5). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-GACUCCAAGUCCAG-3' (SEQ ID NO: 6). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-UGACUCCAAGUCCAG-3' (SEQ ID NO: 7). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'- CUGACUCCAAGUCCAG-3' (SEQ ID NO: 8). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-UCUGACUCCAAGUCCAG-3' (SEQ ID NO: 9). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'- UUCUGACUCCAAGUCCAG-3' (SEQ ID NO: 10). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-CUUCUGACUCCAAGUCCAG-3' (SEQ ID NO: 11). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'- CCUUCUGACUCCAAGUCCAG-3' (SEQ ID NO: 12). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-AGUCCAGU-3'. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-AAGUCCAGU-3'. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-CAAGUCCAGU-3' (SEQ ID NO: 13). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'- CCAAGUCCAGU-3' (SEQ ID NO: 14). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'- UCCAAGUCCAGU-3' (SEQ ID NO: 15). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-CUCCAAGUCCAGU-3' (SEQ ID NO: 16). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-ACUCCAAGUCCAGU-3' (SEQ ID NO: 17). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-
GACUCCAAGUCCAGU-3' (SEQ ID NO: 18). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-UGACUCCAAGUCCAGU-3' (SEQ ID NO: 19). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-CUGACUCCAAGUCCAGU-3' (SEQ ID NO: 20). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-UCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 21). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'- UUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 22). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'- CUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 23). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-
CCUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 24). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which comprises the sequence 5'-
GCCUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 25). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which consists essentially of the sequence 5'- GCCUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 25). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence which consists of the sequence 5'- GCCUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 25).
[0105] In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence as set forth in 5'-AGTCCAG-3', 5'-AAGTCCAG-3', 5'-CAAGTCCAG -3', 5'- CCAAGTCCAG-3' (SEQ ID NO: 26), 5'-TCCAAGTCCAG-3' (SEQ ID NO: 27), 5'- CTCCAAGTCCAG-3' (SEQ ID NO: 28), 5'-ACTCCAAGTCCAG-3' (SEQ ID NO: 29), 5'- GACTCCAAGTCCAG-3' (SEQ ID NO: 30), 5'-TGACTCCAAGTCCAG-3' (SEQ ID NO: 31), 5'- CTGACTCCAAGTCCAG-3' (SEQ ID NO: 32), 5'-TCTGACTCCAAGTCCAG-3' (SEQ ID NO: 33), 5'- TTCTGACTCCAAGTCCAG-3' (SEQ ID NO: 34), 5'- CTTCTGACTCCAAGTCCAG-3' (SEQ ID NO: 35), 5'-CCTTCTGACTCCAAGTCCAG-3' (SEQ ID NO: 36), 5'-AGTCCAGT-3', 5'-AAGTCCAGT-3', 5'-CAAGTCCAGT-3' (SEQ ID NO: 37), 5'-CCAAGTCCAGT-3' (SEQ ID NO: 38), 5'- TCCAAGTCCAGT-3' (SEQ ID NO: 39), 5'-CTCCAAGTCCAGT-3' (SEQ ID NO: 40), 5'- ACTCCAAGTCCAGT-3' (SEQ ID NO: 41), 5'-GACTCCAAGTCCAGT-3' (SEQ ID NO: 42), 5'- TGACTCCAAGTCCAGT-3' (SEQ ID NO: 43), 5'-CTGACTCCAAGTCCAGT-3' (SEQ ID NO: 44), 5'- TCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 45), 5'-TTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 46), 5'-CTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 47), 5'-CCTTCTGACTCCAAGTCCAGT-3'
(SEQ ID NO: 48), or 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'- AGTCCAG-3'. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-AAGTCCAG-3'. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-CAAGTCCAG-3'. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'- CCAAGTCCAG-3' (SEQ ID NO: 26). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-TCCAAGTCCAG-3' (SEQ ID NO: 27). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-CTCCAAGTCCAG-3' (SEQ ID NO: 28). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-ACTCCAAGTCCAG-3' (SEQ ID NO: 29). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'- GACTCCAAGTCCAG-3' (SEQ ID NO: 30). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-TGACTCCAAGTCCAG-3' (SEQ ID NO: 31). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-CTGACTCCAAGTCCAG-3' (SEQ ID NO: 32). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-TCTGACTCCAAGTCCAG-3' (SEQ ID NO: 33). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'- TTCTGACTCCAAGTCCAG-3' (SEQ ID NO: 34). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-
CTTCTGACTCCAAGTCCAG-3' (SEQ ID NO: 35). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-
CCTTCTGACTCCAAGTCCAG-3' (SEQ ID NO: 36). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-AGTCCAGT-3'. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-AAGTCCAGT-3'. In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-CAAGTCCAGT-3' (SEQ ID NO: 37). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'- CCAAGTCCAGT-3' (SEQ ID NO: 38). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-TCCAAGTCCAGT-3' (SEQ ID NO: 39). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising
the sequence 5'-CTCCAAGTCCAGT-3' (SEQ ID NO: 40). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'- ACTCCAAGTCCAGT- 3' (SEQ ID NO: 41). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-GACTCCAAGTCCAGT-3' (SEQ ID NO: 42). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-TGACTCCAAGTCCAGT-3' (SEQ ID NO: 43). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-CTGACTCCAAGTCCAGT-3' (SEQ ID NO: 44). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-TCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 45). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-TTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 46). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'- CTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 47). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-
CCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 48). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence comprising the sequence 5'-
GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence consisting essentially of the sequence 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence consisting of the sequence 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49).
[0106] In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence that is at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% identical to the sequence 5'-GCCUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 25) or 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49). In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence that has at least 90% similarity to the sequence 5'-GCCUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 25) or 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49).
IL A.2. Chemically Modified Oligonucleotides
[0107] In some aspects, oligonucleotides of the present disclosure comprises at least one chemically modified nucleoside and/or nucleotide. When the oligonucleotides of the present disclosure are chemically modified, the nucleic acids can be referred to as "modified nucleic acids." For instance, the term "modified ASO" refers to an antisense oligonucleotide that has been chemically modified. Oligonucleotides that have not been chemically modified are referred to herein as "naked" oligonucleotides (e.g., naked ASO).
[0108] A "nucleoside" refers to a compound containing a sugar molecule (e.g., a pentose or ribose) or a derivative thereof in combination with an organic base (e.g., a purine or pyrimidine) or a derivative thereof (also referred to herein as "nucleobase").
[0109] A “nucleotide" refers to a nucleoside including a phosphate group. Modified nucleotides can be synthesized by any useful method, such as, for example, chemically, enzymatically, or recombinantly, to include one or more modified or non-natural nucleosides.
[0110] Nucleic acids can comprise a region or regions of linked nucleosides. Such regions can have variable backbone linkages. The linkages can be standard phosphodiester linkages, in which case the nucleic acids would comprise regions of nucleotides.
[OHl] The modified nucleic acids disclosed herein can comprise various distinct modifications. In some aspects, the modified nucleic acids contain one, two, or more (optionally different) nucleoside or nucleotide modifications. In some aspects, a modified polynucleotide can exhibit one or more desirable properties, e.g., improved thermal or chemical stability, reduced immunogenicity, reduced degradation, increased binding to the target microRNA, reduced nonspecific binding to non-target microRNA or other molecules, as compared to an unmodified polynucleotide.
[0112] In some aspects, one or more nucleic acids in the oligonucleotide of the present disclosure are chemically modified. As used herein in reference to a polynucleotide, the terms "chemical modification" or, as appropriate, "chemically modified" refer to modification with respect to adenosine (A), guanosine (G), uridine (U), thymidine (T) or cytidine (C) ribo- or deoxyribonucleosides in one or more of their position, pattern, percent or population, including, but not limited to, its nucleobase, sugar, backbone, or any combination thereof.
[0113] In some aspects, an oligonucleotide of the present disclosure can have a uniform chemical modification of all or any of the same nucleoside type or a population of modifications produced by downward titration of the same starting modification in all or any of the same nucleoside type, or a measured percent of a chemical modification of all any of the same nucleoside
type but with random incorporation. In some aspects, the oligonucleotide of the present disclosure can have a uniform chemical modification of two, three, or four of the same nucleoside type throughout the entire polynucleotide (such as all uridines and/or all cytidines, etc. are modified in the same way).
[0114] Modified nucleotide base pairing encompasses not only the standard adeninethymine, adenine-uracil, or guanine-cytosine base pairs, but also base pairs formed between nucleotides and/or modified nucleotides comprising non-standard or modified bases, wherein the arrangement of hydrogen bond donors and hydrogen bond acceptors permits hydrogen bonding between a non-standard base and a standard base or between two complementary non-standard base structures. One example of such non-standard base pairing is the base pairing between the modified nucleobase inosine and adenine, cytosine, or uracil. Any combination of base/sugar or linker can be incorporated into nucleic acids of the present disclosure.
[0115] The skilled artisan will appreciate that, except where otherwise noted, polynucleotide sequences set forth in the instant application will recite "T"s in a representative DNA sequence but where the sequence represents RNA, the "T"s would be substituted for "U"s. For example, TD’s of the present disclosure can be administered as RNAs, as DNAs, or as hybrid molecules comprising both RNA and DNA units.
[0116] In some aspects, the oligonucleotide of the disclosure includes a combination of at least two (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more) modified nucleobases. In some aspects, the oligonucleotide has two modified nucleobases. In some aspects, the oligonucleotide has three modified nucleobases. In some aspects, the oligonucleotide has four modified nucleobases. In some aspects, the oligonucleotide has five modified nucleobases. In some aspects, the oligonucleotide has six modified nucleobases. In some aspects, the oligonucleotide has seven modified nucleobases. In some aspects, the oligonucleotide has eight modified nucleobases. In some aspects, the oligonucleotide has nine modified nucleobases. In some aspects, the oligonucleotide has 10 modified nucleobases. In some aspects, the oligonucleotide has 11 modified nucleobases. In some aspects, the oligonucleotide has 12 modified nucleobases. In some aspects, the oligonucleotide has 13 modified nucleobases. In some aspects, the oligonucleotide has 14 modified nucleobases. In some aspects, the oligonucleotide has 15 modified nucleobases. In some aspects, the oligonucleotide has 16 modified nucleobases. In some aspects, the oligonucleotide has 17 modified nucleobases. In some aspects, the oligonucleotide has 18 modified nucleobases. In some aspects, the oligonucleotide has 19 modified nucleobases. In some aspects, the
oligonucleotide has 20 modified nucleobases. In some aspects, the oligonucleotide has more than 20 modified nucleobases.
[0117] In some aspects, the nucleobases, sugars, backbone linkages, or any combination thereof in an oligonucleotide are modified by at least about 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% or 100%.
ILA.3. Base Modifications
[0118] In some aspects, the chemical modification is at nucleobases in an oligonucleotide of the present disclosure. In some aspects, the chemically modified nucleoside is a modified uridine (e.g., pseudouridine (y), 2-thiouridine (s2U), 1-methyl-pseudouridine (mly), 1-ethyl- pseudouridine (ely), or 5-methoxy-uridine (mo5U)), a modified cytosine (e.g., 5-methyl-cytidine (m5C)) a modified adenosine (e.g, 1-methyl-adenosine (ml A), N6-methyl-adenosine (m6A), or 2- methyl-adenine (m2A)), a modified guanosine e.g., 7-methyl-guanosine (m7G) or 1-methyl- guanosine (mlG)), a 5'-methyl pyrimidine e.g., 5-methyl-cytidine (m5C), 5-methyl-thymidine (m5T), or 5-methyl-uridine (m5U)), or a combination thereof. In some aspects, the chemically modified nucleoside is a 5-methyl-pryimidine.
[0119] In some aspects, the oligonucleotide of the present disclosure is uniformly modified (e.g., fully modified, modified throughout the entire sequence) for a particular modification. For example, an oligonucleotide can be uniformly modified with the same type of base modification, e.g., 5-methyl-cytidine (m5C), meaning that all cytidine residues in the oligonucleotide sequence are replaced with 5-methyl-cytidine (m5C). Similarly, an oligonucleotide can be uniformly modified for any type of nucleoside residue present in the sequence by replacement with a modified nucleoside, such as any of those set forth above.
[0120] In some aspects, the oligonucleotide of the present disclosure e.g., an antimir, e.g., a miR378a antimir) includes a combination of at least two (e.g., 2, 3, 4 or more) modified nucleobases. In some aspects, at least about 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about
50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about
75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about
96%, at least about 97%, at least about 98%, at least about 99% or 100% of a type of nucleobase
in an oligonucleotide of the present disclosure e.g., an antimir, e.g., a miR378a inhibitor) are modified nucleobases.
IL A.4. Backbone modifications
[0121] In some aspects, the "oligonucleotide of the present disclosure" (for example an antimir, e.g., a miR378a inhibitor), comprises any useful modification to the linkages between the nucleosides. Such linkages, including backbone modifications, that are useful in the oligonucleotide of the present disclosure include, but are not limited to the following: 3'-alkylene phosphonates, 3 '-amino phosphoramidate, alkene containing backbones, aminoalkylphosphoramidates, aminoalkylphosphotriesters, boranophosphates, -CH2-O-N(CH3)- CH2-, -CH2-N(CH3)-N(CH3)-CH2-, -CH2-NH-CH2-, chiral phosphonates, chiral phosphorothioates, formacetyl and thioformacetyl backbones, methylene (methylimino), methylene formacetyl and thioformacetyl backbones, methyleneimino and methylenehydrazino backbones, morpholino linkages, -N(CH3)-CH2-CH2-, oligonucleosides with heteroatom internucleoside linkage, phosphinates, phosphoramidates, phosphorodithioates, phosphorothioate internucleoside linkages, phosphorothioates, phosphotriesters, PNA, siloxane backbones, sulfamate backbones, sulfide sulfoxide and sulfone backbones, sulfonate and sulfonamide backbones, thionoalkylphosphonates, thionoalkylphosphotriesters, and thionophosphoramidates.
Boranophosphates
[0122] In some aspects, the presence of a backbone linkage disclosed above increase the stability (e.g., thermal stability) and/or resistance to degradation (e.g., enzyme degradation) of an oligonucleotide of the present disclosure (e.g., an antimir, e.g., a miR378a inhibitor). In some aspects, the stability and/or resistance to degradation increases by at least about 10%, at least about
15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about
40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about
65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about
90%, at least about 95%, or at least about 100% in the modified oligonucleotide compared to a corresponding oligonucleotide without the modification (reference or control oligonucleotide) [0123] In some aspects, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% or 100%
of the backbone linkages in an oligonucleotide of the present disclosure ((e.g., an antimir, e.g., a miR378a inhibitor) are modified (e.g., all of them are phosphorothioate).
[0124] In some aspects, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21 backbone linkages in an oligonucleotide of the present disclosure (e.g., an antimir, e.g., a miR378a inhibitor) are modified (e.g., phosphorothioate).
[0125] In some aspects, the backbone comprises linkages selected from the group consisting of phosphodiester linkage, phosphotriesters linkage, methylphosphonate linkage, phosphoramidate linkage, phosphorothioate linkage, and combinations thereof.
ILA.5. Sugar Modifications
[0126] The modified nucleosides and nucleotides which can be incorporated into an oligonucleotide of the present disclosure (e.g., an antimir, e.g., a miR378a inhibitor), can be modified on the sugar of the nucleic acid. Thus, in some aspects, the oligonucleotide comprises a nucleic acid, wherein the nucleic acid comprises at least one nucleoside analog (e.g., a nucleoside with a sugar modification).
[0127] In some aspects, the sugar modification increases the affinity of the binding of the oligonucleotide to its target miRNA. Incorporating affinity-enhancing nucleotide analogues in the oligonucleotide, such as LNA or 2 ’-substituted sugar can allow the length of oligonucleotide to be reduced, and also may reduce the upper limit of the size an oligonucleotide can be before nonspecific or aberrant binding takes place.
[0128] In some aspects, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100% of the nucleotides in an oligonucleotide of the present disclosure (e.g., an antimir, e.g., a miR378a inhibitor) contain sugar modifications (e.g., LNA).
[0129] In some aspects, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, or 22 nucleotide units in an oligonucleotide of the present disclosure (e.g., an antimir, e.g., a miR378a inhibitor) are sugar modified (e.g., LNA). In some aspects, one of the nucleotide units in an oligonucleotide of the present disclosure is sugar modified (e.g., LNA). In some aspects, two of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA). In some aspects, three of the nucleotide units in an oligonucleotide of the present disclosure are
sugar modified (e.g., LNA). In some aspects, four of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA). In some aspects, five of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA). In some aspects, six of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA). In some aspects, seven of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA). In some aspects, eight of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA). In some aspects, nine of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA). In some aspects, 10 of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA). In some aspects, 11 of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA). In some aspects, 12 of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA). In some aspects, 13 of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA). In some aspects, 14 of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA). In some aspects, 15 of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA). In some aspects, 16 of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA). In some aspects, 17 of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA). In some aspects, 18 of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA). In some aspects, 19 of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA). In some aspects, 20 of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA). In some aspects, more than 20 of the nucleotide units in an oligonucleotide of the present disclosure are sugar modified (e.g., LNA).
[0130] Generally, RNA includes the sugar group ribose, which is a 5-membered ring having an oxygen. Exemplary, non-limiting modified nucleotides include replacement of the oxygen in ribose (e.g., with S, Se, or alkylene, such as methylene or ethylene); addition of a double bond (e.g., to replace ribose with cyclopentenyl or cyclohexenyl); ring contraction of ribose (e.g., to form a 4-membered ring of cyclobutane or oxetane); ring expansion of ribose (e.g., to form a 6- or 7-membered ring having an additional carbon or heteroatom, such as for anhydrohexitol, altritol, mannitol, cyclohexanyl, cyclohexenyl, and morpholino that also has a phosphoramidate backbone); multicyclic forms (e.g., tricyclo; and "unlocked" forms, such as glycol nucleic acid (GNA) (e.g., R-GNA or S-GNA, where ribose is replaced by glycol units attached to
phosphodiester bonds), threose nucleic acid (TNA, where ribose is replace with a -L- threofuranosyl-(3'->2')) , and peptide nucleic acid (PNA, where 2-amino-ethyl-glycine linkages replace the ribose and phosphodiester backbone). The sugar group can also contain one or more carbons that possess the opposite stereochemical configuration than that of the corresponding carbon in ribose. Thus, an oligonucleotide molecule can include nucleotides containing, e.g., arabinose, as the sugar.
[0131] The 2' hydroxyl group (OH) of ribose can be modified or replaced with a number of different substituents. Exemplary substitutions at the 2'-position include, but are not limited to, H, halo, optionally substituted Ci-6 alkyl; optionally substituted Ci-6 alkoxy; optionally substituted Ce-io aryloxy; optionally substituted C3-8 cycloalkyl; optionally substituted C3-8 cycloalkoxy; optionally substituted Ce-io aryloxy; optionally substituted Ce-io aryl-Ci-6 alkoxy; optionally substituted C1-12 (heterocyclyl)oxy; a sugar (e.g., ribose, pentose, or any described herein); a polyethyleneglycol (PEG), -O(CH2CH2O)nCH2CH2OR, where R is H or optionally substituted alkyl, and n is an integer from 0 to 20 (e.g., from 0 to 4, from 0 to 8, from 0 to 10, from 0 to 16, from 1 to 4, from 1 to 8, from 1 to 10, from 1 to 16, from 1 to 20, from 2 to 4, from 2 to 8, from 2 to 10, from 2 to 16, from 2 to 20, from 4 to 8, from 4 to 10, from 4 to 16, and from 4 to 20); "locked" nucleic acids (LNA) in which the 2'-hydroxyl is connected by a C1-6 alkylene or C1-6 heteroalkylene bridge to the 4'-carbon of the same ribose sugar, where exemplary bridges include methylene, propylene, ether, amino bridges, aminoalkyl, aminoalkoxy, amino, and amino acid.
[0132] In some aspects, nucleoside analogues present in an oligonucleotide of the present disclosure (e.g., an antimir, e.g., a miR378a inhibitor) comprise, e.g., 2’-O-alkyl-RNA units, 2’- OMe-RNA units, 2’-O-alkyl-SNA units, 2’-amino-DNA units, 2’-fluoro-DNA units, LNA units, arabino nucleic acid (ANA) units, 2’ -fluoro- ANA units, HNA units, INA (intercalating nucleic acid) units, 2’MOE units, or any combination thereof. In some aspects, the LNA is, e.g., oxy-LNA (such as beta-D-oxy-LNA, or alpha-L-oxy-LNA), amino-LNA (such as beta-D-amino-LNA or alpha-L-amino-LNA), thio-LNA (such as beta-D-thio-LNA or alpha-L-thio-LNA), ENA (such a beta-D-ENA or alpha-L-ENA), or any combination thereof.
[0133] In some aspects, nucleoside analogs present in an oligonucleotide of the present disclosure comprise Locked Nucleic Acid (LNA), 2'-O-alkyl-RNA, 2'-amino-DNA, 2'-fluoro- DNA, arabino nucleic acid (ANA), 2'-fluoro-ANA, hexitol nucleic acid (HNA), intercalating
nucleic acid (INA), constrained ethyl nucleoside (cEt), 2'-O-methyl nucleic acid (2'-0Me), 2'-O- methoxyethyl nucleic acid (2'-M0E), or any combination thereof.
[0134] In some aspects, an oligonucleotide of the present disclosure (e.g., an antimir, e.g., a miR378a inhibitor) can comprise both modified RNA nucleotide analogues (e.g., LNA) and DNA units. In some aspects, an oligonucleotide of the present disclosure is a gapmer. See, e.g., U.S. Pat. Nos. 8,404,649; 8,580,756; 8,163,708; 9,034,837; all of which are herein incorporated by reference in their entireties. In some aspects, an oligonucleotide of the present disclosure is a micromir. See U.S. Pat. Appl. Publ. No. US20180201928, which is herein incorporated by reference in its entirety.
ILA.6. Non-limiting Examples of Chemically Modified Oligonucleotides
[0135] In some aspects, an oligonucleotide of the present disclosure comprises a miRNA inhibitor.
[0136] In some aspects, the miRNA inhibitor of the present disclosure has a nucleotide sequence comprising the sequence 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49) and a backbone modification comprising one or more phosphorothioate linkages (SEQ ID NO: 55).
[0137] In some aspects, the miRNA inhibitor of the present disclosure comprises the ASO sequence and design of ASO Ml as shown in FIG. 12B. In some aspects, the miRNA inhibitor of the present disclosure comprises a nucleotide sequence comprising the sequence 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein (from 5'- end) nucleotide residues 1, 2, 3, and 22 are a LNA, and nucleotide residues 4-21 are a DNA (SEQ ID NO: 57).
[0138] In some aspects, the miRNA inhibitor of the present disclosure has a nucleotide sequence comprising the sequence 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49) and a backbone modification comprising one or more phosphorothioate linkages, wherein (from 5'- end) nucleotide residues 1, 2, 3, and 22 are a LNA, and nucleotide residues 4-21 are a DNA (SEQ ID NO: 58).
[0139] In some aspects, the disclosure comprises an oligonucleotide comprising a contiguous nucleotide sequence of 10 to 30 nucleic acids in length that are complementary to a nucleic acid sequence within miRNA 378a-3p, wherein the contiguous nucleotide sequence comprises the sequence 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein the first, second, and third nucleotides from the 5’ to 3’ are LNAs (SEQ ID NO: 63).
[0140] In some aspects, the oligonucleotide comprises a contiguous nucleotide sequence of 10 to 30 nucleic acids in length that are complementary to a nucleic acid sequence within miRNA 378a-3p, wherein the contiguous nucleotide sequence comprises the sequence 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein the first, second, third, and 22nd nucleotides from the 5’ to 3’ are LNAs (SEQ ID NO: 57). In some aspects, the 4th, 5th, 6th, 7th, 8th, 9th, 10th, 11th, 12th, 13th, 14th, 15th, 16th, 17th, 18th, 19th, 20th, or 21st nucleotides from the 5’ to 3’ are DNAs. In some aspects, the base of the 2nd and 3rd nucleotides from 5’ to 3’ are 5-methyl- pyrimidine (SEQ ID NO: 64).
[0141] In some aspects, the disclosure comprises an oligonucleotide comprising a contiguous nucleotide sequence of 10 to 30 nucleic acids in length that are complementary to a nucleic acid sequence within miRNA 378a-3p, wherein the contiguous nucleotide sequence comprises the sequence 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein the first, second, third, and 22nd nucleotides from the 5’ to 3’ are LNAs, wherein the 4th, 5th, 6th, 7th, 8th, 9th, 10th, 11th, 12th, 13th, 14th, 15th, 16th, 17th, 18th, 19th, 20th, or 21st nucleotides from the 5’ to 3’ are DNAs, and the base of the 2nd and 3rd nucleotides from 5’ to 3’ are 5-methyl-pyrimidine (SEQ ID NO: 64). In some aspects, each of the nucleotides is linked by a phosphothioate bond (SEQ ID NO: 50). Accordingly, in some aspects, a miRNA 387a-3p inhibitor comprises a contiguous nucleotide sequence comprising the sequence 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein (from the 5'- end) the 1st, 2nd, 3rd, and 22nd nucleotides are LNA, wherein the 4th- 21st nucleotides are DNA, and the base of the 2nd and 3rd nucleotides are 5-methyl-pyrimidine, and wherein each of the nucleotides is linked by a phosphothioate bond (SEQ ID NO: 50).
[0142] In some aspects, the miRNA inhibitor of the present disclosure has a nucleotide sequence comprising 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49) and a backbone modification comprising one or more phosphorothioate linkages wherein (from the 5'- end) nucleotide residues 1, 2, 3, and 22 are a LNA, nucleotide residues 4-21 are a DNA, and nucleotide residues 2 and 3 comprise a 5-methyl-pyrimidine nucleobase modification (SEQ ID NO: 56).
[0143] In some aspects, the miRNA inhibitor of the present disclosure has a nucleotide sequence comprising 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), a backbone modification wherein 100% of the backbone linkages are phosphorothioate linkages, and wherein (from 5'- end) nucleotide residues 1, 2, 3, and 22 are a LNA, nucleotide residues 4-21 are a DNA, and nucleotide residues 2 and 3 comprise a 5-methyl-pyrimidine nucleobase modification (e.g.,
ASO Ml provided herein (the phrase “ASO Ml” is used interchangeably with “ASO #1”, “Modified ASO #1”, and “Ml”)) (SEQ ID NO: 50).
[0144] In some aspects, the ASO Ml induces an increased suppression of miR378a-3p in a cell, e.g., HepG2 or HepG3 cells, compared to a reference ASO (e.g., M2, Ml’, M5, M6, or M8). The structures of ASOs M2, Ml’, M5, M6, and M8 are provided in FIGs. 12D, 12C, 12F, 12G, and 121 respectively. In some aspects, the induced suppression level is at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 100%, as compared to the reference ASO.
[0145] In some aspects, the ASO Ml induces loss of body fat mass at a higher percentage than lean muscle mass compared to a reference ASO (e.g., M2, Ml’, M5, M6, or M8). In some aspects, the ASO Ml induces loss of body fat mass at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least aout 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or about 100% more than lean muscle mass compared to a reference ASO (e.g., M2, Ml’, M5, M6, or M8). In some aspects, the subject that received ASO Ml loses body fat mass more efficiently than a corresponding subject that received a control, e.g., a GLP-1 agonist, e.g., semaglutide or tirzepatide, or a reference ASO (e.g., M2, Ml’, M5, M6, or M8).
[0146] In some aspects, the ASO Ml is stable in mouse plasma when administered up to (from the administration to) about 1 day, about 2 days, about 3 days, about 4 days, about 5 days, about 6 days, or about 7 days.
[0147] In some aspects, the miRNA inhibitor comprises the ASO sequence and design of ASO M7 as shown in FIG. 12H. In some aspects, the miRNA inhibitor of the present disclosure comprises a nucleotide sequence comprising 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein (from 5'- end) each of nucleotide residues 1, 2, 3, 4, 5, 18, 19, 20, 21, and 22 is a LNA, and each of nucleotide residues 6-17 is a DNA (SEQ ID NO: 74).
[0148] In some aspects, the miRNA inhibitor of the present disclosure has a nucleotide sequence comprising 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49) and a backbone modification comprising one or more phosphorothioate linkages wherein (from 5'- end) each of nucleotide residues 1, 2, 3, 4, 5, 18, 19, 20, 21, and 22 is a LNA, and each of nucleotide residues 6-17 is a DNA (SEQ ID NO: 77). In some aspects, the miRNA inhibitor of the present disclosure has a nucleotide sequence comprising 5'-GCC C GAC CCAAG CCAG -3' (SEQ ID NO: 49),
wherein the backbone of the nucleotide sequence comprises phosphorothioate linkages and wherein (from 5'- end) each of nucleotide residues 1, 2, 3, 4, 5, 18, 19, 20, 21, and 22 is a LNA, and each of nucleotide residues 6-17 is a DNA (SEQ ID NO: 78).
[0149] In some aspects, the disclosure comprises an oligonucleotide comprising a contiguous nucleotide sequence of 10 to 30 nucleic acids in length that are complementary to a nucleic acid sequence within miRNA 378a-3p, wherein the contiguous nucleotide sequence comprises the sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein each of the first, second, third, fourth, fifth, 18, 19, 20, 21, and 22 nucleotides from the 5’ to 3’ is a nucleic acid comprising a LNA (SEQ ID NO: 74).
[0150] In some aspects, the oligonucleotide comprising a contiguous nucleotide sequence of 10 to 30 nucleic acids in length that are complementary to a nucleic acid sequence within miRNA 378a-3p, wherein the contiguous nucleotide sequence comprises the sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein each of the first, second, third, fourth, fifth, 18th, 19th, 20th, 21st, and 22nd nucleotides from the 5’ to 3’ is a LNA (SEQ ID NO: 74). In some aspects, each of the 6th, 7th, 8th, 9th, 10th, 11th, 12th, 13th, 14th, 15th, 16th, and 17th, nucleotides from the 5’ to 3’ is a DNA. In some aspects, each of the base of the 2nd, 3rd, 6th, 10th, 12th, 13th, 18th, and 19th nucleotides from 5’ to 3’ is a nucleic acid comprising 5-methyl-pyrimidine (SEQ ID NO: 75).
[0151] In some aspects, the disclosure comprises an oligonucleotide comprising a contiguous nucleotide sequence of 10 to 30 nucleic acids in length that are complementary to a nucleic acid sequence within miRNA 378a-3p, wherein the contiguous nucleotide sequence comprises the sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein each of the first, second, third, fourth, fifth, 18th, 19th, 20th, 21st, and 22nd nucleotides from the 5’ to 3’ is a nucleic acid comprising LNAs, wherein each of the 6th, 7th, 8th, 9th, 10th, 11th, 12th, 13th, 14th, 15th, 16th, and 17th nucleotides from the 5’ to 3’ is a DNA, and each of the base of the 2nd, 3rd, 6th, 10th, 12th, 13th, 18th, and 19th nucleotides from 5’ to 3’ is a nucleic acid comprising a 5- methyl-pyrimidine (SEQ ID NO: 75). In some aspects, each of the nucleotides is linked by a phosphothioate bond (SEQ ID NO: 70). Accordingly, in some aspects, a miRNA 387a-3p inhibitor comprises a contiguous nucleotide sequence comprising the sequence 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein each of the lst-5th and 18th-22nd nucleotides is a LNA, wherein each of the 6th- 17th nucleotides is a DNA, and each of the base of
the 2nd, 3rd, 6th, 10th, 12th, 13th, 18th, and 19th nucleotides comprises a 5-methyl-pyrimidine. In some aspects, each of the nucleotides is linked by a phosphothioate bond (SEQ ID NO: 70).
[0152] In some aspects, the miRNA inhibitor of the present disclosure has a nucleotide sequence comprising 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49) and a backbone modification comprising one or more phosphorothioate linkages wherein (from the 5'- end) each of nucleotide residues 1, 2, 3, 4, 5, 18, 19, 20, 21, and 22 is a nucleic acid comprising a LNA, each of nucleotide residues 6-17 is a DNA, and each of nucleotide residues 2, 3, 6, 10, 12, 13, 18, and 19 comprises a nucleic acid comprising a 5-methyl-pyrimidine (SEQ ID NO: 76).
[0153] In some aspects, the miRNA inhibitor of the present disclosure has a nucleotide sequence comprising 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), a backbone modification wherein 100% of the backbone linkages are phosphorothioate linkages, and wherein each of nucleotide residues 1, 2, 3, 4, 5, 18, 19, 20, 21, and 22 is a nucleic acid comprising a LNA, each of nucleotide residues 6-17 is a DNA, and each of nucleotide residues 2, 3, 6, 10, 12, 13, 18, and 19 comprises a nucleic acid comprising a 5-methyl-pyrimidine (ASO M7 (the phrase “ASO M7” is used interchangeably with “ASO #7”, “Modified ASO #7” and “M7”)) (SEQ ID NO: 70). [0154] In some aspects, the ASO M7 induces an increased suppression of miR378a-3p in a cell, e.g., HepG2 or HepG3 cells, compared to a reference ASO (e.g., M2, ME, M5, M6, or M8). In some aspects, the induced suppression level is at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 100%.
[0155] In some aspects, the ASO M7 induces loss of body fat mass at a higher percentage than lean muscle mass compared to a reference ASO (e.g., M2, Ml’, M5, M6, or M8). In some aspects, the ASO-M1 induces loss of body fat mass at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least aout 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or about 100% more than lean muscle mass compared to a reference ASO (e.g., M2, Ml’, M5, M6, or M8). In some aspects, the subject loses body fat mass more efficiently than a corresponding subject that received a control, e.g., a GLP-1 agonist, e.g., semaglutide or tirzepatide, or a reference ASO (e.g., M2, Ml’, M5, M6, or M8).
[0156] In some aspects, the ASO M7 is stable in mouse plasma when administered up to (from the administration to) about 1 day, about 2 days, about 3 days, about 4 days, about 5 days, about 6 days, about 7 days, about 8 days, about 9 days, about 10 days, about 11 days, about 12
days, about 13 days, about 14 days, or about 15 days. In some aspects, the stability of an miRNA inhibitor provided herein can be determined by measuring the absorbance value of the inhibitor present in a sample (e.g., mouse plasma). For instance, in some aspects, a miRNA inhibitor is determined to be stable if the absorbance value of the ASO in the sample is at least half the absorbance value measured in a sample immediately after the administration.
[0157] In some aspects, the miRNA inhibitor of the present disclosure comprises the ASO sequence and design of ASO M4 as shown in FIG. 12E. In some aspects, the oligonucleotide comprising a contiguous nucleotide sequence of 10 to 30 nucleic acids in length that are complementary to a nucleic acid sequence within miRNA 378a-3p, wherein the contiguous nucleotide sequence comprises the sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein the first, second, third, and 22nd nucleotides from the 5’ to 3’ are LNAs (SEQ ID NO: 57), wherein the 4th, 5th, 6th, 7th, 8th, 9th, 10th, 11th, 12th, 13th, 14th, 15th, 16th, 17th, 18th, 19th, 20th, or 21st nucleotides from the 5’ to 3’ are DNAs, and wherein the base of the 2nd, 3rd, 6th, 10th, 12th, 13th, 18th, and 19th nucleotides from 5’ to 3’ are 5-methyl-pyrimidine (SEQ ID NO: 72). In some aspects, each of the nucleotides is linked by a phosphothioate bond (SEQ ID NO: 79). Accordingly, in some aspects, a miRNA 387a-3p inhibitor comprises a contiguous nucleotide sequence comprising the sequence 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein (from the 5'- end) the 1st, 2nd, 3rd, and 22nd nucleotides are LNA, wherein the 4th-21st nucleotides are DNA, wherein the based of the 2nd, 3rd, 6th, 10th, 12th, 13th, 18th, and 19th nucleotides are 5-methyl-pyrimidine, and wherein each of the nucleotides is linked by a phosphothioate bond (SEQ ID NO: 67).
[0158] In some aspects, the miRNA inhibitor of the present disclosure has a nucleotide sequence comprising 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49) and a backbone modification comprising one or more phosphorothioate linkages wherein (from the 5'- end) nucleotide residues 1, 2, 3, and 22 are a LNA, nucleotide residues 4-21 are a DNA, and nucleotide residues 2, 3, 6, 10, 12, 13, 18, and 19 comprise a 5-methyl-pyrimidine nucleobase modification (SEQ ID NO: 73).
[0159] In some aspects, the miRNA inhibitor of the present disclosure has a nucleotide sequence comprising 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), a backbone modification wherein 100% of the backbone linkages are phosphorothioate linkages, and wherein (from the 5'- end) nucleotide residues 1, 2, 3, and 22 are a LNA, nucleotide residues 4-21 are a DNA, and nucleotide residues 2, 3, 6, 10, 12, 13, 18, and 19 comprise a 5-methyl-pyrimidine
nucleobase modification (ASO M4 (the phrase “ASO M4” is used interchangeably with “ASO #4”, “Modified ASO #4”, and “M4”)) (SEQ ID NO: 67).
[0160] In some aspects, the ASO M4 induces an increased suppression of miR378a-3p in a cell, e.g., HepG2 or HepG3 cells, compared to a reference ASO (e.g., M2, Ml’, M5, M6, or M8). In some aspects, the induced suppression level is at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or at least 100%, as compared to that observed with the reference ASO.
[0161] In some aspects, the ASO M4 induces loss of body fat mass at a higher percentage than lean muscle mass compared to a reference ASO (e.g., M2, Ml’, M5, M6, or M8). In some aspects, the ASO-M1 induces loss of body fat mass at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least aout 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or about 100% more than lean muscle mass compared to a reference ASO (e.g., M2, Ml’, M5, M6, or M8). In some aspects, the subject loses body fat mass more efficiently than a corresponding subject that received a control, e.g., a GLP-1 agonist, e.g., semaglutide or tirzepatide, or a reference ASO (e.g., M2, Ml’, M5, M6, or M8).
[0162] In some aspects, the ASO M4 is stable in mouse plasma when administered up to (from the administration to) about 1 day, about 2 days, about 3 days, about 4 days, about 5 days, about 6 days, or about 7 days.
[0163] In some aspects, a miRNA inhibitor comprises ASO M2. In some aspects, a miRNA inhibitor comprises a nucleotide sequence comprising 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein (from 5'- end) each of nucleotide residues 1, 2, 3, and 22 is a nucleic acid comprising a 2’-M0E, and each of nucleotide residues 4- 21 is a DNA (SEQ ID NO: 59).
[0164] In some aspects, a miRNA inhibitor has a nucleotide sequence comprising 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49) and a backbone modification comprising one or more phosphorothioate linkages wherein (from 5'-end) each of nucleotide residues 1, 2, 3, and 22 is a 2’-M0E, and each of nucleotide residues 4-21 is a DNA (SEQ ID NO: 60). In some aspects, a miRNA inhibitor of the present disclosure has a nucleotide sequence comprising 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein the backbone of the nucleotide sequence comprises phosphorothioate linkages and wherein (from 5'- end) each of nucleotide
residues 1, 2, 3, and 22 is a nucleic acid comprising a 2’-M0E, and each of nucleotide residues 4- 21 is a DNA (SEQ ID NO: 60).
[0165] In some aspects, provided herein is an oligonucleotide comprising a contiguous nucleotide sequence of 10 to 30 nucleic acids in length that are complementary to a nucleic acid sequence within miRNA 378a-3p, wherein the contiguous nucleotide sequence comprises the sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein (from 5'- end) each of the first, second, and third nucleotides from the 5’ to 3’ is a nucleic acid comprising a 2’-M0E (SEQ ID NO: 65).
[0166] In some aspects, provided herein is an oligonucleotide comprising a contiguous nucleotide sequence of 10 to 30 nucleic acids in length that are complementary to a nucleic acid sequence within miRNA 378a-3p, wherein the contiguous nucleotide sequence comprises the sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein (from 5'- end) each of the first, second, third, and 22nd nucleotides is a nucleic acid comprising a 2’ -MOE (SEQ ID NO: 59). In some aspects, each of the 4th, 5th, 6th, 7th, 8th, 9th, 10th, 11th, 12th, 13th, 14th, 15th, 16th, 17th, 18th, 19th, 20th, or 21st nucleotides from the 5’ to 3’ is a DNA. In some aspects, each of the base of the 2nd and 3rd nucleotides from 5’ to 3’ is a nucleic acid comprising 5-methyl- pyrimidine (SEQ ID NO: 66).
[0167] In some aspects, provided herein is an oligonucleotide comprising a contiguous nucleotide sequence of 10 to 30 nucleic acids in length that are complementary to a nucleic acid sequence within miRNA 378a-3p, wherein the contiguous nucleotide sequence comprises the sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein (from the 5'- end) each of the first, second, third, and 22nd nucleotides is a nucleic acid comprising 2’- MOEs, wherein each of the 4th, 5th, 6th, 7th, 8th, 9th, 10th, 11th, 12th, 13th, 14th, 15th, 16th, 17th, 18th, 19th, 20th, or 21st nucleotides from the 5’ to 3’ is a DNA, and each of the base of the 2nd and 3rd nucleotides from 5’ to 3’ is a nucleic acid comprising a 5-methyl-pyrimidine (SEQ ID NO: 66). In some aspects, each of the nucleotides is linked by a phosphothioate bond (SEQ ID NO: 62).
[0168] In some aspects, a miRNA inhibitor has a nucleotide sequence comprising 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49) and a backbone modification comprising one or more phosphorothioate linkages wherein (from the 5'- end) each of nucleotide residues 1, 2, 3, and 22 is a nucleic acid comprising a 2’ -MOE, each of nucleotide residues 4-21 is a DNA, and each of nucleotide residues 2 and 3 comprises a nucleic acid comprising a 5-methyl-pyrimidine (SEQ ID NO: 61).
[0169] In some aspects, a miRNA inhibitor has a nucleotide sequence comprising 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), a backbone modification wherein 100% of the backbone linkages are phosphorothioate linkages, and wherein (from the 5'- end) each of nucleotide residues 1, 2, 3, and 22 is a nucleic acid comprising a 2’-M0E, each of nucleotide residues 4-21 is a DNA, and each of nucleotide residues 2 and 3 comprises a nucleic acid comprising a 5-methyl-pyrimidine (ASO M2 (the phrase “ASO M2” is used interchangeably with “ASO #2”, “Modified ASO #2” and “M2”)) (SEQ ID NO: 62). In some aspects, ASO M2 is a reference ASO as used herein compared to ASO Ml, ASO M4, and/or ASO M7.
[0170] In some aspects, a miRNA inhibitor comprise ASO ME. In some aspects, the miRNA inhibitor comprises a nucleotide sequence comprising 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), a backbone modification wherein 100% of the backbone linkages are phosphorothioate linkages, and wherein (from 5'- end) nucleotide residues 1, 2, 3, and 22 are a LNA, nucleotide residues 4-21 are a DNA, nucleotide residues 2 and 3 comprise a 5-methyl-pyrimidine nucleobase modification, and a cholesteryl moiety is attached to the 3 ’ end of the nucleotide sequence (ASO Ml’ (the phrase “ASO Ml’” is used interchangeably with “ASO #1’”, “Modified ASO #1’”, and “Ml ’”)) (SEQ ID NO: 50). In some aspects, ASO Ml’ is a reference ASO compared to ASO Ml, ASO M4, and/or ASO M7.
[0171] In some aspects, a miRNA inhibitor comprises ASO M5. In some aspects, a miRNA inhibitor comprises a nucleotide sequence comprising 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), a backbone modification wherein 100% of the backbone linkages are phosphorothioate linkages, and wherein (from 5'- end) each of nucleotide residues 1, 2, 3, 4, 5, 18, 19, 20, 21, and 22 is a nucleic acid comprising a 2’ -MOE, each of nucleotide residues 6-17 is a DNA, and each of nucleotide residues 2, 3, 6, 10, 12, 13, 18, and 19 comprises a nucleic acid comprising a 5-methyl-pyrimidine (ASO M5 (the phrase “ASO M5” is used interchangeably with “ASO #5”, “Modified ASO #5” and “M5”)) (SEQ ID NO: 68). In some aspects, ASO M5 is a reference ASO compared to ASO Ml, ASO M4, and/or ASO M7.
[0172] In some aspects, a miRNA inhibitor comprises ASO M6. In some aspects, the miRNA inhibitor comprises a nucleotide sequence comprising 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), a backbone modification wherein 100% of the backbone linkages are phosphorothioate linkages, and wherein (from 5'- end) each of nucleotide residues 1, 2, 3, 4, 5, 18, 19, 20, 21, and 22 is a nucleic acid comprising a 2’-M0E, each of nucleotide residues 6-17 is a DNA, and each of nucleotide residues 2, 3, 6, 10, 12, 13, 18, and
19 comprises a nucleic acid comprising a 5-methyl-pyrimidine (ASO M6 (the phrase “ASO M6” is used interchangeably with “ASO #6”, “Modified ASO #6” and “M6”)) (SEQ ID NO: 69). In some aspects, ASO M6 is a reference ASO compared to ASO Ml, ASO M4, and/or ASO M7.
[0173] In some aspects, a miRNA inhibitor comprises ASO M8. In some aspects, a miRNA inhibitor comprises a nucleotide sequence comprising 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), a backbone modification wherein 100% of the backbone linkages are phosphorothioate linkages, and wherein (from 5'- end) each of nucleotide residues 1-22 is a nucleic acid comprising a 2’-M0E, and each of nucleotide residues 2, 3, 6, 7, 10, 11, 12, 13, 17, 18, and 19 comprises a nucleic acid comprising a 5-methyl-pyrimidine (ASO M8 (the phrase “ASO M8” is used interchangeably with “ASO #8”, “Modified ASO #8” and “M8”)) (SEQ ID NO: 71). In some aspects, ASO M8 is a reference ASO compared to ASO Ml, ASO M4, and/or ASO M7.
IIB. Targeting moiety
[0174] In some aspects, the conjugate comprises a targeting moiety, which is linked to the oligonucleotide, optionally via a linker. As used herein, the term "targeting moiety" refers to a biorecognition molecule that binds to a specific biological substance or site. In some aspects, the targeting moiety is specific for a certain target molecule (e.g., a ligand targeting a receptor, or an antibody targeting a surface protein) or tissue (e.g., a molecule that would preferentially carry the conjugate to a specific organ or tissue, e.g., liver, brain, or endothelium), or facilitates transport through a physiological barrier (e.g., a peptide or other molecule that may facilitate transport across the brain blood barrier or plasma membrane).
[0175] For targeting a payload (e.g., a nucleotide molecule, e.g., an antisense oligonucleotide that binds to a microRNA) according to the present disclosure, a targeting moiety can be coupled to the payload, either directly or indirectly through a linker.
[0176] In some aspects, the targeting moiety is capable of targeting the conjugate of the present disclosure to a tissue. In some aspects, the tissue is liver, brain, kidney, lung, ovary, pancreas, thyroid, breast, stomach, or any combination thereof. In some aspects, the tissue is cancer tissue, e.g., liver cancer, brain cancer, kidney cancer, lung cancer, ovary cancer, pancreas cancer, thyroid cancer, breast cancer, stomach cancer, or any combination thereof.
[0177] In a specific aspect, the tissue is liver. In a specific aspect, the targeting moiety targeting liver is cholesterol. In other aspects, the targeting moiety targeting liver is a ligand that binds an asialoglycoprotein receptor targeting moiety.
[0178] In some aspects, a targeting moiety comprises glucose, e.g., D-glucose, which can bind to Glucose transporter 1 (or GLUT1). GLUT1, also known as solute carrier family 2, facilitated glucose transporter member 1 (SLC2A1), is a uniporter protein that, in humans, is encoded by the SLC2A1 gene. GLUT1 facilitates the transport of glucose across the plasma membranes of mammalian cells.
[0179] In some aspects, a targeting moiety comprises galactose, e.g., D-galactose, which can bind to GLUT1. In some aspects, a targeting moiety comprises glutamic acid, which can bind to acetylcholinesterase inhibitor (AChEI) and/or EAATs inhibitors. Acetylcholinesterase is the enzyme that is the primary member of the cholinesterase enzyme family. An acetylcholinesterase inhibitor (AChEI) is the inhibitor that inhibits acetylcholinesterase from breaking down acetylcholine into choline and acetate. Acetylcholinesterase inhibitors are one of two types of cholinesterase inhibitors; the other being butyryl-cholinesterase inhibitors.
[0180] In some aspects, a targeting moiety is GABA, which can bind to GABA receptors. The GABA receptors are a class of receptors that respond to the neurotransmitter gamma- aminobutyric acid (GABA), the chief inhibitory compound in the mature vertebrate central nervous system. There are two classes of GABA receptors: GABAA and GAB AB. GABAA receptors are ligand-gated ion channels (also known as ionotropic receptors); whereas GAB AB receptors are G protein-coupled receptors, also called metabotropic receptors.
[0181] In some aspects, a targeting moiety comprises tyrosine. In some aspects, a targeting moiety comprises lysine. In some aspects, a targeting moiety comprises glutamine. In some aspects, a targeting moiety comprises phenylalanine, which can bind to GABA receptors, CNS reverse transcriptase inhibitors, and/or dopamine (DA) receptors. Dopamine receptors are a class of G protein-coupled receptors that are prominent in the vertebrate central nervous system (CNS). Dopamine receptors activate different effectors through not only G-protein coupling, but also signaling through different protein (dopamine receptor-interacting proteins) interactions. The neurotransmitter dopamine is the primary endogenous ligand for dopamine receptors.
[0182] In some aspects, a targeting moiety comprises valine, which can bind to CNS reverse transcriptase inhibitors. In some aspects, a targeting moiety comprises tryptophan, which can bind to GABA receptors and/or CNS reverse transcriptase inhibitors. In some aspects, a targeting moiety comprises leucine, which can bind to GABA receptors and/or CNS reverse transcriptase inhibitors. In some aspects, a targeting moiety comprises methionine, which can bind to GABA receptors and/or CNS reverse transcriptase inhibitors. In some aspects, a targeting moiety comprises histidine, which can bind to GABA receptors. In some aspects, a targeting moiety
comprises isoleucine, which can bind to CNS reverse transcriptase inhibitors. In some aspects, a targeting moiety comprises Glutathione, which can bind to GSH transporter. In some aspects, a targeting moiety comprises Glutathi one-Met, which can bind to GSH transporter. In some aspects, a targeting moiety comprises Urea/Thiourea, which can bind to Nitric oxide synthase (NOS). In some aspects, a targeting moiety comprises NAD+/NADH. In some aspects, a targeting moiety comprises purine. Additional examples of targeting moieties for CNS targeting are shown in Sutera et al. (2016): Small endogenous molecules as moiety to improve targeting of CNS drugs, Expert Opinion on Drug Delivery, DOI: 10.1080/17425247.2016.1208651, which is incorporated herein by reference in its entirety.
II.B.1. Ligands
[0183] A ligand functions as a type of targeting moiety defined as a selectively bindable material that has a selective (or specific), affinity for another substance. The ligand is recognized and bound by a usually, but not necessarily, larger specific binding body or "binding partner," or "receptor." Examples of ligands suitable for targeting are antigens, haptens, biotin, biotin derivatives, lectins, galactosamine and fucosylamine moieties, receptors, substrates, coenzymes and cofactors among others.
[0184] When applied to the oligonucleotides of the present disclosure that is conjugated to a ligand, the ligand includes an antigen or hapten that is capable of being bound by, or to, its corresponding antibody or fraction thereof. Also included are viral antigens or hemagglutinins and neuraminidases and nucleocapsids including those from any DNA and RNA viruses, AIDS, HIV and hepatitis viruses, adenoviruses, alphaviruses, arenaviruses, coronaviruses, flaviviruses, herpesviruses, myxoviruses, oncornaviruses, papovaviruses, paramyxoviruses, parvoviruses, picornaviruses, poxviruses, reoviruses, rhabdoviruses, rhinoviruses, togaviruses and viroids; any bacterial antigens including those of gram-negative and gram-positive bacteria, Acinetobacter, Achromobacler. Bacteroides, Clostridium, Chlamydia, enterobacteria, Haemophilus, Lactobacillus, Neisseria, Staphyloccus, or Streptoccocus,' any fungal antigens including those of Aspergillus, Candida, Coccidiodes, mycoses, phycomycetes, and yeasts; any mycoplasma antigens; any rickettsial antigens; any protozoan antigens; any parasite antigens; any human antigens including those of blood cells, virus infected cells, genetic markers, heart diseases, oncoproteins, plasma proteins, complement factors, rheumatoid factors. Included are cancer and tumor antigens such as alpha-fetoproteins, prostate specific antigen (PSA) and CEA, cancer markers and oncoproteins, among others.
[0185] Other substances that can function as ligands for targeting an oligonucleotide of the present disclosure are certain vitamins (i.e. folic acid, B12), steroids, prostaglandins, carbohydrates, lipids, antibiotics, drugs, digoxins, pesticides, narcotics, neuro-transmitters, and substances used or modified such that they function as ligands.
[0186] In some aspects, the targeting moiety comprises a protein or protein fragment (e.g., hormones, toxins), and synthetic or natural polypeptides with cell affinity. Ligands also include various substances with selective affinity for ligators that are produced through recombinant DNA, genetic and molecular engineering. Except when stated otherwise, ligands of the instant disclosure also include ligands as defined in U.S. Pat. No. 3,817,837, which is herein incorporated by reference in its entirety.
ILB.2. Ligators
[0187] A ligator functions as a type of targeting moiety defined for this disclosure as a specific binding body or "partner" or "receptor," that is usually, but not necessarily, larger than the ligand it can bind to. For the purposes of this disclosure, it can be a specific substance or material or chemical or "reactant" that is capable of selective affinity binding with a specific ligand. A ligator can be a protein such as an antibody, a nonprotein binding body, or a "specific reactor." [0188] When applied to this disclosure, a ligator includes an antibody, which is defined to include all classes of antibodies, monoclonal antibodies, chimeric antibodies, Fab fractions, fragments and derivatives thereof. The term "antibody" encompasses an immunoglobulin whether natural or partly or wholly synthetically produced, and fragments thereof. The term also covers any protein having a binding domain that is homologous to an immunoglobulin binding domain. "Antibody" further includes a polypeptide comprising a framework region from an immunoglobulin gene or fragments thereof that specifically binds and recognizes an antigen. Use of the term antibody is meant to include whole antibodies, polyclonal, monoclonal and recombinant antibodies, fragments thereof, and further includes single-chain antibodies, humanized antibodies, murine antibodies, chimeric, mouse-human, mouse-primate, primate-human monoclonal antibodies, anti-idiotype antibodies, antibody fragments, such as, e.g., scFv, scFab, (scFab)2, (SCFV)2, Fab, Fab', and F(ab')2, F(abl)2, Fv, dAb, and Fd fragments, diabodies, and antibody-related polypeptides. Antibody includes bispecific antibodies and multispecific antibodies so long as they exhibit the desired biological activity or function. In some aspects of the present disclosure, the targeting moiety is an antibody or a molecule comprising an antigen binding fragment thereof. In some aspects, the antibody is a nanobody. In some aspects, the antibody is an ADC. The terms
"antibody-drug conjugate" and "ADC" are used interchangeably and refer to an antibody linked, e.g., covalently, to a therapeutic agent (sometimes referred to herein as agent, drug, or active pharmaceutical ingredient) or agents. In some aspects of the present disclosure, the targeting moiety is an antibody-drug conjugate.
[0189] Under certain conditions, the instant disclosure is also applicable to using other substances as ligators. For instance, other ligators suitable for targeting include naturally occurring receptors, any hemagglutinins and cell membrane and nuclear derivatives that bind specifically to hormones, vitamins, drugs, antibiotics, cancer markers, genetic markers, viruses, and histocompatibility markers. Another group of ligators includes any RNA and DNA binding substances such as polyethylenimine (PEI) and polypeptides or proteins such as histones and protamines.
[0190] Other ligators also include enzymes, especially cell surface enzymes such as neuraminidases, plasma proteins, avidins, streptavidins, chalones, cavitands, thyroglobulin, intrinsic factor, globulins, chelators, surfactants, organometallic substances, staphylococcal protein A, protein G, ribosomes, bacteriophages, cytochromes, lectins, certain resins, and organic polymers.
[0191] Targeting moieties also include various substances such as any proteins, protein fragments or polypeptides with affinity for the surface of any cells, tissues or microorganisms that are produced through recombinant DNA, genetic and molecular engineering. Thus, in some aspects, the targeting moiety directs a conjugate of the present disclosure to a specific tissue (i.e., liver tissue or brain tissue), to a specific type of cell (e.g., a certain type of cancer cells), or to a physiological compartment or physiological barrier (e.g., the plasma membrane).
II. C. Linkers
[0192] As described above, an oligonucleotide disclosed herein is optionally conjugated to a targeting moiety via one or more linkers. As used herein, the term "linker" refers to a peptide or polypeptide sequence (e.g., a synthetic peptide or polypeptide sequence), or a non-peptide linker for which its main function is to connect two moieties with an oligonucleotide disclosed herein. In some aspects, oligonucleotides conjugated to a targeting moiety can comprise at least one linker connecting thetissue-specific targeting moiety (TM) with the oligonucleotide.
[0193] Generally, linkers provide flexibility to the oligonucleotide and targeting moiety conjugate. Linkers are not typically cleaved; however, in certain aspects, such cleavage can be desirable. Accordingly, in some aspects a linker can comprise one or more protease-cleavable sites,
which can be located within the sequence of the linker or flanking the linker at either end of the linker sequence. In some aspects, the cleavable linker is cleavable by a protease. In some aspects, the linker is a bioreducible linker, an acid cleavable linker, a click-to-release linker, a pyrophosphatase cleavable linker, a beta-glucuronidase cleavable linker, or any combination thereof.
[0194] In one aspect, the linker is a peptide linker.
[0195] In some aspects, the linker comprises a non-peptide linker. In other aspects, the linker consists of a non-peptide linker. In some aspects, the non-peptide linker can be, e.g., maleimido caproyl (MC), maleimido propanoyl (MP), methoxyl polyethyleneglycol (MPEG), succinimidyl 4-(N-maleimidomethyl)-cyclohexane-l -carboxylate (SMCC), m-maleimidobenzoyl- N-hydroxysuccinimide ester (MBS), succinimidyl 4-(p-maleimidophenyl)butyrate (SMPB), N- succinimidyl(4-iodoacetyl)aminobenzonate (SIAB), succinimidyl 6-[3-(2-pyridyldithio)- propionami de] hexanoate (LC-SPDP), 4-succinimidyloxycarbonyl-alpha-methyl-alpha-(2- pyridyldithio)toluene (SMPT), etc. (see, e.g., U.S. Pat. No. 7,375,078).
[0196] In some aspects, a linker for the oligonucleotide and targeting moiety conjugate of the present disclosure has a formula:
wherein Ri R2, X = CH2, O, or CN, n = 0 to 10, and each of Ri and R2 =
[0197] In some aspects, non-limiting examples of the linkers include, but are not limited to:
III. Pharmaceutical Compositions
[0198] The present disclosure also provides pharmaceutical compositions comprising the oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates of the present disclosure that are suitable for administration to a subject. As discussed above, oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates of the present disclosure can be homogeneous (i.e., all oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates comprises the same type of oligonucleotide with the same targeting moiety). However, in other aspects, the oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates can comprise multiple targeting moieties, multiple payloads, etc.
[0199] The pharmaceutical compositions generally comprise an oligonucleotide (e.g., ASO Ml, M7, and/or M4) or a conjugate of the present disclosure and a pharmaceutically-acceptable excipient or carrier in a form suitable for administration to a subject. Pharmaceutically acceptable excipients or carriers are determined in part by the particular composition being administered, as well as by the particular method used to administer the composition.
[0200] There is a wide variety of suitable formulations for pharmaceutical compositions comprising oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates of the present
disclosure (See, e.g., Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa. 18th ed. (1990)). The pharmaceutical compositions are generally formulated sterile and in full compliance with all Good Manufacturing Practice (GMP) regulations of the U.S. Food and Drug Administration. In some aspects, the pharmaceutical composition comprises one or more oligonucleotides or conjugates described herein.
[0201] In certain aspects, the oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates described herein are co-administered with one or more additional therapeutic agents, in a pharmaceutically acceptable carrier. In some aspects, the pharmaceutical composition comprising the oligonucleotides or conjugates described herein is administered prior to administration of the additional therapeutic agent(s). In other aspects, the pharmaceutical composition comprising the oligonucleotides or conjugates described herein is administered after the administration of the additional therapeutic agent(s). In further aspects, the pharmaceutical composition comprising the oligonucleotides or conjugates described herein is administered concurrently with the additional therapeutic agent(s).
[0202] Acceptable carriers, excipients, or stabilizers are nontoxic to recipients (e.g., animals or humans) at the dosages and concentrations employed, and include buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid and methionine; preservatives (such as octadecyldimethylbenzyl ammonium chloride; hexamethonium chloride; benzalkonium chloride, benzethonium chloride; phenol, butyl or benzyl alcohol; alkyl parabens such as methyl or propyl paraben; catechol; resorcinol; cyclohexanol; 3-pentanol; and m-cresol); low molecular weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, histidine, arginine, or lysine; monosaccharides, di saccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugars such as sucrose, mannitol, trehalose or sorbitol; salt-forming counter-ions such as sodium; metal complexes (e.g., Zn-protein complexes); and/or non-ionic surfactants such as TWEEN™, PLURONICS™ or polyethylene glycol (PEG).
[0203] Examples of carriers or diluents include, but are not limited to: water, saline, Ringer's solutions, dextrose solution, and 5% human serum albumin. The use of such media and compounds for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or compound is incompatible with the oligonucleotides or conjugates disclosed herein, use thereof in the compositions is contemplated.
[0204] Supplementary therapeutic agents can also be incorporated into the compositions of the present disclosure. Typically, a pharmaceutical composition is formulated to be compatible with its intended route of administration. The oligonucleotides or conjugates described herein can be administered by parenteral, topical, intravenous, oral, subcutaneous, intra-arterial, intradermal, transdermal, rectal, intracranial, intraperitoneal, intranasal, intratumoral, and/or intramuscular route or as inhalants. In certain aspects, the pharmaceutical composition comprising oligonucleotides or conjugates described herein are administered intravenously, e.g. by injection. The oligonucleotides or conjugates described herein can optionally be administered in combination with other therapeutic agents that are at least partly effective in treating the disease, disorder or condition for which the oligonucleotides or conjugates described herein are intended.
[0205] Solutions or suspensions can include the following components: a sterile diluent such as water, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial compounds such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating compounds such as ethylenediaminetetraacetic acid (EDTA); buffers such as acetates, citrates or phosphates, and compounds for the adjustment of tonicity such as sodium chloride or dextrose. The pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide. The preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.
[0206] Pharmaceutical compositions suitable for injectable use include sterile aqueous solutions (if water soluble) or dispersions and sterile powders. For intravenous administration, suitable carriers include physiological saline, bacteriostatic water, Cremophor EL™ (BASF, Parsippany, N.J.) or phosphate buffered saline (PBS). The composition is generally sterile and fluid to the extent that easy syringeability exists. The carrier can be a solvent or dispersion medium containing, e.g., water, ethanol, polyol (e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like), and suitable mixtures thereof. The proper fluidity can be maintained, e.g., by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal compounds, e.g., parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like. If desired, isotonic compounds, e.g., sugars, polyalcohols such as mannitol, sorbitol, and sodium chloride can be added to the composition. Prolonged absorption of the injectable compositions can be brought about by including in the composition a compound which delays absorption, e.g., aluminum monostearate and gelatin.
[0207] Pharmaceutical compositions of the present disclosure can be sterilized by conventional, well known sterilization techniques. Aqueous solutions can be packaged for use or filtered under aseptic conditions and lyophilized, the lyophilized preparation being combined with a sterile aqueous solution prior to administration.
[0208] Sterile injectable solutions can be prepared by incorporating the oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates described herein in an effective amount and in an appropriate solvent with one or a combination of ingredients enumerated herein, as desired. Generally, dispersions are prepared by incorporating the oligonucleotides or conjugates described herein into a sterile vehicle that contains a basic dispersion medium and any desired other ingredients. In the case of sterile powders for the preparation of sterile injectable solutions, methods of preparation are vacuum drying and freeze-drying that yields a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof. The oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates described herein can be administered in the form of a depot injection or implant preparation which can be formulated in such a manner to permit a sustained or pulsatile release of the oligonucleotides or conjugates described herein.
[0209] Systemic administration of compositions comprising oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates described herein can also be by transmucosal means. For transmucosal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art, and include, e.g., for transmucosal administration, detergents, bile salts, and fusidic acid derivatives. Transmucosal administration can be accomplished through the use of, e.g., nasal sprays.
[0210] In some aspects the pharmaceutical composition comprising oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates described herein is administered intravenously into a subject that would benefit from the pharmaceutical composition. In some aspects, the composition is administered to the lymphatic system, e.g., by intralymphatic injection or by intranodal injection (see e.g., Senti et al., PNAS 105(46): 17908 (2008)), or by intramuscular injection, by subcutaneous administration, by intratumoral injection, by direct injection into the thymus, or into the liver.
[0211] In some aspects, the pharmaceutical composition comprising oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates described herein is administered as a liquid suspension. In some aspects, the pharmaceutical composition is administered as a formulation that is capable
of forming a depot following administration. In some aspects, the depot slowly releases the conjugates described herein into circulation, or remains in depot form.
[0212] Typically, pharmaceutically-acceptable compositions are highly purified to be free of contaminants, are biocompatible and not toxic, and are suited to administration to a subject. If water is a constituent of the carrier, the water is highly purified and processed to be free of contaminants, e.g., endotoxins.
[0213] The pharmaceutically-acceptable carrier can be lactose, dextrose, sucrose, sorbitol, mannitol, starch, gum acacia, calcium phosphate, alginates, gelatin, calcium silicate, microcrystalline cellulose, polyvinylpyrrolidone, cellulose, water, syrup, methyl cellulose, methylhydroxy benzoate, propylhydroxy benzoate, talc, magnesium stearate, and/or mineral oil, but is not limited thereto. The pharmaceutical composition can further include a lubricant, a wetting agent, a sweetener, a flavor enhancer, an emulsifying agent, a suspension agent, and/or a preservative.
[0214] The pharmaceutical compositions described herein comprise the oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates described herein and optionally a pharmaceutically active or therapeutic agent. The therapeutic agent can be a biological agent, a small molecule agent, or a nucleic acid agent.
[0215] Dosage forms are provided that comprise oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates described herein. In some aspects, the dosage form is formulated as a liquid suspension for intravenous injection.
[0216] The oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates disclosed herein or pharmaceutical composition comprising the oligonucleotides or conjugates may be used concurrently with other drugs. To be specific, the oligonucleotides (e.g., ASO Ml, M7, and/or M4), conjugates or pharmaceutical compositions of the present disclosure may be used together with medicaments such as hormonal therapeutic agents, chemotherapeutic agents, immunotherapeutic agents, medicaments inhibiting the action of cell growth factors or cell growth factor receptors and the like.
IV. Methods of Manufacture
[0217] The present disclosure also provides methods of making an oligonucleotide (e.g., ASO Ml, M7, and/or M4) or a conjugate of the present disclosure. In general, the present disclosure provides a method of preparing an oligonucleotide (e.g., ASO Ml, M7, and/or M4) or a conjugate of the present disclosure comprising synthesizing the oligonucleotide (e.g., ASO Ml,
M7, and/or M4) or conjugate as described, e.g., in the Examples section. As used herein, the term "synthesizing" refers the assembling the oligonucleotide (e.g., ASO Ml, M7, and/or M4) or conjugate using methods known in the art. In some aspects, each one of the components of the oligonucleotide (e.g., ASO Ml, M7, and/or M4) or conjugate can be prepared using methods known in the art, e.g., recombinant protein production, solid phase peptide or nucleic acid synthesis, chemical synthesis, enzymatic synthesis, or any combination thereof, and the resulting component can be conjugated using chemical and/or enzymatic methods known in the art.
[0218] The oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates of the present disclosure can be purified to remove contaminants. In some aspects, the oligonucleotide (e.g., ASO Ml, M7, and/or M4) or conjugate composition comprises a uniform population of oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates. However, in other aspects, the oligonucleotide (e.g., ASO Ml, M7, and/or M4) or conjugate composition can comprise multiple species (e.g., some of them comprising a targeting moiety, and some comprising the remaining moieties but without a targeting moiety). In some aspects, the manufacture of the oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates of the present disclosure comprise lyophilization or any other form of dry storage suitable for reconstitution.
[0219] In some aspects, the oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates of the present disclosure can be purified, e.g., to remove contaminants and/or to generate a uniform population of oligonucleotides or conjugates (e.g., oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugates having the same size, or conjugates having the same payload or the same targeting moiety).
V. Methods of Treatment and Use
[0220] The present disclosure also provides methods of treating a disease or condition in a subject in need thereof comprising administering an oligonucleotide or a conjugate of the present disclosure or a combination thereof (e.g., ASO Ml, M7, and/or M4) to the subject, e.g., a mammal, such as human subject. In some aspects the disease or disorder is cirrhosis, type 2 diabetes mellitus, hepatitis, fibrosis, fibrosis of the liver, obesity (e.g., abdominal obesity), dyslipidemia (hypercholesterolemia, hypertriglyceridemia), atherosclerosis, type 2 diabetes (T2D), hepatocellular carcinoma (HCC), hypertension, polycystic ovary syndrome (PCOS), chronic kidney disease (CKD), or cardiovascular disease (CVD). In some aspects, the present disclosure provides a method of treating a liver disease or disorder in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of an oligonucleotide or a conjugate
of the present disclosure (e.g., ASO Ml, M7, and/or M4), or a pharmaceutical composition of the present disclosure. In some aspects the liver disease or disorder is metabolic dysfunction-associated fatty liver disease (MAFLD) or metabolic dysfunction-associated steatohepatitis (MASH). In some aspects, the present disclosure provides a method of treating obesity (e.g., abdominal obesity) in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of an oligonucleotide or a conjugate of the present disclosure (e.g., ASO Ml, M7, and/or M4), or a pharmaceutical composition of the present disclosure.
[0221] In some aspects, the oligonucleotides or conjugates of the present disclosure (e.g., ASO Ml, M7, and/or M4) can administered via intravenous, intramuscular, intraarterial, intrathecal, intracapsular, intraorbital, intracardiac, intradermal, intraperitoneal, transtracheal, subcutaneous, subcuticular, intraarticular, subcapsular, subarachnoid, intraspinal and intrasternal injection and infusion. In some aspects, the oligonucleotides or conjugates of the present disclosure can administered via subcutaneous or intravenous injection.
[0222] In some aspects, the oligonucleotides or conjugates of the present disclosure (e.g., ASO Ml, M7, and/or M4) can be used concurrently with other medicaments or treatment suitable for the treatment of the diseases and conditions disclosed herein.
[0223] In some aspects, the oligonucleotides or conjugates of the present disclosure (e.g., ASO Ml, M7, and/or M4) can be used to target liver cells and tissue, e.g., to deliver therapeutic molecules (e.g., an oligonucleotide or antimir). In other aspects, the oligonucleotides or conjugates of the present disclosure (e.g., ASO Ml, M7, and/or M4) can be used to treat MASH and/or MAFLD. For example, oligonucleotides or conjugates of the present disclosure can target a marker specific for MASH and/or MAFLD (e.g. miR-378a-3p), and may additionally carry as payload a therapeutic molecule (e.g., a therapeutic polynucleotide, a peptide, an antimir, an oligonucleotide, or a small molecule).
[0224] In some aspects, the oligonucleotides or conjugates of the present disclosure (e.g., ASO Ml , M7, and/or M4) can be used to target adipose tissue, e.g., to deliver therapeutic molecules (e.g., an oligonucleotide or antimir). In some aspects, the oligonucleotides or conjugates of the present disclosure (e.g., ASO Ml, M7, and/or M4) can be used to treat obesity (e.g., abdominal obesity). For example, oligonucleotides or conjugates of the present disclosure can target a marker specific for obesity (e.g., abdominal obesity), and may additionally carry as payload a therapeutic molecule (e.g., a therapeutic polynucleotide, a peptide, an antimir, an oligonucleotide, or a small molecule).
[0225] In some aspects, the oligonucleotides or conjugates of the present disclosure (e.g., ASO Ml, M7, and/or M4) treats obesity e.g., abdominal obesity). In some aspects, the oligonucleotides or conjugates of the present disclosure (e.g., ASO Ml, M7, and/or M4) are capable of reducing a body weight or inducing a weight loss in a subject in need thereof comprising administering the oligonucleotides or conjugates described herein (e.g., ASO Ml, M7, and/or M4) to the subject. In some aspects, the disclosure provides a method of reducing a body weight or inducing a weight loss in a subject in need thereof comprising administering the oligonucleotides or conjugates described herein (e.g., ASO Ml, M7, and/or M4) to the subject.
[0226] In some aspects, the subject loses body fat mass at a higher percentage than lean muscle mass. In some aspects, the subject loses body fat mass at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least aout 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or about 100% more than lean muscle mass. In some aspects, the subject loses body fat mass more efficiently than a corresponding subject that received a control, e.g., a GLP-1 agonist, e.g., semaglutide or tirzepatide or a reference ASO, e.g., ASO Ml’, ASO M2, ASO M5, ASO M6, or ASO M8.
[0227] In some aspects, the subject after administration of the oligonucleotide (e.g., ASO Ml, M7, and/or M4) or conjugate of the present disclosure reduces body fat mass without changing lean muscle mass. Loss of muscle mass is indeed a major side effect of GLP-1 agonists. The STEP 1 and SUSTAIN 8 of semaglutide trials found 39-40% of weight lost on the GLP-1 drugs was lean mass. Often, twenty-five percent or more of the weight loss on these drugs is muscle. Unlike semaglutide, the oligonucleotides (e.g., ASO Ml, M7, and/or M4) and conjugates of the present disclosure are capable of maintaining the lean muscle mass in a subject administered with the oligonucleotides. In addition, in some aspects, the subject after administration of the oligonucleotide disclosure (e.g., ASO Ml, M7, and/or M4) or conjugate of the present disclosure reduces white adipose tissue (WAT). In mammals, white adipose tissue (WAT) stores and releases lipids, whereas brown adipose tissue (BAT) oxidizes lipids to fuel thermogenesis. In obese individuals, WAT undergoes profound changes; it expands, becomes dysfunctional, and develops a low-grade inflammatory state. Therefore, the oligonucleotides disclosure (e.g., ASO Ml, M7, and/or M4) and conjugates of the present surprisingly reduces WAT, without affecting the BAT. In some aspects, the subject after administration of the oligonucleotide (e.g., ASO Ml, M7, and/or M4) or conjugate of the present disclosure does not significantly lose brown adipose tissue.
[0228] In addition, visceral fat, also known as toxic fat, is hidden inside your body on and around your vital organs. Visceral fat can cause health issues such as high blood pressure, heart disease, diabetes and some cancers. Visceral fat is caused by eating more calories than you burn and not moving enough. In some aspects, the oligonucleotides (e.g., ASO Ml, M7, and/or M4) or conjugate of the present disclosure reduces visceral fat.
[0229] In some aspects, the subject after administration of the oligonucleotide (e.g., ASO Ml, M7, and/or M4) or conjugate of the present disclosure reduces hepatic steatosis and/or lipid accumulation.
VI. Kits
[0230] The present disclosure also provides kits, or products of manufacture, comprising an oligonucleotide (e.g., ASO Ml, M7, and/or M4), a conjugate, or a pharmaceutical composition of the present disclosure and optionally instructions for use. In some aspects, the kit or product of manufacture comprises an oligonucleotide (e.g., ASO Ml, M7, and/or M4), a conjugate, or a pharmaceutical composition of the present disclosure in one or more containers. In some aspects, the kit or product of manufacture comprises an oligonucleotide (e.g., ASO Ml, M7, and/or M4), a conjugate, or a pharmaceutical composition of the present disclosure and a brochure. In some aspects, the kit or product of manufacture comprises an oligonucleotide (e.g., ASO Ml, M7, and/or M4), a conjugate, or a pharmaceutical composition of the present disclosure and instructions for use. One skilled in the art will readily recognize that an oligonucleotide (e.g., ASO Ml , M7, and/or M4), a conjugate, or a pharmaceutical composition of the present disclosure, or combinations thereof, can be readily incorporated into one of the established kit formats which are well known in the art.
[0231] In some aspects, the kit or product of manufacture comprises an oligonucleotide (e.g., ASO Ml, M7, and/or M4) or a conjugate of the present disclosure in dry form in a container (e.g., a glass vial), and optionally a vial with a solvent suitable to hydrate the oligonucleotide (e.g., ASO Ml, M7, and/or M4) or conjugate, and optionally instructions for the hydration of the oligonucleotide (e.g., ASO Ml, M7, and/or M4) or conjugate. In some aspects, the kit or product of manufacture comprises an oligonucleotide (e.g., ASO Ml, M7, and/or M4) or a conjugate of the present disclosure in a dry form. In some aspects, the kit or product of manufacture comprises an oligonucleotide (e.g., ASO Ml, M7, and/or M4) or a conjugate of the present disclosure in solution. In some aspects, the kit or product of manufacture comprises an oligonucleotide (e.g., ASO Ml, M7, and/or M4) or a conjugate of the present disclosure in solution, and instructions for use. In
some aspects, the kit or product of manufacture comprises an oligonucleotide (e.g., ASO Ml, M7, and/or M4) or a conjugate of the present disclosure in dry form, and instructions for use (e.g., instructions for reconstitution and administration).
***
[0232] The practice of the present disclosure will employ, unless otherwise indicated, conventional techniques of cell biology, cell culture, molecular biology, transgenic biology, microbiology, recombinant DNA, and immunology, which are within the skill of the art. Such techniques are explained fully in the literature. See, for example, Sambrook et al., ed. (1989) Molecular Cloning A Laboratory Manual (2nd ed.; Cold Spring Harbor Laboratory Press); Sambrook et al., ed. (1992) Molecular Cloning: A Laboratory Manual, (Cold Springs Harbor Laboratory, NY); D. N. Glover ed., (1985) DNA Cloning, Volumes I and II; Gait, ed. (1984) Oligonucleotide Synthesis; Mullis et al. U.S. Pat. No. 4,683,195; Hames and Higgins, eds. (1984) Nucleic Acid Hybridization; Hames and Higgins, eds. (1984) Transcription And Translation; Freshney (1987) Culture Of Animal Cells (Alan R. Liss, Inc.); Immobilized Cells And Enzymes (IRL Press) (1986); Perbal (1984) A Practical Guide To Molecular Cloning; the treatise, Methods In Enzymology (Academic Press, Inc., N.Y.); Miller and Calos eds. (1987) Gene Transfer Vectors For Mammalian Cells, (Cold Spring Harbor Laboratory); Wu et al., eds., Methods In Enzymology, Vols. 154 and 155; Mayer and Walker, eds. (1987) Immunochemical Methods In Cell And Molecular Biology (Academic Press, London); Weir and Blackwell, eds., (1986) Handbook Of Experimental Immunology, Volumes I-IV; Manipulating the Mouse Embryo, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., (1986); ); Crooke, Antisense drug Technology: Principles, Strategies and Applications, 2nd Ed. CRC Press (2007) and in Ausubel et al. (1989) Current Protocols in Molecular Biology (John Wiley and Sons, Baltimore, Md.).
[0233] All of the references cited above, as well as all references cited herein, are incorporated herein by reference in their entireties.
[0234] The following examples are offered by way of illustration and not by way of limitation.
Examples
Example 1: In vitro Efficacy of ASO Ml in HepG2 Cells
[0235] The results from the in vitro efficacy test of ASO Ml is shown in FIG. 1A. HepG2 cells were obtained from the Korean Cell Line Bank (KCLB®, Seoul, South Korea) and cultured
in suspension at 37°C with a 5% CO2 atmosphere. The cells were grown in Dulbecco's Modified Eagle Medium (DMEM; Welgene, LM001-05) supplemented with 10% fetal bovine serum (FBS; HyClone, Sh30919.03) and a penicillin-streptomycin mix (Gibco, 15140-122). HepG2 cells were seeded at a density of 40,000 cells/well in a 12-well plate and incubated overnight. The cells were then administered a combination of .22 |JM oleic acid (OA; Sigma-Aldrich, 01383) and .11 |JM palmitic acid (PA; Sigma-Aldrich, P0500) at a molar ratio of 2: 1 (.22 pM OA: .11 pM PA) to induce lipid accumulation. Concurrently, transfection of ASO Ml (Ml) was performed at concentrations of 500nM using lipofectamine RNAiMAX (Invitrogen™, 13778450).
[0236] HepG2 cells were collected, and total RNA was extracted using QIAzol Lysis Reagent (Qiagen, 79306) and then reverse transcribed into cDNA using a miScript RT II Kit (Qiagen, 218161). To detect miR-378a-3p and RNU6 miRNA (U6) (reference/normalized) expression, cDNA was amplified by RT-qPCR using TOPreal™ Probe qPCR PreMIX (Enzynomics, RT600M). The primer sequences (5'— >3 ') used in this study were as follows: miR- 378a-3p forward: 5’-ACTGGACTTGGAGTCAGAAGGCAA-3’ (SEQ ID NO: 51), RNU6 forward (reference/normalized): 5’-GCTTCGGCAGCACATATACTAAAAT-3’ (SEQ ID NO: 52), Reverse primer: 5’-GAATCGAGCACCAGTTACG-3’ (SEQ ID NO: 53), probe: FAM-
CGAGGTCGACTTCCTAGA (SEQ ID NO: 54) . The RT-qPCR was carried out for 40 cycles under the following conditions: pre-denaturation at 95°C for 15 minutes, denaturation at 95°C for 10 seconds, annealing at 60°C for 1 minute, and extension at 72°C for 10 seconds. Relative miRNA levels were determined using the 2-AACt method.
[0237] FIG. 1A shows that ASO Ml reduced the expression of miR-378a-3p in cells induced by oleic acid/palmitic acid. miR-378a-3p expression was significantly upregulated following the OA/PA (oleic acid: palmitic acid = 0.22pM/0.1 IpM) administration in HepG2 cells compared to the control group at all three time points (6, 12, and 24 hours). The overexpressed levels of miR-378a-3p were down-regulated when samples were additionally transfected with ASO Ml (500nM) at all three time points (6, 12, and 24 hours). miR-378a-3p overexpression in the OA/PA group compared to the control group was +84% ± 7.6 at the 6 hour time point, +53% ± 5.9 at the 12 hour time point, and +63% ± 5.2 at the 24 hour time point (the difference between the two groups was statistically significant at all 3 time points). miR-378a-3p inhibition in the OA/PA + ASO Ml group compared to the OA/PA group was -62% ± 3.8 at the 6 hour time point, -43% ±
1.0 at the 12 hour time point, and -63% ± 1.8 at the 24 hour time point (the difference between the two groups was statistically significant at all 3 time points) (each group, n=3).
[0238] Data represent the mean ± standard error of the mean (SEM). GraphPad Prism 8.0 software was used for statistical analysis. Differences between the two groups were analyzed using a Student’s unpaired t-test. Group differences were detected using a one-way analysis of variance (ANOVA). Differences between the pathological condition and the control group were considered statistically significant at *P < 0.05, **P < 0.01, ***P< 0.001, and ****P< 0.0001. Differences between the pathological condition and the adminstration group were considered statistically significant at #P< 0.05, ##P < 0.01, ###P < 0.001, and ####P < 0.0001.
[0239] Oil red O staining in HepG2 is shown in FIG. IB. To stain HepG2 cells, first wash the cells three times with PBS to remove any unbound stain. Then, fix the cells with 4% PFA in PB (Biosesang, Cat No: PC2205- 100-74) for 30 minutes. Afterward, remove the PFA and wash the cells twice using distilled water. Add 60% isopropanol to the cells and let them incubate for 5 minutes. Next, discard the isopropanol and incubate the cells with Oil Red O solution (Sigma- Aldrich, Cat No: O1391-250ML) at room temperature for 15 minutes. Briefly rinse the cells with distilled water before staining them with hematoxylin (Sigma-Aldrich, Cat No: 03971-250ML) for 1 minute. Remove the hematoxylin and wash the cells three times with distilled water. Finally, examine the stained cells using a light microscope (Leica Biosystems, DM500). All images were obtained under lOOx magnification.
[0240] FIG. IB shows that ASO Ml reduced the deposition of lipid droplets in cells induced by oleic acid/palmitic acid. The left column, representing the control group, shows very few lipid droplet deposits (indicated by red staining) at the 6, 12, and 24 hour time points. The middle column, representing the OA/PA administered group, shows many lipid droplet deposits, with the amount of deposits increasing across the 6, 12, and 24 hour time points. The right column, representing the OA/PA + ASO Ml administered group, shows some lipid droplet deposits, with the amount of deposits increasing across the 6, 12, and 24 hour time points. This indicates that ASO Ml is able to partially counteract the deposition of lipid droplets induced by the OA/PA administration, and return the cells to a state more similar to the control group. Each group, n=3.
Example 2: In vivo Expression of miR-378a-3p in HFD-fed Mice
[0241] The experimental schedule for the in vivo expression of miR-378a-3p in HFD-fed mice experiment is shown in FIG. 2A. Seven-week-old wild-type male C57BL/6N mice (koatech) were maintained on either a standard diet (SD; samtako, S-01010) or a high-fat diet (HFD; Open Source, DI 2492) for 5 weeks. Mice were not subjected to fasting and re-feeding. Mice were
sacrificed after 5 weeks elapsed. After such time, the brain, liver, heart, lung, kidney, and spleen were collected for gene expression analysis, protein analysis, and histological analysis. All procedures involving mice were approved by the institutional animal care committee at Biorchestra.
[0242] Mouse tissues were collected, and total RNA was extracted using QIAzol Lysis Reagent (Qiagen, 79306) and then reverse transcribed into cDNA using a miScript RT II Kit (Qiagen, 218161). To detect miR-378a-3p and RNU6 miRNA (U6) (reference/normalized) expression, cDNA was amplified by RT-qPCR using TOPreal™ Probe qPCR PreMIX (Enzynomics, RT600M). The primer sequences (5'— >3') used in this study were as follows: miR- 378a-3p forward: 5’-ACTGGACTTGGAGTCAGAAGGCAA-3’ (SEQ ID NO: 51), RNU6 forward (reference/normalized): 5’-GCTTCGGCAGCACATATACTAAAAT-3’ (SEQ ID NO: 52), Reverse primer: 5’-GAATCGAGCACCAGTTACG-3’ (SEQ ID NO: 53), probe: FAM-
CGAGGTCGACTTCCTAGA (SEQ ID NO: 54). The RT-qPCR was carried out for 40 cycles under the following conditions: pre-denaturation at 95°C for 15 minutes, denaturation at 95°C for 10 seconds, annealing at 60°C for 1 minute, and extension at 72°C for 10 seconds. Relative miRNA levels were determined using the 2-AACt method.
[0243] Liver miR-378a-3p expression in HFD-fed mice is shown in FIG 2B. miR-378a-3p was robustly induced in HFD-fed mice, especially in the in fatty liver of HFD-fed mice. miR-378a- 3p expression in the liver of HFD-fed mice compared to the SD-fed mice was +217% ± 15.5 (a statistically significant difference) (each group, n=4).
[0244] Brain, heart, lung, spleen, and kidney miR-378a-3p expression in HFD-fed mice is shown in FIG 2C. miR-378a-3p expression in HFD-fed mice compared to the SD-fed mice was - 13.3% ± 4.6 for the brain, +108.7% ± 114.0 for the heart, +67.8% ± 22.8 for the lungs, +19.56% ± 11.1 in the spleen, and -9.6% ± 34.3 in the kidneys. The differences in the miR-378a-3p expression in the heart and lungs were statistically significant (each group, n=5).
[0245] Data represent the mean ± standard error of the mean (SEM). GraphPad Prism 8.0 software was used for statistical analysis. Differences between the two groups were analyzed using a Student’s unpaired t-test. Group differences were detected using a one-way analysis of variance (ANOVA). Differences were considered statistically significant at *P < 0.05. **P < 0.01, ***P< 0.001, and ****P< 0.0001.
Example 3: In vivo Efficacy of ASO Ml in induced MAFLD and MASH Mice
[0246] The experimental schedule for the in vivo efficacy of ASO Ml in induced MAFLD and MASH mice experiment is shown in FIG. 3A. Seven-week-old wild-type male C57BL/6N mice (koatech) were divided into six groups: SD (standard diet), HFD (High-fat diet), HFD+ASO Ml, LPS (Lipopolysaccharide), HFD+LPS, and (HFD+LPS) + ASO Ml (each group, n=3). The mice were maintained on either a standard diet (SD; samtako, S-01010) or a high-fat diet (HFD; Open Source, D12492) for 5 weeks. In the HFD+ASO Ml and HFD+ASO Ml+LPS groups, mice received a dose of 2.5mg/kg ASO Ml (Ml) complexed with in vivo-jetPEI (Polyplus Transfection, 1010000030), which was adminsiterd via intraperitoneal injection 3 times (every 5 days starting at week 3) before sacrifice. In the LPS, HFD+LPS, and HFD+ASO Ml+LPS groups, 5mg/kg LPS (Siga-Aldrich, L2630-10MG) was administered via intraperitoneal injection 24h before sacrifice. Mice were not subjected to fasting and re-feeding. Mice were sacrificed after 5 weeks elapsed. After such time, the liver, and whole blood were collected for gene expression analysis, protein analysis, and histological analysis. MAFLD was induced in the mice by feeding the mice a HFD. MASH was induced in the mice by feeding the mice a HFD and additionally injecting the mice with LPS. All procedures involving mice were approved by the institutional animal care committee at Biorchestra.
[0247] The morphology of the bodies and livers of the mice for the SD, HFD, and HFD + ASO Ml groups are shown in FIG. 3B. The body and organs, notably the liver, were larger and heavier in the HFD-induced MAFLD mice when compared to the SD mice. The body and organs, notably the liver, were smaller and lighter in HFD +ASO Ml mice when compared to the HFD- induced MAFLD mice (each group, n=4). This indicates that ASO Ml is able to partially counteract the change in morphology caused by the MAFLD induced by the HFD, and return the mice to a state more similar to the control group.
[0248] The biometrics of induced MAFLD mice administered with ASO Ml are shown in FIGs. 3C and 3D. FIG. 3C shows that body weight was significantly reduced in HFD-fed+ASO Ml mice compared to the HFD-fed mice. It should be noted that the body weight reduction in the HFD-fed+ASO Ml mice only began after injections with ASO Ml began 3 weeks into the experiment., before that the HFD-fed+ASO Ml mice and the HFD-fed mice were at essentially the same body weight. Following the ASO Ml injections, the HFD-fed+ASO Ml mice body weight value trending down and approached the SD-fed mice body weight value (each group, n=4). FIG. 3D shows that body weight and liver weight was significantly reduced, and body temperature remained the same, in HFD-fed+ASO Ml mice compared to the HFD-fed mice. The increase in
body weight of the HFD-fed mice was statistically significant when compared to both the SD and HFD-fed+ASO Ml mice. The increase in liver weight of the HFD-fed mice was statistically significant when compared to both the SD and HFD-fed+ASO Ml mice. The difference in body temperature of the HFD-fed mice was statistically non-significant when compared to both the SD and HFD-fed+ASO Ml mice (each group, n=4).
[0249] H&E staining and Oil red O staining of mouse liver samples for both induced MAFLD and MASH mice are shown in FIG. 3E. The liver samples were fixed in 4% PFA in PB (Biosesang, PC2205- 100-74), then embedded in OCT compound (SAKURA Tissue-Tek, 4583). For hematoxylin & eosin (H&E) staining, OCT-embedded liver tissues were coronally sectioned into 25pm slices using a cryostat microtome (Leica Biosystems, CM1860). OCT-embedded sections were stained using an H&E staining kit according to the manufacturer’s instructions (abeam, ab245880). To examine hepatic lipid accumulation, the liver tissues embedded in OCT compound were sectioned (10pm), mounted on slides, and allowed to dry for 1-2 hours. After drying, the sections were rinsed with distilled water 3 times. The slides were then placed in 60% isopropanol for 30 sec, and stained in Oil Red O solution in isopropanol for 10 min. The slides were transferred to a 60% isopropanol solution for 10 sec, rinsed in distilled water 3 times, stained in hematoxylin for 2min, and then rinsed in distilled water 3 times. Then, slides were mounted onto glass slides, air-dried, and coverslipped with an aqueous mounting medium. Stained slides were observed under a digital microscope (Leica Biosystems, DM500). All images were obtained under lOOx magnification.
[0250] FIG. 3E shows that ASO Ml ameliorated liver histopathologies of mice with induced MAFLD. H&E staining revealed that hepatic steatosis (fatty liver disease) was increased in the HFD-fed group compared to the SD-fed group, whereas hepatic steatosis decreased in the HFD+ASO Ml group compared to the HFD-fed group. Oil red O staining revealed that fat deposition (lipid droplets) increased in the HFD-fed group compared to the SD-fed group. Histological results showed no significant differences between the HFD+ASO Ml and SD-fed groups (each group, n=4).
[0251] FIG. 3E shows that ASO Ml ameliorated liver histopathology of mice with induced
MASH. H&E staining revealed that hepatic steatosiswas increased in the HFD+LPS-fed group compared to the SD+LPS-fed group, whereas hepatic steatosis decreased in the HFD+LPS+ASO Ml group compared to the HFD+LPS-fed group. Oil red O staining revealed that the size of fat deposits (lipid droplets) increased in the HFD+LPS-fed group compared to the SD+LPS-fed group
whereas the size of fat deposits decreased in the HFD+LPS+ASO Ml group compared to the HFD+LPS-fed group (each group, n=4).
[0252] HepG2 cells and mouse tissue were collected, and total RNA was extracted using QIAzol Lysis Reagent (Qiagen, 79306) and then reverse transcribed into cDNA using a miScript RT II Kit (Qiagen, 218161). To detect miR-378a-3p and RNU6 miRNA (U6) (reference/normalized) expression, cDNA was amplified by RT-qPCR using TOPreal™ Probe qPCR PreMIX (Enzynomics, RT600M). The primer sequences (5'— >3') used in this study were as follows: miR-378a-3p forward: 5’-ACTGGACTTGGAGTCAGAAGGCAA-3’ (SEQ ID NO: 51), RNU6 forward (reference/normalized): 5’-GCTTCGGCAGCACATATACTAAAAT-3’ (SEQ ID NO: 52), Reverse primer: 5’-GAATCGAGCACCAGTTACG-3’ (SEQ ID NO: 53), probe: FAM- CGAGGTCGACTTCCTAGA (SEQ ID NO: 54). The RT-qPCR was carried out for 40 cycles under the following conditions: pre-denaturation at 95°C for 15 minutes, denaturation at 95°C for 10 seconds, annealing at 60°C for 1 minute, and extension at 72°C for 10 seconds. Relative miRNA levels were determined using the 2-AACt method. Data generated is shown in FIG. 3F.
[0253] FIG. 3F shows that ASO Ml has an effect on miR-378a-3p expression in the liver of induced MAFLD and MASH mice. miR-378a-3p expression in the liver was significantly higher in the HFD and HFD+LPS groups compared to the SD and SD+LPS control groups respectively. The high levels of miR-378a-3p expression were significantly reduced when samples from the HFD and HFD+LPS groups were additionally transfected with ASO Ml (500nM) (each group, n=4). This indicates that ASO Ml is able to reduce the level of miR-378a-3p expression in the liver of induced MAFLD and MASH mice.
[0254] Mouse whole blood was collected via cardiac puncture, and left at room temperature
(RT) for 20 min for coagulation before centrifugation at 13000 rpm for 15 min at 4°C. The supernatant (serum) was collected. ELISA kits for mouse TNF-a (TNF-a; R&D systems) were used to measure cytokines in the serum according to the manufacturer’s instruction. The level of TNF-a was evaluated by comparison with the regression curve for its cytokine standard. Cytokine concentration is reported as pg of cytokine per milliliter of serum. Data generated is shown in FIG.
3G
[0255] FIG. 3G shows that ASO Ml has an anti-inflammatory effect in the induced MAFLD and MASH mice, as evidenced by the concentration of TNF-a in serum. TNF- a in serum was significantly higher in the HFD and HFD+LPS groups compared to the SD and SD+LPS control groups respectively. The high levels of TNF-a were significantly reduced when samples
from the HFD and HFD+LPS groups were additionally transfected with ASO Ml (500nM) (each group, n=4). This indicates that ASO Ml is able to reduce the level of inflammatory cytokine TNF- a in serum and thus reduce inflammation.
[0256] Data represent the mean ± standard error of the mean (SEM). GraphPad Prism 8.0 software was used for statistical analysis. Differences between the two groups were analyzed using a Student’s unpaired t-test. Group differences were detected using a one-way analysis of variance (ANOVA). Differences between the pathological condition and the control group were considered statistically significant at *P < 0.05. **P < 0.01, ***P < 0.001, and ****P < 0.0001. Differences between the pathological condition and the administered group were considered statistically significant at #P< 0.05, ##P < 0.01 and ###P < 0.001.
Example 4: in vitro Knockdown Efficacy of miR-378a-3p after Transfection of Naked ASO, Modified ASO Ml, and Modified ASO M2 in HepG2 and BV-2 Cells
[0257] in vitro knockdown efficacy of miR-378a-3p was investigated. For overexpression of miR-378a-3p, miR-378a-3p mimics were transfected for 2 hours. The media was replaced after 2 hours and an ASOs in vitro efficacy test was conducted. ASOs were transfected with 2-fold dilution at each step (15.625, 31.25, 61.25, 125, 250, 500 nM) in HepG2 and BV-2 cells.
[0258] As shown in FIG. 5A and 5B, Modified ASO #1 reduced target miR-378a-3p mRNA 25.87% more than naked ASO and 40.73% more than modified ASO #2 in HepG2 cells (human liver cell line). The chemical modifications of Modified ASO #1 can result in improved therapeutic effects in a liver disease model compared to a naked ASO and Modified ASO #2 as Modified ASO #1 targets miR-378a-3p better than the naked ASO and Modified ASO #2.
[0259] As shown in FIG. 5C and 5D, Modified ASO #1 reduced the miR-378a-3p mRNA by 38.46% more than the naked ASO and 29.04% more than modified ASO #2 in BV-2 cells (Mouse brain microglia cell line). The chemical modifications of Modified ASO #1 can result in improved therapeutic effects in a brain disease model as Modified ASO #1 targets miR-378a-3p better than the naked ASO and Modified ASO #2. Modified ASO #1 reduced the expression of miR-378a-3p more effectively than the naked ASO and Modified ASO #2.
Example 5: in vitro Anti-Inflammatory Effect after Transfection of Naked ASO, Modified ASO Ml, and Modified ASO M2 in BV-2 Cells
[0260] To measure the anti-inflammatory effects of the ASOs, mouse whole blood was collected from the mice that are administered with Modified ASO #1, the naked ASO, or Modified
ASO #2 via cardiac puncture, and left at room temperature (RT) for 20 min for coagulation before centrifugation at 13000 rpm for 15 min at 4°C. The supernatant (serum) of BV-2 cells were collected. ELISA kits for mouse TNF-a, IL-ip, and IL-18 (TNF-a, IL-ip, and IL-18; R&D systems) were used to measure cytokines in the serum according to the manufacturer’s instruction. The level of TNF-a, IL-ip, and IL-18 were evaluated by comparison with the regression curve for its cytokine standard. Cytokine concentration is reported as pg of cytokine per milliliter of serum. [0261] As shown in FIGs. 6A-6C, Modified ASO #1 administered groups had significantly lower concentrations of TNF-a, IL-ip, and IL-18 than the naked ASO and Modified ASO #2. Modified ASO #1 reduced the pro-inflammatory cytokines more effectively than the naked ASO and Modified ASO #2. Modified ASO #1 effectively reduced excessive TNF-a induced by LPS, and NLRP3 inflammasome activation induced by LPS+ATP. Therefore, based on the antiinflammatory effects, Modified ASO #1 can be expected to have superior therapeutic effects for MAFLD and MASH by effectively reducing inflammation.
Example 6: Comparative Evaluation of the Therapeutic Efficacy of Various Weight Loss Methods in MAFLD Model
[0262] For Examples 6-10, all animals were individually housed in a temperature- controlled (~24 °C) facility with 12h/12h light/dark cycle. Animal protocols were approved by Biorchestra and Co. IACUC (Institutional Animal Care and Use Committee). All studies were conducted in obese male mice (C57/BL6J). The body weight of all mice was measured daily at a consistent time. Animals were maintained on a high-fat diet (consisting of 60% fat, D12492; Research Diets) for 16-weeks, with free access to food and water before randomization by weight. Mice in the HFD group were fed for 8 to 12 weeks before injection. All animals were injected subcutaneously (SC) with vehicle, semaglutide (910463-68-2; Coldspring), tizepatide (2023788-19-2; Coldspring) or ASO-M1 (Example 6 only). Semaglutide and Tirzepatide were administered daily via SC injection for a duration of two weeks, with one injection each day (Example 6 only). The injection schedule for ASO-M1 varied according to the experimental conditions. ASO Ml was injected without transfection reagent (Gymnotic delivery). For the repeat injection conditions, injections were administered every three days, every seven days, or daily. In the case of a single injection, there was a schedule where the subject was sacrificed two weeks after the injection. Mice were not subjected to fasting and re-feeding. After such time, the brain, liver, heart, lung, kidney, spleen, and whole blood were collected for gene expression analysis, protein analysis, clinical chemistry analysis and histological analysis.
[0263] For Examples 6 and 7, mice were deeply anaesthetized with isoflurane, and the organs were immediately isolated from the mice bodies. Inguinal WAT (iWAT), interscapular WAT (isWAT), perigonadal WAT (pWAT), mesenteric WAT (mW AT), liver, quad muscle, kidney, spleen and heart were isloared. After measuring the weight of each organ, iBAT, iWAT, pWAT and liver tissues were fixed with 4% paraformaldehyde (Sigma-Aldrich) overnight and then further processes were conducted. FIG. 7A shows the schedule of the administration.
[0264] For Examples 6 and 7, the body composition measurement, fat mass, and lean mass of each mouse were measured by an EchoMRI700, quantitative nuclear resonance system (Echo Medical Systems).
[0265] FIGs 7B-7G show the results of the Therapeutic Efficacy of Various Weight Loss Methods in MAFLD Model test. As shown in FIG. 7B, daily ASO-M1 administration resulted in about 25% weight loss, outperforming semaglutide (19%) and closely maching tirzepatide efficacy (29%) (compared to control). As shown in FIG. 7C, semaglutide and tirzepatide reduced body weight by reducing food intake, but ASO-M1 caused only moderate reduction of food intake. As shown in FIG. 7D, ASO-M1 induced efficient weight loss by specifically reducing fat mass without changing lean muscle mass. As shown in FIGs. 7E-7G, ASO-M1 administration revealed overall benefits, compared with semaglutide and tizepatide, in reducing hepatic steatosis and lipid accumulation, specifically reducing white adipose tissue (WAT) and visceral fat (FIGs. 7E and 7F) without negatively impacting on brown adipose tissue (BAT) (FIG. 7G).
Example 7: Comparative Evaluation of the Therapeutic Efficacy of Various Schedules of ASO Ml in MAFLD Model
[0266] A MAFLD Model test was conducted to show the results of the therapeutic efficacy of various schedules of ASO ML This test shows that the weight loss effect by ASO-M1 is due to reducing fat mass (e.g., visceral fat), and not due to reducing food intake (FIGs. 8B-8D). Doses of 1.5 mg/kg ASO-M1 were administered three times a week, and 5 mg/kg ASO-M1 were administered once a week. See FIG. 8A. The administrations of ASO-M1 resulted in significantly better and comparable weight loss compared to the daily injection of Semaglutide and Tirzepatide, respectively (FIGs 8B-8G). As shown in FIG. 8B, doses of 1.5 mg/kg ASO-M1 three times a week, and 5 mg/kg ASO-M1 once a week resulted in about 34% and about 21% weight loss respectively compared to the control. FIG. 8C shows that doses of 1.5 mg/kg ASO-M1 three times a week, and 5 mg/kg ASO-M1 once a week resulted in about 27% and about 15% reduction in food intake respectively. FIG. 8D shows that ASO-M1 at both dosing schedules induced efficient
weight loss by specifically reducing fat mass without changing lean muscle mass. Doses of 1.5 mg/kg AS0-M1 three times a week outperformed 5 mg/kg AS0-M1 once a week in reducing fat mass. As shown in FIGs. 8E-8G, AS0-M1 at both dosing schedules revealed overall benefits, in reducing hepatic steatosis and lipid accumulation, specifically reducing white adipose tissue (WAT) and visceral fat (FIGs. 8E and 8F) without negatively impacting brown adipose tissue (BAT) (FIG. 8G).
Example 8: Comparative Evaluation of the Expression of miRNA and mRNA for Various Schedules of ASO Ml in MAFLD Model
[0267] miRNA and mRNA expressions as a result of various schedules of ASO Ml administration were measured. FIG. 9A shows the schedule of the ASO Ml administration. FIGs 9B-9G show that ASO Ml maintains a continuous therapeutic effect for up to two weeks after a single injection by regulating the genes related to lipid clearance and metabolism. As shown in FIG. 9B, doses of ASO Ml (10 mg/kg) weekly for 4 weeks (weeks 8-11) and a dose of ASO Ml (30 mg/kg) once (week 10) resulted in about 32% and about 24% weight loss respectively compared to control. As shown in FIG. 9C, the HFD significantly elevated miR-378 levels in the liver. However, ASO Ml at both dosing schedules restored the miR-378 level back to substantially the normal level. As shown in FIGs 9D, 9F, and 9G, ASO-M1 administration at both dosing schedules restored altered (lowered) expression of ATG2a, IGF-1, and IGF-1R, which are potential targets of miR-378, to the substantially normal level in the liver. As shown in FIG. 9E, ASO-M1 administration at both dosing schedules significantly up-regulated GLP-2Rcompared to control. Down-regulation of GLP-2R is strongly associated with hepatic inflammation and steatosis.
Example 9: Evaluation of MAFLD Progression in a HFD Mouse MAFLD Model via H&E and Oil Red O Staining
[0268] H&E staining and Oil red O staining of mouse liver samples for both induced MAFLD and MASH mice are shown in FIG. 10A and 10B. The liver samples were fixed in 4% PFA in PB (Biosesang, PC2205-100-74), then embedded in OCT compound (SAKURA Tissue- Tek, 4583). For hematoxylin & eosin (H&E) staining, OCT-embedded liver tissues were coronally sectioned into 25pm slices using a cryostat microtome (Leica Biosystems, CM1860). OCT- embedded sections were stained using an H&E staining kit according to the manufacturer’s instructions (abeam, ab245880). To examine hepatic lipid accumulation, the liver tissues embedded in OCT compound were sectioned (10pm), mounted on slides, and allowed to dry for
1-2 hours. After drying, the sections were rinsed with distilled water 3 times. The slides were then placed in 60% isopropanol for 30 sec, and stained in Oil Red O solution in isopropanol for 10 min. The slides were transferred to a 60% isopropanol solution for 10 sec, rinsed in distilled water 3 times, stained in hematoxylin for 2min, and then rinsed in distilled water 3 times. Then, slides were mounted onto glass slides, air-dried, and coverslipped with an aqueous mounting medium. Stained slides were observed under a digital microscope (Leica Biosystems, DM500). All images were obtained under lOOx magnification.
[0269] FIGs. 10A and 10B show the results of the evaluation of MAFLD Progression via H&E and Oil Red O Staining test. The results show that ASO-M1 reduces the lipid droplet, fat accumulation and ballooned hepatocytes in the livers of the mice in the HFD mouse MAFLD model. In FIG. 10A, the arrows indicate lipid droplets. FIG. 10A shows that the amount of lipid droplets was significantly increased in all HFD conditions compared to all HFD+ASO-M1 conditions which mirrors the control condition. In FIG. 10B the ballooned hepatocytes and the areas of fat accumulation were circled. FIG. 10B shows that the amount of ballooned hepatocytes and the areas of fat accumulation were significantly increased in all HFD conditions compared to all HFD+ASO-M1 conditions which mirrors the control condition.
Example 10: Evaluation of MAFLD Progression in a HFD Mouse MAFLD Model via Lipid Profile Examination
[0270] MAFLD Progression via Lipid Profile Examination test was evaluated. Mice used in the tests of Example 10 were administered ASO-M1 as described in FIG. 9A. The results are shown in FIGs. 11A-11F. ASO-M1 administration at both dosing schedules reversed abnormal lipid profiles induced by the HFD, such as high Low-density lipoprotein (LDL) (FIG. HA), high triglyceride (TG) (FIG. 11C), and high total cholesterol (TC) levels (FIG. HD). ASO-M1 administration at both dosing schedules did not affect the lipid profile of beneficial High-density lipoprotein (HDL) (FIG. 11B). ASO-M1 administration at both dosing schedules also normalized the increased levels of Alanine transaminase (ALT) (FIG. HE) and Aspartate transaminase (AST) (FIG. HF) activities, both of which are markers for liver damage. ASO-M1 administration at both dosing schedules was able to reverse elevated levels of malign lipids and maintain stable levels of benign lipids, which is predicted to improve liver health and prevent liver damage.
Example 11: Inhibitory Activity of Modified miR-378a-3p ASOs
[0271] For FIGs. 13A, 13B, 14A, 14B, 15A, and 15B, HepG2 and Hep3B cells were obtained from the Korean Cell Line Bank (KCLB®, Seoul, South Korea) and cultured in suspension
at 37°C with a 5% C02 atmosphere. The cells were grown in Dulbecco's Modified Eagle Medium (DMEM; Welgene, LM001-05) supplemented with 10% fetal bovine serum (FBS; HyClone, Sh30919.03) and a penicillin-streptomycin mix (Gibco, 15140-122). HepG2 and Hep3B cells were seeded at a density of 40,000 cells/well in a 24-well plate and incubated overnight. The cells were then pre-adminstered with 378a-3p mimic (25 nM) overnight. Concurrently, miR-378a-3p-mimic- administered HepG2 and Hep3B cells were exposued at various concentration of modified miR- 378a-3p ASOs between .927 nM to 1000 nM, either with or without the presence of RNAiMAX (Invitrogen™, 13778450).
[0272] For FIG. 16, all animals were individually housed in a temperature-controlled (~24 °C) facility with 12h/12h light/dark cycle. Animal protocols were approved by BIORCHESTRA and Co. IACUC. All studies were conducted in male mice (C57BL/6). All animals were intraperitoneally injected with control (PBS), or modified miR-378a-3p ASOs. The mice were sacrificed 7 days after the injection. Mice were not subjected to fasting and re-feeding. After such time, the liver was collected for gene expression analysis.
[0273] HepG2 and Hep3B cells and mouse tissue were collected, and total RNA was extracted using QIAzol Lysis Reagent (Qiagen, 79306) and then reverse transcribed into cDNA using a miScript RT II Kit (Qiagen, 218161). To detect miR-378a-3p miRNA expression, cDNA was amplified by RT-qPCR using TOPreal™ Probe qPCR PreMIX (Enzynomics, RT600M). The primer sequences (5'— >3') used in this study were as follows: miR-378a-3p forward: 5’- ACTGGACTTGGAGTCAGAAGGCAA-3’ (SEQ ID NO: 51), RNU6 forward (reference): 5’- GCTTCGGCAGCACATATACTAAAAT-3’ (SEQ ID NO: 52), Reverse: 5’-
GAATCGAGCACCAGTTACG-3’ (SEQ ID NO: 53), probe: FAM-CGAGGTCGACTTCCTAGA (SEQ ID NO: 54). The RT-qPCR was carried out for 40 cycles under the following conditions: predenaturation at 95°C for 15 minutes, denaturation at 95°C for 10 seconds, annealing at 60°C for 1 minute, and extension at 72°C for 10 seconds. Relative miRNA levels were determined using the 2~AACt method. Data generated is shown in FIGs. 13A, 13B, 14A, 14B, 15A, 15B, and 16.
[0274] FIGs. 13A and 13B show that modified ASO #1 (Ml), #4 (M4) and #7 (M7) were most effective in reducing miR-378a-3p expression levels in both HepG2 and Hep3B cell lines compared to the control. FIGs. 14A and 14B show that in the absence of a transfection reagent (gymnotic) modified ASO #1 (Ml), #4 (M4) and #7 (M7) were most effective in reducing miR- 378a-3p expression levels in the Hep3B cell line compared to the control. It also shows that greater dose concentration increased the effectiveness of the reduction in expression. FIGs. 15A and 15B
show that modified ASO #7(M7) was more effective in reducing miR-378a-3p than modified ASO #1 (Ml) in the Hep3B cell line. M7 was shown to more effective than Ml in reducing miR-378a- 3p in the Hep3B cell line at nearly all tested concentrations, and in both the presence and absence of a transfection reagent. FIG. 16 shows that in the absence of a transfection reagent modified ASO #1 (Ml), #4 (M4) and #7 (M7) were most effective in reducing miR-378a-3p expression levels in C57BL/6 mice compared to the control.
Example 12: Stability of Modified miR-378a-3p ASOs in Mouse Plasma
[0275] The stability of modified miR-378a-3p ASO #1 (Ml), #2 (M2), #4 (M4), #5 (M5), #6 (M6), #7 (M7), and #8 (M8) in mouse plasma, 500 pL of mouse plasma was mixed with 500 pL of modified miR-378a-3p ASO (200 pM) in a 1 : 1 ratio. The ASO in the mixed plasma was incubated at 37°C, and samples were collected at 0 minutes, 30 minutes, 1 hour, 1 day, 3 days, 7 days, 15 days, and 30 days. At each time point, 150 pL of the incubated sample was collected, filtered with a 0.2 pm PES (poly ethersulfone) filter, and washed with 100 pL of nuclease-free water. The recovery (%) of the samples was measured by HPLC (1260 Infinity II, Agilent). Data generated is shown in FIG. 17.
[0276] FIG. 17 shows that miR-378a-3p ASO #7 maintains stability in mouse plasma from 0 minutes to at least 15 days post injection and that ASO #1 maintains stability in mouse plasma from 0 minutes to at least 7 days post injection. ASO #2, #5, #6, and #8 were also stable from 0 minutes to at least 7 days post injection, with ASO #8 remaining stable up to at least 30 days post injection.
[0277] It is to be appreciated that the Detailed Description section, and not the Summary and Abstract sections, is intended to be used to interpret the claims. The Summary and Abstract sections may set forth one or more but not all exemplary aspects of the present disclosure as contemplated by the inventor(s), and thus, are not intended to limit the present disclosure and the appended claims in any way.
[0278] The present disclosure has been described above with the aid of functional building blocks illustrating the implementation of specified functions and relationships thereof. The boundaries of these functional building blocks have been arbitrarily defined herein for the convenience of the description. Alternate boundaries can be defined so long as the specified functions and relationships thereof are appropriately performed.
[0279] The foregoing description of the specific aspects will so fully reveal the general nature of the disclosure that others can, by applying knowledge within the skill of the art, readily
modify and/or adapt for various applications such specific aspects, without undue experimentation, without departing from the general concept of the present disclosure. Therefore, such adaptations and modifications are intended to be within the meaning and range of equivalents of the disclosed aspects, based on the teaching and guidance presented herein. It is to be understood that the phraseology or terminology herein is for the purpose of description and not of limitation, such that the terminology or phraseology of the present specification is to be interpreted by the skilled artisan in light of the teachings and guidance.
[0280] The breadth and scope of the present disclosure should not be limited by any of the above-described exemplary aspects, but should be defined only in accordance with the following claims and their equivalents.
Claims
1. An oligonucleotide comprising a contiguous nucleotide sequence of 10 to 30 nucleic acids in length that are complementary to a nucleic acid sequence within miRNA 378a-3p (5 - ACUGGACUUGGAGUCAGAAGGC-3' (SEQ ID NO: 1)), wherein the contiguous nucleotide sequence comprises at least one nucleic acid analog.
2. The oligonucleotide of claim 1, wherein the nucleotide sequence comprises a nucleotide sequence comprising 5'-AGUCCAG-3'.
3. The oligonucleotide of claim 1 or 2, wherein the nucleotide sequence comprises about 6 to about 30 nucleotides in length.
4. The oligonucleotide of any one of claims 1 to 3, wherein the oligonucleotide comprises at least 1 nucleotide, at least 2 nucleotides, at least 3 nucleotides, at least 4 nucleotides, at least 5 nucleotides, at least 6 nucleotides, at least 7 nucleotides, at least 8 nucleotides, at least 9 nucleotides, at least 10 nucleotides, at least 11 nucleotides, at least 12 nucleotides, at least 13 nucleotides, at least 14 nucleotides, at least 15 nucleotides, at least 16 nucleotides, at least 17 nucleotides, at least 18 nucleotides, at least 19 nucleotides, or at least 20 nucleotides at the 5' of the nucleotide sequence.
5. The oligonucleotide of any one of claims 1 to 4, wherein the oligonucleotide comprises at least 1 nucleotide, at least 2 nucleotides, at least 3 nucleotides, at least 4 nucleotides, at least 5 nucleotides, at least 6 nucleotides, at least 7 nucleotides, at least 8 nucleotides, at least 9 nucleotides, at least 10 nucleotides, at least 11 nucleotides, at least 12 nucleotides, at least 13 nucleotides, at least 14 nucleotides, at least 15 nucleotides, at least 16 nucleotides, at least 17 nucleotides, at least 18 nucleotides, at least 19 nucleotides, or at least 20 nucleotides at the 3' of the nucleotide sequence.
6. The oligonucleotide of any one of claims 1 to 5, wherein the nucleotide sequence comprises the sequence as set forth in 5'-AGUCCAG-3', 5'-AAGUCCAG-3', 5'-CAAGUCCAG-3', 5'- CCAAGUCCAG-3' (SEQ ID NO: 2), 5'-UCCAAGUCCAG-3' (SEQ ID NO: 3), 5'-CUCCAAGUCCAG- 3' (SEQ ID NO: 4), 5'-ACUCCAAGUCCAG-3' (SEQ ID NO: 5), 5'-GACUCCAAGUCCAG-3' (SEQ ID NO: 6), 5'-UGACUCCAAGUCCAG-3' (SEQ ID NO: 7), 5'-CUGACUCCAAGUCCAG-3' (SEQ ID NO: 8), 5'-UCUGACUCCAAGUCCAG-3' (SEQ ID NO: 9), 5'-UUCUGACUCCAAGUCCAG-3' (SEQ ID NO:
10), 5'-CUUCUGACUCCAAGUCCAG-3' (SEQ ID NO: 11), 5'-CCUUCUGACUCCAAGUCCAG-3' (SEQ ID NO: 12); 5'-AGUCCAGU-3', 5'-AAGUCCAGU-3', 5'-CAAGUCCAGU-3' (SEQ ID NO: 13), 5'- CCAAGUCCAGU-3' (SEQ ID NO: 14), 5'-UCCAAGUCCAGU-3' (SEQ ID NO: 15), 5'- CUCCAAGUCCAGU-3' (SEQ ID NO: 16), 5'-ACUCCAAGUCCAGU-3' (SEQ ID NO: 17), 5'- GACUCCAAGUCCAGU-3' (SEQ ID NO: 18), 5'-UGACUCCAAGUCCAGU-3' (SEQ ID NO: 19), 5'- CUGACUCCAAGUCCAGU-3' (SEQ ID NO: 20), 5'-UCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 21), 5'-UUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 22), 5'- CUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 23), 5'-CCUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 24), or 5'- GCCUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 25).
7. The oligonucleotide of any one of claims 1 to 5, wherein the nucleotide sequence comprises the sequence as set forth in 5'-AGTCCAG-3', 5'-AAGTCCAG-3', 5'-CAAGTCCAG -3', 5'- CCAAGTCCAG-3' (SEQ ID NO: 26), 5'-TCCAAGTCCAG-3' (SEQ ID NO: 27), 5'- CTCCAAGTCCAG-3' (SEQ ID NO: 28), 5'-ACTCCAAGTCCAG-3' (SEQ ID NO: 29), 5'- GACTCCAAGTCCAG-3' (SEQ ID NO: 30), 5'-TGACTCCAAGTCCAG-3' (SEQ ID NO: 31), 5'- CTGACTCCAAGTCCAG-3' (SEQ ID NO: 32), 5'-TCTGACTCCAAGTCCAG-3' (SEQ ID NO: 33), 5'- TTCTGACTCCAAGTCCAG-3' (SEQ ID NO: 34), 5'- CTTCTGACTCCAAGTCCAG-3' (SEQ ID NO: 35), 5'-CCTTCTGACTCCAAGTCCAG-3' (SEQ ID NO: 36); 5'-AGTCCAGT-3', 5'-AAGTCCAGT-3', 5'-CAAGTCCAGT-3' (SEQ ID NO: 37), 5'-CCAAGTCCAGT-3' (SEQ ID NO: 38), 5'- TCCAAGTCCAGT-3' (SEQ ID NO: 39), 5'-CTCCAAGTCCAGT-3' (SEQ ID NO: 40), 5'- ACTCCAAGTCCAGT-3' (SEQ ID NO: 41), 5'-GACTCCAAGTCCAGT-3' (SEQ ID NO: 42), 5'- TGACTCCAAGTCCAGT-3' (SEQ ID NO: 43), 5'-CTGACTCCAAGTCCAGT-3' (SEQ ID NO: 44), 5'- TCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 45), 5'-TTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 46), 5'-CTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 47), 5'-CCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 48), or 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49).
8. The oligonucleotide of any one of claims 1 to 7, wherein the nucleotide sequence has at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% sequence identity to 5'-GCCUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 25) or 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49).
9. The oligonucleotide of claim 8, wherein the nucleotide sequence has at least 90% similarity to 5'-GCCUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 25) or 5'-GCCTTCTGACTCCAAGTCCAGT- 3' (SEQ ID NO: 49).
10. The oligonucleotide of claim 8 or 9, wherein the nucleotide sequence comprises the sequence as set forth in 5'-GCCUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 25) or 5'- GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49) with one substitution or two substitutions.
11. The oligonucleotide of any one of claims 1 to 10, wherein the nucleotide sequence comprises the sequence as set forth in 5'-GCCUUCUGACUCCAAGUCCAGU-3' (SEQ ID NO: 25) or 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49).
12. The oligonucleotide of claim 11, wherein the nucleotide sequence comprises the sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49).
13. The oligonucleotide of any one of claims 1 to 12, wherein the nucleic acid analog is a locked nucleic acid (LNA), an unlocked nucleic acid (UNA), an arabino nucleic acid (ABA), a bridged nucleic acid (BNA), or a peptide nucleic acid (PNA).
14. The oligonucleotide of any one of claims 1 to 13, wherein the nucleic acid analog comprises LNA.
15. The oligonucleotide of any one of claims 1 to 14, wherein the nucleic acid analog comprises 2'-O-alkyl-RNA, 2'-amino-DNA, 2'-fluoro-DNA, arabino nucleic acid (ANA), 2'-fluoro-ANA, hexitol nucleic acid (HNA), intercalating nucleic acid (INA), constrained ethyl nucleoside (cEt), 2'-O-methyl nucleic acid (2'-0Me), or 2'-O-methoxyethyl nucleic acid (2'-M0E).
16. The oligonucleotide of any one of claims 1 to 15, wherein the nucleic acid analog comprises a base modification.
17. The oligonucleotide of claim 16, wherein the base modification comprises a 5-methyl- pyrimidine nucleobase.
18. The oligonucleotide of any one of claims 1 to 17, wherein the nucleotide sequence is 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26 nucleotides in length.
19. The oligonucleotide of any one of claims 1 to 18, wherein the nucleotide sequence is a gapmer, a mixmer, a totalmer, or any combination thereof.
20. The oligonucleotide of any one of claims 1 to 19, wherein the nucleotide sequence comprises a backbone modification.
21. The oligonucleotide of claim 20, wherein the backbone modification is a phosphodiester linkage, a phosphotriester linkage, a methylphosphonate linkage, a phosphoramidate linkage, a phosphorothioate linkage, a phosphorodiamidate morpholino oligomer (PMO), or any combination thereof.
22. The oligonucleotide of claim 21, the nucleotide sequence comprises the sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49); wherein: the nucleotide sequence comprises one or more phosphorothioate linkages (SEQ ID NO: 55).
23. An oligonucleotide comprising, consisting essentially of, or consisting of the nucleotide sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein each of nucleotide residues 1, 2, 3, and 22 is a LNA; each of nucleotide residues 4-21 is a DNA (SEQ ID NO: 57).
24. The oligonucleotide of claim 23, wherein each of nucleotide residues 2 and 3 comprises a 5-methyl-pyrimidine nucleobase modification (SEQ ID NO: 56).
25. The oligonucleotide of claim 23 or 24, wherein the nucleotide sequence comprises one or more phosphorothioate linkages (SEQ ID NO: 58).
26. An oligonucleotide comprising, consisting essentially of, or consisting of the nucleotide sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49); wherein: the nucleotide sequence comprises a fully phosphorothioate modified backbone structure; each of nucleotide residues 1, 2, 3, and 22 is a LNA; each of nucleotide residues 4-21 is a DNA; and each of nucleotide residues 2 and 3 comprises a 5-methyl-pyrimidine nucleobase modification (SEQ ID NO: 50).
27. The oligonucleotide of claim 23, wherein each of nucleotide residues 2, 3, 6, 10, 12, 13, 18 and 19 comprise a 5-methyl-pyrimidine nucleobase modification (SEQ ID NO: 72).
28. The oligonucleotide of claim 27, wherein the nucleotide sequence comprises one or more phosphorothioate linkages (SEQ ID NO: 73).
29. An oligonucleotide comprising, consisting essentially of, or consisting of the nucleotide sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49); wherein: the nucleotide sequence comprises a fully phosphorothioate modified backbone structure; each of nucleotide residues 1, 2, 3, and 22 is a LNA; each of nucleotide residues 4-21 is a DNA; and each of nucleotide residues 2, 3, 6, 10, 12, 13, 18 andl9 comprises a 5-methyl-pyrimidine nucleobase modification (SEQ ID NO: 67).
30. An oligonucleotide comprising, consisting essentially of, or consisting of the nucleotide sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49), wherein each of nucleotide residues 1, 2, 3, 4, 5, 18, 19, 20, 21, and 22 is a LNA; each of nucleotide residues 4-21 is a DNA (SEQ ID NO: 74).
31. The oligonucleotide of claim 30, wherein each of nucleotide residues 2, 3, 6, 10, 12, 13, 18, and 19comprises a 5-methyl-pyrimidine nucleobase modification (SEQ ID NO: 75).
32. The oligonucleotide of claim 30 or 31, wherein the nucleotide sequence comprises one or more phosphorothioate linkages (SEQ ID NO: 76 and 77).
33. An oligonucleotide comprising, consisting essentially of, or consisting of the nucleotide sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49); wherein: the nucleotide sequence comprises a fully phosphorothioate modified backbone structure; each of nucleotide residues 1, 2, 3, 4, 5, 18, 19, 20, 21, and 22 is a LNA; each of nucleotide residues 6-17 is a DNA; and each of nucleotide residues 2, 3, 6, 10, 12, 13, 18 and 19 comprises a 5-methyl-pyrimidine nucleobase modification (SEQ ID NO: 70).
34. The oligonucleotide of any one of claims 1 to 33, wherein the oligonucleotide is formulated to be delivered to a tissue, wherein the tissue comprises liver tissue, brain tissue, kidney tissue, lung tissue, ovary tissue, pancreas tissue, thyroid tissue, breast tissue, stomach tissue, or any combination thereof.
35. The oligonucleotide of claim 34, wherein the tissue is liver tissue.
36. The oligonucleotide of any one of claims 1 to 35, wherein the oligonucleotide is conjugated to a targeting moiety.
37. The oligonucleotide of claim 36, wherein the targeting moiety is linked to the oligonucleotide by a linker.
38. The oligonucleotide of any one of claims 1 to 37, wherein the linker comprises a non- cleavable linker.
39. The oligonucleotide of claim 37 or 38, wherein the linker comprises a cleavable linker.
40. The oligonucleotide of claim 39, wherein the cleavable linker comprises cleavable by a protease.
41. The oligonucleotide of claim 37, wherein the linker comprises a bioreducible linker, an acid cleavable linker, a click-to-release linker, a pyrophosphatase cleavable linker, a betaglucuronidase cleavable linker, or any combination thereof.
42. A pharmaceutical composition comprising the oligonucleotide of any one of claims 1 to 41 and a pharmaceutically acceptable carrier.
43. A method of preparing an oligonucleotide targeting miRNA 378a-3p comprising mixing nucleic acids to form the oligonucleotide of any one of claims 1 to 41 or the pharmaceutical composition of claim 42.
44. The method of claim 43, further comprising purifying the oligonucleotide.
45. A method of treating a disease or condition in a subject in need thereof comprising administering the oligonucleotide of any one of claims 1 to 41 or the pharmaceutical composition of claim 44 to the subject.
46. The method of claim 45, wherein the disease or condition is cirrhosis, type 2 diabetes mellitus, hepatitis, fibrosis, fibrosis of the liver, obesity (e.g., abdominal obesity), dyslipidemia (hypercholesterolemia, hypertriglyceridemia), atherosclerosis, type 2 diabetes (T2D), hepatocellular carcinoma (HCC), hypertension, polycystic ovary syndrome (PCOS), chronic kidney disease (CKD), or cardiovascular disease (CVD).
47. The method of claim 46, wherein the disease or condition is a liver disease or condition.
48. The method of claim 47, wherein the liver disease or condition is metabolic dysfunction- associated fatty liver disease (MAFLD) or metabolic dysfunction-associated steatohepatitis (MASH).
49. A method of treating metabolic dysfunction-associated fatty liver disease (MAFLD) or metabolic dysfunction-associated steatohepatitis (MASH) in a subject in need thereof comprising administering the oligonucleotide of any one of claims 1 to 41 or the pharmaceutical composition of claim 42 to the subject.
50. A method of treating metabolic dysfunction-associated fatty liver disease (MAFLD) or metabolic dysfunction-associated steatohepatitis (MASH) in a subject in need thereof comprising administering an oligonucleotide comprising, consisting essentially of, or consisting of the nucleotide sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49); wherein: the nucleotide sequence comprises a fully phosphorothioate modified backbone structure; each of nucleotide residues 1, 2, 3, and 22 is a LNA; each of nucleotide residues 4-21 is a DNA; and each of nucleotide residues 2 and 3 comprises a 5-methyl-pyrimidine nucleobase modification (SEQ ID NO: 50).
51. A method of treating metabolic dysfunction-associated fatty liver disease (MAFLD) or metabolic dysfunction-associated steatohepatitis (MASH) in a subject in need thereof comprising administering an oligonucleotide comprising, consisting essentially of, or consisting of the nucleotide sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49); wherein: the nucleotide sequence comprises a fully phosphorothioate modified backbone structure; each of nucleotide residues 1, 2, 3, 4, 5, 18, 19, 20, 21, and 22 is a LNA; each of nucleotide residues 6-17 is a DNA; and each of nucleotide residues 2, 3, 6, 10, 12, 13, 18, and 19 comprises a 5-methyl-pyrimidine nucleobase modification (SEQ ID NO: 70).
52. A method of treating metabolic dysfunction-associated fatty liver disease (MAFLD) or metabolic dysfunction-associated steatohepatitis (MASH) in a subject in need thereof comprising administering an oligonucleotide comprising, consisting essentially of, or consisting of the
nucleotide sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49); wherein: the nucleotide sequence comprises a fully phosphorothioate modified backbone structure; each of nucleotide residues 1, 2, 3, and 22 is a nucleic acid comprising a LNA; each of nucleotide residues 4-21 is a DNA; and each of nucleotide residues 2, 3, 6, 10, 12, 13, 18, and 19 comprises a 5-methyl-pyrimidine (SEQ ID NO: 67).
53. A method of treating cirrhosis, type 2 diabetes mellitus, hepatitis, fibrosis, fibrosis of the liver, obesity (e.g., abdominal obesity), dyslipidemia (hypercholesterolemia, hypertriglyceridemia), atherosclerosis, type 2 diabetes (T2D), hepatocellular carcinoma (HCC), hypertension, polycystic ovary syndrome (PCOS), chronic kidney disease (CKD), or cardiovascular disease (CVD) in a subject in need thereof comprising administering an oligonucleotide comprising a miR-378a-3p inhibitor.
54. A method of treating obesity (e.g., abdominal obesity) in a subject in need thereof comprising administering the oligonucleotide of any one of claims 1 to 41 or the pharmaceutical composition of claim 42 to the subject.
55. A method of treating obesity (e.g., abdominal obesity) in a subject in need thereof comprising administering an oligonucleotide comprising, consisting essentially of, or consisting of the nucleotide sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49); wherein: the nucleotide sequence comprises a fully phosphorothioate modified backbone structure; each of nucleotide residues 1, 2, 3, and 22 is a LNA; each of nucleotide residues 4-21 is a DNA; and each of nucleotide residues 2 and 3 comprises a 5-methyl-pyrimidine nucleobase modification (SEQ ID NO: 50).
56. A method of treating obesity (e.g., abdominal obesity) in a subject in need thereof comprising administering an oligonucleotide comprising, consisting essentially of, or consisting of the nucleotide sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49); wherein: the nucleotide sequence comprises a fully phosphorothioate modified backbone structure; each of nucleotide residues 1, 2, 3, 4, 5, 18, 19, 20, 21, and 22 is a LNA;
each of nucleotide residues 6-17 is a DNA; and each of nucleotide residues 2, 3, 6, 10, 12, 13, 18, and 19 comprises a 5-methyl-pyrimidine nucleobase modification (SEQ ID NO: 70).
57. A method of treating obesity (e.g., abdominal obesity) in a subject in need thereof comprising administering an oligonucleotide comprising, consisting essentially of, or consisting of the nucleotide sequence as set forth in 5'-GCCTTCTGACTCCAAGTCCAGT-3' (SEQ ID NO: 49); wherein: the nucleotide sequence comprises a fully phosphorothioate modified backbone structure; each of nucleotide residues 1, 2, 3, and 22 is a nucleic acid comprising a LNA; each of nucleotide residues 4-21 is a DNA; and each of nucleotide residues 2, 3, 6, 10, 12, 13, 18, and 19 comprises a 5-methyl-pyrimidine (SEQ ID NO: 67).
58. A method of reducing a body weight or inducing a weight loss in a subject in need thereof comprising administering the oligonucleotide of any one of claims 1 to 41 to the subject.
59. The method of any one of claims 45 to 58, wherein the subject loses body fat mass at a higher percentage than lean muscle mass.
60. The method of claim 59, wherein the subject loses body fat mass at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least aout 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or about 100% more than lean muscle mass.
61. The method of any one of claims 45 to 60, wherein the subject reduces body fat mass without changing lean muscle mass.
62. The method of any one of claims 45 to 61, wherein the subject reduces hepatic steatosis and/or lipid accumulation.
63. The method of any one of claims 45 to 62, wherein the subj ect reduces white adipose tissue (WAT) and/or visceral fat.
64. The method of any one of claims 45 to 63, wherein the subject does not significantly lose brown adipose tissue.
65. The method of any one of claims 45 to 64, wherein the oligonucleotide or the pharmaceutical composition is administered orally, parenterally, intrathecally, intra- cerebroventricularly, pulmonarily, subcutaneously, intravenously, topically, or intraventricularly.
66. The method of any one of claims 45 to 65, wherein the oligonucleotide or the pharmaceutical composition is administered subcutaneously or intravenously.
67. The method of any one of claims 45 to 66, wherein the subject is a mammal.
68. The method of any one of claims 45 to 67, wherein the subject is a human.
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| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO2012145374A1 (en) * | 2011-04-19 | 2012-10-26 | Regulus Therapeutics Inc. | TARGETING miR-378 FAMILY MEMBERS FOR THE TREATMENT OF METABOLIC DISORDERS |
| US20130150427A1 (en) * | 2010-06-04 | 2013-06-13 | Board Of Regents, The University Of Texas System | Regulation of metabolism by mir-378 |
| US20180127755A1 (en) * | 2007-10-29 | 2018-05-10 | Regulus Therapeutics Inc. | Targeting micrornas for the treatment of liver cancer |
| US20180273944A1 (en) * | 2012-06-21 | 2018-09-27 | MiRagen Therapeutics, Inc. | Oligonucleotide-based inhibitors comprising locked nucleic acid motif |
| US20200071698A1 (en) * | 2018-08-29 | 2020-03-05 | Korea Institute Of Science And Technology | Therapeutic agent for treating cancer comprising anti-mirna-albumin composite |
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| US20180127755A1 (en) * | 2007-10-29 | 2018-05-10 | Regulus Therapeutics Inc. | Targeting micrornas for the treatment of liver cancer |
| US20130150427A1 (en) * | 2010-06-04 | 2013-06-13 | Board Of Regents, The University Of Texas System | Regulation of metabolism by mir-378 |
| WO2012145374A1 (en) * | 2011-04-19 | 2012-10-26 | Regulus Therapeutics Inc. | TARGETING miR-378 FAMILY MEMBERS FOR THE TREATMENT OF METABOLIC DISORDERS |
| US20180273944A1 (en) * | 2012-06-21 | 2018-09-27 | MiRagen Therapeutics, Inc. | Oligonucleotide-based inhibitors comprising locked nucleic acid motif |
| US20200071698A1 (en) * | 2018-08-29 | 2020-03-05 | Korea Institute Of Science And Technology | Therapeutic agent for treating cancer comprising anti-mirna-albumin composite |
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