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  • C12N15/1135—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 against oncogenes or tumor suppressor genes
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Definitions

• Acute myeloid leukemia is characterized by accumulation of immature myeloid progenitor cells.
• Leukemogenesis results from deregulation of oncogenes, tumor suppressors or transcription factors which control myeloid lineage differentiation, self -renewal and/or proliferation.
• the transcription factor CCAAT/enhancer binding protein alpha (C/EBPa) promotes differentiation of granulocyte and macrophages and negatively regulates hematopoietic stem cell self-renewal.
• C/EBPa transcription factor CCAAT/enhancer binding protein alpha
• C/EBPa is substituted by transcriptional activity of C/ ⁇ and STAT3 transcription factors. Mutations or down-regulation of C/EBPa are frequently observed in patients with AML.
• Short activating RNAs are capable of inducing gene expression.
• a factor in the clinical application of saRNA and other oligonucleotide therapeutics is difficulty in their targeted delivery, additionally complicated by the inherent sensitivity of the immune system to nucleic acids.
• STAT3 operates in both cancer cells and non-malignant tumor-associated cells.
• targeting transcription factors such as STAT3 is complicated by their lack of enzymatic activity and requires non-pharmacologic approaches.
• Antisense technology for suppressing STAT3 has limited effect because available antisense oligonucleotides lack cell selectivity.
• the present disclosure relates to compounds, compositions, and methods of treating cancer, e.g.
• the present disclosure also relates to compounds, compositions, and methods of treating cancer, e.g. , prostate cancer and glioblastoma with antisense oligonucleotides conjugated to phosphorothioated
• the current disclosure provides, inter alia, an isolated compound including a phosphorothioated oligodeoxynucleotide (ODN) conjugated to an oligonucleotide for modulating expression of a target gene.
• ODN phosphorothioated oligodeoxynucleotide
• the present disclosure includes an isolated compound including a phosphorothioated oligodeoxynucleotide (ODN), conjugated to an antisense nucleic acid sequence or to a short-activating RNA (saRNA) of a gene of interest.
• the ODN is a 15 to 30 bases long, single-stranded, partly or completely phosphorothioated oligodeoxynucleotide.
• the compound of the present disclosure include a short- activating RNA (saRNA) for enhancing gene expression, or an antisense sequence for suppressing gene expression.
• saRNA short- activating RNA
• the present disclosure includes a method of treating cancer in a subject with the compound or a composition including the compound, with or without stimulating an immune response in a subject with a compound or a composition including a compound of the present disclosure.
• the present disclosure includes a method of enhancing C/EBPa expression in a cell with a compound or a composition including a compound including saRNA of C/EBPa conjugated to a phosphorothioated oligonucleotide of the present disclosure.
• the present disclosure includes a method of suppressing expression of transcription factor Signal Transducer and Activator of
• STAT Transcription
• STAT1 - STAT6 with a compound or a composition including a compound including an antisense oligonucleotide (ASO) of one or more of STAT1 - STAT6 conjugated to a phosphorothioated oligonucleotide of the present disclosure.
• ASO antisense oligonucleotide
• the present disclosure includes a method of inhibiting cell growth by contacting the cell with an effective amount of the compound or a composition including the compound.
• the short- activating RNA is capable of activating a CCAAT/enhancer- binding protein-a (C/EBPa).
• the method includes treating myeloma, acute myeloid leukemia, prostate cancer, breast cancer, glioblastoma, ovarian cancer, lung cancer, head and neck cancer, esophageal cancer, skin cancer, melanoma, brain cancer, colorectal cancer, leukemia, or lymphoma.
• the composition may be administered to the subject by intravenous, parenteral, subcutaneous, intramuscular, transdermal, intraperitoneal, intranasal, aerosol, oral, or topical administration.
• FIG. 1A depicts a conjugate sequence comprising SEQ ID NO: 103 and duplex strand SEQ ID NO:2.
• FIG. 1A depicts a conjugate sequence comprising SEQ ID NO: 103 and duplex strand SEQ ID NO:2.
• IB depicts a conjugate sequence comprising SEQ ID NO: 104 and duplex strand SEQ ID NO: 105.
• FIG. 1C depicts a conjugate sequence comprising SEQ ID NO: 103.
• FIG. ID depicts a conjugate sequence comprising SEQ ID NO: 104.
• FIG. IE depicts a conjugate sequence comprising SEQ ID NO: 106 and duplex strand SEQ ID NO: 107.
• FIG. IF depicts a conjugate sequence comprising SEQ ID NO: 108 and duplex strand SEQ ID NO: 109.
• FIGs. 2A and 2B are bar graphs of mRNA expression levels measured by real-time quantitative PCR (qPCR).
• FIGs. 2C and 2D are western blot images of protein expression levels.
• Fresh bone marrow cells isolated from wild-type (WT) or TLR9-deficient (TLR9KO) mice were incubated in the process of 500 nM of various CpG-saRNA conjugates or transfected with 50 nM of unconjugated saRNA using Lipofectamine 2000.
• the mRNA and protein levels of C/EBPa were measured using qPCR (FIGs. 2A-2B) and western blotting (FIGs. 2C-2D), respectively.
• FIG. 3 shows bar graphs showing CpG-CEBPA saRNA triggers transcriptional activity of C/EBPa in target human cancer cells.
• Human DU145 prostate cancer cells expressing C/EBPa-specific promoter-luciferase construct were incubated in the presence of 500 nM of various CpG-saRNA conjugates or transfected with 50 nM of unconjugated saRNA using Lipofectamine 2000 as indicated; CpG-FLUC-RNA conjugates with a sequence matching firefly luciferase were used as a negative control. 72 h later cells were lysed and analyzed levels using Cignal C/EBP Reporter Assay Kit (Qiagen).
• FIGs. 4A and 4B show bar graphs human DU145 prostate cancer cells
• MOLM13 leukemia cell respectively in an assay to show TLR9-dependent effect of CpG- CEBPA saRNA on the C/EBPa mRNA and protein levels in human and mouse cells.
• Human DU145 prostate cancer cells (FIG. 4A) and MOLM13 leukemia cells (FIG. 4B) were incubated in the process of 500 nM of various CpG-saRNA conjugates or transfected with 50 nM of unconjugated saRNA using Lipofectamine 2000; CpG-FLUC-RNA conjugates with a sequence matching firefly luciferase were uses as a negative control. 72 hours later cells were lysed to isolated RNA for the analysis of CEBPA mRNA levels using real-time quantitative PCR (qPCR).
• qPCR real-time quantitative PCR
• FIGs. 5A-5C are flow cytometry spectra of Human MV4-11 AML cells incubated with 500 nM CpG-CEBPA saRNA or transfected with CEBP saRNA alone in vitro for 48 h.
• the expression of HLADR and costimulatory molecules CD86 and CD40 was assessed using flow cytometry.
• FIGs. 6A-6B show line graphs and flow-cytometry data of dose-dependent effect of CpG-CEBPA saRNA on syngeneic leukemia cells in mice. After Cbfb/MYHl 1/Mpl leukemia was established (>1%, ranging 1-5% of AML cells in blood), C57BL/6 mice were injected twice using various doses of CpG-CEBPA saRNA every other day and euthanized one day after last treatment.
• FIG. 6A shows line graphs of percentages of AML cells in peripheral blood were assessed using flow cytometry before and after treatment.
• 6B shows flow cytometry spectrums showing CpG-CEBPA saRNA treatment reduces the percentage of AML cells in bone marrow and spleen in dose-dependent manner. Shown are representative results of the flow cytometric analysis of GFP+c-Kit+ AML cells in various organs.
• FIGs. 7A-7B show flow cytometry and histrograms data of intravenous injection of CpG-CEBPA saRNA inducing target gene expression in AML cells in the bone marrow. Mice with established Cbfb/MYHl 1/Mpl leukemia were injected three times every other day using 1 mg/kg of CpG-CEBPA saRNA and euthanized one day after last treatment.
• FIG. 7 A shows representative results of flow cytometry;
• FIG. 7B shows bar graphs of the levels of CEBPA mRNA were measured in c-Kit+AML cells enriched from the bone marrow using real-time qPCR.
• FIGs. 7A-7B show flow cytometry and histrograms data of intravenous injection of CpG-CEBPA saRNA inducing target gene expression in AML cells in the bone marrow. Mice with established Cbfb/MYHl 1/Mpl leukemia were injected three
• FIGS. 8A-8B show line graphs and flow cytometry data of intravenous injections of CpG-CEBPA saRNA induce target gene expression in AML cells in the bone marrow.
• Mice with established Cbfb/MYHl 1/Mpl leukemia were injected four times every other day using 5 mg/kg of CpG-CEBPA saRNA and euthanized one day after last treatment ( day 20).
• FIG. 8A shows line graphs of percentages of AML cells in peripheral blood assessed using flow cytometry before, during and after treatment.
• FIG. 8B shows flow cytometric analysis of AML percentages in peripheral blood, bone marrow and spleen at the end of experiment.
• FIGs. 9A-9C show exemplary sequence design and PAGE gel data of CpG-STAT3 ASO conjugates.
• An example of the single- stranded CpG-STAT3 ASO design is shown in FIG. 9A.
• Phosphorothioated nucleotides are underlined; (CH 2 )3 units of the carbon linker are in blue; 2'OMe-modified nucleotides in the gapmer sequence of STAT3AS02 are in red.
• CpG-STAT3AS02 (FIG. 9B) and CpG-STAT3AS04 (FIG. 9C) conjugates were incubated in 50% human serum at 37C for up to 5 days. The samples were then resolved on 7.5M Urea/20% PAGE gel and stained using ethidium bromide; the representative gel images are shown; M indicates position of DNA marker.
• FIGs. 10A-10B show flow cytometry data of CpG-STAT3 ASO Cy3 by human immune and prostate cancer cells in vitro.
• Human prostate cancer cells FIG. 10A
• splenocytes FIG. 10B
• CpG-STAT3 ASO Cy3 was rapidly internalized by mouse immune and prostate cancer cells in vitro.
• FIGs. 1 lA-1 IB show flow cytometry data of CpG-STAT3 ASO Cy3 by mouse immune and prostate cancer cells in vitro.
• Mouse prostate cancer cells (FIG. 11 A) and splenocytes (FIG. 1 IB) were incubated with the indicated concentrations of fluorescently- labeled CpG-STAT3 ASO Cy3 for one hour without any transfection reagents.
• the oligonucleotide uptake by cancer cells, dendritic cells (DCs; CDl lc), macrophages (MAC; F4/80+Grl-), B cells (B220+CDl lc-) and T cells (CD3+) was assessed using flow cytometry.
• CpG-STAT3 ASO Cy3 was rapidly internalized by mouse immune and prostate cancer cells in vitro.
• FIGs. 12A-12D shows confocal microscopy images showing the intracellular localization of CpG-STAT3 ASO Cy3 after uptake by prostate cancer cells in vitro.
• DU-145 prostate cancer cells were incubated with 500 nM of fluorescently-labeled CpG-STAT3 ASO Cy3 at different times, as indicated (15 min (FIG. 12A) 1 hour (FIG. 12B), 2 hours (FIG. 12C), and 4 hours (FIG. 12D)).
• the intracellular localization of the conjugate was assessed using confocal microscopy after nuclear staining with DRAQ5 ® . Representative images from one of two independent experiments are shown.
• FIGs. 13A-13D are bar graphs and expression data showing that CpG-STAT3 ASO Cy3 induced potent STAT3 knockdown in androgen-independent DU-145 (FIG. 13 A) and LNCaP-S17 (FIG. 13B) prostate cancer cells.
• DU-145 (FIG. 13A) and LNCaP-S17 (FIG. 13B) prostate cancer cells were incubated in vitro for 24 hours with 500 nM of various CpG/GpC-STAT3ASOs, unconjugated STAT3ASOs or non-targeting CpG-scrambled ODN.
• FIG. 13C shows dose-dependent effect of CpG-STAT3ASO compared to the unconjugated STAT3ASO on prostate cancer cells.
• DU145 cells were treated using different concentration of STAT3 ASO (left panel) or CpG-STAT3ASO (right panel) before analyzing STAT3 mRNA levels using qPCR assay.
• FIG. 13D shows CpG-STAT3ASO induced a faster STAT3 knock-down than STAT3 ASO alone.
• Cells were treated with 500 nM of CpG-STAT3 ASO, unconjugated STAT3ASO or the negative control CpG-STAT3SSO for 24 or 48 h, as indicated.
• the activation and protein levels of STAT3 were assessed using Western blotting; ⁇ -actin was used as a loading control.
• FIGs. 14A-14B are flow cytometry data showing that CpG-STAT3ASO conjugates were more effective than the STAT3ASO alone in the induction of apoptosis in prostate cancer cells in vitro.
• Cells DU-145 (FIG. 14A), and LNCaP S17 (FIG. 14B)
• CpG-scrambled ODN CpG-scbODN
• the percentages of apoptotic cells were measured using flow cytometry after staining for 7AAD and Annexin V.
• FIGs. 15A-15C show flow cytometry data of the in vivo biodistribution of systemically injected CpG-STAT3ASO Cy3 .
• C57BL/6 mice were injected intravenously using 5 mg/kg of Cy3-labeled CpG-STAT3 ASO Cy3 and euthanized 3 hours later.
• FIG. 15A-15C show flow cytometry data of the in vivo biodistribution of systemically injected CpG-STAT3ASO Cy3 .
• C57BL/6 mice were injected intravenously using 5 mg/kg of Cy3-lab
• 15C shows C57BL/6 mice with established RM9 prostate tumors were injected intravenously using 2.5 mg /kg of Cy3-labeled CpG-STAT3 ASO Cy3 and euthanized 3 h later.
• FIGs. 16A-16C are flow cytometry data and bar graphs showing that CpG-STAT3 ASO conjugates effectively targeted STAT3 and reduced viability of TLR+ B cell lymphoma.
• FIG. 16A shows flow cytometry data of Non-Hodgkin' s lymphoma B cells incubated with 500 nM of fluorescently-labeled CpG-STAT3 ASO Cy3 for one hour without any transfection reagents. The oligonucleotide uptake was measured using flow cytometry.
• FIG. 16B is a bar graph showing the expression of STAT3 mRNA measured using quantitative real-time PCR (Taqman).
• FIG. 16C is a bar graph showing results of OCI-Ly3 cells treated daily with 500 nM of CpG-STAT3ASO for 3 days. Their viability was measured using an XTT (second generation tetrazolium dye; (2,3-bis-(2-methoxy-4-nitro-5- sulfophenyl)-2H-tetrazolium-5-carboxanilide) ) assay; results from one of two independent experiments in triplicates is shown; means +/- SEM.
• XTT second generation tetrazolium dye; (2,3-bis-(2-methoxy-4-nitro-5- sulfophenyl)-2H-tetrazolium-5-carboxanilide
• FIGs. 17A-17C are flow cytometry data and bar graphs showing microglia and glioma cell-specific uptake and STAT3 inhibition by CpG-STAT3ASO.
• Mouse TLR9+ BV2 and K-luc cells (FIG. 17A) and human primary glioma stem-like cells (FIG. 17B) quickly internalize CpG-STAT3ASO and to lesser extent the unconjugated STAT3ASO in vitro (250 nM/1 h).
• Cells were incubated with 250 nM CpG-STAT3ASO Alexa488 or unconjugated STAT3ASO Alexa488 for indicated times and percentages of Alexa488-positive cells were measured using flow cytometry.
• FIG. 17C shows CpG-STAT3ASO induces potent and rapid knockdown of STAT3 at mRNA and protein levels in primary human glioma stem-like cells. Shown are representative results of real time qPCR for STAT3 mRNA levels.
• FIGs. 18A-18C are bar graphs and flow cytometry data showing biodistribution of CpG-STAT3 inhibitors in glioma-bearing mice after administration using various routes of delivery.
• FIG. 18A shows biodistribution studies of fluorescently labeled CSIs demonstrate cell- selective oligonucleotide uptake by TLR9+ GL261 glioma and myeloid cells
• FIG. 18B shows representative dot plots showing gating strategy and levels of fluorescent signal in various tested cell populations isolated from IV injected animals.
• FIG. 18C shows intracranial/IT injections of CpG-STAT3ASO induced STAT3 knockdown in GL261 tumors in vivo.
• FIGs. 19A-19E shows that local administration of the CpG-STAT3ASO reduces tumor growth in the distant location and inhibits PD-L1 immune checkpoint regulation.
• FIG. 19A shows anti-tumor effect of CpGSTAT3ASO conjugated in vivo is more pronounced than STAT3ASO alone.
• FIG. 19B shows that CpG-STAT3ASO but not STAT3ASO inhibits STAT3 expression in distant, untreated site. Levels of STAT3 mRNA were assessed using qPCR in whole RM9 tumors harvested from differently treated mice.
• FIGs 19C - 19D shows CpG-STAT3ASO reduces STAT3 activation (FIG. 19C) and PD-L1 immune checkpoint expression (FIG. 19D) on tumor- infiltrating myeloid derived suppressor cells (MDSCs).
• FIGs 19C - 19D shows CpG-STAT3ASO reduces STAT3 activation (FIG. 19C) and PD-L1 immune checkpoint expression (FIG. 19D) on tumor- infiltrating myeloid derived suppressor cells (MDSCs).
• Levels of pSTAT3 (right panels) and PD-L1 surface expression (left panels) were assessed by flow cytometry in MDSCs
• FIG. 19E shows that CpG-STAT3ASO but not STAT3ASO inhibits STAT3 expression in distant, untreated site. Levels of STAT3 mRNA were assessed using qPCR in whole RM9 tumors harvested from differently treated mice.
• FIGs. 20A-20B are images (FIG. 20 A) and flow cytometry data (FIG. 20B) showing that intravenous administration of the CpG-STAT3ASO results in complete regression of the experimental bone metastatic model of RM9 prostate cancer.
• RM9 prostate cancer cells were injected intratibially in C57BL/6 mice. Animals with established tumors were treated using daily i.v. injections 5 mg/kg of CpG-STAT3 ASO conjugated, STAT3 ASO alone or CpG-scrambled ASO for up to 15 days. Tumor burden and mice condition were monitored using the bioluminescent imaging (BLI) on AmiX (Spectral) imaging system or body condition scoring (BCS), respectively (FIG. 20A).
• BLI bioluminescent imaging
• AmiX Spectral
• BCS body condition scoring
• FIG. 21 shows that the two pronged action of CpG-STAT3ASO inhibitors can augment therapeutic efficacy of human cancer immunotherapies.
• TLR9 is expressed not only by tumor-associated myeloid cells (macrophages, microglia and G-MDSCs) but also certain cancer cells (tumor-propagating cells).
• Treatment-induced cancer cell death e.g. after CAR T cell treatment or radiation therapy
• leads to release of TLR9 ligands which indirectly activating STAT3 in the tumor microenvironment.
• TLR9/STAT3 signaling inhibits macrophages/microglia differentiation, while stimulating angiogenesis and suppressing immune responses.
• STAT3 activation in tumor-propagating cells supports cancer self-renewal and resistance to therapies.
• CSIs allows for targeting of STAT3 in both TLR9+ cell compartments thereby enhancing overall therapeutic efficacy.
• isolated compound targeting moieties and antisense oligonucleotides.
• isolated compounds include a phosphorothioated
• ODN oligodeoxynucleotide nucleic acid sequence conjugated to short- activating RNAs (saRNA) or an antisense oligonucleotide (ASO).
• saRNA and/or the ASO may be modified with 2' OMe, locked nucleic acid.
• the term "short activating RNAs (saRNAs)" is used according to its plain and ordinary meaning and refers to RNA that is capable of activating or inducing gene expression.
• Gene specific saRNAs target sequences in the promoter of a target gene and induce expression of the gene.
• the saRNA oligomer may be a double stranded oligomer of 15-30 bases.
• the saRNA oligomer may be partially double stranded, with single stranded overhangs (see, e.g. , FIGs. 1A-1F).
• the double strand includes a guide strand (antisense, AS) and a passenger strand (sense strand, SS).
• the saRNA may target regions between nucleotides -75 to +25 relative to a transcription start site of a target gene.
• the oligomer may have a 2'chemical modification.
• the oligomer may have serum stability-enhancing chemical modification, e.g. , a phosphothioate internucleotide linkage, a 2'-0-methyl ribonucleotide, a 2'-deoxy-2'fluoro ribonucleotide, a 2'-deoxy ribonucleotide, a universal base nucleotide, a 5-C methyl nucleotide, an inverted deoxybasic residue incorporation, or a locked nucleic acid.
• antisense oligonucleotide As used herein antisense oligonucleotide (ASO) is used according to its plain and ordinary meaning and refers to an oligonucleotide that targets a transcript of a gene to reduce expression of the gene product.
• the antisense oligonucleotide is an anti- Gene X antisense oligonucleotide sequence.
• an ASO of STAT can be referred to as an "anti-STAT antisense oligonucleotide sequence.
• Anti-STATl oligonucleotide is an oligonucleotide that reduces or inhibits translation level of messenger RNA (mRNA) of Signal transducer and activator of transcription 1 (STAT1) transcription factor, which in humans is encoded by the STAT1 gene. It is a member of the STAT protein family.
• Anti- STAT2 oligonucleotide is an oligonucleotide that reduces or inhibits translation level of messenger RNA (mRNA) of Signal transducer and activator of transcription 2 (STAT2).
• Anti-STAT3 oligonucleotide is an oligonucleotide that reduces or inhibits translation level of messenger RNA (mRNA) of Signal transducer and activator of transcription 3 (STAT3).
• Anti-STAT4 oligonucleotide is an oligonucleotide that reduces or inhibits translation level of messenger RNA (mRNA) of Signal transducer and activator of transcription 4 (STAT4).
• Anti-STAT5A oligonucleotide is an oligonucleotide that reduces or inhibits translation level of messenger RNA (mRNA) of Signal transducer and activator of transcription 5A
• Anti-STAT5B oligonucleotide is an oligonucleotide that reduces or inhibits translation level of messenger RNA (mRNA) of Signal transducer and activator of transcription 5B (STAT5B).
• Anti-STAT6 oligonucleotide is an oligonucleotide that reduces or inhibits translation level of messenger RNA (mRNA) of Signal transducer and activator of transcription 6 (STAT6).
• the oligomer may have a 2'chemical modification.
• the oligomer may have serum stability-enhancing chemical modification, e.g. , a phosphothioate intemucleotide linkage, a 2'-0-methyl ribonucleotide, a 2'-deoxy-2'fluoro ribonucleotide, a 2'-deoxy ribonucleotide, a universal base nucleotide, a 5-C methyl nucleotide, an inverted deoxybasic residue incorporation, or a locked nucleic acid (LNA).
• serum stability-enhancing chemical modification e.g. , a phosphothioate intemucleotide linkage, a 2'-0-methyl ribonucleotide, a 2'-deoxy-2'fluoro ribonucleotide, a 2'-deoxy ribonucleotide, a universal base nucleotide, a 5-C methyl nucleotide, an inverted deoxybasic residue incorporation,
• phosphorothioated oligodeoxynucleotide refers to a nucleic acid sequence, e.g. , "CpG nucleic acid sequence", “GpC nucleic acid sequence” or “PS (phosphorothioated) nucleic acid sequence” in which some or all the intemucleotide linkages constitute a phosphorothioate linkage.
• phosphorothioated oligodeoxynucleotide (ODN) is 15 to 30 bases long, single-stranded, and/or partly or completely phosphorothioated.
• the partly phosphorothioated ODN may be an ODN in which 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, or 28, intemucleotide linkages constitute a phosphorothioate linkage.
• phosphorothioation can be in string on 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or all nucleotides. In embodiments, some oligodeoxynucleotides are not phosphorothioated.
• CpG nucleic acid sequence refers to nucleic acid including a CpG motif in which a 5' C nucleotide connected to a 3' G nucleotide through a phosphodiester intemucleotide linkage or a phosphodiester derivative intemucleotide linkage.
• a CpG motif includes a phosphodiester intemucleotide linkage.
• a CpG motif includes a phosphodiester derivative intemucleotide linkage.
• a CpG motif includes a phosphorothioate linkage.
• GpC nucleic acid sequence refers to nucleic acid including a GpC motif in which a 5' G nucleotide connected to a 3' C nucleotide through a phosphodiester intemucleotide linkage or a phosphodiester derivative intemucleotide linkage.
• a GpC motif includes a phosphodiester intemucleotide linkage.
• a GpC motif includes a phosphodiester derivative internucleotide linkage.
• a GpC motif includes a phosphorothioate linkage.
• oligonucleotide e.g., CpG-ODN or GpC-ODN
• all internuclotide linkage are phosphorothioate linkages.
• Class A CpG ODN or "A-class CpG ODN” or “D-type CpG ODN” or “Class A CpG DNA sequence” is used in accordance with its common meaning in the biological and chemical sciences and refers to a CpG motif including oligodeoxynucleotide having one or more of a poly-G sequence at the 5', 3' , or both ends; an internal palindrome sequence including CpG motif; having one or more phosphodiester derivatives linking deoxy nucleotides.
• a Class A CpG ODN includes poly-G sequence at the 5' , 3' , or both ends; an internal palindrome sequence including CpG motif; and one or more phosphodiester derivatives linking deoxynucleotides.
• the phosphodiester derivative is phosphorothioate.
• Examples of Class A CpG ODNs include ODN D19, ODN 1585, ODN 2216, and ODN 2336.
• Class B CpG ODN or "B-class CpG ODN” or “K-type CpG ODN” or “Class B CpG DNA sequence” is used in accordance with its common meaning in the biological and chemical sciences and refers to a CpG motif including oligodeoxynucleotide including one or more of a 6mer motif including a CpG motif;
• a Class B CpG phosphodiester derivatives linking all deoxynucleotides.
• a Class B CpG phosphodiester derivatives linking all deoxynucleotides.
• ODN includes one or more copies of a 6mer motif including a CpG motif and phosphodiester derivatives linking all deoxynucleotides.
• the phosphodiester derivative is phosphorothioate.
• a Class B CpG ODN includes one 6mer motif including a CpG motif.
• a Class B CpG ODN includes two copies of a 6mer motif including a CpG motif.
• a Class B CpG ODN includes three copies of a 6mer motif including a CpG motif.
• a Class B CpG ODN includes four copies of a 6mer motif including a CpG motif. Examples of Class B CpG ODNs include ODN 1668, ODN 1826, ODN 2006, and ODN 2007.
• Class C CpG ODN or “C-class CpG ODN” " or “C-type CpG DNA sequence” is used in accordance with its common meaning in the biological and chemical sciences and refers to an oligodeoxynucleotide including a palindrome sequence including a CpG motif and phosphodiester derivatives (phosphorothioate) linking all deoxynucleotides.
• Class C CpG ODNs include ODN 2395 and ODN M362.
• the abbreviations used herein have their conventional meaning within the chemical and biological arts. The chemical structures and formulae set forth herein are constructed according to the standard rules of chemical valency known in the chemical arts.
• alkyl by itself or as part of another substituent, means, unless otherwise stated, a straight (i.e., unbranched) or branched non-cyclic carbon chain (or carbon), or combination thereof, which may be fully saturated, mono- or polyunsaturated and can include di- and multivalent radicals, having the number of carbon atoms designated (i.e., C 1 -C 10 means one to ten carbons).
• saturated hydrocarbon radicals include, but are not limited to, groups such as methyl, ethyl, n-propyl, isopropyl, n-butyl, t-butyl, isobutyl, sec- butyl, (cyclohexyl)methyl, homologs and isomers of, for example, n-pentyl, n-hexyl, n- heptyl, n-octyl, and the like.
• An unsaturated alkyl group is one having one or more double bonds or triple bonds.
• unsaturated alkyl groups include, but are not limited to, vinyl, 2-propenyl, crotyl, 2-isopentenyl, 2-(butadienyl), 2,4-pentadienyl, 3-(l,4-pentadienyl), ethynyl, 1- and 3-propynyl, 3-butynyl, and the higher homologs and isomers.
• An alkoxy is an alkyl attached to the remainder of the molecule via an oxygen linker (-0-).
• alkylene by itself or as part of another substituent, means, unless otherwise stated, a divalent radical derived from an alkyl, as exemplified, but not limited by, -CH 2 CH 2 CH 2 -. Typically, an alkyl (or alkylene) group will have from 1 to 24 carbon atoms.
• a "lower alkyl” or “lower alkylene” is a shorter chain alkyl or alkylene group, generally having eight or fewer carbon atoms.
• alkenylene by itself or as part of another substituent, means, unless otherwise stated, a divalent radical derived from an alkene.
• heteroalkyl by itself or in combination with another term, means, unless otherwise stated, a stable non-cyclic straight or branched chain, or combinations thereof, including at least one carbon atom and at least one heteroatom selected from the group consisting of O, N, P, Si, and S, and wherein the nitrogen and sulfur atoms may optionally be oxidized, and the nitrogen heteroatom may optionally be quaternized.
• the heteroatom(s) O, N, P, S, and Si may be placed at any interior position of the heteroalkyl group or at the position at which the alkyl group is attached to the remainder of the molecule.
• heteroalkylene by itself or as part of another substituent, means, unless otherwise stated, a divalent radical derived from heteroalkyl, as exemplified, but not limited by, -CH 2 -CH 2 -S-CH 2 -CH 2 - and -CH 2 -S-CH 2 -CH 2 -NH-CH 2 -.
• heteroalkylene groups heteroatoms can also occupy either or both of the chain termini (e.g., alkyleneoxy, alkylenedioxy, alkyleneamino, alkylenediamino, and the like). Still further, for alkylene and heteroalkylene linking groups, no orientation of the linking group is implied by the direction in which the formula of the linking group is written. For example, the formula -C(0) 2 R'- represents both -C(0) 2 R'- and -R'C(0) 2 -.
• heteroalkyl groups include those groups that are attached to the remainder of the molecule through a heteroatom, such as -C(0)R', -C(0)NR, -NR'R", -OR', -SR',
• heteroalkyl is recited, followed by recitations of specific heteroalkyl groups, such as -NR'R” or the like, it will be understood that the terms heteroalkyl and -NR'R" are not redundant or mutually exclusive. Rather, the specific heteroalkyl groups are recited to add clarity. Thus, the term “heteroalkyl” should not be interpreted herein as excluding specific heteroalkyl groups, such as -NR'R” or the like.
• cycloalkyl and heterocycloalkyl by themselves or in combination with other terms, mean, unless otherwise stated, cyclic non-aromatic versions of “alkyl” and “heteroalkyl,” respectively, wherein the carbons making up the ring or rings do not necessarily need to be bonded to a hydrogen due to all carbon valencies participating in bonds with non-hydrogen atoms. Additionally, for heterocycloalkyl, a heteroatom can occupy the position at which the heterocycle is attached to the remainder of the molecule.
• cycloalkyl examples include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, 1-cyclohexenyl, 3-cyclohexenyl, cycloheptyl, and the like.
• heterocycloalkyl examples include, but are not limited to, l-(l,2,5,6-tetrahydropyridyl), 1-piperidinyl, 2-piperidinyl, 3-piperidinyl, 4-morpholinyl, 3-morpholinyl, tetrahydrofuran-2-yl, tetrahydrofuran-3-yl, tetrahydrothien-2-yl, tetrahydrothien-3-yl, 1-piperazinyl, 2-piperazinyl, and the like.
• halo(Ci-C4)alkyl includes, but is not limited to, fluoromethyl, difluoromethyl, trifluoromethyl, 2,2,2-trifluoroethyl, 4-chlorobutyl, 3-bromopropyl, and the like.
• acyl means, unless otherwise stated, -C(0)R where R is a substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.
• aryl means, unless otherwise stated, a polyunsaturated, aromatic, hydrocarbon substituent, which can be a single ring or multiple rings (preferably from 1 to 3 rings) that are fused together (i.e., a fused ring aryl) or linked covalently (e.g., biphenyl).
• a fused ring aryl refers to multiple rings fused together wherein at least one of the fused rings is an aryl ring.
• heteroaryl refers to aryl groups (or rings) that contain at least one heteroatom such as N, O, or S, wherein the nitrogen and sulfur atoms are optionally oxidized, and the nitrogen atom(s) are optionally quaternized.
• heteroaryl includes fused ring heteroaryl groups (i.e., multiple rings fused together wherein at least one of the fused rings is a heteroaromatic ring).
• a 5,6-fused ring heteroarylene refers to two rings fused together, wherein one ring has 5 members and the other ring has 6 members, and wherein at least one ring is a heteroaryl ring.
• a 6,6-fused ring heteroarylene refers to two rings fused together, wherein one ring has 6 members and the other ring has 6 members, and wherein at least one ring is a heteroaryl ring.
• a 6,5-fused ring heteroarylene refers to two rings fused together, wherein one ring has 6 members and the other ring has 5 members, and wherein at least one ring is a heteroaryl ring.
• a heteroaryl group can be attached to the remainder of the molecule through a carbon or heteroatom.
• Non-limiting examples of aryl and heteroaryl groups include phenyl, 1-naphthyl, 2-naphthyl, 4-biphenyl, 1-pyrrolyl, 2- pyrrolyl, 3-pyrrolyl, 3-pyrazolyl, 2-imidazolyl, 4-imidazolyl, pyrazinyl, 2-oxazolyl, 4- oxazolyl, 2-phenyl-4-oxazolyl, 5-oxazolyl, 3-isoxazolyl, 4-isoxazolyl, 5-isoxazolyl, 2- thiazolyl, 4-thiazolyl, 5-thiazolyl, 2-furyl, 3-furyl, 2-thienyl, 3-thienyl, 2-pyridyl, 3-pyridyl, 4-pyridyl, 2-pyrimidyl, 4-pyrimidyl, 5-benzothiazolyl, purinyl, 2-benzimidazolyl, 5-indolyl, 1-is
• arylene and heteroarylene are selected from the group of acceptable substituents described below.
• heteroaryl groups include pyridinyl, pyrimidinyl, thiophenyl, thienyl, furanyl, indolyl, benzoxadiazolyl, benzodioxolyl, benzodioxanyl, thianaphthanyl, pyrrolopyridinyl, indazolyl, quinolinyl, quinoxalinyl, pyridopyrazinyl, quinazolinonyl, benzoisoxazolyl, imidazopyridinyl, benzofuranyl, benzothienyl, benzo thiophenyl, phenyl, naphthyl, biphenyl, pyrrolyl, pyrazolyl, imidazolyl, pyrazinyl, oxazolyl, isoxazolyl, thiazolyl, furylthienyl, pyridyl, pyrimidyl,
• a fused ring heterocyloalkyl-aryl is an aryl fused to a heterocycloalkyl.
• a fused ring heterocycloalkyl -heteroaryl is a heteroaryl fused to a heterocycloalkyl.
• a fused ring heterocycloalkyl-cycloalkyl is a heterocycloalkyl fused to a cycloalkyl.
• a fused ring heterocycloalkyl-heterocycloalkyl is a heterocycloalkyl fused to another heterocycloalkyl.
• Fused ring heterocycloalkyl-aryl, fused ring heterocycloalkyl-heteroaryl, fused ring heterocycloalkyl-cycloalkyl, or fused ring heterocycloalkyl-heterocycloalkyl may each independently be unsubstituted or substituted with one or more of the substitutents described herein.
• oxo means an oxygen that is double bonded to a carbon atom.
• alkylsulfonyl means a moiety having the
• R' is a substituted or unsubstituted alkyl group as defined above.
• R' may have a specified number of carbons (e.g., "C 1 -C4 alkylsulfonyl").
• alkyl includes both substituted and unsubstituted forms of the indicated radical. Preferred substituents for each type of radical are provided below.
• R, R', R", R'", and R" each preferably independently refer to hydrogen, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl (e.g., aryl substituted with 1-3 halogens), substituted or unsubstituted heteroaryl, substituted or unsubstituted alkyl, alkoxy, or thioalkoxy groups, or arylalkyl groups.
• each of the R groups is independently selected as are each R', R", R'", and R"" group when more than one of these groups is present.
• R' and R" are attached to the same nitrogen atom, they can be combined with the nitrogen atom to form a 4-, 5-, 6-, or 7-membered ring.
• -NR'R includes, but is not limited to, 1-pyrrolidinyl and 4-morpholinyl.
• alkyl is meant to include groups including carbon atoms bound to groups other than hydrogen groups, such as haloalkyl (e.g., -CF 3 and -CH 2 CF 3 ) and acyl
• substituents for the aryl and heteroaryl groups are varied and are selected from, for
• each of the R groups is independently selected as are each R', R", R'", and R"" groups when more than one of these groups is present.
• Two or more substituents may optionally be joined to form aryl, heteroaryl, cycloalkyl, or heterocycloalkyl groups.
• Such so-called ring-forming substituents are typically, though not necessarily, found attached to a cyclic base structure.
• the ring-forming substituents are attached to adjacent members of the base structure.
• two ring-forming substituents attached to adjacent members of a cyclic base structure create a fused ring structure.
• the ring-forming substituents are attached to a single member of the base structure.
• two ring- forming substituents attached to a single member of a cyclic base structure create a spirocyclic structure.
• the ring-forming substituents are attached to non-adjacent members of the base structure.
• Two of the substituents on adjacent atoms of the aryl or heteroaryl ring may optionally form a ring of the formula -T-C(0)-(CRR') q -U-, wherein T and U are
• q is an integer of from 0 to 3.
• two of the substituents on adjacent atoms of the aryl or heteroaryl ring may optionally be replaced with a substituent of the formula -A-(CH 2 ) r -B-, wherein A and B are independently -CRR'-, -0-, -NR-, -S-, -S(O) -, -S(0) 2 -, -S(0) 2 NR-, or a single bond, and r is an integer of from 1 to 4.
• One of the single bonds of the new ring so formed may optionally be replaced with a double bond.
• two of the substituents on adjacent atoms of the aryl or heteroaryl ring may optionally be replaced with a substituent of the
• R, R, R", and R" are preferably independently selected from hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl.
• heteroatom or "ring heteroatom” are meant to include, oxygen (O), nitrogen (N), sulfur (S), phosphorus (P), and silicon (Si).
• a "substituent group,” as used herein, means a group selected from the following moieties: (A) oxo, halogen, -CF 3 , -CN, -OH, -NH 2 , -COOH, -CONH 2 , -N0 2 , -SH, -S0 2 C1, -S0 3 H, -
• a "size-limited substituent” or " size-limited substituent group,” as used herein, means a group selected from all of the substituents described above for a "substituent group,” wherein each substituted or unsubstituted alkyl is a substituted or unsubstituted Ci-C 20 alkyl, each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 20 membered heteroalkyl, each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C 3 -C8 cycloalkyl, each substituted or unsubstituted heterocycloalkyl is a substituted or unsubstituted 3 to 8 membered heterocycloalkyl, each substituted or unsubstituted aryl is a substituted or unsubstituted C 6 -Cio aryl, and each substituted or unsubstituted heteroaryl
• a "lower substituent” or " lower substituent group,” as used herein, means a group selected from all of the substituents described above for a "substituent group,” wherein each substituted or unsubstituted alkyl is a substituted or unsubstituted Ci-C 8 alkyl, each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 8 membered heteroalkyl, each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C 3 - C 7 cycloalkyl, each substituted or unsubstituted heterocycloalkyl is a substituted or unsubstituted 3 to 7 membered heterocycloalkyl, each substituted or unsubstituted aryl is a substituted or unsubstituted C 6 -Cio aryl, and each substituted or unsubstituted heteroaryl is a
• each substituted group described in the compounds herein is substituted with at least one substituent group. More specifically, in some embodiments, each substituted alkyl, substituted heteroalkyl, substituted cycloalkyl, substituted
• heterocycloalkyl substituted aryl, substituted heteroaryl, substituted alkylene, substituted heteroalkylene, substituted cycloalkylene, substituted heterocycloalkylene, substituted arylene, and/or substituted heteroarylene described in the compounds herein are substituted with at least one substituent group. In other embodiments, at least one or all of these groups are substituted with at least one size-limited substituent group. In other embodiments, at least one or all of these groups are substituted with at least one lower substituent group.
• each substituted or unsubstituted alkyl may be a substituted or unsubstituted C 1 -C 20 alkyl
• each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 20 membered heteroalkyl
• each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C 3 -C 8 cycloalkyl
• each substituted or unsubstituted heterocycloalkyl is a substituted or unsubstituted 3 to 8 membered
• each substituted or unsubstituted aryl is a substituted or unsubstituted C 6 - C 10 aryl
• each substituted or unsubstituted heteroaryl is a substituted or unsubstituted 5 to 10 membered heteroaryl.
• each substituted or unsubstituted alkylene is a substituted or unsubstituted C 1 -C 20 alkylene
• each substituted or unsubstituted heteroalkylene is a substituted or unsubstituted 2 to 20 membered
• each substituted or unsubstituted cycloalkylene is a substituted or unsubstituted C 3 -C 8 cycloalkylene
• each substituted or unsubstituted heterocycloalkylene is a substituted or unsubstituted 3 to 8 membered heterocycloalkylene
• each substituted or unsubstituted arylene is a substituted or unsubstituted C 6 -Cio arylene
• each substituted or unsubstituted heteroarylene is a substituted or unsubstituted 5 to 10 membered heteroarylene.
• each substituted or unsubstituted alkyl is a substituted or unsubstituted Ci-C 8 alkyl
• each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 8 membered heteroalkyl
• each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C 3 -C7 cycloalkyl
• each substituted or unsubstituted or unsubstituted alkyl is a substituted or unsubstituted Ci-C 8 alkyl
• each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 8 membered heteroalkyl
• each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C 3 -C7 cycloalkyl
• heterocycloalkyl is a substituted or unsubstituted 3 to 7 membered heterocycloalkyl
• each substituted or unsubstituted aryl is a substituted or unsubstituted C 6 -Cio aryl
• each substituted or unsubstituted heteroaryl is a substituted or unsubstituted 5 to 9 membered heteroaryl.
• each substituted or unsubstituted alkylene is a substituted or unsubstituted Ci-C 8 alkylene
• each substituted or unsubstituted hetero alkylene is a substituted or unsubstituted 2 to 8 membered heteroalkylene
• unsubstituted cycloalkylene is a substituted or unsubstituted C 3 -C7 cycloalkylene
• each substituted or unsubstituted heterocycloalkylene is a substituted or unsubstituted 3 to 7 membered heterocycloalkylene
• each substituted or unsubstituted arylene is a substituted or unsubstituted C 6 -Cio arylene
• each substituted or unsubstituted heteroarylene is a substituted or unsubstituted 5 to 9 membered heteroarylene.
• the compound is a chemical species set forth in the Examples section below.
• conjugated when referring to two moieties means the two moieties are bonded, wherein the bond or bonds connecting the two moieties may be covalent or non-covalent.
• the two moieties are covalently bonded to each other (e.g. directly or through a covalently bonded intermediary).
• the two moieties are non-covalently bonded (e.g. through ionic bond(s), van der waal's
• protecting groups refers to a particular functional moiety (e.g., oxygen, sulfur, nitrogen and carbon) that is temporarily blocked so that a reaction can be carried out selectively at another reactive site in a multifunctional compound.
• Protecting groups may be introduced and removed at appropriate stages during the synthesis of a compound using methods that are known to one of ordinary skill in the art. The protecting groups are applied according to standard methods of organic synthesis as described in the literature (see, e.g.: Theodora W. Green and Peter G. M.
• Exemplary alcohol protecting groups include, but are not limited to, methyl ethers, substituted methyl ethers (e.g., MOM (methoxymethyl ether), MTM (methylthiomethyl ether), BOM (benzyloxymethyl ether), PMBM (p-methoxybenzyloxymethyl ether), optionally substituted ethyl ethers, optionally substituted benzyl ethers, silyl ethers (e.g., TMS (trimethylsilyl ether), TES (triethylsilylether), TIPS (triisopropylsilyl ether), TBDMS (t-butyldimethylsilyl ether), tribenzyl silyl ether, TBDPS (t-butyldiphenyl silyl ether), esters (e.g., formate, acetate, benzoate (Bz), trifluoroacetate, dichloroacetate) carbonates, cyclic acetals and ketals
• R* is substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl (e.g., aryl substituted with 1-3 halogens), or substituted or unsubstituted heteroaryl.
• Exemplary amino protecting groups include, but are not limited to, carbamates (including methyl carbamate, ethyl carbamate, substituted ethyl carbamates (e.g., Troc), t-butyl carbamate (Boc), and benzyl carbamate (Cbz)), amides, cyclic imide derivatives, N-alkyl and N-aryl amines, imine derivatives, enamine derivatives, and the like.
• protected amino groups include nitrogen groups protected as: an amide (—
• R* is, independently, hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl (e.g., aryl substituted with 1-3 halogens), or substituted or unsubstituted hetero
• Exemplary sulfhydryl protecting groups include, but are not limited to thioethers (-SR*), where R* is substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted
• the click chemistry reactive group is or includes an azide groups, an alkene group, an amino groups, an N-hydroxysuccinimide group, a sulfhydryl group, a divinyl sulfone derivative, or a maleimido derivative.
• the linker is substituted with a reactive group (e.g.
• a click chemistry reactive group or a protected reactive group, including, for example, a protected amino group or a N-hydroxysuccinimide group, suitable for conjugation by N-hydroxysuccinimide (NHS) chemistry; a sulfhydryl group that may be conjugated with divinyl sulfone; a protected sulfhydryl group, which may be conjugated with l-alkyl-3-methylacryloyl (acryloyl) chloride or acryloyl derivatives; a protected sulfhydryl group, which may be conjugated with maleimido derivatives.
• a click chemistry reactive group or a protected reactive group, including, for example, a protected amino group or a N-hydroxysuccinimide group, suitable for conjugation by N-hydroxysuccinimide (NHS) chemistry
• a sulfhydryl group that may be conjugated with divinyl sulfone
• a protected sulfhydryl group which may
• a “label” or a “detectable moiety” is a composition detectable by spectroscopic, photochemical, biochemical, immunochemical, chemical, magnetic resonance imaging, or other physical means.
• useful detectable moieties include 32 P, fluorescent dyes, electron-dense reagents, enzymes (e.g.
• biotin as commonly used in an ELISA, biotin, digoxigenin, paramagnetic molecules, paramagnetic nanoparticles, ultrasmall superparamagnetic iron oxide (“USPIO”) nanoparticles, USPIO nanoparticle aggregates, superparamagnetic iron oxide (“SPIO”) nanoparticles, SPIO nanoparticle aggregates, monochrystalline SPIO, monochrystalline SPIO aggregates, monochrystalline iron oxide nanoparticles, monochrystalline iron oxide, other nanoparticle contrast agents, liposomes or other delivery vehicles containing Gadolinium chelate (“Gd-chelate”) molecules, Gadolinium,
• radioisotopes examples include radionuclides (e.g. carbon-11, nitrogen-13, oxygen-15, fluorine-18, rubidium- 82), fluorodeoxyglucose (e.g. fluorine-18 labeled), any gamma ray emitting radionuclides, positron-emitting radionuclide, radiolabeled glucose, radiolabeled water, radiolabeled ammonia, biocolloids, microbubbles (e.g.
• microbubble shells including albumin, galactose, lipid, and/or polymers
• microbubble gas core including air, heavy gas(es), perfluorcarbon, nitrogen, octafluoropropane, perflexane lipid microsphere, perflutren, etc.
• iodinated contrast agents e.g.
• Detectable moieties also include any of the above compositions encapsulated in nanoparticles, particles, aggregates, coated with additional compositions, derivatized for binding to a targeting agent (e.g.
• oligonucleotide or protein to the label may be employed, e.g., using methods described in Hermanson, Bioconjugate Techniques 1996, Academic Press, Inc., San Diego.
• cell as used herein also refers to individual cells, cell lines, or cultures derived from such cells.
• a “culture” refers to a composition comprising isolated cells of the same or a different type.
• nucleic acids or polypeptide sequences refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same (i.e.
• sequences are then said to be “substantially identical.”
• This definition also refers to, or may be applied to, the compliment of a test sequence.
• the definition also includes sequences that have deletions and/or additions, as well as those that have substitutions.
• the preferred algorithms can account for gaps and the like.
• identity exists over a region that is at least about 10 amino acids or 20 nucleotides in length, or more preferably over a region that is 10-50 amino acids or 20-50 nucleotides in length.
• percent (%) amino acid sequence identity is defined as the percentage of amino acids in a candidate sequence that are identical to the amino acids in a reference sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity.
• Alignment for purposes of determining percent sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN, ALIGN-2 or Megalign (DNASTAR) software. Appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full-length of the sequences being compared can be determined by known methods.
• sequence comparisons typically one sequence acts as a reference sequence, to which test sequences are compared.
• test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated.
• sequence algorithm program parameters Preferably, default program parameters can be used, or alternative parameters can be designated.
• sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters.
• Patient refers to a living organism suffering from or prone to a disease or condition that can be treated by administration using the methods and
• compositions provided herein include humans, other mammals, bovines, rats, mice, dogs, monkeys, goat, sheep, cows, deer, and other non-mammalian animals.
• a patient is human.
• Tissues, cells and their progeny of a biological entity obtained in vitro or cultured in vitro are also contemplated.
• administering means oral administration, administration as a suppository, topical contact, intravenous, parenteral, intraperitoneal, intramuscular, intralesional, intrathecal, intranasal or subcutaneous administration, or the implantation of a slow-release device, e.g., a mini-osmotic pump, to a subject.
• Administration is by any route, including parenteral and transmucosal (e.g., buccal, sublingual, palatal, gingival, nasal, vaginal, rectal, or transdermal).
• Parenteral administration includes, e.g., intravenous, intramuscular, intra-arteriole, intradermal, subcutaneous, intraperitoneal, intraventricular, and intracranial.
• Other modes of delivery include, but are not limited to, the use of liposomal formulations, intravenous infusion, transdermal patches, etc.
• the terms "treat,” “treating” or “treatment,” and other grammatical equivalents as used herein, include alleviating, abating, ameliorating, or preventing a disease, condition or symptoms, preventing additional symptoms, ameliorating or preventing the underlying metabolic causes of symptoms, inhibiting the disease or condition, e.g. , arresting the development of the disease or condition, relieving the disease or condition, causing regression of the disease or condition, relieving a condition caused by the disease or condition, or stopping the symptoms of the disease or condition, and are intended to include prophylaxis.
• the terms further include achieving a therapeutic benefit and/or a prophylactic benefit.
• therapeutic benefit is meant eradication or amelioration of the underlying disorder being treated.
• a therapeutic benefit is achieved with the eradication or amelioration of one or more of the physiological symptoms associated with the underlying disorder such that an improvement is observed in the patient, notwithstanding that the patient may still be afflicted with the underlying disorder.
• the terms "prevent,” “preventing,” or “prevention,” and other grammatical equivalents as used herein, include to keep from developing, occur, hinder or avert a disease or condition symptoms as well as to decrease the occurrence of symptoms.
• the prevention may be complete (i.e., no detectable symptoms) or partial, so that fewer symptoms are observed than would likely occur absent treatment.
• the terms further include a prophylactic benefit.
• the compositions may be administered to a patient at risk of developing a particular disease, or to a patient reporting one or more of the physiological symptoms of a disease, even though a diagnosis of this disease may not have been made.
• inhibiting also means reducing an effect (disease state or expression level of a gene/protein/mRNA) relative to the state in the absence of a compound or composition of the present disclosure.
• test compound refers to an experimental compound used in a screening process to identify activity, non-activity, or other modulation of a particularized biological target or pathway.
• Control or "control experiment” is used in accordance with its plain ordinary meaning and refers to an experiment in which the subjects or reagents of the experiment are treated as in a parallel experiment except for omission of a procedure, reagent, or variable of the experiment. In some instances, the control is used as a standard of comparison in evaluating experimental effects. In some embodiments, a control is the measurement of the activity of a protein in the absence of a compound as described herein (including
• Disease or “condition” refer to a state of being or health status of a patient or subject capable of being treated with the compounds or methods provided herein. In some instances, “disease” or “condition” refers to a "cancer”.
• cancer refers to all types of cancer, neoplasm, malignant or benign tumors found in mammals, including leukemia, carcinomas and sarcomas.
• Exemplary cancers include breast cancer, ovarian cancer, colon cancer, liver cancer, kidney cancer and pancreatic cancer. Additional examples include leukemia (e.g. acute myeloid leukemia ("AML”) or chronic myelogenous leukemia (“CML”)), cancer of the brain, lung cancer, non-small cell lung cancer, melanoma, sarcomas, and prostate cancer, cervix cancers, stomach cancers, head & neck cancers, uterus cancers, mesothelioma, metastatic bone cancer, Medulloblastoma, Hodgkin's Disease, Non-Hodgkin's Lymphoma, multiple myeloma, neuroblastoma, rhabdomyosarcoma, primary thrombocytosis, primary macroglobulinemia, primary brain tumors, malignant pancreatic insulanoma, malignant carcinoid, urinary bladder cancer, premalignant skin lesions, testicular cancer, lymphomas, thyroid cancer,
• Contacting is used in accordance with its plain ordinary meaning and refers to the process of allowing at least two distinct species (e.g. chemical compounds including biomolecules or cells) to become sufficiently proximal to react, interact or physically touch. It should be appreciated; however, the resulting reaction product can be produced directly from a reaction between the added reagents or from an intermediate from one or more of the added reagents which can be produced in the reaction mixture.
• species e.g. chemical compounds including biomolecules or cells
• contacting includes allowing a compound described herein to interact with a protein or enzyme.
• phenotype and “phenotypic” as used herein refer to an organism's observable characteristics such as onset or progression of disease symptoms, biochemical properties, or physiological properties.
• the word "expression” or “expressed” as used herein in reference to a DNA nucleic acid sequence means the transcriptional and/or translational product of that sequence.
• the level of expression of a DNA molecule in a cell may be determined on the basis of either the amount of corresponding mRNA that is present within the cell or the amount of protein encoded by that DNA produced by the cell (Sambrook et al., 1989
• expression includes any step involved in the production of a polypeptide including, but not limited to, transcription, post-transcriptional modification, translation, post- translational modification, and secretion.
• Expression can be detected using conventional techniques for detecting protein (e.g. , ELISA, Western blotting, flow cytometry,
• the term "gene” means the segment of DNA involved in producing a protein; it includes regions preceding and following the coding region (leader and trailer) as well as intervening sequences (introns) between individual coding segments (exons).
• the leader, the trailer as well as the introns include regulatory elements that are necessary during the transcription and the translation of a gene.
• a "protein gene product” is a protein expressed from a particular gene.
• an amount of in reference to a polynucleotide or polypeptide refers to an amount at which a component or element is detected. The amount may be measured against a control, for example, wherein an increased level of a particular polynucleotide or polypeptide in relation to the control, demonstrates enrichment of the polynucleotide or polypeptide. Thus, in embodiments, an increased amount indicates a greater level or efficiency of grafting HSPCs described herein into a host (e.g. mouse). The term refers to quantitative measurement of the enrichment as well as qualitative measurement of an increase or decrease relative to a control.
• a derivative may be a conjugate with a pharmaceutically acceptable agent, for example, phosphate or phosphonate.
• salt refers to acid or base salts of the agents used herein.
• acceptable salts are mineral acid (hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid, and the like) salts, organic acid (acetic acid, propionic acid, glutamic acid, citric acid, and the like) salts, and quaternary ammonium (methyl iodide, ethyl iodide, and the like) salts.
• salts are meant to include salts of the active compounds that are prepared with relatively nontoxic acids or bases, depending on the particular substituents found on the compounds described herein.
• base addition salts can be obtained by contacting the neutral form of such compounds with a sufficient amount of the desired base, either neat or in a suitable inert solvent.
• pharmaceutically acceptable base addition salts include sodium, potassium, calcium, ammonium, organic amino, or magnesium salt, or a similar salt.
• acid addition salts can be obtained by contacting the neutral form of such compounds with a sufficient amount of the desired acid, either neat or in a suitable inert solvent.
• pharmaceutically acceptable acid addition salts include those derived from inorganic acids like hydrochloric, hydrobromic, nitric, carbonic,
• salts of amino acids such as arginate and the like, and salts of organic acids like glucuronic or galactunoric acids and the like (see, e.g. , Berge et al , Journal of Pharmaceutical Science 66: 1-19 (1977)).
• Certain specific compounds of the present disclosure contain both basic and acidic functionalities that allow the compounds to be converted into either base or acid addition salts.
• Other pharmaceutically acceptable carriers known to those of skill in the art are suitable for the present disclosure. Salts tend to be more soluble in aqueous or other protonic solvents that are the corresponding free base forms.
• the preparation may be a lyophilized powder in 1 mM-50 mM histidine, 0.1%-2% sucrose, 2%-7% mannitol at a pH range of 4.5 to 5.5, that is combined with buffer prior to use.
• the compounds of the present disclosure may exist as salts, such as with pharmaceutically acceptable acids.
• the present disclosure includes such salts.
• examples of such salts include hydrochlorides, hydrobromides, sulfates, methanesulfonates, nitrates, maleates, acetates, citrates, fumarates, tartrates (e.g., (+) -tartrates, (-)-tartrates, or mixtures thereof including racemic mixtures), succinates, benzoates, and salts with amino acids such as glutamic acid.
• These salts may be prepared by methods known to those skilled in the art.
• An "adjuvant” (from Latin, adiuvare: to aid) is a pharmacological and/or immunological agent that modifies the effect of other agents.
• a "diluent” (also referred to as a filler, dilutant or thinner) is a diluting agent.
• administering refers to the act of providing an agent of the current embodiments or pharmaceutical composition including an agent of the current embodiments to the individual in need of treatment.
• co- administer it is meant that a composition described herein is administered at the same time, just prior to, or just after the administration of additional therapies.
• the compound or the composition of the disclosure can be administered alone or can be coadministered to the patient.
• Co- administration is meant to include simultaneous or sequential administration of the compound individually or in combination (more than one compound or agent).
• the preparations can also be combined, when desired, with other active substances (e.g. to reduce metabolic degradation).
• simultaneous administration includes that the administration of two agents (e.g. , the compounds or compositions described herein) occurs separately on the same day or do not occur on a same day (e.g., occurs on consecutive days).
• “concurrent administration” includes overlapping in duration at least in part.
• two agents e.g. , any of the agents or class of agents described herein that has bioactivity
• their administration occurs within a certain desired time.
• the agents' administration may begin and end on the same day.
• the administration of one agent can also precede the administration of a second agent by day(s) as long as both agents are taken on the same day at least once.
• the administration of one agent can extend beyond the administration of a second agent as long as both agents are taken on the same day at least once.
• the bioactive agents/agents do not have to be taken at the same time each day to include concurrent administration.
• intermittent administration includes the administration of an agent for a period of time (which can be considered a “first period of administration”), followed by a time during which the agent is not taken or is taken at a lower maintenance dose (which can be considered “off-period") followed by a period during which the agent is administered again (which can be considered a "second period of administration”).
• first period of administration a period of time
• second period of administration a period during which the agent is administered again
• the dosage level of the agent will match that administered during the first period of administration but can be increased or decreased as medically necessary.
• administering means oral administration, administration as a suppository, topical contact, intravenous, parenteral, intraperitoneal, intramuscular, intralesional, intrathecal, intranasal or subcutaneous administration, or the implantation of a slow-release device, e.g. , a mini-osmotic pump, to a subject.
• Administration is by any route, including parenteral and transmucosal (e.g. , buccal, sublingual, palatal, gingival, nasal, vaginal, rectal, or transdermal).
• Parenteral administration includes, e.g.
• compositions disclosed herein can be delivered transdermally, by a topical route, formulated as applicator sticks, solutions, suspensions, emulsions, gels, creams, ointments, pastes, jellies, paints, powders, and aerosols.
• Oral preparations include tablets, pills, powder, dragees, capsules, liquids, lozenges, cachets, gels, syrups, slurries, suspensions, etc., suitable for ingestion by the patient.
• Solid form preparations include powders, tablets, pills, capsules, cachets, suppositories, and dispersible granules.
• Liquid form preparations include solutions, suspensions, and emulsions, for example, water or water/propylene glycol solutions.
• the compositions of the present disclosure may additionally include components to provide sustained release and/or comfort. Such components include high molecular weight, anionic mucomimetic polymers, gelling polysaccharides and finely-divided drug carrier substrates.
• compositions disclosed herein can also be delivered as microspheres for slow release in the body.
• microspheres can be administered via intradermal injection of drug-containing microspheres, which slowly release subcutaneously (see Rao, /. Bioniater Sci. Polym. Ed. 7:623-645, 1995; as biodegradable and injectable gel formulations (see, e.g., Gao Phann. Res. 12:857-863, 1995); or, as microspheres for oral administration (see, e.g., Eyles, /. Phann. Pharmacol. 49:669- 674, 1997).
• an "effective amount” or “therapeutically effective amount” is that amount sufficient to affect a desired biological effect, such as beneficial results, including clinical results. As such, an “effective amount” depends upon the context in which it is being applied. An effective amount may vary according to factors known in the art, such as the disease state, age, sex, and weight of the individual being treated. Several divided doses may be administered daily or the dose may be proportionally reduced as indicated by the exigencies of the therapeutic situation. In addition, the compositions/formulations of this disclosure can be administered as frequently as necessary to achieve a therapeutic amount.
• compositions may include compositions wherein the therapeutic drug (e.g., agents described herein, including embodiments or examples) is contained in a therapeutically effective amount, i.e., in an amount effective to achieve its intended purpose.
• a therapeutically effective amount i.e., in an amount effective to achieve its intended purpose.
• the actual amount effective for a particular application will depend, inter alia, on the condition being treated.
• compositions When administered in methods to treat a disease, such compositions will contain an amount of therapeutic drug effective to achieve the desired result, e.g., modulating the activity of a target molecule, and/or reducing, eliminating, or slowing the progression of disease symptoms.
• the dosage and frequency (single or multiple doses) administered to a mammal can vary depending upon a variety of factors, for example, whether the mammal suffers from another disease, and its route of administration; size, age, sex, health, body weight, body mass index, and diet of the recipient; nature and extent of symptoms of the disease being treated, kind of concurrent treatment, complications from the disease being treated or other health-related problems.
• Other therapeutic regimens or agents can be used in conjunction with the methods and agents of this disclosure. Adjustment and manipulation of established dosages (e.g., frequency and duration) are well within the ability of those skilled in the art.
• the therapeutically effective amount can be initially determined from cell culture assays.
• Target concentrations will be those concentrations of therapeutic drug(s) that are capable of achieving the methods described herein, as measured using the methods described herein or known in the art.
• therapeutically effective amounts for use in humans can also be determined from animal models.
• a dose for humans can be formulated to achieve a concentration that has been found to be effective in animals.
• the dosage in humans can be adjusted by monitoring agent's effectiveness and adjusting the dosage upwards or downwards, as described above. Adjusting the dose to achieve maximal efficacy in humans based on the methods described above and other methods is well within the capabilities of the ordinarily skilled artisan.
• Dosages may be varied depending upon the requirements of the patient and the therapeutic drug being employed.
• the dose administered to a patient should be sufficient to effect a beneficial therapeutic response in the patient over time.
• the size of the dose also will be determined by the existence, nature, and extent of any adverse side-effects.
• Determination of the proper dosage for a particular situation is within the skill of the practitioner. Generally, treatment is initiated with smaller dosages which are less than the optimum dose of the agent. Thereafter, the dosage is increased by small increments until the optimum effect under circumstances is reached. Dosage amounts and intervals can be adjusted individually to provide levels of the administered agent effective for the particular clinical indication being treated. This will provide a therapeutic regimen that is commensurate with the severity of the individual's disease state.
• Excipient is used herein to include any other agent that may be contained in or combined with a disclosed agent, in which the excipient is not a therapeutically or biologically active agent/agent. As such, an excipient should be pharmaceutically or biologically acceptable or relevant (for example, an excipient should generally be non-toxic to the individual). “Excipient” includes a single such agent and is also intended to include a plurality of excipients.
• the term "excipient” and “carrier” are used interchangeably in some embodiments of the present disclosure and said terms are defined herein as, “ingredients which are used in the practice of formulating a safe and effective pharmaceutical composition.”
• the term “about” refers to any minimal alteration in the concentration or amount of an agent that does not change the efficacy of the agent in preparation of a formulation and in treatment of a disease or disorder.
• the term “about” with respect to concentration range of the agents (e.g. , therapeutic/active agents) of the current disclosure also refers to any variation of a stated amount or range which would be an effective amount or range.
• Ranges can be expressed herein as from “about” one particular value, and/or to "about” another particular value. When such a range is expressed, another aspect includes from the one particular value and/or to the other particular value. Similarly, when values are expressed as approximations, by use of the antecedent "about,” it is understood that the particular value forms another aspect. It is further understood that the endpoints of each of the ranges are significant both in relation to the other endpoint, and independently of the other endpoint. It is also understood that there are a number of values disclosed herein, and that each value is also herein disclosed as "about” that particular value in addition to the value itself.
• the present disclosure includes an isolated compound including a phosphorothioated oligodeoxynucleotide (ODN), conjugated to an antisense nucleic acid sequence or to a short- activating RNA (saRNA) of a gene of interest.
• ODN phosphorothioated oligodeoxynucleotide
• saRNA short- activating RNA
• the isolated compound has the formula: PODN-L-ANA (I) or PODN-L-saRNA (II).
• PODN is the phosphorothioated ODN and L is a linker such as a covalent linker.
• ANA is the antisence nucleic acid sequence.
• saRNA is the short- activating RNA.
• the isolated compound includes a nucleic acid sequence having about 80%-100% sequence identity with a continuous 15 nucleobase sequence of one of phosphorothioated oligodeoxynucleotides (ODN) having a sequence of SEQ ID NOs: 7-18, 29-30, and 98-101, conjugated to an antisense oligonucleotide (ASO).
• ODN phosphorothioated oligodeoxynucleotides
• ASO antisense oligonucleotide
• the present disclosure provides an isolated compound including a nucleic acid sequence having about 80%-100% sequence identity with a continuous 15 nucleobase sequence of one of phosphorothioated oligodeoxynucleotides (ODN) having a sequence of SEQ ID NOs: 7-18, 29-30, and 98-101, conjugated to a saRNA.
• ODN phosphorothioated oligodeoxynucleotides
• the nucleic acid sequence having about 80%-100% sequence identity with a continuous 15 nucleobase sequence of one of phosphorothioated oligodeoxynucleotides (ODN) having a sequence of SEQ ID NOs: 7- 18, 29-30, and 98-101 includes a 15 to 30 bases long, single-stranded, partly or completely phosphorothioated oligonucleotide conjugated to a saRNA or an ASO.
• the antisense oligonucleotide is a STAT (STAT1 - STAT6) antisense oligonucleotide.
• the antisense oligonucleotide is a STAT-3 antisense oligonucleotide.
• the saRNA is a saRNA of CEBP/a, p21, or p53.
• the isolated compound of the present disclosure includes a nucleic acid sequence having about 80-85%, about 85-90%, about 90-95%, about 95%-100% sequence identity with a continuous 15 nucleobase sequence of one of phosphorothioated oligodeoxynucleotides (ODN) having a sequence of SEQ ID NOs: 7-18, 29-30, and 98-101, conjugated to a saRNA or an antisense oligonucleotide (ASO).
• ODN phosphorothioated oligodeoxynucleotides
• ASO antisense oligonucleotide
• the nucleic acid sequence having about 80-85%, about 85-90%, about 90-95%, about 95%-100% sequence identity with a continuous 15 nucleobase sequence of one of phosphorothioated oligodeoxynucleotides (ODN) having a sequence of SEQ ID NOs: 7-18, 29-30, and 98-101 includes a 15 to 30 bases long, single-stranded, partly or completely phosphorothioated oligonucleotide conjugated to a saRNA or an antisense oligonucleotide (ASO).
• ODN phosphorothioated oligodeoxynucleotides
• ASO antisense oligonucleotide
• the present disclosure provides an isolated compound including a
• phosphorothioated oligodeoxynucleotide having a sequence of SEQ ID NOs: 7-18, 29-30, and 98-101 conjugated to a short-activating RNA (saRNA) or an ASO.
• the present disclosure includes a phosphorothioated oligodeoxynucleotide (ODN) having a sequence of SEQ ID NOs: 7-18, 29-30, and 98-101 conjugated to a short- activating RNA (saRNA) that is capable of activating a CCAAT/enhancer-binding protein-a (C/EBPa).
• the disclosure provides a phosphorothioated oligodeoxynucleotide (ODN) having a sequence of SEQ ID NOs: 7-18, 29-30, and 98-101 conjugated to a saRNA or an ASO with a linker between the phosphorothioated oligodeoxynucleotide (ODN) having a sequence of SEQ ID NOs: 7-18, 29-30, and 98-101, and the saRNA or the ASO.
• the linker may be a covalent linker.
• the linker is or includes a substituted or unsubstituted alkylene or heteroalkylene linker.
• the nucleic acid conjugated to saRNA includes more than one substituted or unsubstituted heteroalkylene linkers.
• Linkers may be added during the synthesis in sequence.
• heteroalkylene linkers are connected to each other with an intervening phosphate bond.
• the linker is a substituted or unsubstituted heteroalkylene or substituted or unsubstituted cyclo-heteroalkylene.
• a "cyclo-heteroalkylene,” as used herein is a heteroalkylene having a one or more divalent cyclic moieties within the heteroalkylene chain.
• the cyclic moiety may be a substituted or unsubstituted cycloalklylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene or substituted or unsubstituted heteroarylene.
• the cyclic moiety is a substituted or unsubstituted ribose (e.g., a nucleoside).
• the cyclic moiety serves as a branch point of the linker thereby forming a branched linker.
• the cyclic moiety branch point may be used to attach additional functional moieties to the conjugates provided herein, such as detectable moieties, drug moieties or biomolecule. As explained in more detail below, the additional functional moieties may be connected using click chemistry techniques as known in the art.
• the linker e.g., L in Formula (I) and (II)
• the linker is or contains a moiety having the formula:
• n is an integer from 1 to 5 (e.g., 3) and the symbol z is an integer from 0 to 50 (e.g. from 0 to 25, 0 to 10, or 0 to 5).
• n is 3 and z is 0 to 5 or 1 to 5.
• n is 3 and z is 0 to 4 or 1 to 4.
• n is 3 and z is 0 to 3 or 1 to 3.
• n is 3 and z is 3.
• the linker e.g., L in Formula (I) and (II)
• nl, n2 and n3 are independently an integer from 1 to 5 (e.g., 3) and the symbol z is an integer from 0 to 50 (e.g. from 0 to 25, 0 to 10, or 0 to 5).
• nl, n2 and n3 are 3 and z is 0 to 5 or 1 to 5.
• nl, n2 and n3 are 3 and z is 0 to 4 or 1 to 4.
• nl, n2 and n3 are 3 and z is 0 to 3 or 1 to 3.
• nl, n2 and n3 are 3 and z is 3.
• the linker may have the structure below, where the linker connects with the 3' phosphate of the guanine on one end and the 5' phosphate of the thymidine on the other end:
• guanine and thymidine in the above structure may be replaced with any nucleic acid monomer/nucleobase.
• the linker comprises a heteroalkylene having three carbons (-OCH 2 CH 2 CH 2 O-) conjugated to a phosphate moiety.
• the heteroalkylene moiety can be varied (e.g., the linker can comprise a heteroalkyene having two, four, five, six, seven, or eight carbons).
• the guanosine above is connected to the ODN nucleic acid sequence and the thymidine is connected to the short- activating RNA (saRNA) or an ASO.
• saRNA short- activating RNA
• the linker e.g., linker may be an heteroalkylene linker
• a reactive group e.g. a click chemistry reactive group
• the reactive group may be used to conjugate the phosphorothioated oligodeoxynucleotide (ODN)-saRNA/ASO compound to an additional functional moiety as described herein, such as a detectable moiety or biomolecule (e.g. a targeting moiety).
• heteroalkylene linker may include further modification, conjugation, or attachment of additional moieties.
• the reactive group used to conjugate the phosphorothioated oligodeoxynucleotide (ODN)-saRNA/ASO compound to an additional functional moiety may be any applicable reactive group useful in bioconjugate chemistry. See Hermanson, Bioconjugate Techniques 1996, Academic Press, Inc., San Diego. [0134] In embodiments, the reactive group is a click chemistry reactive group. Click chemistry refers to a group of reactions that are fast, simple to use, easy to purify, versatile, regiospecific, and give high product yields.
• Cycloadditions - these primarily refer to 1,3-dipolar cycloadditions, but also include hetero-Diels-Alder cycloadditions;
• Nucleophilic ring-openings - these refer to the opening of strained heterocyclic electrophiles, such as aziridines, epoxides, cyclic sulfates, aziridinium ions, episulfonium ions;
• carbonyl chemistry of the non-aldol type - examples include the formations of ureas, thioureas, hydrazones, oxime ethers, amides, aromatic heterocycles;
• additions of carbon-carbon multiple bonds - examples include epoxidations, aziridinations, dihydrooxylations, sulfenyl halide additions, nitrosyl halide additions, and certain Michael additions.
• the click reaction used may be Cu ! -catalyzed Huisgen 1,3-dipolar cycloaddition (HDC) of azides or terminal alkynes to form 1,2,3- triazoles.
• the click reaction may be a copper-free reaction.
• the click chemistry reactive group is or includes an azide group, an alkene group, an amino groups, an N-hydroxysuccinimide group, a sulfhydryl group, a divinyl sulfone derivative, or a maleimido derivative.
• the linker is substituted with a reactive group (e.g.
• a click chemistry reactive group or a protected reactive group, including, for example, a protected amino group or a N-hydroxysuccinimide group, suitable for conjugation by N-hydroxysuccinimide (NHS) chemistry; a sulfhydryl group that may be conjugated with divinyl sulfone; a protected sulfhydryl group, which may be conjugated with l-alkyl-3-methylacryloyl (acryloyl) chloride or acryloyl derivatives; a protected sulfhydryl group, which may be conjugated with maleimido derivatives.
• a cyclo-heteroalkylene branched linker is provided below.
• a cyclo-heteroalkylene branched linker connects with the 3 ' phosphate of the guanine on one end and the 5' phosphate of the thymidine on the other end.
• the moiety of the cyclo-heteroalkylene branched linker is a branch point and is a 5- substituted thymidine.
• the thymidine is substitued in position 5 with a reactive group containing an NHS moiety, which can serve as a reactive group to connect to an additional fucntional moiety.
• the linker branch point may be non-cyclic.
• An example of a compound that can be used to serve as non-cyclic moiety branch point within the linker that contains a reactive functional group and protected reactive functional groups is provided below.
• the reactive group may be used to conjugate the
• ODN phosphorothioated oligodeoxynucleotide
• ASO phosphorothioated oligodeoxynucleotide
• Additional functional moieties include a fluorescent label, a targeting compound (bone targeting bisphosphonates), a drug, or an antibody.
• additional moiety is a chemically reactive moiety, detectable moiety, therapeutic moiety (e.g. anti-cancer agent or anti- viral agent), nucleic acid sequence, DNA sequence, or nucleic acid analogs.
• the detectable moiety is a fluorescent dye, electron-dense reagent, enzyme, biotin, digoxigenin, paramagnetic molecule, paramagnetic nanoparticle, contrast agent, magnetic resonance contrast agent, X-ray contrast agent, Gadolinium, radioisotope, radionuclide, fluorodeoxy glucose, gamma ray emitting radionuclide, positron-emitting radionuclide, biocolloid, microbubble, iodinated contrast agent, barium sulfate, thorium dioxide, gold, gold nanoparticle, gold nanoparticle aggregate, fluorophore, two-photon fluorophore, hapten, protein, or fluorescent moiety.
• an additional moiety is a therapeutic moiety (e.g. anti-cancer agent or anti- viral agent).
• the additional functional moiety is a substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.
• the additional moiety is a substituted or unsubstituted C1-C4 0 alkyl, substituted or unsubstituted 2 to 40 membered heteroalkyl, substituted or unsubstituted C 3 -C 8 cycloalkyl, substituted or unsubstituted 3 to 8 membered heterocycloalkyl, substituted or unsubstituted C 6 -Cio aryl, or substituted or unsubstituted 5 to 10 membered heteroaryl.
• the additional moiety is a substituted C1-C4 0 alkyl, substituted 2 to 40 membered heteroalkyl, substituted C 3 -C 8 cycloalkyl, substituted 3 to 8 membered heterocycloalkyl, substituted C 6 -Cio aryl, or substituted 5 to 10 membered heteroaryl.
• the additional functional moiety is an R ⁇ -substituted C1-C4 0 alkyl, R ⁇ -substituted 2 to 40 membered heteroalkyl, R ⁇ substituted C 3 -C 8 cycloalkyl, R 1 -substituted 3 to 8 membered heterocycloalkyl, R 1 -substituted C 6 -Cio aryl, or
• the additional functional moiety is an R ⁇ substituted C1-C4 0 alkyl. In embodiments, the additional functional moiety is an -(unsubstituted C1-C4 0 alkylene)-R 1 . In embodiments, the additional functional moiety is an -(unsubstituted linear C1-C4 0 alkylene)-R 1 . In embodiments, the additional functional moiety is an -(unsubstituted C 3 -C21 alkylene)-R 1 . In embodiments, the additional functional moiety is an -(unsubstituted C 3 -C1 8 alkylene)-R 1 .
• the additional functional moiety is an -(unsubstituted linear C 3 -C15 alkylene)-R 1 . In embodiments, the additional functional moiety is an -(unsubstituted linear C6-C21 alkylene)-R 1 . In embodiments, the additional functional moiety is an -(unsubstituted linear C9-C21 alkylene)-R 1 . In
• the additional functional moiety is an -(unsubstituted linear C9-C1 8
• the additional functional moiety is an -(unsubstituted linear C9-C15 alkylene)-R 1 . In embodiments, the additional functional moiety is an -(unsubstituted linear C12-C15 alkylene)-R 1 . In embodiments, the additional functional moiety is
• the additional functional moiety is an -(unsubstituted linear Ci 2 alkylene)-R 1 .
• the additional functional moiety is an -(unsubstituted linear C1 3 alkylene)-R 1 .
• the additional functional moiety is an -(unsubstituted linear Ci 4 alkylene)-R 1 .
• the additional functional moiety is an -(unsubstituted linear C15 alkylene)-R 1 .
• the additional functional moiety is an R ⁇ substituted 2 to 40 membered heteroalkyl.
• the additional functional moiety is an -(unsubstituted 2 to 40 membered heteroalkylene)-R 1 .
• the additional functional moiety is a -(substituted linear 2 to 40 membered heteroalkylene)-R 1 . In embodiments, the additional functional moiety is a -( substituted 5 to 40 membered heteroalkylene)-R 1 . In embodiments, the additional functional moiety is a -( substituted 10 to 40 membered heteroalkylene)-R 1 . In embodiments, the additional functional moiety is a -( substituted 15 to 40 membered heteroalkylene)-R 1 . In embodiments, the additional functional moiety is a -( substituted 20 to 40 membered heteroalkylene)-R 1 .
• the additional functional moiety is a -( substituted 30 to 40 membered heteroalkylene)-R 1 . In embodiments, the additional functional moiety is a -( substituted 2 to 35 membered heteroalkylene)-R 1 . In embodiments, the additional functional moiety is a -( substituted 2 to 30 membered heteroalkylene)-R 1 . In embodiments, the additional functional moiety is a -( substituted 2 to 25 membered heteroalkylene)-R 1 . In embodiments, the additional functional moiety is a -( substituted 2 to 20 membered heteroalkylene)-R 1 .
• the additional functional moiety is a -( substituted 2 to 10 membered heteroalkylene)-R 1 . In embodiments, the additional functional moiety is a -( substituted 2 to 50 membered heteroalkylene)-R 1 . In embodiments, the additional functional moiety is a -( substituted 2 to 60 membered heteroalkylene)-R 1 . In embodiments, the additional functional moiety is a substituted 2 to 40 membered heteroalkyl. In embodiments, the additional functional moiety is a substituted 10 to 50 membered heteroalkyl. In embodiments, the additional functional moiety is a substituted 20 to 40 membered heteroalkyl. In embodiments, the additional functional moiety is a substituted 25 to 40 membered heteroalkyl. In embodiments, the additional functional moiety is a substituted 30 to 40 membered heteroalkyl.
• R 1 in an additional functional moiety is a detectable moiety or a therapeutic moiety. In embodiments, R 1 in an additional functional moiety is a detectable moiety. In embodiments, the detectable moiety is a fluorescent dye, electron-dense reagent, enzyme, biotin, digoxigenin, paramagnetic molecule, paramagnetic nanoparticle, contrast agent, magnetic resonance contrast agent, X-ray contrast agent, Gadolinium, radioisotope, radionuclide, fluorodeoxyglucose, gamma ray emitting radionuclide, positron-emitting radionuclide, biocolloid, microbubble, iodinated contrast agent, barium sulfate, thorium dioxide, gold, gold nanoparticle, gold nanoparticle aggregate, fluorophore, two-photon fluorophore, hapten, protein, or fluorescent moiety.
• the detectable moiety is a fluorescent dye, electron-dense reagent, enzyme, bio
• R 1 in an additional functional moiety is a therapeutic moiety (e.g. anti-cancer agent or anti- viral agent).
• R 1 in an additional functional moiety is H.
• an additional functional moiety is oxo.
• an additional functional moiety is oxygen.
• an additional functional moiety is sulfur.
• the further linking substituent includes a substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene or substituted or unsubstituted heteroarylene.
• the further linking substituent may include a PEG moiety attached to the reactive group or additional moiety.
• the linker includes an unsubstituted C 3 alkylene (e.g. as described above separated by phosphate diester linker groups). In embodiments, the linker may be unsubstituted C15 alkylene. In embodiments, the linker includes an unsubstituted C 6 to Ci 6 alkylene. In embodiments, the linker may be a substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene.
• the linker may be a substituted or unsubstituted C1-C4 0 alkylene, substituted or unsubstituted 2 to 40 membered heteroalkylene, substituted or unsubstituted C 3 -C 8 cycloalkylene, substituted or unsubstituted 3 to 8 membered heterocycloalkylene, substituted or unsubstituted C 6 -Cio arylene, or substituted or unsubstituted 5 to 10 membered heteroarylene.
• the linker may be an unsubstituted C1-C4 0 alkylene, unsubstituted 2 to 40 membered heteroalkylene, unsubstituted C 3 -C 8 cycloalkylene, unsubstituted 3 to 8 membered heterocycloalkylene, unsubstituted C 6 - C1 0 arylene, or unsubstituted 5 to 10 membered heteroarylene.
• the linker may be a substituted 2 to 40 membered heteroalkylene.
• a linker may be a bond, nucleic acid sequence, two nucleic acid sequences, DNA sequence, two DNA sequences, nucleic acid analog sequence, substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted
• cycloalkylene substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene.
• the linker is or contains a substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene (e.g. substituted or unsubstituted alkylene groups connected by phosphate diester linker groups), substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene.
• substituted or unsubstituted alkylene substituted or unsubstituted heteroalkylene (e.g. substituted or unsubstituted alkylene groups connected by phosphate diester linker groups), substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene.
• the linker is a substituted or unsubstituted C1-C2 0 alkylene, substituted or unsubstituted 2 to 20 membered heteroalkylene, substituted or unsubstituted C 3 -C 8 cycloalkylene, substituted or unsubstituted 3 to 8 membered heterocycloalkylene, substituted or unsubstituted C 6 -Cio arylene, or substituted or unsubstituted 5 to 10 membered heteroarylene.
• the linker is an
• the linker is an unsubstituted C1-C2 0 alkylene.
• the linker is a substituted or unsubstituted C1-C4 0 alkylene, substituted or unsubstituted 2 to 40 membered heteroalkylene, substituted or unsubstituted C 3 -C 8 cycloalkylene, substituted or unsubstituted 3 to 8 membered
• the linker is a substituted or unsubstituted C1-C4 0 alkylene. In embodiments, the linker is a substituted or unsubstituted 2 to 40 membered heteroalkylene. In embodiments, the linker is a substituted 2 to 40 membered heteroalkylene. In embodiments, the linker includes alkyl phosphates (e.g., propyl phosphates).
• the linker consists of alkyl phosphates (e.g., propyl phosphates) bonded to the reminder of the compound by phosphates at both ends. In embodiments, the linker consists of 1-5 alkyl phosphates (e.g., propyl phosphates) bonded to the reminder of the compound by phosphates at both ends. In embodiments, the linker consists of 1-4 alkyl phosphates (e.g., propyl phosphates) bonded to the reminder of the compound by phosphates at both ends.
• the linker consists of 4 alkyl phosphates (e.g., propyl phosphates) bonded to the reminder of the compound by phosphates at both ends.
• alkyl phosphates e.g., propyl phosphates
• a linker consisting of alkyl phosphates that is bonded to the remainder of the compound by phosphates on both ends will have one more phosphate than alkylene groups (e.g., a linker consisting of 4 alkyl phosphates that is bonded to the reminder of the compound by phosphates at both ends will have five phosphates and four alkyl groups with alternating phosphate groups and alkyl groups).
• saRNA may include modifications such as 2' O-Methyl, 2'-deoxy- 2'fluoro, 2'-deoxy, a universal base, 5-C-methyl, an inverted deoxy abasic residue incorporation, or a locked nucleic acid, or any combination(s) thereof.
• the saRNA may have a modification positioned at the terminal nucleobase of the saRNA.
• the saRNA may not have a modification positioned at the terminal nucleobase of the saRNA.
• the modification of the saRNA protects the compound against serum-derived nucleases.
• the saRNA includes a guide strand (antisense or AS) sequence of 5 ' GACC AGUGAC AAUGACCGC UU 3' [SEQ ID NO: 1] or a sequence having 90%-99% homology to SEQ ID NO: 1, and a passenger strand (sense strand or SS) sequence of 3' ⁇ CUGG?7CAC£/G£/UAC£/GGCG 5' [SEQ ID NO: 2] or a sequence having 90%-99% homology to SEQ ID NO: 2.
• a saRNA of the present disclosure may include a guide strand (AS) sequence of 5 '
• the saRNA includes a guide strand (AS) sequence of 5'UUAGGAAGGCUUUCCGUAA 3' [SEQ ID NO: 5] or a sequence having 90%-99% homology to SEQ ID NO: 5, and a passenger strand (SS) sequence of
• SEQ ID NO: 6 3'AAUCCUUCCGAAAGGCAUU 5' [SEQ ID NO: 6] or a sequence having 90%-99% homology to SEQ ID NO: 6.
• the phosphorothioated oligodeoxynucleotide (ODN)-saRNA/ASO conjugate has a terminal moiety.
• a terminal moiety is a chemically reactive moiety, detectable moiety, therapeutic moiety (e.g. anti-cancer agent or anti-viral agent), nucleic acid sequence, DNA sequence, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted
• heterocycloalkyl substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.
• a terminal moiety is a chemically reactive moiety, detectable moiety, therapeutic moiety (e.g. anti-cancer agent or anti-viral agent), nucleic acid sequence, DNA sequence, nucleic acid analogs, R ⁇ substituted or unsubstituted alkyl, R ⁇ substituted or unsubstituted heteroalkyl, R ⁇ substituted or unsubstituted cycloalkyl, R ⁇ substituted or unsubstituted heterocycloalkyl, R ⁇ substituted or unsubstituted aryl, or R 1 -substituted or unsubstituted heteroaryl.
• therapeutic moiety e.g. anti-cancer agent or anti-viral agent
• an phosphorothioated oligodeoxynucleotide (ODN)-saRNA/ASO conjugate includes a terminal moiety, which is a detectable moiety.
• the phosphorothioated oligodeoxynucleotide (ODN)-saRNA/ASO conjugate includes terminal detectable moiety such as, a fluorescent dye, electron-dense reagent, enzyme, biotin, digoxigenin, paramagnetic molecule, paramagnetic nanoparticle, contrast agent, magnetic resonance contrast agent, X-ray contrast agent, Gadolinium, radioisotope, radionuclide, fluorodeoxyglucose, gamma ray emitting radionuclide, positron-emitting radionuclide, biocolloid, microbubble, iodinated contrast agent, barium sulfate, thorium dioxide, gold, gold nanoparticle, gold nanoparticle aggregate, fluoro
• the phosphorothioated oligodeoxynucleotide (ODN)-saRNA/ASO conjugate includes a terminal moiety, which is a therapeutic moiety (e.g. , anti-cancer agent or anti- viral agent).
• the phosphorothioated oligodeoxynucleotide (ODN)-saRNA/ASO conjugate includes a terminal moiety, which is a substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or
• the phosphorothioated oligodeoxynucleotide (ODN)-saRNA/ASO conjugate includes a terminal moiety, which is a substituted or unsubstituted C1-C4 0 alkyl, substituted or unsubstituted 2 to 40 membered heteroalkyl, substituted or unsubstituted C 3 -C 8 cycloalkyl, substituted or unsubstituted 3 to 8 membered heterocycloalkyl, substituted or unsubstituted C 6 -Cio aryl, or substituted or unsubstituted 5 to 10 membered heteroaryl.
• the phosphorothioated oligodeoxynucleotide (ODN)-saRNA/ASO conjugate includes a terminal moiety, which is a substituted C1-C4 0 alkyl, substituted 2 to 40 membered heteroalkyl, substituted C 3 -C 8 cycloalkyl, substituted 3 to 8 membered heterocycloalkyl, substituted C 6 -Cio aryl, or substituted 5 to 10 membered heteroaryl.
• the terminal moiety is an R ⁇ substituted C1-C4 0 alkyl
• the terminal moiety is an R ⁇ substituted C1-C4 0 alkyl. In embodiments, the terminal moiety is an -(unsubstituted C1-C4 0 alkylene)-R 1 .
• the terminal moiety is an -(unsubstituted linear C1-C4 0 alkylene)-R 1 . In embodiments, the terminal moiety is an -(unsubstituted C 3 -C21 alkylene)-R 1 . In
• the terminal moiety is an -(unsubstituted C 3 -C1 8 alkylene)-R 1 .
• the terminal moiety is an -(unsubstituted linear C 3 -Q5 alkylene)-R 1 . In embodiments, the terminal moiety is an -(unsubstituted linear C6-C21 alkylene)-R 1 . In embodiments, the terminal moiety is an -(unsubstituted linear C9-C21 alkylene)-R 1 . In embodiments, the terminal moiety is an -(unsubstituted linear C9-C18 alkylene)-R 1 . In embodiments, the terminal moiety is an -(unsubstituted linear C9-C15 alkylene)-R 1 .
• the terminal moiety is an -(unsubstituted linear C12-C15 alkylene)-R 1 . In embodiments, the terminal moiety is an -(unsubstituted linear Ci 2 alkylene)-R 1 . In embodiments, the terminal moiety is an -(unsubstituted linear C 13 alkylene)-R 1 . In embodiments, the terminal moiety is an -(unsubstituted linear Ci 4 alkylene)-R 1 . In embodiments, the terminal moiety is an -(unsubstituted linear C 15 alkylene)-R 1 . In embodiments, the terminal moiety is an R 1 -substituted 2 to 40 membered heteroalkyl. In embodiments, the terminal moiety is an -(unsubstituted 2 to 40 membered
• the terminal moiety is a -(substituted linear 2 to 40 membered heteroalkylene)-R 1 . In embodiments, the terminal moiety is a -( substituted 5 to 40 membered heteroalkylene)-R 1 . In embodiments, the terminal moiety is a -( substituted 10 to 40 membered heteroalkylene)-R 1 . In embodiments, the terminal moiety is a -( substituted 15 to 40 membered heteroalkylene)-R 1 . In embodiments, the terminal moiety is a -( substituted 20 to 40 membered heteroalkylene)-R 1 .
• the terminal moiety is a -( substituted 30 to 40 membered heteroalkylene)-R 1 . In embodiments, the terminal moiety is a -( substituted 2 to 35 membered heteroalkylene)-R 1 . In embodiments, the terminal moiety is a -( substituted 2 to 30 membered heteroalkylene)-R 1 . In embodiments, the terminal moiety is a -( substituted 2 to 25 membered heteroalkylene)-R 1 . In embodiments, the terminal moiety is a -( substituted 2 to 20 membered heteroalkylene)-R 1 . In embodiments, the terminal moiety is a -( substituted 2 to 10 membered heteroalkylene)-R 1 .
• the terminal moiety is a -( substituted 2 to 50 membered heteroalkylene)-R 1 . In embodiments, the terminal moiety is a -( substituted 2 to 60 membered heteroalkylene)-R 1 .
• the phosphorothioated oligodeoxynucleotide (ODN)-saRNA/ASO conjugate includes a terminal moiety, which is a substituted 2 to 40 membered heteroalkyl. In embodiments, the phosphorothioated oligodeoxynucleotide (ODN)-saRNA/ASO conjugate includes a terminal moiety, which is a substituted 10 to 50 membered heteroalkyl. In embodiments, the phosphorothioated oligodeoxynucleotide (ODN)-saRNA/ASO conjugate includes a terminal moiety, which is a substituted 20 to 40 membered heteroalkyl.
• the phosphorothioated oligodeoxynucleotide (ODN)-saRNA/ASO conjugate includes a terminal moiety, which is a substituted 25 to 40 membered heteroalkyl. In embodiments, the phosphorothioated oligodeoxynucleotide (ODN)-saRNA/ASO conjugate includes a terminal moiety, which is a substituted 30 to 40 membered heteroalkyl.
• the phosphorothioated oligodeoxynucleotide (ODN)-saRNA/ASO conjugate includes a terminal moiety with a R 1 group, in which R 1 is a detectable moiety or a therapeutic moiety.
• ODN-saRNA/ASO conjugate terminal moiety is a detectable moiety.
• R 1 in the phosphorothioated oligodeoxynucleotide (ODN)-saRNA/ASO conjugate is a detectable moiety, which is a fluorescent dye, electron-dense reagent, enzyme, biotin, digoxigenin, paramagnetic molecule, paramagnetic nanoparticle, contrast agent, magnetic resonance contrast agent, X-ray contrast agent, Gadolinium, radioisotope, radionuclide,
• oligodeoxynucleotide (ODN)-saRNA/ASO conjugate terminal moiety is a therapeutic moiety (e.g. , anti-cancer agent or anti- viral agent).
• R 1 in the phosphorothioated oligodeoxynucleotide (ODN)-saRNA/ASO conjugate terminal moiety is H.
• R 1 in the phosphorothioated oligodeoxynucleotide (ODN)-saRNA/ASO conjugate terminal moiety is oxo.
• R 1 in the phosphorothioated oligodeoxynucleotide (ODN)- saRNA/ASO conjugate terminal moiety is oxygen.
• R 1 in the phosphorothioated oligodeoxynucleotide (ODN)- saRNA/ASO conjugate terminal moiety is oxygen. In embodiments, R 1 in the
• phosphorothioated oligodeoxynucleotide (ODN)-saRNA/ASO conjugate terminal moiety is sulfur.
• the ODN nucleic acid sequence of the compound includes unmethylated CpG or GpC motif.
• the CpG nucleic acid sequence includes a Class A CpG nucleic acid sequence, a Class B CpG nucleic acid sequence, or a Class C CpG nucleic acid sequence.
• the GpC nucleic acid sequence includes a Class A GpC nucleic acid sequence, a Class B GpC nucleic acid sequence, or a Class C GpC nucleic acid sequence.
• the compound includes phosphorothioated oligodeoxynucleotide (ODN) in which C and G (CpG or GpC) are nucleotides connected by a phosphodiester internucleotide linkage.
• ODN phosphorothioated oligodeoxynucleotide
• the compound includes CpG or GpC, wherein C and G are nucleotides connected by a phosphodiester derivative internucleotide linkage.
• a Toll-like receptor (TLR)-binding DNA substituent is a Class A CpG oligodeoxynucleotide (ODN).
• a TLR-binding DNA substituent is a Class B CpG oligodeoxynucleotide (ODN).
• a TLR-binding DNA substituent is a Class C CpG oligodeoxynucleotide (ODN).
• a TLR-binding DNA substituent e.g., TLR9-binding DNA substituent
• phoshorothioation one non-bridging oxygen on the 3' adjacent phosphate replaced with sulfur
• nucleotides for example GGGGGG is GG*G*G*G*G in 5'- G*G*TGCATCGATGCAG G*G*G*G-3', where the asterix (*) is placed between the bases (more accurately: nucleosides) and the phosphorothioated phosphate is also placed between bases);
• the compounds of the present disclosure include combination of one of phosphorothioated oligodeoxynucleotides (ODN) of SEQ ID NOs: 7-18, 29-30, and 98-101 with CEBPA saRNA (SEQ ID NOs: 1-2), p21 saRNA (SEQ ID NOs: 3-4), or p53 saRNA (SEQ ID NOs: 5-6), joined by a linker, as described in the present disclosure.
• ODN phosphorothioated oligodeoxynucleotides
• the compounds of the present disclosure include combination of one of phosphorothioated oligodeoxynucleotides (ODN) of SEQ ID NOs: 7-18, 29-30, and 98-101, with one of SEQ ID NOs: 31-42 and 110-113, joined by a linker, as described in the present disclosure. Examples of combination of the compounds are listed in Tables 2-4.
• the compound binds an endosomal TLR. In embodiments, the compound preferentially binds an endosomal TLR over other TLR. In embodiments, the compound specifically binds an endosomal TLR. In embodiments, the compound binds TLR3. In embodiments, the compound preferentially binds TLR3 over other TLR. In embodiments, the compound specifically binds TLR3. In embodiments, the compound binds TLR7. In embodiments, the compound preferentially binds TLR7 over other TLR. In embodiments, the compound specifically binds TLR7. In embodiments, the compound binds TLR8. In embodiments, the compound preferentially binds TLR8 over other TLR.
• the compound specifically binds TLR8. In embodiments, the compound binds TLR9. In embodiments, the compound preferentially binds TLR9 over other TLR. In embodiments, the compound specifically binds TLR9. In embodiments, the compound includes CpG, wherein C and G are nucleotides connected by a phosphodiester
• internucleotide linkage or phosphodiester derivative internucleotide linkage.
• the TLR-binding DNA substituent is a Class A CpG
• the TLR-binding DNA substituent is a Class B CpG oligodeoxynucleotide (ODN). In embodiments, the TLR-binding DNA substituent is a Class C CpG oligodeoxynucleotide (ODN). In embodiments, the TLR-binding DNA substituent is ODN 1585, ODN 2216, ODN D19, or ODN 2336. In embodiments, the TLR- binding DNA substituent is ODN 1668, ODN 1826, ODN 2006, or ODN 2007. In embodiments, the TLR-binding DNA substituent is ODN 2395 or ODN M362.
• the TLR-binding DNA substituent is a derivative of ODN 1585, ODN 2216, ODN D19, ODN 2336, ODN 1668, ODN 1826, ODN 2006, ODN 2007, ODN 2395 or ODN M362.
• a derivative of ODN 1585, ODN 2216, ODN D19, ODN 2336, ODN 1668, ODN 1826, ODN 2006, ODN 2007, ODN 2395 or ODN M362 includes one or more (e.g. , 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10) nucleotide substitutions (e.g. , A, C, G, or T substituted with a different nucleotide).
• a derivative of ODN 1585, ODN 2216, ODN D19, ODN 2336, ODN 1668, ODN 1826, ODN 2006, ODN 2007, ODN 2395 or ODN M362 includes one or more (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10) internucleotide linkage replacements (e.g. , phosphodiester replaced with a phosphodiester derivative or a phosphodiester derivative replaced with a phosphodiester).
• a derivative of ODN 1585, ODN 2216, ODN D19, ODN 2336, ODN 1668, ODN 1826, ODN 2006, ODN 2007, ODN 2395 or ODN M362 includes one or more (e.g.
• nucleotide deletions 1, 2, 3, 4, 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, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100) nucleotide deletions.
• a derivative of ODN 1585, ODN 2216, ODN D19, ODN 2336, ODN 1668, ODN 1826, ODN 2006, ODN 2007, ODN 2395 or ODN M362 includes one or more (e.g. , 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10) nucleotide additions.
• the compound includes a phosphodiester derivative linkage (e.g., phosphoramidate, phosphorodiamidate, phosphorothioate, phosphorodithioate,
• the compound includes a plurality of phosphodiester derivative linkages (e.g., phosphoramidate, phosphorodiamidate, phosphorothioate, phosphorodithioate,
• the compound includes a phosphodiester derivative linkage (e.g., phosphoramidate, phosphorodiamidate, phosphorothioate, phosphorodithioate, phosphonocarboxylic acids, phosphonocarboxylates, phosphonoacetic acid, phosphonoformic acid, methyl phosphonate, boron phosphonate, or O-methylphosphoroamidite linkages) in the TLR9-binding DNA substituent.
• a phosphodiester derivative linkage e.g., phosphoramidate, phosphorodiamidate, phosphorothioate, phosphorodithioate, phosphonocarboxylic acids, phosphonocarboxylates, phosphonoacetic acid, phosphonoformic acid, methyl phosphonate, boron phosphonate, or O-methylphosphoroamidite linkages
• the compound includes a phosphodiester derivative linkage (e.g., phosphoramidate, phosphorodiamidate, phosphorothioate, phosphorodithioate, phosphonocarboxylic acids, phosphonocarboxylates, phosphonoacetic acid, phosphonoformic acid, methyl phosphonate, boron phosphonate, or O- methylphosphoroamidite linkages) in the TLR-binding nucleic acid (e.g. , endosomal TLR-, TLR3-, TLR7-, TLR8-, or TLR9-binding nucleic acid) substituent.
• a phosphodiester derivative linkage e.g., phosphoramidate, phosphorodiamidate, phosphorothioate, phosphorodithioate, phosphonocarboxylic acids, phosphonocarboxylates, phosphonoacetic acid, phosphonoformic acid, methyl phosphonate, boro
• the phosphodiester derivative linkage in the CpG nucleic acid sequence may be phosphoramidate linkage, phosphorodiamidate linkage, phosphorothioate linkage, phosphorodithioate linkage, phosphonocarboxylic acid linkage,
• one or more of the nucleic acid internucleotide linkages in the compound is a phosphodiester derivative linkage (e.g., phosphoramidate,
• the present disclosure includes a compound linking CpG to an antisense oligonucleotide targeting CEBPA.
• the OND-saRNA is present in the cytoplasm (and in the cell nucleus).
• Antisense oligonucleotide conjugates affects gene expression as a result of RNaseH-mediated effects on the antisense oligonucleotides.
• the present disclosure includes a compound linking an OND to an antisense oligonucleotide targeting STAT.
• present disclosure includes compounds of ODN-STAT3-ASO (antisense), as listed in Tables 2, 3, and/or 4.
• the present disclosure provides pharmaceutical compositions including a pharmaceutically acceptable excipient and a compound disclosed herein.
• the composition includes a second therapeutic agent.
• the second therapeutic agent is an anti-cancer agent.
• the second therapeutic agent may be part of the same unit dosage or part of a separate unit dosage. The second therapeutic agent is not one of compounds listed in Tables 1-4 or derivatives thereof.
• the present disclosure includes compositions of a combination of a compound of the present disclosure with one or more additional anti-cancer therapies, e.g. , an anti-VEGF antibody, or anti-STAT agents.
• additional anti-cancer therapies include, without limitation, surgery, radiation therapy (radiotherapy), biotherapy, immunotherapy, chemotherapy (e.g., temozolomide), or a combination of these therapies.
• cytotoxic agents, anti-angiogenic and anti-proliferative agents can be used in combination with a composition including a compound of the present disclosure.
• the disclosure includes treating cancer, by administering effective amounts of a compound of the present disclosure and a chemotherapeutic agents to a subject diagnosed with cancer.
• chemotherapeutic agents may be used in the combined treatment methods and uses of the present disclosure.
• the chemotherapeutic agent may be temolozolomide.
• the chemotherapeutic agent may be administered concommitantly with radiotherapy.
• the combined treatment may involve administration which includes simultaneous administration, using separate formulations or a single pharmaceutical formulation, and consecutive administration in either order, where there may be a time period when both (or all) active agents simultaneously exert their biological activities.
• Preparation and dosing schedules for such chemotherapeutic agents may be used according to
• the chemotherapeutic agent may precede, or follow administration of a compound or composition of the present disclosure or may be given simultaneously therewith.
• other therapeutic agents useful for combination tumor therapy with a compound of the present disclosure include antagonist of other factors that are involved in tumor growth, such as VEGF, EGFR, ErbB3, ErbB4, STAT or TNF. Sometimes, it may be beneficial to also administer one or more cytokines to the subject.
• a compound or composition of the present disclosure is co-administered with a growth inhibitory agent.
• the growth inhibitory agent may be administered first, followed by the compound or composition of the present disclosure.
• simultaneous administration or administration of a compound or composition of the present disclosure first may be possible. Suitable dosages for the growth inhibitory agent are those presently used and may be lowered due to the combined action (synergy) of the growth inhibitory agent and a compound of the present disclosure.
• the formulation herein may also contain more than one active compound as necessary for the particular indication being treated, e.g. , those with complementary activities that do not adversely affect each other.
• active compound e.g., those with complementary activities that do not adversely affect each other.
• the composition may include a chemotherapeutic agent, or a cytotoxic agent.
• Such molecules may be suitably present in combination in amounts that are effective for the purpose intended.
• other therapeutic agents useful for combination cancer therapy with a compound or composition of the present disclosure include other anti- angiogenic agents.
• Many anti-angiogenic agents have been identified and are known in the arts, including those listed by Carmeliet and Jain (2000).
• a compound or composition of the present disclosure is used in combination with another CEBPA antagonist, neutralizing anti-CEBPA antibodies, low molecule weight inhibitors of CEBPA, and any combinations thereof.
• the present disclosure includes a composition including a CpG nucleic acid sequence conjugated to a short- activating RNA (saRNA) and a compound including a TLR-binding nucleic acid substituent conjugated to a STAT-binding DNA substituent.
• the STAT is human STAT1, STAT2, STAT3, STAT4, STAT5A, STAT5B, or STAT6.
• the TLR9-binding DNA substituent includes a CpG motif.
• the TLR9-binding DNA substituent includes an unmethylated CpG motif.
• the TLR9-binding DNA substituent includes a DNA sequence capable of forming a G-quadruplex.
• the TLR9- binding DNA substituent includes a Class A CpG DNA sequence, a Class B CpG DNA sequence, or a C-type CpG DNA sequence.
• the STAT3-binding DNA substituent includes a first STAT3 -binding DNA sequence covalently bound to a second STAT3 -binding DNA sequence by a linker;
• the present disclosure includes a composition linking CpG to an antisense oligonucleotide targeting CEBPA.
• the ODN-saRNA is present in the cytoplasm (and in the cell nucleus).
• the nuclear delivery of ODN- Antisense oligonucleotide conjugates affects gene expression as a result of RNaseH-mediated effects on the antisense oligonucleotides.
• the present disclosure includes a composition linking ODN to an antisense oligonucleotide targeting STAT.
• a composition linking ODN to an antisense oligonucleotide targeting STAT for example, three ODN-STAT3-ASO
• the linker represented by "x" in Table 2 is -(CH 2 )n-P0 4 -[(CH2)n-P0 4 ] z -(CH 2 )n, in which the symbol n is an integer from 1 to 5 (e.g., 3) and the symbol z is an integer from 0 to 50 (e.g. from 0 to 25, 0 to 10, or 0 to 5).
• n is 3 and z is 0 to 5 or 1 to 5.
• n is 3 and z is 0 to 4 or 1 to 4.
• n is 3 and z is 0 to 3 or 1 to 3.
• n is 3 and z is 3.
• the nucleobases in the CpG sequence may include a phosphorothioate internucleotide linkage.
• the linker may have the structure below, where the linker connects with the 3' phosphate of the guanine on one end and the 5' phosphate of the thymidine on the other end, and the nucleobases in the antisense part may be modified with 2'OMe.
• the linker is a substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene.
• a linker connects the TLR9-binding DNA substituent and the STAT3-binding DNA substituent.
• the linker is a substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene.
• the present disclosure includes a composition including a CpG nucleic acid sequence conjugated to a short- activating RNA (saRNA) and a compound listed in Table 3.
• saRNA short- activating RNA
• Table 3 Compound and component sequences.
• GpC(A)-ODN- 5' GGT GCA TGC ATG CAG GGGGG xxxxx CTA TTT 61 STAT3 ASOl GGA TGT CAGC 3'
• GpC(A)-ODN- 5' GGT GCA TGC ATG CAG GGGGG xxxxx 62 STAT3 AS02 CAGCAGATCAAGTCCAGGGA 3'
• GpC(A)-ODN- 5' GGT GCA TGC ATG CAG GGGGG xxxxx TTTTG 63 STAT3 AS03 CATGATGTAA CCACT 3'
• GpC(A)-ODN- 5' GGT GCA TGC ATG CAG GGGGG xxxxx 65 STAT3 LNA ASOl GCA ACC TGA CTT TAGT 3'
• GpC(A)-ODN- 5' GGT GCA TGC ATG CAG GGGGG xxxxx 66 STAT3 LNA AS02 GAT TCT GCT AAT GACG 3'
• GpC(A)-ODN- 5' GGT GCA TGC ATG CAG GGGGG xxxxx 69 STAT3 LNA AS05 GTC AAT GCA CAC T7TA 3'
• GpC(B)-ODN-STAT3 5' TGCTGCTTTTGTGCTTTTGTGCTT xxxxx 71 AS02 CAGCAGATCAAGTCCAGGGA 3'
• GpC(B)-ODN-STAT3 5' TGCTGCTTTTGTGCTTTTGTGCTT xxxxx TTTTG 72 AS03 CATGATGTAACCACT 3'
• GpC(B)-ODN-STAT3 5' TGCTGCTTTTGTGCTTTTGTGCTT xxxxx 73 AS04 ATC AAA GTC ATC CTG GAG 3
• GpC(B)-ODN-STAT3 5' TGCTGCTTTTGTGCTTTTGTGCTT xxxxx 76 LNA AS03 TGA CGG GTC TGA AGTT 3'
• GpC(B)-ODN-STAT3 5' TGCTGCTTTTGTGCTTTTGTGCTT xxxxx 77 LNA AS04 AGA TAG CAG AAG TAGG 3'
• PS-CpG-ODN Sequences (phosphorothioated ASO) PS-CDG-ODN (GGTGCATCGATGCAGGGGGG) rSEO ID NO:1021
• phoshorothioation one non-bridging oxygen on the 3' adjacent phosphate replaced with sulfur
• nucleotides for example GGGGGG is GG*G*G*G*G in 5'- G*G*TGCATCGATGCAG G*G*G*G-3', where the asterix (*) is placed between the bases (more accurately: nucleosides) and the phosphorothioated phosphate is also placed between bases);
• the linker represented by "x" in Table 3 and in Table 4 is -(CH 2 ) n -P0 4 -[(CH 2 ) n - ⁇ 0 4 ] ⁇ -( ⁇ 3 ⁇ 4) ⁇ , in which the symbol n is an integer from 1 to 5 (e.g., 3) and the symbol z is an integer from 0 to 50 (e.g. from 0 to 25, 0 to 10, or 0 to 5). In embodiments, n is 3 and z is 0 to 5, or 1 to 5. In embodiments, n is 3 and z is 0 to 4, or 1 to 4. In embodiments, n is 3 and z is 0 to 3, or 1 to 3. In embodiments, n is 3 and z is 3. Linker "x" may be present multiple times in concatenation (e.g., 1, 2, 3, 4, 5 or even 6 times), wherein n and z are independent for each occurrence of linker "x.”
• the present disclosure includes compositions with an effective dose of a compound of the present disclosure.
• the effective dose may be between about 0.001 mg/kg to about 100 mg/kg of the agent.
• the effective dose of a compound of the present disclosure for treating cancer, enhancing C/EBPA expression in a cell, inhibiting cell growth, and/or reducing STAT transcription factor activity may be between about 0.001 mg/kg to about 0.01 mg/kg of the compound, between about 0.01 mg/kg to about 0.1 mg/kg of the compound, between about 0.1 mg/kg to about 1.0 mg/kg of the compound, between about 1.0 mg/kg to about 5.0 mg/kg of the compound, between about 5.0 mg/kg to about 10 mg/kg of the compound, between about 10 mg/kg to about 15 mg/kg of the compound, between about 15 mg/kg to about 20 mg/kg of the compound, between about 20 mg/kg to about 25 mg/kg of the compound, between about 25 mg/kg to about 30 mg/kg of the compound, between about 30 mg/kg to
• the present disclosure includes compositions with an effective dose of a compound of the present disclosure in which the compound may be between about 0.1% to about 20% w/v of the composition.
• the effective dose of a compound disclosed herein may be between about 0.001% - about 0.01%, between about 0.01% - about 0.1%, between about 0.1% - about 1.0%, between about 1.0% - about 2.0%, between about 2.0% - about 3.0%, between about 3.0% - about 4.0%, between about 4.0% - about 5.0%, between about 5.0% - about 6.0%, between about 6.0% - about 7.0%, between about 7.0% - about 8.0%, between about 8.0% - about 9.0%, between about 9.0% - about 10%, between about 10% - about 11%, between about 11% - about 12%, between about 12% - about 13%, between about 13% - about 14%, between about 14% - about 15%, between about 15% - about 16%, between about 16% - about 17%, between about 17% - about 18%, between about 18% - about 19%, or between about 19% - about 20% w/v of the composition.
• the present disclosure includes a method of enhancing expression gene expression and stimulating immune response, with a compound and/or composition of the disclosure.
• the enhancing expression of a gene and stimulating immune response is achieved with a saRNA conjugated with a phosphorothioated
• oligodeoxynucleotide (ODN) sequence having a CpG sequence oligodeoxynucleotide (ODN) sequence having a CpG sequence.
• ODN oligodeoxynucleotide
• expression of C/EBPA, p21, and p53 is enhanced and immune response is stimulated with saRNA of C/EBPA, p21, and p53, respectively, conjugated with a phosphorothioated
• ODN oligodeoxynucleotide
• the present disclosure includes a method of enhancing expression gene expression, without stimulating immune response, with a compound and/or composition of the disclosure.
• the enhancing expression of a gene without stimulating immune response is achieved with a saRNA conjugated with a phosphorothioated oligodeoxynucleotide (ODN) sequence having a GpC or PS sequence of the present disclosure.
• ODN phosphorothioated oligodeoxynucleotide
• expression of C/EBPA, p21, and p53 is enhanced, without stimulating immune response, with saRNA of C/EBPA, p21, and p53, respectively, conjugated with a phosphorothioated oligodeoxynucleotide (ODN) sequence, e.g., one of SEQ ID NO: 29-30.
• ODN phosphorothioated oligodeoxynucleotide
• the present disclosure includes a method of suppressing a gene with a compound and/or composition while inducing an immunogenic effect.
• the present disclosure provides a method of suppressing a gene, e.g., a STAT, with a compound of one of phosphorothioated oligodeoxynucleotides (ODN) of SEQ ID NOs: 7-18 and 98-101 linked to one of SEQ ID NOs: 31-42 and 110-113.
• ODN phosphorothioated oligodeoxynucleotides
• the method of suppressing STAT gene is achieved with a compound of SEQ ID NOs: 43-60.
• Intravenous (IV) injection of the compound may deliver the compound to the majority of myeloid cells in the bone marrow and significant proportion of myeloid cells, including DCs, in the peripheral lymph nodes (FIGs. 15A - 15B).
• STAT expression is suppressed, while stimulating immune response, in malignant cells and/or tumor-associated immune cells, e.g., myeloid-derived suppressor cells (MDSCs).
• MDSCs are heterogeneous population of immature and potentially immunosuppressive myeloid cells, which play pivotal role in prostate cancer progression and poor patient survival.
• STAT expression is suppressed in hormone -refractory/castration-resistant prostate cancer (CRPC), while simultaneously stimulating immune response.
• CRPC hormone -refractory/castration-resistant prostate cancer
• the present disclosure includes a method of suppressing a gene with a compound and/or composition without inducing an immunogenic effect.
• the present disclosure provides a method of suppressing a gene, e.g., a STAT (one of STATl - STAT5), with a compound, e.g. , of one of phosphorothioated oligodeoxynucleotides
• ODN OTN of SEQ ID NOs: 29-30 linked to, e.g. , one of SEQ ID NOs: 31-42 and 110-113.
• suppression of STAT1-STAT5 is achieved with a compound of SEQ ID NOs: 61- 95, without stimulating an immunogenic effect.
• the compounds of SEQ ID NOs: 78-95 have higher stability compared to compounds of SEQ ID NOs: 61-77.
• STAT expression is suppressed, without stimulating immune response, in malignant cells and/or tumor-associated immune cells, e.g., myeloid-derived suppressor cells (MDSCs).
• STAT expression is suppressed in hormone -refractory/castration-resistant prostate cancer (CRPC), without stimulating immune response.
• CRPC hormone -refractory/castration-resistant prostate cancer
• the present disclosure includes a method of suppressing a gene with a compound and/or composition of the present disclosure while inducing apoptosis.
• the present disclosure provides a method of suppressing a gene, e.g., a STAT (STATl - STAT5), with a compound of, e.g. , one of phosphorothioated
• oligodeoxynucleotides of SEQ ID NOs: 7-18 and 98-101 linked to, e.g. , one of SEQ ID NOs: 31-42 and 110-113.
• ODN oligodeoxynucleotides
• the method of suppressing STATl - STAT5 is achieved with a compound of, e.g. , SEQ ID NOs: 43-60, while inducing apoptosis of the target cells.
• the present disclosure includes a method of suppressing a gene with a compound and/or composition without inducing apoptosis.
• the present disclosure provides a method of suppressing a gene, e.g., a STAT (STATl - STAT5), with a compound of, e.g. , one of phosphorothioated oligodeoxynucleotides (ODN) of SEQ ID NOs: 29-30 linked to, e.g. , one of SEQ ID NOs: 31-42 and 110-113, without inducing apoptosis.
• the method of suppressing STATl - STAT5 is achieved with a compound of, e.g. , SEQ ID NOs: 61-95, without inducing apoptosis of the target cell.
• the present disclosure includes a method of treating cancer and/or a tumor with a compound and/or composition of the disclosure, while inducing an
• the method includes treating cancer and/or a tumor with a compound and/or composition of the disclosure, without inducing an immunogenic effect.
• the cancer may be a hematopoietic cell cancer. In embodiments, the cancer is not a hematopoietic cell cancer. In embodiments, the cancer is myeloma or acute myeloid leukemia. In embodiments, the cancer is prostate cancer (e.g., hormone- refractory/castration-resistant prostate cancer (CRPC)), breast cancer, glioblastoma, ovarian cancer, lung cancer, head and neck cancer, esophageal cancer, skin cancer, melanoma, brain cancer, colorectal cancer, leukemia, lymphoma, or myeloma.
• prostate cancer e.g., hormone- refractory/castration-resistant prostate cancer (CRPC)
• breast cancer glioblastoma, ovarian cancer, lung cancer, head and neck cancer, esophageal cancer, skin cancer, melanoma, brain cancer, colorectal cancer, leukemia, lymphoma, or myeloma.
• the compound or the composition is administered to the subject by intravenous, parenteral, subcutaneous, intramuscular, transdermal, intraperitoneal, intranasal, aerosol, oral, or topical administration.
• the treatment is dose- dependent of the compound or composition. In embodiments, about 0.001 mg/kg to about
• the present disclosure provides a method of treating cancer in a subject in need thereof, the method including administering to the subject an effective amount of a compound or the pharmaceutical composition including a compound disclosed herein.
• the present disclosure provides a method of treating cancer and stimulating an immune response in a subject in need thereof, the method including administering to the subject an effective amount of a compound or a pharmaceutical composition including a compound of one of phosphorothioated oligodeoxynucleotides (ODN) of, e.g. , SEQ ID NOs: 7-18 and 98-
• ODN phosphorothioated oligodeoxynucleotides
• CEBPA saRNA SEQ ID NOs: 1-2
• p21 saRNA SEQ ID NOs: 3- 4
• p53 saRNA SEQ ID NOs: 5-6
• STAT ASOs of, e.g. , SEQ ID NOs: 31-42 and 110-113.
• the method of treating cancer includes administering a subject in need thereof, compound or a composition of a compound of a combination of one of phosphorothioated oligodeoxynucleotides (ODN) of, e.g. , SEQ ID NOs: 7-18, 29-30, and 98- 101, with CEBPA saRNA (SEQ ID NOs: 1-2), p21 saRNA (SEQ ID NOs: 3-4), or p53 saRNA (SEQ ID NOs: 5-6), joined by a linker, as described in the present disclosure.
• ODN phosphorothioated oligodeoxynucleotides
• the method of treating cancer includes administering a subject in need thereof, a compound or a composition of a compound of a combination of one of phosphorothioated oligodeoxynucleotides (ODN) of, e.g. , SEQ ID NOs: 7-18, 29-30, and 98-101, with one of, e.g. , SEQ ID NOs: 31-42 and 110-113, joined by a linker, as described in the present disclosure.
• ODN phosphorothioated oligodeoxynucleotides
• the stimulation of immune response includes maturation, differentiation, or proliferation of natural killer cells, T cells, B cells or myeloid cells.
• the stimulation of immune response includes an increase in Tnl-type immune response.
• the stimulation of immune response may recruit dendritic cells and CD 8+ T cells into an organ of the subject.
• the stimulation of immune response expands population of antigen-presenting cells in the subject.
• the stimulation of immune response suppresses proliferation of cancer cells in the subject.
• the compound or the composition is administered to the subject by intravenous, parenteral, subcutaneous, intramuscular, transdermal, intraperitoneal, intranasal, aerosol, oral, or topical administration in order to stimulate immune response.
• the present disclosure provides a method of enhancing C/EBPa, p21, and/or p53 expression in a cell, and simultaneously inducing immunogenic effect, the method including contacting the cell with an effective amount of a compound or a pharmaceutical composition of a compound of one of phosphorothioated oligodeoxynucleotides (ODN) of, e.g. , SEQ ID NOs: 7-18 and 98-101 linked to one of CEBPA saRNA (SEQ ID NOs: 1-2), p21 saRNA (SEQ ID NOs: 3-4), and p53 saRNA (SEQ ID NOs: 5-6), respectively .
• ODN phosphorothioated oligodeoxynucleotides
• the present disclosure provides a method of inhibiting cell growth including contacting the cell with an effective amount of a compound or a pharmaceutical composition of a compound of one of phosphorothioated oligodeoxynucleotides (ODN) of, e.g. , SEQ ID NOs: 7-18 and 98-101 linked to one of CEBPA saRNA (SEQ ID NOs: 1-2), p21 saRNA (SEQ ID NOs: 3-4), and p53 saRNA (SEQ ID NOs: 5-6), respectively.
• ODN phosphorothioated oligodeoxynucleotides
• the present disclosure provides a method of reducing the activity of a STAT transcription factor in a cell including contacting the cell with an effective amount of a compound or a pharmaceutical composition of one of phosphorothioated oligodeoxynucleotides (ODN) of, e.g. , SEQ ID NOs: 7-18 and 98-101 linked to one of, e.g. , SEQ ID NOs: 31-42 and 110-113.
• ODN phosphorothioated oligodeoxynucleotides
• the cell is a cancer cell.
• the cell is an acute myeloid lymphoid (AML) cell or a prostate cancer cell.
• AML cell is from the bone marrow.
• the cell is a cultured cell in vitro, the cell is in situ in a host, the cell is in a cultured tissue ex vivo.
• the contacting step is free of viral transduction.
• the contacting step is free of viral transduction and the cell is contacted with a compound of the present disclosure or a pharmaceutical composition including a compound of the present disclosure.
• the cell is contacted with about 1 nanomolar to about 100 nanomolar of the compound. All digits and various ranges within this range are also implied.
• CpG-CEBPA saRNA Intravenous injections of CpG-CEBPA saRNA induced expression of C/EBPa protein and led to dose-dependent reduction in the percentage of leukemic cells in blood and in various organs. At 2.5 mg/kg and above repeated injections of CpG-CEBPA saRNA resulted in complete AML eradication. The antitumor efficacy of this strategy seems to be further enhanced by immunostimulatory effect of combined TLR9-triggering and C/EBPa upregulation. In Cbft/MYHll/Mpll leukemia model, i.v. injections of CpG-CEBPA saRNA resulted in recruitment of dendritic cells and CD 8+ T cells into various organs.
• CpG- CEBPA saRNA strategy can provide a novel and cell- selective strategy for therapy of AML and potentially prostate cancer.
• CpG-CEBPA saRNA could allow for expanding population of antigen-presenting cells in cancer patients, while suppressing proliferation of cancer cells.
• CpG ODN part of the conjugate trigger internalization by target cells.
• the endosomal uptake of CpGCEBPA saRNA is mediated through scavenger receptors and leads to interaction with TLR9.
• TLR9 activation generates immunostimulatory signal (signal 1) while also enables release of the conjugate into cytoplasm.
• CpG- CEBPA saRNA eventually reaches nucleus interacting with gene expression machinery and thereby leading to expression of the target gene.
• the C/EBPa protein acts as a transcriptional activator of cell differentiation (signal 2).
• the combination of both immunostimulation and differentiation signals enhance the antigen presentation and result in potent antitumor immune responses.
• STAT3 activity is often triggered by cytokines released in response to stress and inflammation, downstream from Toll-like receptor (TLR) and NF- ⁇ signaling.
• TLR Toll-like receptor
• TLR9/NF-KB/STAT3 signaling axis has a role in the prostate cancer cell self -renewal, tumorigenic potential and therapeutic resistance.
• STAT3 is activated in both malignant cells and tumor-associated immune cells such as myeloid-derived suppressor cells (MDSCs).
• MDSCs myeloid-derived suppressor cells
• the MDSCs are heterogeneous population of immature and potently immunosuppressive myeloid cells which play pivotal role in prostate cancer progression and poor patients' survival.
• TLR9 + granulocytic MDSCs are a population of cells with highly activated STAT3 which accumulated in blood of prostate cancer patients during progression of the disease from localized to metastatic/castration- resistant prostate cancer (mCRPC).
• the strategy is for targeted gene suppression, e.g., in TLR9+ cells in the tumor microenvironment such as myeloid immune cells and B lymphocytes.
• TLR9-positive hematologic malignancies and cancer stem-like cells in solid tumors such as prostate cancers and glioblastoma is treated.
• STAT expression is suppressed, without stimulating immune response, in malignant cells and/or tumor-associated immune cells, e.g., myeloid-derived suppressor cells (MDSCs).
• STAT expression is suppressed in hormone- refractory /castration-resistant prostate cancer (CRPC), while simultaneously stimulating immune response, thereby treating CRPC. Treating Cancer without Stimulating an Immune Response
• the present disclosure provides a method of treating cancer without stimulating an immune response in a subject in need thereof, the method including administering to the subject an effective amount of a compound or a pharmaceutical composition including a compound of, e.g. , one of SEQ ID NOs: 29-30 linked to, e.g. , one of CEBPA saRNA (SEQ ID NOs: 1-2), p21 saRNA (SEQ ID NOs: 3-4), p53 saRNA (SEQ ID NOs: 5-6), or one of STAT ASOs of, e.g. , SEQ ID NOs: 31-42 and 110-113.
• a compound of e.g. , one of SEQ ID NOs: 29-30 linked to, e.g. , one of CEBPA saRNA (SEQ ID NOs: 1-2), p21 saRNA (SEQ ID NOs: 3-4), p53 saRNA (SEQ ID NOs: 5-6), or one of STAT ASOs
• the compound or the composition including a compound of, e.g. , SEQ ID NOs: 29-30 linked to one of CEBPA saRNA (SEQ ID NOs: 1-2), p21 saRNA (SEQ ID NOs: 3-4), p53 saRNA (SEQ ID NOs: 5-6), or one of, e.g. , STAT ASOs of SEQ ID NOs: 31-42 and 110-113, is administered to the subject by intravenous, parenteral, subcutaneous, intramuscular, transdermal, intraperitoneal, intranasal, aerosol, oral, or topical administration in order to treat cancer, without stimulating an immune response.
• the present disclosure provides a method of enhancing C/EBPa, p21, and/or p53 expression in a cell, without simultaneously inducing immunogenic effect, the method including contacting the cell with an effective amount of a compound or a pharmaceutical composition of a compound of, e.g. , one of SEQ ID NOs: 29-30 linked to one of CEBPA saRNA (SEQ ID NOs: 1-2), p21 saRNA (SEQ ID NOs: 3-4), and p53 saRNA (SEQ ID NOs: 5-6), respectively .
• the present disclosure provides a method of inhibiting uncontrolled cell growth and/or proliferation, without simultaneously inducing an immune response, including contacting the cell with an effective amount of a compound or a pharmaceutical composition of a compound of, e.g. , one of SEQ ID NOs: 29-30 linked to one of CEBPA saRNA (SEQ ID NOs: 1-2), p21 saRNA (SEQ ID NOs: 3-4), and p53 saRNA (SEQ ID NOs: 5-6), respectively, or one of STAT ASOs of, e.g. , SEQ ID NOs: 31-42 and 110-113.
• a compound of e.g. , one of SEQ ID NOs: 29-30 linked to one of CEBPA saRNA (SEQ ID NOs: 1-2), p21 saRNA (SEQ ID NOs: 3-4), and p53 saRNA (SEQ ID NOs: 5-6), respectively, or one of STAT ASOs of, e.g.
• the present disclosure provides a method of reducing the activity of a STAT transcription factor in a cell, without simultaneously inducing an immune response, including contacting the cell with an effective amount of a compound or a pharmaceutical composition of, e.g. , one of SEQ ID NOs: 29-30 linked to, e.g. , one of SEQ ID NOs: 31-42 and 110-113.
• the present disclosure provides a method of treating cancer, inhibiting uncontrolled cell growth and/or proliferation, and/or reducing activity of STAT transcription factor in a cell, e.g., a STAT, without inducing immune response, with a compound of, e.g. , one of SEQ ID NOs: 29-30 linked to, e.g.
• the method of includes administering a compound of, e.g. , SEQ ID NOs: 61-95, which do not induce immune response.
• STAT expression is suppressed in hormone- refractory /castration-resistant prostate cancer (CRPC), without stimulating immune response, thereby treating CRPC.
• CRPC hormone- refractory /castration-resistant prostate cancer
• conjugates of CpG oligodeoxynucleotide (ODN), a synthetic TLR9 ligand, with various chemically-modified and nuclease-resistant STAT ASO sequences, e.g., CpG/GpC-ODN-STAT3 ASO, are generated (e.g., SEQ ID NOs: 43-95) (Tables 1, 2, and 4; and FIG. 9A).
• conjugates of CpG oligodeoxynucleotide (ODN), a synthetic TLR9 ligand, with various chemically-modified and nuclease-resistant STAT ASO sequences e.g., CpG/GpC-ODN-STAT3 ASO, (e.g., SEQ ID NOs: 43-95) are administered to TLR9+ cells.
• oligodeoxynucleotide ODN
• synthetic TLR9 ligand TLR9 ligand
• STAT ASO sequences e.g., CpG/GpC-ODN-STAT3 ASO, (e.g., SEQ ID NOs: 43-95) are administered to subjects.
• CpG/GpC-ODN-STAT3 ASO e.g., SEQ ID NOs: 43-95
• linking the CpG ODN to STAT ASO e.g., CpG/GpC-ODN-STAT3 ASO, allows for quick internalization by target TLR9 + cells.
• linking the CpG ODN to STAT ASO e.g., CpG-ODN-
• STAT3 ASO allows for quick internalization by target TLR9+ cells within an hour or less of incubation (e.g., 1 minute, 5 minutes, 10 minutes, 15 minutes, 20 minutes, 25 minutes, 30 minutes, 45 minutes, 50 minutes, 55 minutes or 60 minutes).
• TLR9+ cells include human and mouse immune cells as well as prostate cancer cells (FIGs. 10A-10B and FIGs. 11A- 11B).
• the uptake of CpG-STAT ASO, e.g., CpG-ODN-STAT3 ASO, (e.g., SEQ ID NOs: 43-60) by human and mouse myeloid immune cells is detectable at a concentration of 50 nM or less (e.g., 1 nM, 5 nM, 10 nM, 15 nM, 20 nM, 25 nM, 30 nM, 35 nM, 40 nM, 45 nm, or 50 nM) (FIGs. 10A-10B and FIGs. 1 lA-1 IB).
• intracellular uptake of CpG-STAT ASO e.g., CpG/GpC-ODN-STAT3 ASO, (e.g., SEQ ID NOs: 43-95) is verified using confocal microscopy.
• the conjugate is detectable in the cytoplasm of target cells within 15 min after adding it to culture media (e.g., 30 seconds, 1 minute, 2 minutes, 5 minutes, 10 minutes, 12 minutes, or 15 minutes) (FIGs. 12A-12B).
• the efficient uptake of these conjugates corresponded to improved efficacy of STAT3 knockdown in DU145 and LNCaP-S17 cells within 24 h of incubation often exceeding the effect of the respective ASO alone (FIGs.
• a conjugate of ASO to GpC ODN which does not activate TLR9 also strongly inhibits STAT3 expression (FIGs. 13A-13B).
• CpG-STAT3ASO e.g., SEQ ID NOs: 43-60
• CpG-STATASO e.g., CpG-ODN-STAT3 ASO, (e.g., SEQ ID NOs: 43-60, 78-86) internalization and target knock-down is similarly effective in glioma and microglia cells (FIGs. 17A-17C).
• CpG-STAT ASO conjugate e.g., CpG-ODN-STAT3 ASO, (e.g., SEQ ID NOs: 43-60), but not STAT3 ASO alone or control CpG-scrambled ODN, induces cell death in cells (FIGs. 14A-14B).
• CpG- STAT3 ASO conjugate e.g., SEQ ID NOs: 43-60, 78-86
• STAT3 ASO alone or control CpG-scrambled ODN induces cell death in cells within 24 h of culture (e.g., 30 minutes, 1 hour, 1.5 hours, 2 hours, 3 hours, 5 hours, 10 hours, 12 hours, 16 hours, 20 hours, 24 hours).
• CpG-STAT3 ASO conjugate e.g., SEQ ID NOs: 43-60, 78-86
• CpG-STAT3 ASO conjugate induces cell death in cells within 24 h of culture in the presence of oligonucleotides.
• CpG-STAT3 ASO conjugate e.g., SEQ ID NOs: 43-60, 78-86
• STAT3 ASO alone or control CpG- scrambled ODN induces cell death in cells within 24 h of culture in the presence of oligonucleotides at a concentration of 1-1000 nM (e.g., 500 nM).
• CpG- STAT3 ASO conjugate e.g., SEQ ID NOs: 43-60, 78-86
• STAT3 ASO alone or control CpG-scrambled ODN induces cell death in DU145 and LNCaP-S17 cells within 24 h of culture in the presence of 500 nM of oligonucleotides.
• improved nuclease-resistance of CpG-ASOs e.g., SEQ ID NOs: 61-95
• improved nuclease-resistance of CpG-ASOs allows for systemic administration and targeting of TLR9+ cells in distant organs (e.g., spleen or bone marrow).
• a single intravenous (IV) injection of fluorescently-labeled CpG-STAT3ASO is sufficient to deliver conjugate to a majority of myeloid cells (FIGs. 15A-15C).
• a single intravenous (IV) injection of fluorescently-labeled CpG-STAT3ASO is sufficient to deliver to 50% or more of myeloid cells in the bone marrow (e.g., 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99% or more).
• a single intravenous (IV) injection of fluorescently-labeled CpG- STAT3ASO is sufficient to deliver to a significant proportion of myeloid cells (e.g., 25%, 30%, 35%, 40%, 45%, 50% or more) in peripheral lymph nodes, including dendritic cells.
• administration of repeated (e.g., more than one) IV injections of CpG-STAT3ASO allows for penetration of significant fraction of myeloid cells (e.g., 20%, 25%, or 30% of MDSCs) in brain localized glioma tumors (FIGs. 18A-18C).
• administration of a single local IV injection of CpG-STAT3ASO allows for almost complete penetration (e.g., 75%, 80%, 85%, 90%, 95%, 99.5) of the tumor
• CpG-STAT3ASO e.g., SEQ ID NOs: 43-60, 78-86
• administration of CpG-STAT3ASO is utilized against TLR9 + malignancies.
• CpG-STAT3ASO e.g., SEQ ID NOs: 43-60, 78-86
• enhances target gene knock down and cytotoxicity FIGS. 16A-16C.
• CpG-STAT3ASO reduces tumor size in distant untreated locations (FIG. 19A).
• reduction of STAT3 expression in a distant site correlates with a systemic effect of CpG-STAT3ASO (e.g., SEQ ID NOs: 43-60, 78-86) release from an injection site (FIG. 19B and FIG. 19E).
• CpG-STAT3ASO e.g., SEQ ID NOs: 43-60, 78-86
• treatment using CpG-STAT3ASO reduces expression of STAT3 and PD-L1 immune checkpoint molecules (FIGs. 19C-19D).
• treatment using CpG-STAT3ASO reduces expression of STAT3 and PD-L1 immune checkpoint molecules in myeloid-derived suppressor cells (MDSCs) at the distant tumor site.
• CpG-STAT3ASO e.g., SEQ ID NOs: 43-60, 78-86
• is administered systemically FIGs. 20A-20B).
• the administration route of CpG-STAT3ASO may be IP (intra-peritoneal); PO (per-oral); or IV (intra-venous).
• the administration route is transdermal, subcutaneous, intra-muscular, intra-thecal, intra-ocular, intra-nasal, transmucosal, sublabial, insufflation, enteral, suppository, intra-arterial, intra- articular, intracerebral, intra-cranial, intravitreal, or intratibial.
• subjects are treated using daily intravenous injections of 0.5mg/kg to 5 mg/kg of CpG-STAT3ASO (e.g., SEQ ID NOs: 43-60, 78-86).
• CpG-STAT3ASO e.g., SEQ ID NOs: 43-60, 78-86
• CpG-STAT3ASO induces complete regression of tumors.
• CpG-STAT3ASO e.g., SEQ ID NOs: 61-95
• localized tumors e.g., bone, spleen, bladder, pancreas, testis, ovary, prostate, uterus, colon, lymph node, lung, brain, kidney, liver, stomach, large intestines, small intestines, esophagus, spine, head, neck, skin, or heart.
• nuclease-resistant CpG-STAT3 ASO inhibitors allow for simultaneous targeting of STAT3 signaling in disseminated TLR9 + cells and in tolerogenic tumor-associated cells (FIG. 21).
• nuclease-resistant CpG-STAT3 ASO inhibitors allow for simultaneous targeting of STAT3 signaling in disseminated TLR9+ prostate cancer cells and in tolerogenic tumor-associated immune cells (e.g., macrophages, microglia, T cells, B cells, or MDSCs).
• tumor-associated immune cells e.g., macrophages, microglia, T cells, B cells, or MDSCs.
• disruption of signaling cross talk within the tumor microenvironment is effective in treating cancer.
• the present disclosure includes a method of treating an autoimmune disease and/or disorder with a compound and/or composition of the disclosure, without inducing an immunogenic effect.
• the method includes suppressing of a gene in myeloid cells with a compound and/or composition of the disclosure, without inducing an immunogenic effect.
• the myeloid cells are in a tumor microenvironment, involved in autoimmune disease and/or disorder, or in cancer (e.g., prostate cancer).
• the method includes treating an autoimmune disease and/or disorder (e.g., rheumatoid arthritis, Crohn's disease, ulcerative colitis, multiple sclerosis, psoriasis, systemic lupus erythematosus (SLE)), with a compound and/or composition of the disclosure, without inducing an immunogenic effect.
• an autoimmune disease and/or disorder e.g., rheumatoid arthritis, Crohn's disease, ulcerative colitis, multiple sclerosis, psoriasis, systemic lupus erythematosus (SLE)
• SLE systemic lupus erythematosus
• the present disclosure provides a method of treating an autoimmune disease (e.g., rheumatoid arthritis, Crohn's disease, ulcerative colitis, multiple sclerosis, psoriasis, systemic lupus erythematosus (SLE)) without stimulating an immune response in a subject in need thereof, the method including administering to the subject an effective amount of a compound or a pharmaceutical composition including a compound of, e.g. , one of SEQ ID NOs: 29-30 linked to, e.g. , one of STAT ASOs of SEQ ID NOs: 31-42 and 110-113.
• an autoimmune disease e.g., rheumatoid arthritis, Crohn's disease, ulcerative colitis, multiple sclerosis, psoriasis, systemic lupus erythematosus (SLE)
• SLE systemic lupus erythematosus
• the present disclosure provides a method of treating an autoimmune disease (e.g., rheumatoid arthritis, Crohn's disease, ulcerative colitis, multiple sclerosis, psoriasis, systemic lupus erythematosus (SLE)), without simultaneously inducing an immune response, including contacting the cell with an effective amount of a compound or a pharmaceutical composition of, e.g. , one of SEQ ID NOs: 29-30 linked to, e.g. , one of SEQ ID NOs: 31-42 and 110-113.
• an autoimmune disease e.g., rheumatoid arthritis, Crohn's disease, ulcerative colitis, multiple sclerosis, psoriasis, systemic lupus erythematosus (SLE)
• SLE systemic lupus erythematosus
• the present disclosure provides a method of treating an autoimmune disease (e.g., rheumatoid arthritis, Crohn's disease, ulcerative colitis, multiple sclerosis, psoriasis, systemic lupus erythematosus (SLE)), inhibiting uncontrolled cell growth and/or
• an autoimmune disease e.g., rheumatoid arthritis, Crohn's disease, ulcerative colitis, multiple sclerosis, psoriasis, systemic lupus erythematosus (SLE)
• the method of includes administering a compound of, e.g. , SEQ ID NOs: 61-95, which do not induce immune response.
• the present disclosure provides a method of treating Crohn's disease, without simultaneously inducing an immune response, including contacting the cell with an effective amount of a compound or a pharmaceutical composition of, e.g. , one of SEQ ID NOs: 29-30 linked to, e.g. , one of SEQ ID NOs: 31-42 and 110-113.
• a compound or a pharmaceutical composition of, e.g. , one of SEQ ID NOs: 29-30 linked to, e.g. , one of SEQ ID NOs: 31-42 and 110-113.
• the present disclosure provides a method of treating Crohn's disease, without inducing immune response, with a compound of, e.g. , one of SEQ ID NOs: 29-30 linked to, e.g. , one of SEQ ID NOs: 31-42 and 110-113.
• the method of includes administering a compound of, e.g. , SEQ ID NOs: 61-95, which do not induce immune response.
• the present disclosure includes a method of treating paraplegia in a subject in need thereof, by administering a compound and/or composition of the disclosure, with or without inducing an immunogenic effect.
• the method includes suppressing of a gene in mesenchymal stem cells (MSCs) with a compound and/or composition of the disclosure, with or without inducing an immunogenic effect.
• MSCs mesenchymal stem cells
• the present disclosure provides a method of treating paraplegia without stimulating an immune response in a subject in need thereof, the method including administering to the subject an effective amount of a compound or a pharmaceutical composition including a compound of, e.g. , one of SEQ ID NOs: 29-30 linked to, e.g. , one of STAT ASOs of SEQ ID NOs: 31-42 and 110-113.
• the present disclosure provides a method of treating paraplegia, while
• ODN phosphorothioated oligodeoxynucleotides
• CpG-CEBPA saRNA (SS, sense strand) and CEBPA saRNA (AS, antisense strand) may be synthesized using a cycle including four steps. After the complete synthesis, deprotection, purification and desalting of CpG-CEBPA saRNA (SS) and CEBPA saRNA (AS), the two components may be annealed to produce a compound of the present disclosure CpG-CEBPA saRNA (SS/AS).
• the starting point of the synthesis may be a protected nucleoside linked via its 3'- oxygen to a polystyrene-based solid support.
• Nucleoside phosphoramidite chemistry may be used for this synthesis.
• the synthesis cycle may include the following four steps:
• Step (4) can be substituted with a sulfurization step for the synthesis of phosphorothioated oligonucleotides.
• the synthetic pathway may be as shown in scheme 1 below:
• the heteroalkylene linker allow for further modification, conjugation, or attachment of additional moieties after completion of the synthesis and while the oligonucleotide is still attached to the support.
• the present disclosure includes a CpG nucleic acid sequence conjugated to a saRNA with a substituted heteroalkylene linker, which may allow further modification, conjugation, or attachment during synthesis and while the oligonucleotide is attached to a support.
• the substituted heteroalkylene linker is modified, conjugated, or attached to substituents.
• a modification may include the conversion of the original substituent into a different substituent.
• a bromo-alkane substituent may be converted into an azido-alkane. Conjugation may result in bonding of two large moieties together.
• an NHS derivative may be conjugated with PEG-NH 2 .
• a peptide may also be conjugated with an oligonucleotide or an antibody may be conjugated to an oligonucleotide. Attachment may result in bonding of the small molecule to a large molecule.
• NHS-ester of biotin might be attached to the amino derivative of an oligo.
• the present disclosure includes a CpG nucleic acid sequence conjugated to a saRNA with linkers multiple different linkers, multiple identical linkers, or a substitution of linkers selected from the following groups:
• Fmoc amino-modifier C6 dT introduction of the amino group
• NHS ester and divinyl sulfone and its analogues by reacting with NHS ester and divinyl sulfone and its analogues.
• Amino-modifier Serinol Phosphoramidite introduction of the amino group
• NHS ester and divinyl sulfone and its analogues by reacting with NHS ester and divinyl sulfone and its analogues.
• CpG- CEBPa-saRNA uptake 1 x 10 5 cells were incubated in 500 ⁇ media with indicated saRNA (500 ⁇ , final concentration). 3 h later, cells were washed with PBS twice. PBMCs were stained with anti-CD 14 and anti-CD 19 antibodies to assess uptake by different cell types. Cy3 uptake level was analyzed by flow cytometry.
• CpG-saRNA(-Cy3) localization in DU145 1 x 10 5 DU145 cells were plated on cover slips in a 24-well plate. When cells were -60% confluent, Cy3-labeled CpG-saRNA conjugates were added to the culture at final concentration 500 ⁇ . 2 h or 24 h post transfection, cells were gently washed with PBS with 1 mM MgCl 2 and 0.1 mM CaCl 2 twice and fixed with 0.25 ml 2% paraformaldehyde for 20 min at room temperature.
• the iScript cDNA Synthesis kit (BioRad) was used for reverse transcription.
• a SsoAdvancedTM Universal Probes Supermix (Biorad) was used for Taqman quantitative real-time PCR and results were quantified with a CFX96 Real Time PCR Detection system (BioRad).
• mRNA expression level of CEBPA was normalized to TBP expression.
• the primer sequences used for human CEBPA were:
• CEBP Reporter Assay was performed according to the manufacturer's protocol (Qiagen CCS-OOIL). Briefly, 4 x 10 4 DU145 cells /well were seeded in 96-well plates at 150 ⁇ volume of RPMI supplemented with 2.5% FCS only. 0.6 ⁇ Lipofectamine2000, 1 ⁇ Lucif erase or control plasmid and non-CpG conjugated saRNA (final cone. 50 ⁇ ) in 50 ⁇ OptiMem media (Life Technologies) were added. Luciferase- or control plasmid is only transfected once.
• CpG-conjugated saRNA were added in 50 ⁇ RPMI media directly to wells at final concentration 500 ⁇ every 24 h. Three days later, cells were gently washed with PBS and 50 ⁇ of Passive Lysis Buffer (Promega E194A) was added directly into each well. The lysates were then transferred into white 96-well Optiplates (Perkin Elmer) for Renilla/Firefly Dual Luciferase assay with 50 ⁇ of Luciferase Assay Reagent II (Promega E1910). The plate was then measured for firefly and then for Renilla luciferase. Values were normalized to the activity in the untreated sample. The experiment was performed in triplicates.
• MV4;11 maturation 1 x 10 5 MV4-11 cells were transfected with indicated saRNA (final concentration 500 ⁇ ) every 24 h except for SS/AS which was transfected using Lipofectamine2000 only once. 96 h later, cells were harvested, washed with FACS buffer (PBS with 2% FBS) twice and stained with antibodies specific to hCD86 (FITC), hCD40 (PE), HLADR (APC) and 7-AAD as a viability marker. Expression levels were measured by flow cytometry.
• Cbfbl/56M/Mx-Crel mice were backcrossed to wild-type C57BL/6 mice for >10 generations to generate the syngeneic AML model.
• CpG-STAT3 ASO Design and Synthesis The CpG-ASOs were synthesized in the DNA/RNA Synthesis Core (COH) by linking CpG(D19)-ODN to Stat3 or Scramble ASOs similarly as previously described (Kortylewski et al. Nat. Biotech. 2009).
• Biodistribution C57BL/6 mice (6-8 weeks old) were purchased from the NCI (Frederick, MD). C57BL/6 mice were injected intravenously with 5 mg/Kg with CpG- STAT3Cy3 and euthanized 3 h later. The lymph node and bone marrow were harvested. Single cell suspensions were prepared by mechanic tissue disruption and collagenase D/DNase I treatment as described (Kortylewski et al. Nat. Med 2005) and stained using CD1 lb, CD3, B220, CD1 lc and F4/80 antibodies. The uptake by different population was accessed by flow cytometry.
• Confocal Microscopy DU-145 cells were treated using 500 nM CpG-STAT3 ASO Cy3 labeled for different time points. Cells were fixed with 2% paraformadehyde for 20 min, permeabilized in PBS containing 0.1% Triton X-100 and the nuclei were stained using DRAQ5® 5 min. Slides were mounted in mounting medium (Vector Labs, Burlingame, CA). Confocal imaging was carried out using C-Apochromat 40 x/1.2 water-immersed objectives on cLSM510-Meta inverted confocal microscope (Zeiss, Thornwood, NY). LSM software v.4.2 SP1 was used for image acquisition, and LSM Image Browser v.4,2,0,121 for post- acquisition analysis (Zeiss).
• CpG-CEBPA saRNA (SS, sense strand) and CEBPA saRNA (AS, antisense strand) were synthesized using a cycle consisting of four steps as described in the following sections. After the complete synthesis, deprotection, purification and desalting of CpG-CEBPA saRNA (SS) and CEBPA saRNA (AS), the two components were annealed to produce the drug product CpG-CEBPA saRNA (SS/AS).
• the starting point of the synthesis was a protected nucleoside linked via its 3'- oxygen to a polystyrene-based solid support. Nucleoside phosphoramidite chemistry was used for this synthesis.
• the synthesis cycle consisted of the following four steps:
• Oxidation* *Step (4) can be substituted with a sulfurization step for the synthesis of phosphorothioated oligonucleotides.
• the acid labile dimethoxytrityl (DMT) group of the support-bound monomer was removed with a 5% solution of dichloroacetic acid (DCA) in toluene.
• DCA dichloroacetic acid
• the resulting DMT cation chromophore was quantitated to determine coupling efficiency of the synthetic cycle.
• An orange color was produced by the cleaved DMT carbocation, which absorbed in the visible region at 495 nm. The intensity of this absorbance was used to determine the coupling efficiency.
• Most commercially available DNA synthesizers have hardware to measure and record the detritylation yield for each cycle so that the efficiency of synthesis can be monitored in real time. As the DNA bases are acid- labile, the detritylation step must only be as long as is necessary to ensure complete detritylation.
• CEBPA saRNA The solid support used for the synthesis of CEBPA saRNA (AS) was LCAA-CPG from Prime Synthesis. Synthesis of CEBPA saRNA (AS) at the scale of 0.75 mmole required 9.5 g of support placed in a 46 mL sized column. The product from this reaction should have a mass gain of 11 g. Coupling
• the Coupling Mechanism was a nucleophilic attack by the free 5 ' -hydroxyl group on the 3'-0-phosphorus of the incoming activated monomer. For this reason, a totally hydroxyl-free environment in the column was important to have. To ensure this, dry acetonitrile was used as the general solvent, and all the reagents and solvents were maintained in the anhydrous state. Under these conditions the coupling efficiencies were very high, thereby permitting synthesis of long oligonucleotides.
• CAP A was a 20% solution of 1-methyl-imidazole in anhydrous ACN
• CAP B was generated by mixing equal volumes of CAP B 1 and CAP B2 prior to use, where CAP B 1 as a 40% solution acetic anhydride in anhydrous ACN, and CAP B2 was a 60% solution of 2,6- lutidine in anhydrous ACN.
• the internucleotide linkage was a trivalent phosphite triester that was unstable and must be oxidized to a phosphotriester. This step can be substituted with a sulfurization step for the synthesis of phosphorothioate oligonucleotides. Oxidation Conditions
• Oxidation was conducted with 0.05 M solution of iodine in pyridine: water, 9: 1. Oxidative sulfurization was conducted in a 0.3 M solution of xanthane hydride in anhydrous pyridine.
• Final detritylation is conducted on the synthesizer by wash with a solution of 5% DC A in toluene.
• the oligonucleotide must be removed (cleaved) from the support and fully deprotected prior to use.
• the resin was treated with a solution of 20% diethylamine (DEA) in ACN to deprotect the phosphorus by ⁇ -elimination of the cyanoethyl group.
• DEA diethylamine
• a 60 minute, 55°C treatment with 600 mL of methylamine-ammonium hydroxide mixture (AMA) was used to cleave the oligonucleotide from the support and to remove the protecting groups of the exocyclic amino groups.
• the resulting crude mixture contained the full length oligonucleotide, still carrying the 2' -TBDMS protection on ribose residues, the truncated failure sequences with free 5'-hydroxyl ends and biproducts of deprotection (benzamide, isobutyramide, acrylonitrile, and acetamide).
• the TBDMS protecting groups were removed at the final deprotection step by the basic fluoride ion.
• Deprotection was conducted by treatment with 700 mL of a mixture of triethylamine trihydrofluoride/triethylamine/DMSO, 10:2: 1, at 60°C for 1.5 hrs. The reaction was then cooled to ambient temperature, mixed with 3L of acetone, left at ambient temperature overnight, and centrifuged. The supernatant was separated, representative samples of supernatant were taken (5 x 20 ⁇ _,), evaporated to dryness under the reduced pressure, re- dissolved, and the absorption was measured at 258 nm. If a significant amount of products are still present in the supernatant, another 1 ,000 mL of acetone was added and the mixture was kept at room temperature for an additional 2 hours. After the final centrifugation the supernatant was discarded and pellets were kept under vacuum at room temperature until dry.
• RNA chemical synthesis was identical to that used for DNA, with the exception for the need of an additional protecting group at the 2'-hydroxyl of ribose. This position is usually protected with i ⁇ ?ri-butyldimethyl silyl groups, which are stable throughout the synthesis. They were removed at the final deprotection step by the basic fluoride ion. The remaining positions on both the sugar and the bases were protected in the same fashion as for DNA.
• Annealing complementary strands of nucleic acid comprised the following four steps: 1. Mixed concentrated complementary oligonucleotides together at a 1: 1 molar ratio in a pear shaped round bottomed 1 ,000 mL flask.
• EXAMPLE 3 Targeted CpG-STAT3ASO as an Inhibitor of Tumorigenic and Immunosuppressive Signaling for Metastatic Prostate Cancer Immunotherapy
• the STAT3 transcription factor is a multifaceted oncogene and a master regulator of immunosupression commonly activated in human cancers.
• tumors such as advanced prostate cancers
• STAT3 for their survival, vascularization and metastasis, whereas normal cells do not (Mora, L.B. et al. Cancer Res 62, 6659-66 (2002), Dhir, R. et al. Prostate 51, 241-6 (2002), Lee, S.O. et al. Prostate 60, 303-9 (2004),and Hedvat, M. et al. Cancer Cell 16, 487-97 (2009)).
• STAT3 activation results in tumor progression towards hormone-refractory/castration-resistant prostate cancer (CRPC) phenotype and poor patients' survival.
• STAT3 activity is often triggered by cytokines released in response to stress and inflammation, downstream from Toll-like receptor (TLR) and NF- ⁇ signaling.
• TLR Toll-like receptor
• TLR9/NF-KB/STAT3 signaling axis plays a role in the prostate cancer cell self- renewal, tumorigenic potential and therapeutic resistance. As a unique a point of
• STAT3 is activated in both malignant cells and tumor-associated immune cells such as myeloid-derived suppressor cells (MDSCs).
• MDSCs myeloid-derived suppressor cells
• immunosuppressive myeloid cells which play pivotal role in prostate cancer progression and poor patients' survival.
• a population of TLR9+ granulocytic MDSCs (G-MDSCs; Lin-HLA-DR-CD 14- CD15HICD33LO) have highly activated STAT3 which accumulates in blood of prostate cancer patients during progression of the disease from localized to metastatic/castration- resistant prostate cancer (mCRPC).
• the inhibitory effects of these G-MDSCs on T cell proliferation rely on the STAT3-mediated expression of Arginase-1 (ARG-1), thereby potently inhibiting T-cell proliferation and activity. Rapid internalization of CpG ODN conjugates in immune and prostate cancer cells
• Conjugates of CpG oligodeoxynucleotide (ODN) were generated, a synthetic TLR9 ligand, with various chemically-modified and nuclease-resistant STAT3 ASO sequences (Tables 1-4, and FIGs. 9A-9C).
• Linking of the CpG ODN to STAT3 ASO allowed for quick internalization by target TLR9+ cells such as human and mouse immune cells as well as prostate cancer cells within one hour of incubation (FIGs. 10A-10B (human), and FIGs. 11A- 11B (mouse), respectively).
• target TLR9+ cells such as human and mouse immune cells as well as prostate cancer cells within one hour of incubation
• FIGs. 10A-10B human
• FIGs. 11A- 11B mouse
• FIGs. 15A- 15B Improved nuclease-resistance of CpG-ASOs, allowed for systemic administration and targeting of TLR9+ cells in distant organs, such as spleen or bone marrow.
• a single intravenous (IV) injection of fluorescently-labeled CpG-STAT3ASO delivered the conjugate to the majority of myeloid cells in the bone marrow and significant proportion of myeloid cells, including DCs, in peripheral lymph nodes (FIGs. 15A-15B).
• the experiments on human B cell lymphoma cells suggest that CpG-STAT3ASO strategy can be utilized against other TLR9+ malignancies, enhancing target gene knock down and cytotoxicity (FIGs. 16A-16C).
• CpG-ASOs were synthesized in the DNA/RNA Synthesis Core (COH) by linking CpG(D19)-ODN to Stat3 or Scramble ASOs similarly as previously described (Kortylewski et al. Nat. Biotech. 2009).
• Healthy PBMCs were derived from anonymous donors under IRB#13378 from the Donor Aphaeresis Center at CoH. Sample acquisition was approved by the institutional review board in accordance with the Declaration of Helsinki.
• Human PC3 and DU-145 prostate cancer cells were purchased from American Type Culture Collection, while the LnCaP S17 stably expressing IL-6 were from Vaccine and Gene Institute, FL.
• Mouse Myc- CaP cells, RM1 and RM9 were obtained from respective original sources.
• Human LNCaP, DU145, PC3 prostate cancer cells were originally derived from ATCC and authenticated.
• Human OCI-Ly3, RL, Jeckol and RECl B cell non-Hodgkin lymphoma cells were obtained from City of Hope. Flow cytometry
• C57BL/6 mice (6-8 weeks old) were purchased from the NCI (Frederick, MD). Animal care/procedures were performed in accordance with established institutional guidance and approved protocols from the IACUC (COH). Mice were injected subcutaneously in two sites with 2xl0 5 RM9 cells. The tumor growth was assessed using a caliper. Mice with established tumors were treated using intratumoral injection with various CpG-conjugates (5mg/kg) every day and euthanized a day after the last treatment. For the experimental metastatic mouse model, C57BL/6 mice were injected intratibially with 2xl0 5 RM9 mcherry/luciferase cells in PBS.
• mice with established tumors were injected intravenously with CpG-conjugates (5mg/kg) every day and euthanized based on the body score following the institution guide line or day after the last treatment.
• Tumor burden was monitored using the bioluminescent imaging (BLI) was measured using AmiX (Spectral) imaging system.
• C57BL/6 mice (6-8 weeks old) were purchased from the NCI (Frederick, MD). Animal care/procedures were performed in accordance with established institutional guidance and approved protocols from the IACUC (COH). C57BL/6 mice with or without established tumors were injected intravenously with 5 mg/kg with CpG-STAT3 Cy3 and euthanized 3 h later. The tumor, lymph node bone marrow, spleen and brain were harvested. Single cell suspensions were prepared by mechanic tissue disruption and collagenase D/DNase I treatment as described (Kortylewski et al. Nat. Med 2005) and stained using CD l ib, CD3, B220, CD19, CD56, CDl lc and F4/80 antibodies. The uptake by different population was accessed by flow cytometry.
• DU-145 cells were treated using 500 nM CpG-STAT3 ASO Cy3 labeled for different time points.
• Cells were fixed with 2% paraformadehyde for 20 min, permeabilized in PBS containing 0.1% Triton X-100 and the nuclei were stained using DRAQ5 ® 5 min.
• Slides were mounted in mounting medium (Vector Labs, Burlingame, CA). Confocal imaging was carried out using C-Apochromat 40 x/1.2 water-immersed objectives on cLSM510-Meta inverted confocal microscope (Zeiss, Thornwood, NY).
• LSM software v.4.2 SP1 was used for image acquisition, and LSM Image Browser v.4,2,0,121 was used for post- acquisition analysis (Zeiss).
• Unpaired t test was used to calculate two-tailed P value to estimate statistical significance of differences between two treatment groups.
• One- or two-way ANOVA plus Bonfeerroni post-test were applied to assess differences between multiple groups or in tumor growth kinetics experiments, respectively.
• Statistically significant P values were indicated in figures as follows: ***, P ⁇ 0.001; **, P ⁇ 0.01 and *, P ⁇ 0.05.
• Data were analyzed using Prism software v. 6.01 (GraphPad).
• the CpG-STAT3ASO showed more rapid induction of STAT3 knock-down at both mRNA (FIG. 13C) and protein (FIG. 13D) levels compared to the unconjugated STAT3ASO. That CpG-STAT3ASO internalization and target knock-down is similarly effective also in glioma and microglia cells were also verified (FIGs. 17A-17C). Importantly, only CpG-STAT3 ASO conjugate, but not STAT3 ASO alone or control CpG-scrambled ODN, was able to induce cell death in DU145 and LNCaP-S17 cells within 24 h of culture in the presence of 500 nM of oligonucleotides (FIGs. 14A-14B).
• CpG-ASOs allows for systemic administration and targeting of TLR9 + cells in distant organs, such as spleen or bone marrow (FIGs. 15A-15C, and FIGs. 18A-18C).
• IV intravenous
• CpG-STAT3ASO fluorescently-labeled CpG- STAT3ASO was sufficient to deliver the conjugate to the majority of myeloid cells in the bone marrow and significant proportion of myeloid cells, including DCs, in peripheral lymph nodes (FIGs. 15A-15C).
• IV injections allowed for CpG-STAT3ASO penetration of significant fraction of myeloid cells (e.g.
• mice were engrafted subcutaneously with RM9 tumors in two locations and tumors in one site were treated using intratumoral injections of CpG-STAT3ASO, STAT3ASO or control oligonucleotides (FIGs. 19A-19D).
• CpG-STAT3ASO and STAT3ASO initially inhibited growth of tumors in the treated site, only CpG-STAT3ASO also reduced tumor size in the distant untreated locations (FIG. 19A).
• CpG-STAT3ASO treatment induced complete regression of bone-localized RM9 tumors compare to limited effect of STAT3 ASO and control CpG-scrODN.
• new nuclease-resistant CpG-STAT3 ASO inhibitors allow for simultaneous targeting of STAT3 signaling in disseminated TLR9 + prostate cancer cells and in tolerogenic tumor-associated immune cells, such as macrophages/microglia/MDSCs (FIG. 21).
• the results demonstrate that immunotherapeutic approach to targeted cancer therapy focused on the disruption of signaling cross talk within the tumor microenvironment can be effective in treating cancer.
• An isolated compound comprising a phosphorothioated oligodeoxynucleotide (ODN) sequence conjugated to a short-activating RNA (saRNA) or an antisense
• ASO oligonucleotide
• saRNA short- activating RNA
• C/EBPa CCAAT/enhancer-binding protein-a
• ASO is an ASO of Signal Transducer and Activator of Transcription (STAT).
• antisense sequence is an anti- STAT1, anti-STAT2, anti-STAT3, anti-STAT4, anti-STAT5A, anti-STAT5B, or anti- STAT6 oligonucleotide sequence.
• the compound further comprising a linker between the ODN sequence and the short-activating RNA (saRNA) or the ASO.
• linker comprises a substituted or unsubstituted alkylene or substituted or unsubstituted heteroalkylene.
• the compound, wherein the acryloyl derivative is acryloyl chloride.
• the linker comprises a repeating unit of a substituted alkylene or heteroalkylene group conjugated to polyethylene glycol (PEG) or bisphosphonate moiety.
• linker is a substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene.
• linker is a substituted or unsubstituted C1-C4 0 alkylene, substituted or unsubstituted 2 to 40 membered heteroalkylene, substituted or unsubstituted C 3 -C 8 cycloalkylene, substituted or unsubstituted 3 to 8 membered heterocycloalkylene, substituted or unsubstituted C 6 -Cio arylene, or substituted or unsubstituted 5 to 10 membered heteroarylene.
• unsubstituted 2 to 40 membered heteroalkylene unsubstituted C 3 -C 8 cycloalkylene, unsubstituted 3 to 8 membered heterocycloalkylene, unsubstituted C 6 -Cio arylene, or unsubstituted 5 to 10 membered heteroarylene.
• the compound, wherein the saRNA or the ASO comprises a chemical modification selected for the group consisting of a 2' O-Methyl, 2'-deoxy-2'fluoro, 2'-deoxy, a universal base, 5-C-methyl, an inverted deoxy abasic residue incorporation, and a locked nucleic acid.
• the compound, wherein the phosphodiester derivative linkage in the ODN nucleic acid sequence is selected from the group consisting of: a phosphoramidate linkage, phosphorodiamidate linkage, phosphorothioate linkage, phosphorodithioate linkage, phosphonocarboxylic acid linkage, phosphonocarboxylate linkage, phosphonoacetic acid linkage, phosphonoformic acid linkage, methyl phosphonate linkage, boron phosphonate linkage, and O-methylphosphoroamidite linkage.
• the compound, wherein the phosphodiester derivative linkage is a phosphorothioate linkage.
• a pharmaceutical composition comprising a pharmaceutically acceptable excipient and the compound of one of claims.
• the pharmaceutical composition further comprising a second therapeutic agent.
• the second therapeutic agent is selected from the group consisting of: anti-tumor or anti-cancer agent, cytotoxic agent, cytostatic agent, anti-inflammatory agent, analgesic, anti-infective agent, growth inhibitory agent, immunogenic agent, immunomodulatory agent, and chemokine.
• composition wherein said anti-cancer agent is a cell death promoting agent.
• the pharmaceutical composition wherein said second therapeutic agent is selected from the group consisting of: Actinomycin D / Dactinomycin, Bleomycin, Daunorubicin, Doxorubicin, Doxorubicin (pegylated liposomal), Epirubicin, Idarubicin, Mitomycin, Mitoxantrone, Etoposide, Docetaxel, Irinotecan, Paclitaxel, Topotecan, Vinblastine,
• Vincristine Vinorelbine, Carboplatin, Cisplantin, Oxaliplatin, Alemtuzamab, BCG,
• Bevacizumab Cetuximab, Denosumab, Erlotinib, Gefitinib, Imatinib, Interferon, Ipilimumab, Lapatinib, Monomethyl auristatin E (MMEA), Mertansine (DM1), Rituximab, Sunitinib, Sorafenib, Temsirolimus, and Trastuzumab, or any combination(s) thereof.
• MMEA Monomethyl auristatin E
• DM1 Mertansine
• Rituximab Sunitinib
• Sorafenib Sunitinib
• Temsirolimus Temsirolimus
• Trastuzumab or any combination(s) thereof.
• a method of treating cancer in a subject in need thereof comprising administering to said subject an effective amount of the compound of one of claims 1-24, or the pharmaceutical composition of one of claims.
• the method of treating cancer wherein the cancer is prostate cancer, breast cancer, glioblastoma, ovarian cancer, lung cancer, head and neck cancer, esophageal cancer, skin cancer, melanoma, brain cancer, colorectal cancer, leukemia, lymphoma, or myeloma.
• the compound comprises: (i) a saRNA of CEBPA, p21, or p53 conjugated to one of phosphorothioated oligodeoxynucleotides (ODN) of SEQ ID NOs: 7-18 and 98-101, or (ii) a STAT ASO of SEQ ID NOs: 31-42 and 110-113 conjugated to a phosphorothioated oligodeoxynucleotides (ODN) of sequence of SEQ ID NO: 7-18 and 98-101.
• ODN phosphorothioated oligodeoxynucleotides
• a method of treating an autoimmune disease in a subject in need thereof comprising administering to said subject an effective amount of the compound of one of claims 1-24, or the pharmaceutical composition of one of claims.
• the method of treating an autoimmune disease wherein the autoimmune disease and/or disorder is rheumatoid arthritis, Crohn's disease, ulcerative colitis, multiple sclerosis, psoriasis, or systemic lupus erythematosus (SLE).
• the autoimmune disease and/or disorder is rheumatoid arthritis, Crohn's disease, ulcerative colitis, multiple sclerosis, psoriasis, or systemic lupus erythematosus (SLE).
• a method of stimulating an immune response in a subject in need thereof comprising administering to said subject an effective amount of the compound comprising one of phosphorothioated oligodeoxynucleotides (ODN) sequence of SEQ ID NO: 7-18 and 98-101 conjugated to (i) a saRNA of CEBP, p21, or p53 or (ii) a ASOs of SEQ ID NO: 31-42 and 110-113; or the pharmaceutical composition comprising the compounds comprising one of a phosphorothioated oligodeoxynucleotides (ODN) sequence of SEQ ID NO: 7-18 and 98-101 conjugated to (i) a saRNA of CEBP, p21, or p53 or (ii) a ASOs of SEQ ID NO: 31-42 and
• the method of stimulating an immune response comprising maturation, differentiation, or proliferation of natural killer cells, T cells, B cells or myeloid cells.
• a method of enhancing C/EBPa expression in a cell comprising contacting the cell with an effective amount of the compound comprising one of a phosphorothioated oligodeoxynucleotide (ODN) sequences of SEQ ID NO: 7-18, 29-30, and 98-101 conjugated to a saRNA of CEBP, or a pharmaceutical composition comprising the compound comprising one of a phosphorothioated oligodeoxynucleotide (ODN) sequences of SEQ ID NO: 7-18, 29-30, and 98-101 conjugated to a saRNA of CEBP.
• ODN phosphorothioated oligodeoxynucleotide
• a method of inhibiting cell growth comprising contacting said cell with an effective amount of the compound of one of claims, or the pharmaceutical composition of one of claims.
• a method of reducing the activity of a STAT transcription factor in a cell comprising contacting the cell with an effective amount of the compound one of a phosphorothioated oligodeoxynucleotide (ODN) sequences of SEQ ID NO: 7-18, 29-30, and 98-101 conjugated to a ASOs of SEQ ID NO: 31-42 and 110-113, or the pharmaceutical composition comprising the compounds comprising one of a phosphorothioated
• ODN phosphorothioated oligodeoxynucleotide
• ODN oligodeoxynucleotide
• AML acute myeloid lymphoid

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