EP4587573A2 - Products and compositions - Google Patents
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- EP4587573A2 EP4587573A2 EP23866589.7A EP23866589A EP4587573A2 EP 4587573 A2 EP4587573 A2 EP 4587573A2 EP 23866589 A EP23866589 A EP 23866589A EP 4587573 A2 EP4587573 A2 EP 4587573A2
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- nucleic acid
- region
- acid portion
- oligomeric compound
- nucleosides
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- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
- C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
- C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
- C12N15/1137—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 enzymes
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- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K31/00—Medicinal preparations containing organic active ingredients
- A61K31/70—Carbohydrates; Sugars; Derivatives thereof
- A61K31/7088—Compounds having three or more nucleosides or nucleotides
- A61K31/7125—Nucleic acids or oligonucleotides having modified internucleoside linkage, i.e. other than 3'-5' phosphodiesters
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- C12N2310/00—Structure or type of the nucleic acid
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- C12N2310/14—Type of nucleic acid interfering nucleic acids [NA]
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- C12N2310/00—Structure or type of the nucleic acid
- C12N2310/30—Chemical structure
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- C12N2310/312—Phosphonates
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- C12N2310/00—Structure or type of the nucleic acid
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- C12N2310/31—Chemical structure of the backbone
- C12N2310/315—Phosphorothioates
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- C12N2310/00—Structure or type of the nucleic acid
- C12N2310/30—Chemical structure
- C12N2310/31—Chemical structure of the backbone
- C12N2310/317—Chemical structure of the backbone with an inverted bond, e.g. a cap structure
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- C12N2310/00—Structure or type of the nucleic acid
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- C12N2310/32—Chemical structure of the sugar
- C12N2310/321—2'-O-R Modification
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- C12N2310/00—Structure or type of the nucleic acid
- C12N2310/30—Chemical structure
- C12N2310/32—Chemical structure of the sugar
- C12N2310/322—2'-R Modification
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- C12Y304/21—Serine endopeptidases (3.4.21)
Definitions
- Nucleic acid products that modulate, interfere with, or inhibit angiotensinogen (AGT) gene expression are provided.
- methods, compounds, and compositions are provided for reducing expression of AGT mRNA and protein in an animal. Such methods, compounds, and compositions are useful to treat, prevent, or ameliorate AGT-associated diseases or disorders, such as hypertension.
- renin-angiotensin-aldosterone system The renin-angiotensin-aldosterone system (RAAS) is known to play an important role in the regulation of blood pressure.
- the RAAS cascade is initiated by the release due to widely known mechanisms of renin into the circulation, in particular into the plasma.
- Active renin in the plasma cleaves angiotensinogen (AGT), which is produced by the liver, to yield angiotensin I.
- AGT angiotensinogen
- Angiotensin I is converted to angiotensin II by the circulating and locally expressed angiotensin-converting enzyme (ACE).
- ACE angiotensin-converting enzyme
- Angiontensin II is a peptide hormone, which causes vasoconstriction, which in turn, can increase blood pressure and may lead to hypertension and associated diseases.
- Dysregulation of angiotensin II causes hypertension and can lead to increased oxidative stress, promotion of inflammation, hypertrophy, and fibrosis in the heart, kidneys, and arteries, and may finally result in left ventricular fibrosis, arterial remodelling and glomerulosclerosis.
- Hypertension can also occur along with PCSK9- and/or APOC3-associated disorders such as dyslipidaemia, more specifically hypercholesterinaemia, hypertriglyceridemia, hyperchylomicronaemia, and atherosclerotic cardiovascular disease (ASCVD).
- dyslipidaemia more specifically hypercholesterinaemia, hypertriglyceridemia, hyperchylomicronaemia, and atherosclerotic cardiovascular disease (ASCVD).
- ASCVD atherosclerotic cardiovascular disease
- anti-hypertensive drugs may reduce hypertension and reduce the diseases, disorders and/or conditions associated with hypertension (Paulis et al., Nat Rev Cardiol, 2012, 9:276-285).
- therapies currently approved for treating hypertension as a significant subset of all hypertensive patients do not achieve adequate blood pressure control.
- drugs such as ACE inhibitors and angiotensin receptor blockers (ARBs) that target parts of the renin-angiotensin system (RAS) pathway are limited in their ability to inhibit the RAAS pathway (Nobakht et al., Nat Rev Nephrol, 2011 , 7:356-359).
- certain anti-hypertensive drugs such as ACE inhibitors are contra-indicated in hypertensive patients with renal disease due to their potential to compromise renal function in patients.
- Double-stranded RNAs also are provided.
- dsRNAs Double-stranded RNAs
- dsRNAs lack a loop connecting antisense and sense portions and therefore contains two strands. The two strands are not covalently connected to each other but form a duplex region where base pairing occurs.
- nucleic acid construct may contain at least:
- a second nucleic acid portion that is at least partially complementary to at least a second portion of an RNA, which is transcribed from an AGT gene, the second portion being different from the first portion;
- nucleobase means a group of atoms that can be linked to a sugar moiety to create a nucleoside that is capable of incorporation into an oligonucleotide, and where the group of atoms is capable of bonding, more specifically hydrogen bonding, with a complementary naturally occurring nucleobase of another oligonucleotide or nucleic acid. Nucleobases may be naturally occurring or may be modified.
- unmodified nucleobase or “naturally occurring nucleobase” means the naturally occurring heterocyclic nucleobases of RNA or DNA: the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) (including 5-methyl C), and uracil (U).
- modified nucleobase means any nucleobase that is not a naturally occurring nucleobase.
- bicyclic nucleoside or "BNA” means a nucleoside having a bicyclic sugar moiety.
- locked nucleic acid nucleoside or "LNA” means a nucleoside having a bicyclic sugar moiety having a 4'-CH2-O-2'bridge.
- 2 '-substituted nucleoside means a nucleoside having a substituent at the 2'- position of the sugar moiety other than H or OH. Unless otherwise indicated, a 2 '-substituted nucleoside is not a bicyclic nucleoside.
- deoxynucleoside means a nucleoside having 2'-H furanosyl sugar moiety, as found in naturally occurring deoxyribonucleosides (DNA).
- a 2'-deoxynucleoside may contain a modified nucleobase or may contain an RNA nucleobase (e.g., uracil).
- oligonucleotide means a compound having a plurality of linked nucleosides.
- an oligonucleotide contains one or more unmodified ribonucleosides (RNA) and / or unmodified deoxyribonucleosides (DNA) and / or one or more modified nucleosides.
- modified oligonucleotide means an oligonucleotide having at least one modified nucleoside and / or at least one modified internucleoside linkage.
- Advantageous positions for such modified internucleoside linkages include the termini and the hairpin loop of single-stranded oligomeric compounds.
- the internucleoside linkages connecting first and second nucleoside and second and third nucleoside counting from the 5' terminus, and/or the internucleoside linkages connecting first and second nucleoside and second and third nucleoside counting from the 3' terminus are modified.
- a linkage connecting the terminal nucleoside of the 3' terminus with a ligand, such as GalNAc may be modified.
- linkages in the hairpin loop designates the linkages between nucleosides, which are not engaged in base pairing.
- linkages in the hairpin loop also extends to the linkages connecting the stem to the loop, i.e., those linkages which connect a base-paired nucleoside to a non-based paired nucleoside.
- linkages connecting the stem to the loop i.e., those linkages which connect a base-paired nucleoside to a non-based paired nucleoside.
- modified internucleoside linkages are at both termini and in the hairpin loop.
- linkage means a group of atoms that link together two or more other groups of atoms.
- nucleoside linkage means a covalent linkage between adjacent nucleosides in an oligonucleotide.
- naturally occurring internucleoside linkage means a 3' to 5' phosphodiester linkage.
- modified internucleoside linkage means any internucleoside linkage other than a naturally occurring internucleoside linkage.
- a “modified internucleoside linkage” as referred to herein can include a modified phosphorous linking group such as a phosphorothioate or phosphorodithioate internucleoside linkage.
- terminal internucleoside linkage means the linkage between the last two nucleosides of an oligonucleotide or defined region thereof.
- phosphorus linking group means a linking group having a phosphorus atom and can include naturally occurring phosphorous linking groups as present in naturally occurring RNA or DNA, such as phosphodiester linking groups, or modified phosphorous linking groups that are not generally present in naturally occurring RNA or DNA, such as phosphorothioate or phosphorodithioate linking groups.
- Phosphorus linking groups can therefore include without limitation, phosphodiester, phosphorothioate, phosphorodithioate, phosphonate, methylphosphonate, phosphoramidate, phosphorothioamidate, thionoalkylphosphonate, phosphotriesters, thionoalkylphosphotriester and boranophosphate.
- nucleoside phosphorus linking group means a phosphorus linking group that directly links two nucleosides.
- oligomeric compound means a polymeric structure having two or more substructures.
- an oligomeric compound contains an oligonucleotide, such as a modified oligonucleotide.
- an oligomeric compound further contains one or more conjugate groups and I or terminal groups and I or ligands.
- an oligomeric compound consists of an oligonucleotide.
- an oligomeric compound contains a backbone of one or more linked monomeric sugar moieties, where each linked monomeric sugar moiety is directly or indirectly attached to a heterocyclic base moiety.
- oligomeric compounds may also include monomeric sugar moieties that are not linked to a heterocyclic base moiety, thereby providing abasic sites.
- Oligomeric compounds may be defined in terms of a nucleobase sequence only, i.e., by specifying the sequence of A, G, C, U (or T). In such a case, the structure of the sugar-phosphate backbone is not particularly limited and may or may not contain modified sugars and/or modified phosphates.
- oligomeric compounds may be more comprehensively defined, i.e., by specifying not only the nucleobase sequence, but also the structure of the backbone, in particular the modification status of the sugars (unmodified, 2'-OMe modified, 2'-F modified etc.) and/or of the phosphates.
- An mxRNA is one non-limiting example for an oligomeric compound.
- nucleic acid construct refers to an assembly of two or more, such as four oligomeric compounds.
- the oligomeric compounds may be connected to each other by covalent bonds such phosphodiester bonds as they occur in naturally occurring nucleic acids or modified versions thereof as disclosed herein, or by non-covalent bonds such as hydrogen bonds, advantageously hydrogen bonds between nucleobases such as Watson-Crick base pairing.
- a construct contains four oligomeric compounds, two of which are connected covalently, thereby giving rise to two nucleic acid strands which nucleic acid strands are bound to each other by hydrogen bonds. Complementarity between the strand may be throughout, but is not necessarily so.
- exemplary embodiments provide for an antisense strand targeting a first region of AGT mRNA to be connected covalently with a sense strand of another AGT- targeting double stranded RNA molecule, and of the antisense strand of the AGT mRNA-targeting double stranded RNA molecule to be connected covalently to a sense strand of the other AGT mRNA-targeting double stranded RNA molecule.
- one construct contains a central region where the 3' regions of the antisense portions of the parent single-target-directed RNA molecules face each other. In that region generally no or only partial base pairing will occur, while full complementarity is not excluded. Otherwise, where antisense and sense portions of the respective parent RNA molecules face each other; there is complementarity, advantageously full complementarity or 1 or 2 mismatches.
- An muRNA is non-limiting example for a nucleic acid construct.
- strand has its art-established meaning and refers to a plurality of linked nucleosides, the linker not being particularly limited, but including phosphodiesters and variants thereof as disclosed herein.
- a strand may also be viewed as a plurality of linked nucleotides in which case the linker would be a covalent bond.
- terminal group means one or more atom attached to either, or both, the 3 ' end or the 5' end, also called “terminus” of an oligonucleotide.
- a terminal group contains one or more terminal group nucleosides, whereas a “terminal nucleoside” is only one nucleotide at the respective end (5' end or 3' end).
- conjugate means an atom or group of atoms bound to an oligonucleotide or oligomeric compound.
- a conjugate group links a ligand to a modified oligonucleotide or oligomeric compound.
- conjugate groups can modify one or more properties of the compound to which they are attached, including, but not limited to pharmacodynamic, pharmacokinetic, binding, absorption, cellular distribution, cellular uptake, charge and I or clearance properties.
- the carbohydrate cluster portion contains 2 GalNAc groups.
- the carbohydrate cluster portion contains 3 GalNAc groups and this is particularly advantageous.
- the carbohydrate cluster portion contains 4 GalNAc groups.
- Such ligand portions are attached to an oligomeric compound via a cleavable moiety, such as a cleavable bond or cleavable nucleoside.
- the ligands can be arranged in a linear or branched configuration, such as a biantennary or triantennary configurations.
- An advantageous carbohydrate cluster has the following formula:
- carbohydrate cluster means a compound having one or more carbohydrate residues attached to a linker group.
- modified carbohydrate means any carbohydrate having one or more chemical modifications relative to naturally occurring carbohydrates.
- carbohydrate derivative means any compound which may be synthesized using a carbohydrate as a starting material or intermediate.
- Carbohydrate means a naturally occurring carbohydrate, a modified carbohydrate, or a carbohydrate derivative.
- a carbohydrate is a biomolecule including carbon (C), hydrogen (H) and oxygen (O) atoms.
- Carbohydrates can include monosaccharide, disaccharides, trisaccharides, tetrasaccharides, oligosaccharides or polysaccharides, such as one or more galactose moieties, one or more lactose moieties, one or more N-Acetyl-Galactosamine moieties, and I or one or more mannose moieties.
- a particularly advantageous carbohydrate is N-Acetyl-Galactosamine.
- short hairpin RNA also denoted as shRNA
- shRNA contains a duplex region and a loop connecting the regions forming the duplex.
- the end of the duplex region, which does not carry the loop, may be blunt-ended or carry (a) 3' and/or (a) 5' overhang(s). Blunt-ended constructs are particularly advantageous.
- shRNA is more generic than "mxRNA", as defined below, and may include compounds in which the loop is not or not exclusively formed out of an antisense strand.
- shRNA includes an antisense strand, also called guide strand, being complementary to a region of a target RNA, and a sense strand, i.e. a passenger strand, being substantially complementary to the antisense strand.
- the antisense strand and the sense strand within the shRNA are directly linked, e.g. by a phosphate or a phosphorothioate, or linked by a third portion of linked nucleosides forming the loop, which means that the 3' end of the antisense strand is linked to the 5' end of the sense strand via covalent bonding over several other groups.
- Such direct linkage does not include a gap or nick.
- nucleobase at a certain position of an oligomeric compound is capable of hydrogen bonding with a nucleobase at a certain position of a target sequence
- the position of hydrogen bonding between the oligomeric compound and the target sequence is considered complementary at that nucleobase pair.
- non-complementary in reference to nucleobases means a pair of nucleobases that do not form hydrogen bonds with one another.
- oligomeric compound or region thereof is capable of pairing with a nucleobase of a complementary nucleic acid target sequence or a self-complementary region of the oligomeric compound.
- a fully complementary oligomeric compound or region thereof contains no mismatches or unhybridized nucleobases with respect to its target sequence or a self- complementary region of the oligomeric compound.
- percent identity means the number of nucleobases in a first nucleic acid that are the same type (independent of chemical modification) as nucleobases at corresponding positions in a second nucleic acid, divided by the total number of nucleobases in the first nucleic acid.
- modulation means a change of amount or quality of a molecule, function, or activity when compared to the amount or quality of a molecule, function, or activity prior to modulation.
- modulation includes the change, either an increase (stimulation or induction) or a decrease (inhibition or reduction) in gene expression.
- nucleoside having a modification of a first type may be an unmodified nucleoside.
- RNA nucleosides that are the same but for the presence of different nucleobases are not differently modified.
- MOE nucleoside and an unmodified naturally occurring RNA nucleoside are “differently modified,” even though the naturally occurring nucleoside is unmodified.
- DNA and RNA oligonucleotides are “differently modified,” even though both are naturally occurring unmodified nucleosides. Nucleosides that are the same but for the presence of different nucleobases are not differently modified.
- alkylene means a saturated straight or branched divalent hydrocarbon radical of the general formula -CnHzn- where n is 1 -6. Methylene or ethylene are typical alkylenes.
- alkynyl means a straight or branched unsaturated C2-6 hydrocarbon radical, with ethynyl being a typical alkynyl as a substituent at the 2'-position of the sugar moiety.
- degree of unsaturation that is present in an alkynyl radical is the presence of at least one carbon to carbon triple bond.
- the alkynyl group typically attaches to an oxygen linking atom at the 2'-position of the sugar, therefore, overall providing a -Oalkynyl substituent on a sugar moiety of an oligomeric compound as described herein.
- alkoxy means a radical formed between an alkyl group, such as a C1-6 alkyl group, and an oxygen atom where the oxygen atom is used to attach the alkoxy group either to a parent molecule (such as at the 2'-position of a sugar moiety), or to another group such as an alkylene group as defined herein.
- alkoxy groups include without limitation, methoxy, ethoxy, propoxy, isopropoxy, n-butoxy, sec-butoxy and tert-butoxy.
- Alkoxy groups as used herein may optionally include further substituent groups.
- alkoxyalkylene means an alkoxy group as defined herein that is attached to an alkylene group also as defined herein, and where the oxygen atom of the alkoxy group attaches to the alkylene group and the alkylene attaches to a parent molecule.
- the alkylene group typically attaches to an oxygen linking atom at the 2'-position of the sugar, therefore, overall providing a - Oalkylenealkoxy substituent, such as an -OCH2CH2OCH3 substituent, on a sugar moiety of an oligomeric compound as described herein. This is generally referred to as an MOE substituent as defined herein and as known in the art.
- amino includes primary, secondary and tertiary amino groups.
- an mxRNA is in particular understood as defined in WO 2020/044186 A2, which is incorporated by reference herein in its entirety.
- an mxRNA is a hairpin-shaped RNA molecule consisting of an antisense portion (also referred to as the guide strand) and a sense portion (also referred to the passenger strand).
- the mxRNA contains duplex region and a hairpin loop, where the mxRNA has approximate length of about 34 nucleotides.
- the duplex region contains a region in which parts of the antisense portion and substantially the entire sense portion, typically 14 or 15 nucleotides of each strand, are base-paired.
- the hairpin loop connects both regions, i.e.
- oligomeric compounds are provided that are capable of inhibiting expression of angiotensinogen (AGT), where the compound contains at least a first region of linked nucleosides having at least a first nucleobase sequence that is at least partially complementary to at least a portion of RNA transcribed from an AGT gene, where the first nucleobase sequence is selected from the following sequences, or a portion thereof: sequences of Table 1 a (SEQ ID NOs: 1 to 100), where the portion advantageously has a length of at least 18 nucleosides.
- the 5' terminal nucleoside of the first nucleobase sequence can contain U instead of A; or U instead of G; or U instead of C, respectively.
- the oligomeric compound including the first and second regions of linked nucleosides may contain at least one complementary duplex region that contains at least a portion of the first region of linked nucleosides directly or indirectly linked to at least a portion of the second region of linked nucleosides, where advantageously the duplex region has a length of 10 to 19, 12 to 19, 12 to 15, or 14 or 15, base pairs, where optionally there is one mismatch within the duplex region.
- each of the first and second regions of linked nucleosides has a 5’ to 3’ directionality thereby defining 5’ and 3’ regions respectively thereof.
- the 5’ region of the first region of linked nucleosides may be directly or indirectly linked to the 3’ region of the second region of linked nucleosides, for example by complementary base pairing, where advantageously the 5' terminal nucleoside of the first nucleoside region base pairs with the 3' terminal nucleoside of the second nucleoside region.
- the oligomeric compound may consist of the first region of linked nucleosides and the second region of linked nucleosides.
- Each ofthe regions may constitute a separate strand, thereby giving rise to a double-stranded RNA (dsRNA).
- dsRNAs particularly advantageous dsRNAs are those with a length of the first strand of 19 nucleosides and a length of the second region of 14 or 15, advantageously 14 nucleosides.
- the terms "nucleoside” and “nucleotide” are used equivalently.
- the oligomeric compound contains a single strand having the first and second nucleoside regions, where at least a portion of the first nucleoside region is directly or indirectly linked to at least a portion of the second nucleoside region so as to form the at least partially complementary duplex region.
- the third region is optional.
- the oligomeric compound may contain or may consist of a single strand having or consisting of the first and second regions of linked nucleosides, where at least a portion of the first region of linked nucleosides is directly or indirectly linked to at least a portion of the second region of linked nucleosides so as to form the at least partially complementary duplex region.
- the additional number of linked nucleosides of the first nucleoside region form a hairpin loop linking the first and second regions of linked nucleosides, where advantageously a part of the first nucleobase sequence of the first nucleobase sequence being complementary RNA transcribed from an AGT gene forms the hairpin loop, where the loop contains 2 to 5, advantageously 4 or 5, nucleosides.
- Such compounds are also referred to as hairpins or mxRNAs herein.
- the compound is optimized in terms of size (or miniaturized) as compared to a conventional siRNA which has two regions of comparable length.
- the loop has 4 or 5 linked nucleosides. Particularly advantageous is a length of the first region of 19 nucleosides, of the second region of 14 nucleosides, and of the hairpin loop of 5 nucleosides, where the 5 nucleosides in the hairpin are the 5 3'-terminal nucleosides of the first region.
- Such molecular architecture of a hairpin or mxRNA is also designated "14-5-14" herein.
- an oligomeric single strand as disclosed earlier herein can be selected from Table 2, in particular selected from the group consisting of SEQ IDs NO: 227, 252, 256, 262, 275, 293 and 3602-3603, where advantageously the 5' terminal nucleoside of the first region of linked nucleosides is substituted by an U as the nucleobase, and the 5' terminal nucleoside of the second region of linked nucleosides is substituted by an A as the nucleobase.
- the single strand is selected from Table 3c, in particular from Construct ID NOs: 527, 552, 556, 562, 575, 593 and 3604-3605, where advantageously the 5' terminal nucleoside of the first region of linked nucleosides is substituted by an U as the nucleobase, and the 5' terminal nucleoside of the second region of linked nucleosides is substituted by an A as the nucleobase.
- the first "13" refers to the region of the guide sequence involved in the duplex
- 5 is the length of the loop which is also formed by the guide sequence
- the second 13 refers to the second region of the duplex and is formed by one nucleobase of the guide sequence and 12 nucleobases of the passenger region in 5' to 3' direction.
- a length of the guide sequence of 19 nucleosides is maintained, but the passenger sequence is shortened to 12 nucleosides.
- oligomeric compounds according to the first aspect disclosed herein may be blunt ended.
- the second region may be selected from the sequences of Table 3b, or a portion thereof, especially a portion having a length of 14 nucleosides, in particular from Construct ID NOs: 427, 452, 456, 462, 475 and 493.
- the one or more ligands in particular two or more or three ligands, may be conjugated to the second region of linked nucleosides and/or the first region of linked nucleosides.
- the one or more ligands may be conjugated at the 3' region, advantageously at the 3' terminal nucleoside of the second region of linked nucleosides and/or of the first region of linked nucleosides, and/or to the 5' terminal nucleoside of the second region of linked nucleosides.
- the ligands may be conjugated to the 3' terminal nucleoside.
- the one or more ligands are any cell directing moiety, such as lipids, carbohydrates, aptamers, vitamins and / or peptides that bind cellular membrane or a specific target on cellular surface.
- the one or more ligands may contain one or more, in particular three, carbohydrates.
- the one or more, in particular three, carbohydrates can be a monosaccharide, disaccharide, trisaccharide, tetrasaccharide, oligosaccharide or polysaccharide.
- the one or more carbohydrates may contain one or more, in particular three, N-Acetyl-Galactosamine moieties.
- the target tissue i.e. the liver where AGT is produced
- the target tissue i.e. the liver where AGT is produced
- the oligomeric compounds can exhibit their inhibition of AGT gene more efficiently.
- the one or more, in particular three, ligands may be attached to the oligomeric compound as a biantennary or triantennary configuration.
- the oligomeric compound according to the first aspect disclosed herein may contain internucleoside linkages and where at least one internucleoside linkage is a modified internucleoside linkage.
- the modified internucleoside linkage may be a phosphorothioate or phosphorodithioate internucleoside linkage.
- the oligomeric compound according to the first aspect disclosed herein may contain 1 to 16 phosphorothioate or phosphorodithioate internucleoside linkages.
- modified internucleoside linkages are the subject of some of the embodiments which follow. Certain modified internucleoside linkages are known in the art and described in, for example, Hu et al., Signal Transduction and Targeted Therapy (2020)5:101 .
- the oligomeric compound may contain 7, 8, 9 or 10 phosphorothioate or phosphorodithioate internucleoside linkages.
- the one or more phosphorothioate or phosphorodithioate internucleoside linkages may present at the 5’ region of the first region of linked nucleosides, where advantageously, the oligomeric compound contains three phosphorothioate internucleoside linkages at three adjacent nucleosides at the 5' region.
- the oligomeric compound may contain phosphorothioate or phosphorodithioate internucleoside linkages between at least two, at least three, at least four, or at least five, adjacent nucleosides of the hairpin loop, dependent on the number of nucleosides present in the hairpin loop.
- the oligomeric compound may contain a phosphorothioate or phosphorodithioate internucleoside linkage between each adjacent nucleoside that is present in the hairpin loop.
- At least one nucleoside may contain a modified sugar.
- modified sugars are the subject of some exemplary embodiments, which follow. Certain modified sugars are known in the art and described in, for example, Hu et al., Signal Transduction and Targeted Therapy (2020)5:101 .
- the 2' modified sugar may be selected from 2'-O-alkyl modified sugar, 2'-O-methyl modified sugar, 2'- O-methoxyethyl modified sugar, 2'-O-allyl modified sugar, 2'-C-allyl modified sugar, 2'-deoxy modified sugar such as 2'-deoxy ribose, 2'-F modified sugar, 2'-arabino-fluoro modified sugar, 2'-O-benzyl modified sugar, and 2'-O-methyl-4-pyridine modified sugar.
- At least one modified sugar may be a 2'- O-methyl modified sugar.
- At least one modified sugar may be a 2'-F modified sugar and, advantageously, at most 16 or 17 sugars are 2'-F modified sugars.
- the sugar is ribose.
- sugars of the nucleosides at any of positions 2 and 14 downstream from the first nucleoside of the 5’ region ofthe first region of linked nucleosides do not contain 2'-O-methyl modifications.
- the 3' terminal position ofthe second region of linked nucleosides does not contain a 2'-O-methyl modification.
- sugars of the nucleosides at any of positions 2 and 14 downstream from the first nucleoside of the 5’ region of the first region of linked nucleosides contain 2'-F modifications.
- sugars of the nucleosides of the second region of linked nucleosides that correspond in position to any of the nucleosides of the first region of linked nucleosides at any of positions 11 to 13 downstream from the first nucleoside of the 5’ region of the first region of linked nucleosides contain 2'-F modifications.
- the 3' terminal nucleoside of the second region of linked nucleosides contains a 2'-F modification.
- one or more of the odd numbered nucleosides starting from the 5’ region of the first region of linked nucleosides may be modified, and I or where one or more of the even numbered nucleosides starting from the 5’ region of the first region of linked nucleosides may be modified, where typically the modification of the even numbered nucleosides is a second modification that is different from the modification of odd numbered nucleosides.
- one or more of the odd numbered nucleosides starting from the 3’ region of the second region of linked nucleosides may be modified by a modification that is different from the modification of odd numbered nucleosides of the first region of linked nucleosides.
- one or more of the even numbered nucleosides starting from the 3’ region of the second region of linked nucleosides are modified by a modification that is different from the modification of even numbered nucleosides of the first region of linked nucleoside.
- At least one or more of the modified even numbered nucleosides ofthe first region of linked nucleosides is adjacent to at least one or more of the differently modified odd numbered nucleosides of the first nucleoside region.
- At least one or more of the modified even numbered nucleosides ofthe second nucleoside region is adjacent to at least one or more of the differently modified odd numbered nucleosides of the second region of linked nucleosides.
- sugars of one or more of the odd numbered nucleosides starting from the 5’ region of the first region of nucleosides may be 2'-O-methyl modified sugars.
- one or more of the even numbered nucleosides starting from the 3’ region of the first region of linked nucleosides may be 2'-F modified sugars.
- one or more of the even numbered nucleosides starting from the 5’ region of the second region of linked nucleosides may be 2'-F modified sugars.
- sugars of a plurality of adjacent nucleosides of the second nucleoside region may be modified by a common or different modification.
- the common modification may be a 2'-O-methyl modified sugar.
- the plurality of adjacent 2'-O-methyl modified sugars may be present in at least eight adjacent nucleosides of the first and / or second nucleoside regions.
- the plurality of adjacent 2'-O-methyl modified sugars may be present in three or four adjacent nucleosides of the hairpin loop.
- hairpin loop may contain at least one nucleoside having a modified sugar.
- the at least one nucleoside is adjacent to a nucleoside with a differently modified sugar, where advantageously all adjacent nucleosides in the hairpin loop have a differently modified sugar.
- the modified sugar is a 2'-O-methyl modified sugar
- the differently modified sugar is a 2'-F modified sugar
- one or more nucleosides of the first region of linked nucleosides and / or the second region of linked nucleosides may be an inverted nucleoside and is attached to an adjacent nucleoside via the 3' carbon of its sugar and the 3' carbon of the sugar of the adjacent nucleoside, and / or one or more nucleosides of the first region of linked nucleosides and / or the second region of linked nucleosides is an inverted nucleoside and is attached to an adjacent nucleoside via the 5' carbon of its sugar and the 5' carbon of the sugar of the adjacent nucleoside.
- nucleic acid construct having at least:
- the construct may be designed such that subsequent to in vivo administration the construct disassembles to yield at least first and second discrete nucleic acid targeting molecules that respectively target the RNA portions transcribed from the target genes of (a) and (b); whereby (i) the first nucleic acid targeting molecule is capable of modulating expression of the target gene of (a), and contains, or is derived from, at least the first nucleic acid portion of (a), and (ii) the second nucleic acid targeting molecule is capable of modulating expression of the target gene of (b), and contains, or is derived from, the second nucleic acid portion of (b).
- the construct according to the second aspect and its aforementioned embodiments may at least contain one labile functionality such that subsequent to in vivo administration the construct is cleaved so as to yield the at least first and second discrete nucleic acid targeting molecules.
- the labile functionality may contain one or more unmodified nucleotides.
- the one or more unmodified nucleotides of the labile functionality represent one or more cleavage positions within the construct whereby subsequent to in vivo administration the construct is cleaved at the one or more cleavage positions so as to yield the at least first and second discrete nucleic acid targeting molecules.
- the cleavage positions may be respectively located within the construct so that subsequent to cleavage the first discrete nucleic acid targeting molecule contains, or is derived from, the first nucleic acid duplex region, and the second discrete nucleic acid targeting molecule contains, or is derived from, the second nucleic acid duplex region.
- the first discrete nucleic acid targeting molecule contains or consists of the first nucleic acid portion of (a) and the third nucleic acid portion of (c), and/or the second discrete nucleic acid targeting molecule contains or consists of the second nucleic acid portion of (b) and the fourth nucleic acid portion of (d).
- the first nucleic acid portion has a nucleobase sequence selected from SEQ ID NOs: 1 to 100 in Table 1a;
- the second nucleic acid portion has a nucleobase sequence selected from Table 1a (SEQ ID NOs: 1 to 100);
- the third nucleic acid portion has a nucleobase sequence selected from Table 1 b SEQ ID NOs: 101 to 200; and/or
- the fourth nucleic acid portion has a nucleobase sequence selected from Table 1 b (SEQ ID NOs: 101 to 200). where the third and fourth nucleobase sequences, to the extent they have a length of 14 nucleobases, may be shorter by one, two or three nucleobases, where advantageously the 5'-terminal nucleobase(s) is/are absent.
- the first nucleic acid portion of (a) may be directly or indirectly linked to the fourth nucleic acid portion of (d) as a primary structure.
- the first and the fourth nucleic acid portions may have the nucleobase sequences of SEQ ID NOs: 27 and 127, 44 and 144, 41 and 141 , 97 and 197, 90 and 190, 62 and 162, 52 and 152, 93 and 193, 49 and 149, 73 and 173, 18 and 118, 37 and 137, 56 and 156, 100 and
- the second and third nucleic acid portions may have the nucleobase sequences of SEQ ID NOs: 27 and 127, 44 and 144, 41 and 141 , 97 and 197, 90 and 190, 62 and 162, 52 and 152, 93 and 193, 49 and 149, 73 and 173, 18 and 118, 37 and 137, 56 and 156, 100 and
- sequences of SEQ ID NOs: 27, 52, 56, 62, 75, and 93 may be shorter by one, two, three or four nucleobases, where advantageously the 5'-terminal nucleobase(s) is/are absent.
- the direct or indirect linking may represent either (i) an internucleotide bond, (ii) an internucleotide nick, or (iii) a nucleic acid linker portion of 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides, the nucleic acid linker advantageously being single stranded.
- the linking may be direct, thereby giving rise to (a) contiguous strand(s).
- (i) may be 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10, advantageously 2, 3, 4 or 5 base pairs; and/or
- the unmodified nucleotide is at position 19.
- one, more of all of the duplex regions independently may have a length of 10 to 19, 13 to 19, 13, 14 or 15 base pairs, where optionally there is one mismatch within the duplex region.
- the first nucleic acid portion of (a), and / or the second nucleic acid portion of (b), and / orthe third nucleic acid portion of (c), and / or the fourth nucleic acid portion of (d), and / or, to the extent present, the 1 to 8 additional nucleic acid portions as defined previously herein, and / or the passenger nucleic acid portions as defined previously herein, respectively may have a 5’ to 3’ directionality thereby defining 5’ and 3’ regions thereof.
- one or more ligands are conjugated at the 3 ' region, advantageously the 3' end, of any of (I) the third nucleic acid portion of (c), and / or (ii) the fourth nucleic acid portion of (d), and / or, to the extent present, the (ill) passenger nucleic acid portions as defined previously herein.
- one or more ligands may be conjugated at one or more regions intermediate of the 5’ and 3’ regions of any of the nucleic acid portions, advantageously of the third nucleic acid portion of (c), and I or the fourth nucleic acid portion of (d), and / orthe passenger nucleic acid portions as defined previously herein.
- the hexose moiety may contain two or three N-Acetyl-Galactosamine moieties.
- the hexose moiety may contain three N-Acetyl-Galactosamine moieties.
- the one or more ligands may be attached in a linear configuration, or in a branched configuration.
- the one or more ligands may be attached as a biantennary or triantennary configuration, or as a configuration based on single ligands at different positions.
- the ligand may have the following structure:
- the nucleic acid construct may contain 1 to 15 phosphorothioate or phosphorodithioate internucleotide linkages.
- the nucleic acid construct may contain phosphorothioate or phosphorodithioate internucleotide linkages between at least two adjacent nucleotides of the nucleic acid linker portion as defined in previously herein.
- nucleic acid construct according to the second aspect as described above and its aforementioned embodiments, at least one nucleotide of at least one of the following may be modified: the first nucleic acid portion of (a); and / or the second nucleic acid portion of (b); and / or the third nucleic acid portion of (c); and I or the fourth nucleic acid portion of (d); and I or to the extent present, the 1 to 8 additional nucleic acid portions as defined previously herein; and I or to the extent present, the passenger nucleic acid portions as defined previously herein; and / or to the extent present, the nucleic acid linker portion as further defined previously herein.
- one or more of the odd numbered nucleotides starting from the 5’ region of one of the following may be modified, and / or where one or more of the even numbered nucleotides starting from the 5' region of one of the following are modified, where typically the modification of the even numbered nucleotides is a second modification that is different from the modification of odd numbered nucleotides: the first nucleic acid portion of (a); and / or the second nucleic acid portion of (b); and / or the third nucleic acid portion of (c); and I or the fourth nucleic acid portion of (d); and I or to the extent present, the 1 to 8 additional nucleic acid portions as defined previously herein; and / or to the extent present, the passenger nucleic acid portions as defined previously herein.
- one or more of the odd numbered nucleotides starting from the 3’ region of the third nucleic acid portion of (c) may be modified by a modification that is different from the modification of odd numbered nucleotides starting from the 5’ region of the first nucleic acid portion of (a); and I or one or more of the odd numbered nucleotides starting from the 3’ region of the fourth nucleic acid portion of (d) may be modified by a modification that is different from the modification of odd numbered nucleotides starting from the 5’ region of the second nucleic acid portion of (b); and / or one or more of the odd numbered nucleotides starting from the 3’ region of the passenger nucleic acid portions as defined previously herein, to the extent present, may be modified by a modification that is different from the modification of odd numbered nucleotides starting from the 5’ region of the 1 to 8 additional nucleic acid portions as defined previously herein; and I or where one or more of the nucleotides of a nucleotides
- one or more of the even numbered nucleotides starting from the 3’ region of: (i) the third nucleic acid portion of (c), and I or (ii) the fourth nucleic acid portion of (d), and I or (iii) the passenger nucleic acid portions as defined previously herein, to the extent present, may be modified by a modification that is different from the modification of odd numbered nucleotides starting from the 3’ region of these respective portions.
- At least one or more of the modified even numbered nucleotides of (I) the first nucleic acid portion of (a), and I or (ii) the second nucleic acid portion of (b), and I or (iii), to the extent present, the 1 to 8 additional nucleic acid portions as defined previously herein, may be adjacent to at least one or more differently modified odd numbered nucleotides of these respective portions.
- At least one or more of the modified even numbered nucleotides of (I) the third nucleic acid portion of (c), and I or (ii) the fourth nucleic acid portion of (d), and I or (iii), to the extent present, the passenger nucleic acid portions as defined previously herein, may be adjacent to at least one or more differently modified odd numbered nucleotides of these respective portions.
- a plurality of adjacent nucleotides of (i) the third nucleic acid portion of (c), and I or (ii) the fourth nucleic acid portion of (d), and I or (iii), to the extent present, the passenger nucleic acid portions as defined previously herein, may be modified by a common modification.
- the plurality of adjacent commonly modified nucleotides may be 2 to 4 adjacent nucleotides, advantageously 3 or 4 adjacent nucleotides.
- the plurality of adjacent commonly modified nucleotides may be located in the 5’ region of (i) the third nucleic acid portion of (c), and I or (ii) the fourth nucleic acid portion of (d), and I or (iii), to the extent present, the passenger nucleic acid portions previously herein.
- the one or more of the modified nucleotides of first nucleic acid portion of (a) may not have a common modification present in the corresponding nucleotide of the third nucleic acid portion of (c) of the first duplex region; and I or one or more of the modified nucleotides of second nucleic acid portion of (b) may not have a common modification present in the corresponding nucleotide of the fourth nucleic acid portion of (d) of the second duplex region; and I or one or more of the modified nucleotides of the 1 to 8 additional nucleic acid portions, to the extent present, as defined previously herein, may not have a common modification present in the corresponding nucleotide of the corresponding passenger nucleic acid portions of the respective duplex regions.
- the one or more of the modified nucleotides ofthe first nucleic acid portion of (a) may be shifted by at least one nucleotide relative to a commonly modified nucleotide of the third nucleic acid portion of (c); and / or one or more of the modified nucleotides of the second nucleic acid portion of (b) may be shifted by at least one nucleotide relative to a commonly modified nucleotide of the fourth nucleic acid portion of (d); and / or one or more of the modified nucleotides of the 1 to 8 additional nucleic acid portions, to the extent present, as defined previously herein may be shifted by at least one nucleotide relative to a commonly modified nucleotide of the passenger nucleic acid portions, to the extent present, as defined previously herein.
- the modification and I or modifications may be each and individually sugar, phosphate, or base modifications.
- the modification may be selected from nucleotides with 2' modified sugars; conformationally restricted nucleotides (CRN) sugar such as locked nucleic acid (LNA), (S)- constrained ethyl bicyclic nucleic acid, and constrained ethyl (cEt), tricyclo-DNA; morpholino, unlocked nucleic acid (UNA), glycol nucleic acid (GNA), D-hexitol nucleic acid (HNA), and cyclohexene nucleic acid (CeNA).
- CRN conformationally restricted nucleotides
- At least one modification may be a 2'-O-methyl modification in a ribose moiety.
- At least one modification may be a 2'-F modification in a ribose moiety.
- one, two or all three nucleotides of (i) the third nucleic acid portion of (c); and or (ii) the fourth nucleic acid portion of (d); and / or (iii), to the extent present, the passenger nucleic acid portions as defined previously herein; that respectively correspond in position to any of the nucleotides at any of positions 11 to 13 downstream from the first nucleotide of the 5’ region of (i) the first nucleic acid portion of (a); and I or (ii) the second nucleic acid portion of (b); and I or (ill), to the extent present, the 1 to 8 additional nucleic acid portions as defined previously herein; may contain 2'- F modifications in ribose moieties.
- the first nucleic acid portion may be selected from Table 3a;
- the second nucleic acid portion is selected from Table 5b;
- the first nucleic acid portion is selected from Table 1 a, in particular Table 3a;
- the second nucleic acid portion is selected from Table 10b, in particular Table 12b;
- the fourth nucleic acid portion is selected from Table 11 b, in particular Table 13b.
- the (a) first nucleic acid portion no matter if selected from Table 1a in its unmodified form or from Table 3a in its modified form, is selected from group consisting of the constructs denoted AGT_27, AGT_62, AGT_52, AGT_56, AGT_93 and AGT_75.
- the corresponding (c) third nucleic acid portion has the corresponding denotation in Table 1 b or 3b.
- the second nucleic acid portion is selected from the group consisting of A28(14-4)mF and A277(12-5) in Table 6a, in particular in Table 6b, where the second portion consists of the first 19 nucleotides of these entries.
- the corresponding (d) fourth portion contains the remaining nucleotides from the corresponding entries in Table 6a, in particular Table 6b.
- the nucleic acid portions targeting the AGT gene can be arbitrarily combined with the nucleic acid portions targeting the APOC3 gene as mentioned above, such as AGT_27+A28(14-4)mF, AGT_27+A277(12-5), AGT_62+A28(14-4)mF etc. in orderto arrive at a muRNA molecule targeting both, AGT and APOC3. Such combination is also plausible due to the activity of the respective compounds as set forth in the Examples.
- the target gene different from the AGT gene may be a PCSK9 gene.
- the (b) second nucleic acid portion is e.g. an PCSK9 antisense strand and (d) the fourth nucleic portion a strand at least partially complementary thereto.
- the first nucleic acid portion is selected from Table 3a;
- the second nucleic acid portion is selected from Table 7a
- the third nucleic acid portion is selected from Table 3b
- the fourth nucleic acid portion is selected from 7b.
- the first nucleic acid portion is selected from Table 1 a, in particular Table 3a;
- the second nucleic acid portion is selected from Table 8a, in particular Table 8b;
- the third nucleic acid portion is selected from Table 1 b, in particular Table 3b;
- the first nucleic acid portion is selected from Table 1 a, in particular Table 3a;
- the second nucleic acid portion is selected from Table 9a, in particular Table 9b;
- the third nucleic acid portion is selected from Table 1 b, in particular Table 3b;
- the fourth nucleic acid portion is selected from Table 9c, in particular Table 9d.
- Table 9c the fourth nucleic acid portion is selected from Table 9c, in particular Table 9d.
- the first nucleic acid portion is selected from Table 1 a, in particular Table 3a;
- the second nucleic acid portion is selected from Table 10a, in particular Table 11 a;
- the third nucleic acid portion is selected from Table 1 b, in particular Table 3b;
- the fourth nucleic acid portion is selected from Table 12a, in particular Table 13a.
- the (a) first nucleic acid portion is selected from group consisting of the constructs denoted AGT_27, AGT_62, AGT_52, AGT_56, AGT_93 and AGT_75.
- the corresponding (c) third nucleic acid portion has the corresponding denotation in Table 1 b or 3b.
- the second nucleic acid portion is selected from the group consisting of PCS29, PCS44 and PCS53 in Table 22, where the second portion consists of the first 19 nucleotides of these entries.
- the corresponding (d) fourth portion contains the remaining nucleotides from the corresponding entries in Table 22.
- the nucleic acid portions targeting the AGT gene can be arbitrarily combined with the nucleic acid portions targeting the APOC3 gene as mentioned above, such as AGT_27+PCS29, AGT_27+PCS44, AGT_27+PCS53, AGT_62+PCS29 etc. in order to arrive at a muRNA molecule targeting both, AGT and PCSK9. Such combination is also plausible due to the activity of the respective compounds as set forth in the Examples.
- the construct further contains 1 to 8 additional nucleic acid portions that are respectively at least partially complementary to an additional 1 to 8 portions of RNA transcribed from one or more target genes, which target genes different to each other, and / or the same or different to the target genes defined in (a) and (b), and where each of the 1 to 8 additional nucleic acid portions respectively form additional duplex regions with respective passenger nucleic acid portions that are respectively at least partially complementary therewith.
- the construct contains 1 additional nucleic acid portion.
- the construct targets the target genes selected from the group consisting of:
- AGT gene (b) APOC3 gene and (e) Lp(a) gene
- (a) is the first nucleic acid portion that is at least partially complementary to at least a first portion of an RNA, which is transcribed from an AGT gene
- (b) is the second nucleic acid portion that is at least partially complementary to a first portion of an RNA which is transcribed from the second gene
- (e) is a fifth nucleic acid portion that is at least partially complementary to a third portion of RNA which is transcribed from the third gene
- (f) is a sixth nucleic acid portion that is at least partially complementary to (e)
- the target genes are (a) AGT gene, (b) APOC3 gene and (e) PCSK9 gene.
- the target genes are (a) an AGT gene, (b) an APOC3 gene and (e) a PCSK9 gene.
- the first nucleic acid portion is selected from Table 1 a, in particular Table 3a;
- the third nucleic acid portion is selected from Table 1b, in particular Table 3b;
- the fifth nucleic acid portion is selected from Table 7a;
- the first nucleic acid portion is selected from Table 1 a, in particular Table 3a;
- the second nucleic acid portion is selected from Table 4a, in particular Table 4b;
- the third nucleic acid portion is selected from Table 1 b, in particular Table 3b;
- the fourth nucleic acid portion is selected from Table 4c, in particular Table 4d;
- the fifth nucleic acid portion is selected from Table 8a, in particular Table 8b; and (d) the sixth nucleic acid portion is selected from Table 8c, in particular Table 8d.
- the first nucleic acid portion is selected from Table 1 a, in particular Table 3a;
- the second nucleic acid portion is selected from Table 4a, in particular Table 4b;
- the third nucleic acid portion is selected from Table 1b, in particular Table 3b;
- the fourth nucleic acid portion is selected from Table 4c, in particular Table 4d;
- the fifth nucleic acid portion is selected from Table 8a, in particular Table 8b;
- the first nucleic acid portion is selected from Table 1 a;
- the second nucleic acid portion is selected from Table 5a;
- the third nucleic acid portion is selected from Table 1b;
- the fifth nucleic acid portion is selected from Table 9a, in particular Table 9b;
- (f) the sixth nucleic acid portion is selected from Table 9c, in particular Table 9d.
- the first nucleic acid portion is selected from Table 3a;
- the second nucleic acid portion is selected from Table 5b;
- the fifth nucleic acid portion is selected from Table 9a, in particular Table 9b;
- the first nucleic acid portion is selected from Table 1 a, in particular Table 3a;
- the second nucleic acid portion is selected from Table 10b, in particular Table 12b;
- the third nucleic acid portion is selected from Table 1 b, in particular Table 3b;
- the fourth nucleic acid portion is selected from Table 11 b, in particular Table 13b;
- the fifth nucleic acid portion is selected from Table 10b, in particular Table 11 b;
- (f) the sixth nucleic acid portion is selected from Table 12b, in particular Table 12b.
- nucleic acid portions to be used are set forth under the headings "AGT and APOC3 muRNA” and “AGT and PCSK9 muRNA” above.
- all combinations are possible, such as AGT_27+A28(14-4)mF+PCS44, AGT_62+277(12-5)+PCS29, as long as it contains or consists of one AGT-targeting construct, one APCO3-targeting construct and one PCSK9-targeting construct among these specific constructs.
- Such combinations are also possible due to the activity of the respective compounds as set forth in the Examples.
- AGT-associated diseases or disorders simultaneously with APOC3- associated diseases or disorders and PCSK9-associated diseases or disorders.
- compositions and pharmaceutical compositions including shRNA, mxRNA and/or muRNA oligomeric constructs
- the composition contains an oligomeric compound according to the first aspect and/or a nucleic acid construct according the second aspect as described above, and a physiologically acceptable excipient.
- a pharmaceutical composition containing an oligomeric compound according to the first aspect and/or a nucleic acid construct according to the second aspect as described above.
- the pharmaceutical composition may further contain a pharmaceutically acceptable excipient, diluent, antioxidant, and/or preservative.
- the oligomeric compound according to the first aspect and/or the construct according to the second aspect may be the only pharmaceutically active agent(s).
- the pharmaceutical composition furthermore contains one or more further pharmaceutically active agents.
- the further pharmaceutically active agent(s) may be (an) agent(s) which decrease hypertension, where the further pharmaceutically active agent(s) is/are optionally selected from the group consisting of a diuretic, an angiotensin converting enzyme (ACE) inhibitor, an angiotensin II receptor antagonist, a beta-blocker, a vasodilator, a calcium channel blocker, an aldosterone antagonist, an alpha2-agonist, a renin inhibitor, an alpha-blocker, a peripheral acting adrenergic agent, a selective D1 receptor partial agonist, a nonselective alpha-adrenergic antagonist, a synthetic, a steroidal antimineralocorticoid agent; a combination of any of the foregoing; and a hypertension therapeutic agent formulated as a combination of agents, more optionally an angiotensin II receptor antagonist selected from the group consisting of losartan, val
- an oligomeric compound is provided according to the first aspect and/or a nucleic acid construct according to the second aspect as described above, for use in human or veterinary medicine or therapy.
- an oligomeric compound according to the first aspect and/or a nucleic acid construct according to the second aspect as described above may be used to treat, ameliorate and/or prevent a disease or disorder.
- One of the diseases may be an AGT-associated disease or disorder as discussed below. However, more diseases may be treated simultaneously by using muRNA constructs as described herein.
- Such diseases may be, for example, ApoB containing atherogenic Lipoprotein-associated diseases or disorders; Inflammatory signalling pathway-related diseases, such as related to IL-6, CRP and IL-11 ; Platelet aggregation and coagulation pathway-associated diseases; Diabetes; Obesity and metabolic syndrome; and/or other pro-atherogenic factor and modifiable risk factors for CVD-related diseases.
- Corresponding targets in particular in terms of dyslipidaemia, may be selected from the group consisting of APOC3, PCSK9, ANGPTL3, ANGPTL4, Lp(a), ANGPTL8 and ASGR1/2.
- AGT-associated disease or disorder may be selected from the group consisting of APOC3, PCSK9, ANGPTL3, ANGPTL4, Lp(a), ANGPTL8 and ASGR1/2.
- the disease or disorder may be a disease or disorder associated AGT or a disease or disorder requiring reduction of AGT expression.
- the disease or disorder is selected from the group consisting of high blood pressure, hypertension, borderline hypertension, primary hypertension, secondary hypertension isolated systolic or diastolic hypertension, pregnancy-associated hypertension, diabetic hypertension, resistant hypertension, refractory hypertension, paroxysmal hypertension, renovascular hypertension, Goldblatt hypertension, ocular hypertension, glaucoma, pulmonary hypertension, portal hypertension, systemic venous hypertension, systolic hypertension, labile hypertension; hypertensive heart disease, hypertensive nephropathy, atherosclerosis, arteriosclerosis, vasculopathy, diabetic nephropathy, diabetic retinopathy, chronic heart failure, cardiomyopathy, diabetic cardiac myopathy, nocturnal hypotension, glomerulosclerosis, coarctation of the aorta, aortic aneurism, ventricular fibrosis, heart failure, myocardial infarction, angina, stroke, renal disease
- the disease or disorder is further an APOC3-associated disease or disorder, or a disease or disorder requiring reduction of APOC3 expression levels, the disease or disorder advantageously being selected from dyslipidaemia including mixed dyslipidaemia; hyperchylomicronaemia including familial hyperchylomicronaemia; hypertriglyceridemia, advantageously severe hypertriglyceridemia and/or hypertriglyceridemia with blood triglyceride levels above 500 mg/dl; inflammation including low-grade inflammation; atherosclerosis; atherosclerotic cardiovascular diseases (ASCVD) including major adverse cardiovascular events (MACE) such as myocardial infarction, stroke and peripheral arterial disease; and pancreatitis including acute pancreatitis.
- dyslipidaemia including mixed dyslipidaemia
- hyperchylomicronaemia including familial hyperchylomicronaemia
- hypertriglyceridemia advantageously severe hypertriglyceridemia and/or hypertriglyceridemia with blood triglyceride levels above 500 mg/dl
- inflammation
- the disease or disorder is further a PCSK9- associated disease or disorder, or a disease or disorder requiring reduction of low-density lipoprotein (LDL) cholesterol, the disease or disorder advantageously being selected from dyslipidaemia including mixed dyslipidaemia, hypercholesterolemia, heterozygous familial hypercholesterolemia, non-familial hypercholesterolemia; atherosclerosis; and atherosclerotic cardiovascular disease (ASCVD) including myocardial infarction, stroke and peripheral arterial disease.
- dyslipidaemia including mixed dyslipidaemia, hypercholesterolemia, heterozygous familial hypercholesterolemia, non-familial hypercholesterolemia; atherosclerosis; and atherosclerotic cardiovascular disease (ASCVD) including myocardial infarction, stroke and peripheral arterial disease.
- dyslipidaemia including mixed dyslipidaemia, hypercholesterolemia, heterozygous familial hypercholesterolemia, non-familial hypercholesterolemia; atherosclerosis; and atheros
- a seventh aspect methods are provided for treating a disease or disorder by administering an oligomeric compound according the first aspect and/or a nucleic acid construct according to the second aspect, to an individual in need of treatment.
- the oligomeric compound and/or the nucleic acid construct may be administered subcutaneously or intravenously to the individual.
- an oligomeric compound according to the first aspect or a nucleic acid construct according to the second aspect may be used in research as a gene function analysis tool.
- an oligomeric compound according to the first aspect and/or a nucleic acid construct according to the second aspect may be used in the manufacture of a medicament for a treatment of a disease or disorder.
- nucleobase sequences of antisense and sense strands of the oligomeric compounds as well as of nucleobase sequences of single-stranded oligomeric compounds, and definitions of modified oligomeric compounds.
- the notation includes nucleobase sequence, sugar modifications, and, where applicable, modified phosphates.
- A represents adenine
- U represents uracil
- C represents cytosine
- G represents guanine.
- 5Phos represents a 5’ terminal phosphate group which is advantageous but not indispensable;
- m represents a methyl modification at the 2' position of the sugar of the underlying nucleoside;
- f represents a fluoro modification at the 2' position of the sugar of the underlying nucleoside;
- r indicates an unmodified (2'-OH) ribonucleotide;
- [Ps] or # represents a phosphorothioate inter-nucleoside linkage;
- I represents an inverted inter-nucleoside linkage, which can be either 3'-3', or 5'-5';
- 3xGalNAc represents a trivalent GalNAc.
- Tables 1 a and 1 b below show nucleobase sequences of antisense and sense strands of 100 oligomeric compounds in accordance with the Examples.
- Table 1a Nucleobase sequences of the antisense strands of 100 constructs
- nucleobase of the 3' terminal nucleotide of each of the sense strands presented within the table can be replaced by A.
- Table 2 below shows the nucleobase sequences of the 100 hairpin constructs as selected in accordance with the Examples.
- the nucleobase sequences are a direct fusion of the antisense sequences of Table 1 a with the corresponding sense sequences of Table 1 b.
- nucleobase of the 3' terminal nucleotide of each of the sense strands presented within the table can be replaced by A.
- Tables 3a to c below shows 100 antisense sequences, sense sequences and hairpins, respectively, with full modification information (modified sugars and, where applicable, modified phosphates).
- each of the above constructs may or may not have a phosphate modification at the 5' end group.
- each of the above constructs may or may not have a "3x GalNAc" coupled to the 3' end group.
- the constructs have a 3x GalNAc ligand, in particular a toothbrush ligand as defined herein.
- each of the above constructs may or may not have a phosphate modification at the 5' end group. Furthermore, and independently, each of the above constructs may or may not have a "3x GalNAc" coupled to the 3' end group.
- the constructs have a 3x GalNAc ligand, in particular a toothbrush ligand as defined herein.
- Particularly advantageous are constructs which in addition have a 5' phosphate, even though this is not a strict requirement, given that in the absence thereof, mammalian cells will add such phosphate in case it is absent from the molecule as administered.
- the term “A277” designates the sequence suitable for RNAi with APOC3, where the first number in the round brackets, i.e. 12 in the present case, designates the number of base pairs within a duplex region within a shRNA, and the second number in the round brackets, in this case 5, designates the number of nucleotides present in the hairpin loop of the shRNA. If there is no designation after the hyphen in the round brackets, it means that the loop consists of 5 nucleotides.
- Tables 4a to 4d below show nucleobase sequences and sugar-phosphate backbone modifications of antisense and sense strands of the 376 APOC3 constructs selected in accordance with the Examples. The disclosed 30 specific oligomeric compounds have been selected from these 376 constructs.
- Table 4a Nucleobase sequences of the APOC3 antisense strands of 376 constructs
- Table 5a Nucleobase sequences of the APOC3 antisense strands of 15 further constructs
- Table 5b Nucleobase sequences and sugar-phosphate backbone modifications of the APOC3 antisense strands of 15 further constructs
- Tables 6a to 6b below show nucleobase sequences and sugar-phosphate backbone modifications of 12 further APOC3 constructs.
- Example 9 the nucleobase sequences of antisense and sense strands of 27 specific oligomeric PCSK9-targeting compounds are given. These are also subject of specific embodiments disclosed further herein. Tables 7a and 7b below shows specific sugar-phosphate backbone modifications of PCSK9 antisense and sense strands of the 27 constructs.
- Table 7a Exemplary sugar-phosphate backbone modifications of PCSK9 antisense strands of the 27 constructs.
- Table 7b Exemplary sugar-phosphate backbone modifications of PCSK9 sense strands of the 27 constructs.
- Tables 8a to 8d below show nucleobase sequences and sugar-phosphate backbone modifications of PCSK9 antisense and sense strands of the 250 constructs selected in accordance with Example 8 below.
- the above disclosed 27 oligomeric PCSK9 compounds have been selected from these 250 constructs.
- Table 8b 250 modified PCSK9 antisense nucleobase sequences corresponding to Table 8a.
- Table 8c 250 PCSK9 unmodified sense nucleobase sequences corresponding to Table 8a.
- Table 8d 250 modified PCSK9 sense strands corresponding to the antisense strands of
- Tables 9a to 9d below show nucleobase sequences and sugar-phosphate backbone modifications of PCSK9 antisense and sense strands of a further 43 constructs.
- Table 9a 43 unmodified PCSK9 antisense nucleobase sequences.
- Table 9c 43 unmodified PCSK9 sense nucleobase sequences corresponding to Table 9a.
- Table 9d 43 modified PSCK9 modified sense strands corresponding to the strands of Table 9a.
- Table 10a shows the nucleobase sequences of PCSK9-targeting antisense portions (e.g. second nucleic acid portions).
- Table 10b shows the nucleobase sequences of APOC3-targeting antisense portions
- Table 11a shows the nucleobase sequences of PCSK9-targeting sense portions (third nucleic acid portions).
- Table 11b shows the nucleobase sequences of APOC3-targeting sense portions (fourth or sixth nucleic acid portions).
- Table 12a shows PCSK9-targeting antisense portions including modification information.
- Table 12b shows APOC3-targeting antisense portions including modification information.
- Table 13a shows PCSK9-targeting sense portions including modification information.
- Table 13b shows APOC3-targeting sense portions including modification information.
- Table 14a shows combination (APOC3 + PSCK9) linked first and fourth nucleic acid portions. Linking is direct to give rise to a single contiguous strand.
- Table 14b shows (combination (APOC3 + PCSK9) linked second and third nucleic acid portions. Linking is direct to give rise to a single contiguous strand.
- the 3' terminal nucleoside of the sense (passenger) strand can include any nucleobase that can be present in an RNA molecule, i.e., can be any of adenine (A), uracil (U), guanine (G) or cytosine (C), advantageously, however, the 3’ terminal residue is a nucleobase that is complementary to the 5' nucleobase of the antisense (guide) strand (first region as defined herein).
- RNAi constructs disclosed herein have been carried out using synthesis methods known to the person skilled in the art, such as synthesis methods disclosed in https://en.wikipedia.org/wiki/Oligonucleotide_synthesis ⁇ retrieved on 16 February 2022 ⁇ , where the methods disclosed on this website are incorporated by reference herein in their entirety .
- the only difference to the synthesis method disclosed in this reference is that GalNAc phosphoramidite immobilized on a support is used in the synthesis method during the first synthesis step.
- Oligomeric compounds targeting AGT were identified by bioinformatics analysis on human AGT mRNA sequence as given in RefSeq sequence ID NM_000029.3 100 compounds were selected for synthesis as mxRNA hairpins. Compounds were dissolved to 50uM in molecular biology grade water. Duplexes were annealed by heating at 95 °C for 5 minutes followed by gradual cooling to room temperature. mxRNAs were annealed by heating at 95 °C for 5 minutes followed by rapid cooling on ice.
- Human primary hepatocytes (5 donor pooled - Sekisui XenoTech, HPCH05+) were thawed immediately prior to experimentation and cultured in 1x complete Williams medium (Gibco, A1217601) supplemented with Hepatocytes plating supplement pack (Gibco, CM3000). FBS concentration was modified from manufacture recipe to a final 2.5% (as opposed to 5%) for compound stability.
- Human primary hepatocytes (5 donor pooled - Sekisui XenoTech, HPCH05+; 2 vials) of cells were thawed by pouring Hepatocyte pellets to warm, 45 ml of Sekisui OptiThaw Hepatocyte Media (K8000), spun at 250xg for 5 min, resuspended in 40 ml of complete 2X WEM 1x Complete WEM: 2.5% FBS, 1 pM Dexamethasone, Pen/Strep (100 U/mL /100 pg/mL), 4 pg/ml Human Insulin, 2 mM GlutaMAX, 15 mM HEPES, pH 7.4.) and counted.Cells were then plated in 50 pL of 2x complete WEM at 25,000 cells per well on 96 well type 1 rat tail Collagen plates and allowed to rest and attach for 5 hours before transfection.
- each 2 pM AGT targeting oligonucleoside compound was added to respective plated hepatocytes for a final concentration of 1 pM in a volume of 100uL 1x complete WEM.
- RNA samples were harvested and RNA isolated using the PureLink Pro 96 total RNA Purification Kit (ThermoFisher, 12173011 A) according to the manufacturer protocol.
- Harvested RNA was assayed for AGT expression via Taqman qPCR using the Luna Universal Probe One-Step RT-qPCR Kit (NEB, E3006).
- a qPCR assay was performed for each sample using a AGT TaqMan probe set (Hs01586213_m-FAM) multiplexed with a common GAPDH VIC probe (ThermoFisher, 4326317E). Thermocycling and data acquisition was performed with an Applied Biosystems Quantstudio 3/5 Real-Time PCR System.
- Example 2 Table 15 below shows IC50 values (in nM) for 30 selected constructs (from Table 3c) selected in accordance with the Examples. Seven serials of 5-fold dilution of these constructs starting at 10OOnM were prepared in basal WEM. Effect of different concentration of constructs on inhibition of AGT mRNA was determined using the protocol described above for the primary screen. Max % KD indicates the maximally achieved knock-down at 1000 nM with 0% being no knock-down and 100% full knock-down. M4K4 was used as reference. Percentage inhibition of construct at different concentration was calculated and the IC50 was determined using GraphPad Prism 9.0.
- Figs. 2a to 2h show the results for inhibiting AGT gene expression for fivefold dilution series for various oligomeric nucleoside compounds targeting AGT (from Table 3c).
- the TMPRSS6 construct used as a positive control, has the following modified structure: 5'vP[mA][fA][mC][fC][mA][fG][mA][fA][mG][fA][mA][fG][mC][fA][mG][fG][mU][fG][iN][fC][mU][fG][fC][ fU][mU][fC][mU][fU][mC][fU][mG][fG][mU][fU]#[3XGalNAc] (SEQ ID NO: 3587).
- HepG2 (ATCC cat. 85011430) cells were maintained by biweekly passing in EMEM supplemented with 10% FBS, 20 mM L-glutamine, 10 mM HEPES pH 7.2, 1 mM sodium pyruvate, 1x MEM non- essential amino acids, and 1x Pen/Strep (EMEM complete).
- Targets to APOC3 were identified by bioinformatic analysis on human APOC3 mRNA sequence as given in RefSeq sequence ID NM_000040, where inter alia it has been taken into consideration that constructs should target APOC3 mRNA irrespective of splice variants and isoforms. 376 targets were selected for synthesis as asymmetric duplexes (14 nucleotide sense strand, 19 nucleotide antisense strand). Compounds were dissolved to 50uM in molecular biology grade water and annealed by heating at 95C for 5 minutes followed by gradual cooling to room temperature.
- RNAiMax ThermoFisher
- 77 oligomeric compounds which exhibit at least 70% target knockdown when assessed with either probe. These 77 compounds are selected from SEQ ID Nos. 601-1352 above in Tables 4a and 4b.
- a yet narrower set of the best performing 30 APOC3 duplexes were tested in dose curves.
- HepG2 cells were collected by trypsinization and seeded in 96 well tissue culture plates at 10,000 cells per well in 50uL complete EMEM with 20% FBS and allowed to rest for 4 hours.
- Transfection complexes were formed by gently mixing 36 pmoles of each duplex in 180 uL OptiMEM with 2.16 uL RNAiMax in 180 uL OptiMEM to make 360 uL total complex. A two fold dilution series was then performed with basal OptiMEM.
- each dilution was added to respective triplicates of HepG2 cells to make a final dilution series of 50 nM down to 0.32 nM in a volume of 100uL, 50/50 EMEM/OptiMEM at 10% FBS.
- Table 16 shows IC50 values (in nM) for the 30 constructs selected in accordance with the Examples.
- Human primary hepatocytes (5 donor pooled - Sekisui XenoTech, HPCH05+) were thawed immediately prior to experimentation and cultured in 1x complete Williams medium (Gibco, A1217601) supplemented with Hepatocytes plating supplement pack (Gibco, CM3000). FBS concentration was modified from manufacture recipe to a final 2.5% (as opposed to 5%) for compound stability.
- 1x Complete WEM 2.5% FBS, 1 pM Dexamethasone, Pen/Strep (100 U/mL /100 pg/mL), 4 pg/ml Human Insulin, 2 mM GlutaMAX, 15 mM HEPES, pH 7.4).
- Hepatocytes were plated on Collagen I (rat tail) coated 96 well tissue culture plates (Gibco, A1142803).
- mice used in this study were human liver-uPA-SCID mice. About 80% of the hepatocytes of each mouse have been replaced by human hepatocytes. The skilled person is aware of ways of producing such mice; where at least some of these ways are shown and referenced in P. Meuleman and G. Leroux-Roels in Antiviral Res. 2008 Dec;80(3):231-8 which is incorporated herein by reference in its entirety.
- mice 36 human liver-uPA-SCID mice. Animals will be grouped by treatment type, dosage, and survival period. Each animal will be treated by subcutaneous injection of test material. Groups 1A and 1 B will have four animals receive a control dose of PBS. Groups
- 2A, 2B, 2C, 3A, 3B, and 3C will receive one dose (10 or 30 mg/kg) with four animals for each dose amount. All animals will be kept alive for 14 or 42 days. See study Table 18 below for details.
- A277(12-5) APOC3-targeting mxRNA construct (SEQ ID Nos. 2169, 2181)
- mice used for the study have to be properly considered.
- an estimated fraction of 20 to 25% of the cells of the humanized liver are sill murine.
- A28(14-4)mF does not target murine APOC3.
- the non-silenced murine APOC3 contributes to the observed levels of triglycerides and total cholesterol.
- the downregulation of these two blood fats in a (purely) human system is expected to exceed what has been observed in this study.
- RNAIMax ThermoFisher
- mice 40 PXB. Animals will be grouped by treatment type, dosage, and survival period. Each animal will be treated by subcutaneous injection of test material.
- Group 1A, 1 B, 1 C, and 1 D will have five animals and receive a single control dose of PBS.
- Group 2A, 2B, 2C, and 2D will have five animals and receive a single dose of AGT-27A at 30 mg/kg.
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Abstract
Nucleic acid products are provided that modulate, in particular interfere with or inhibit AGT gene expression. The products can be oligomeric compounds that comprise at least a first region of linked nucleosides having at least a first nucleobase sequence that is at least partially complementary to at least a portion of RNA transcribed from an AGT gene, wherein said first nucleobase sequence is selected from SEQ ID NOs 1 to 100.
Description
Products and Compositions
Related Applications
This application claims the benefit of and priority to US Provisional Patent Application No. 63/407,353, filed September 16, 2022, which is incorporated herein by reference in its entirety. Sequence Listing
The instant application contains a Sequence Listing which has been submitted electronically in XML format and is hereby incorporated by reference in its entirety. Said XML document, created on September 11 , 2023, is named 4690_0081 i_SL.xml and is 23,336,830 bytes in size. Field
Nucleic acid products that modulate, interfere with, or inhibit angiotensinogen (AGT) gene expression are provided. Specifically, methods, compounds, and compositions are provided for reducing expression of AGT mRNA and protein in an animal. Such methods, compounds, and compositions are useful to treat, prevent, or ameliorate AGT-associated diseases or disorders, such as hypertension.
Background
The renin-angiotensin-aldosterone system (RAAS) is known to play an important role in the regulation of blood pressure. The RAAS cascade is initiated by the release due to widely known mechanisms of renin into the circulation, in particular into the plasma. Active renin in the plasma cleaves angiotensinogen (AGT), which is produced by the liver, to yield angiotensin I. Angiotensin I is converted to angiotensin II by the circulating and locally expressed angiotensin-converting enzyme (ACE). Angiontensin II is a peptide hormone, which causes vasoconstriction, which in turn, can increase blood pressure and may lead to hypertension and associated diseases.
Dysregulation of angiotensin II, in particular excessive angiotensin II production, causes hypertension and can lead to increased oxidative stress, promotion of inflammation, hypertrophy, and fibrosis in the heart, kidneys, and arteries, and may finally result in left ventricular fibrosis, arterial remodelling and glomerulosclerosis.
Disease
Hypertension is the most prevalent, controllable disease in developed countries, affecting 20-50% of adult populations. Hypertension is a major risk factor for various diseases, disorders and conditions such as, shortened life expectancy, chronic kidney disease, stroke, myocardial infarction, heart failure, aneurysms (e.g. aortic aneurysm), peripheral artery disease, heart damage (e.g., heart enlargement or hypertrophy) and other cardiovascular related diseases, disorders, or conditions. In addition, hypertension has been shown to be an important risk factor for cardiovascular morbidity and mortality accounting for, or contributing to, 62% of all strokes and 49% of all cases of heart disease. In 2017, changes in the guidelines for diagnosis, prevention, and treatment of hypertension were developed providing goals for even lower blood pressure to further decrease risk of development of diseases and disorders associated with hypertension (see, e.g., Reboussin et al., Systematic Review for the 2017 ACC/AHA/AAPA/ABC/ACPM/AGS/APhA/ASH/ASPC/NMA/PCNA Guideline forthe Prevention, Detection, Evaluation, and Management of High Blood Pressure in Adults: A Report of the i
American College of Cardiology/American Heart Association Task Force on Clinical Practice Guidelines. J Am Coll Cardiol. 2017 Nov 7. pii: S0735- 1097( 17)41517-8. doi: 10.1016/j.jacc.2O17.11.004; and Whelton et a/., (2017 ACC/AHA/AAPA/ABC/ACPM/AGS/APhA/ASH/ASPC/NMA/PCNA Guideline for the Prevention, Detection, Evaluation, and Management of High Blood Pressure in Adults: A Report of the American College of Cardiology/American Heart Association Task Force on Clinical Practice Guidelines. J Am Coll Cardiol. 2017 Nov 7. pii: S0735- 1097( 17)41519-1 . doi: 10.1016/j.jacc.2O17.11.006). Hypertension can also occur along with PCSK9- and/or APOC3-associated disorders such as dyslipidaemia, more specifically hypercholesterinaemia, hypertriglyceridemia, hyperchylomicronaemia, and atherosclerotic cardiovascular disease (ASCVD). Treatment
Despite the number of anti-hypertensive drugs available for treating hypertension, more than two- thirds of subjects are not controlled with one anti-hypertensive agent and require two or more anti - hypertensive agents selected from different drug classes. This further reduces the number of subjects with controlled blood pressure as adherence is reduced and side effects are increased with increasing numbers of medications. Furthermore, several studies have suggested a potential relationship between chronic use of antihypertensive medications and deterioration in kidney function finding that antihypertensive agents to control blood pressure also impact kidney function independently of their effect on blood pressure (Tomlinson, et al (2013) PLoS ONE 8(11) Article ID e78465; The SPRINT Research Group (2015) NEJM 373(22):2103-2116, ClinicalTrials.gov number, NCT01206062; Kidney Disease: Improving Global Outcomes (KDIGO) CKD Work Group (2013) Kidney International Supplements 3: 1-150; Kamaroff, et a/.,(2018( Hindawi International J Chron Dis Article ID 1382705 | https://doi.Org/10.l 155/2018/1382705).
In addition, anti-hypertensive drugs, renal denervation, baroreceptor activation therapy, diet changes and lifestyle changes may reduce hypertension and reduce the diseases, disorders and/or conditions associated with hypertension (Paulis et al., Nat Rev Cardiol, 2012, 9:276-285). However, there are limitations to the therapies currently approved for treating hypertension as a significant subset of all hypertensive patients do not achieve adequate blood pressure control. For example, drugs such as ACE inhibitors and angiotensin receptor blockers (ARBs) that target parts of the renin-angiotensin system (RAS) pathway are limited in their ability to inhibit the RAAS pathway (Nobakht et al., Nat Rev Nephrol, 2011 , 7:356-359). Additionally, certain anti-hypertensive drugs such as ACE inhibitors are contra-indicated in hypertensive patients with renal disease due to their potential to compromise renal function in patients.
Therefore, there is a need for further compounds and treatments being capable of efficiently reducing the effects of dysregulation in connection with excessive production of angiotensin II, such as hypertension, and overcoming the aforementioned disadvantages.
Summary
Compounds and treatments are provided that efficiently reduce the effects of dysregulation in connection with excessive production of angiotensin II, such as hypertension.
According to a first aspect, an oligomeric compound is provided that inhibits expression of angiotensinogen (AGT), where the compound contains at least a first region of linked nucleosides having at least a first nucleobase sequence that is at least partially complementary to at least a portion of RNA transcribed from an AGT gene, where the first nucleobase sequence is selected from the following sequences, or a portion thereof: sequences of Table 1 a (SEQ ID NOs: 1 to 100), where the portion advantageously has a length of at least 18 nucleosides.
Particularly advantageous embodiments are optimized hairpin RNAs (referred to as mxRNAs); for further details see the embodiments and their discussion further below.
Double-stranded RNAs (dsRNAs) also are provided. In contrast to mxRNAs, dsRNAs lack a loop connecting antisense and sense portions and therefore contains two strands. The two strands are not covalently connected to each other but form a duplex region where base pairing occurs.
In a second aspect, the nucleic acid construct may contain at least:
(a) a first nucleic acid portion that is at least partially complementary to at least a first portion of an RNA, which is transcribed from an AGT gene;
(b) a second nucleic acid portion that is at least partially complementary to at least a second portion of an RNA, which is transcribed from an AGT gene, the second portion being different from the first portion;
(c) a third nucleic acid portion that is at least partially complementary to the first nucleic acid portion of (a), so as to form a first nucleic acid duplex region therewith;
(d) a fourth nucleic acid portion that is at least partially complementary to the second nucleic acid portion of (b), so as to form a second nucleic acid duplex region therewith.
Advantageous and/or exemplary features of constructs according to this second aspect are as follows:
1) they contain multiple (2 or more) at least partially double-stranded agents capable of triggering RNA interference, tied together into a single nano-structure predominantly through complementary (Watson-Crick) interactions;
2) optionally, other (e.g.) covalent bindings may be used to build the constructs and/or add various ligands (e.g. delivery/targeting moieties such as GalNAc and or other carbohydrates, cholesterol, peptides, or small molecules, optionally attached via linkers);
3) the constructs predominantly contain chemically modified nucleotides (e.g. 2’F, 2'OMe, LNO, PNA, MOE, BNA, PMO, phosphorothioate, phosphodithioate, etc.), mostly (but not only) to increase resistance to nucleases;
4) the constructs contain “fragile” components (e.g. chemical linkers, unmodified nucleotides, etc.), which allow the constructs to disassemble upon exposure to certain biologic environments (e.g. exposure to extra- and/or intra-cellular fluids); particular examples could be (but not limited): a) cleavage of the oligo backbone by nucleases in the sites with non-modified nucleotides; b) cleavage of the chemical linkage due to the change of pH (e.g. in endosomes);
5) disassembly upon exposure to the certain biologic environments releases the active components (e.g. the at least partially double-stranded agents capable of triggering RNA interference) to modulate (up- or down-regulate, advantageously down-regulate) target gene expression in cells/organisms;
6) the constructs can be used to modulate, advantageously down-regulate or silence gene expression, to study gene function, or to treat various diseases associated with the target genes to be down regulated.
In a third aspect, the composition contains an oligomeric compound according to the first aspect and/or a nucleic acid construct according to the second aspect, and a physiologically acceptable excipient.
In a fourth aspect, a pharmaceutical composition is provided containing an oligomeric compound according to the first aspect and/or a nucleic acid construct according to the second aspect.
A fifth aspect provides an oligomeric compound according to the first aspect and/or a nucleic acid construct according to the second aspect, for use in human or veterinary medicine or therapy.
A sixth aspect provides an oligomeric compound according to the first aspect and/or a nucleic acid construct according to the second aspect, for use in a method of treating a disease or disorder.
A seventh aspect provides a method of treating a disease or disorder by administering an oligomeric compound according to the first aspect and/or a nucleic acid construct according to the second aspect, to an individual in need of treatment.
In an eighth aspect an oligomeric compound according to the first aspect or according to the second aspect, may be used in research as a gene function analysis tool.
In a ninth aspect, an oligomeric compound according to the first aspect or the second aspect is used to manufacture a medicament for a treatment of a disease or disorder.
Effects achieved by the oligomeric compounds
The oligomeric compounds as described herein cause a significant reduction of gene expression of AGT, e.g. in vitro using 5-donor primary human hepatocytes, as e.g. shown in the examples disclosed herein. The most potent compounds surprisingly produce knockdowns of about 91 % or more, even up to 94.8%, AGT mRNA expression in vitro compared with a negative test. Furthermore, the compounds, as e.g. shown in the examples, are at least capable of producing knockdowns of at least 50% of AGT expression in vitro relative to a negative test. As AGT expression can be successfully reduced, the compounds efficiently reduce the effects of angiotensin II overexpression due to dysregulation of the RAAS cascade, and a significant reduction of AGT leads to a reduced production of angiotensin II, and allows treatment of hypertension.
Furthermore, it was surprisingly found that these effects may be achieved by using oligomeric compounds for inhibiting the expression of AGT gene in the form of mxRNA constructs having a reduced length of e.g. 33 nucleosides compared to conventional shRNA molecules having greater lengths. This can e.g. make a synthesis of mxRNA molecules more cost- and production efficient, because less units are needed.
For certain mxRNA constructs that target expression of the AGT gene, it was surprisingly found that the aforementioned effects can be achieved by using short sense strands within the mxRNA, advantageously having a length of 14 nucleosides, which is shorter than the length of the sense strands in conventional shRNA molecules.
In addition, AGT-targeting nucleic acid sequences disclosed herein also may be used in conjunction with an APOC3-targeting nucleic acid sequence or a PCSK9-targeting nucleic acid sequence as part
of a muRNA, as described below. This is plausible, because mxRNA including AGT-targeting nucleic acid sequences in the form of antisense strands have been proven to exhibit knock down of AGT gene expression as confirmed by in vitro experiments herein (see e.g. Examples 1 and 2). On the other hand, mxRNA constructs including APOC3-targeting nucleic acid sequences in the form of antisense strands or PCSK9-targeting nucleic acids in the form of antisense strands have been confirmed in both, in vitro and in vivo experiments, to be active in terms of APOC3 gene knockdown or PCSK9 gene knock down, respectively (see e.g. Examples 3 to 11 herein). Without wishing to be bound by a particular theory, it is believed that the antisense strands targeting AGT, APOC3 or PCSK9, when being part of muRNA nucleic acid constructs, are also the active species in the respective gene knockdown. Thus, the muRNA constructs disclosed herein, including AGT-targeting antisense strands and APOC3-targetting antisense strands or AGT-targeting antisense strands and PCSK9-targeting antisense strands, are active in knockdown of the respective target gene. This is also evidenced by virtue of the in vivo and in vitro experiments disclosed herein showing the respective target knockdown for muRNA molecules including APOC3-targeting antisense strands and PCSK9-targeting antisense strands (see for example Examples 12 and 13). Because it is assumed, without wishing to be bound by a particular theory, that the active species are the same for muRNA as for mxRNA molecules, if the respective targeting antisense strands are included, the experiments of the present application also demonstrate that an muRNA molecule targeting AGT, APOC3, and PCSK9 using the strands disclosed herein, is active in the gene knockdown of AGT, APCO3 and PCSK9 at the same time. Accordingly, the muRNA molecules may be used to treat PCSK9- and/or APOC3-associated disorders such as dyslipidaemia, more specifically hypercholesterinaemia, hypertriglyceridemia, hyperchylomicronaemia, and atherosclerotic cardiovascular disease (ASCVD), along with hypertension.
In addition, it has been found that muRNA constructs may be used to simultaneously inhibit both, AGT and APOC3 where the constructs include the AGT-targeting nucleic acid portions disclosed herein and APOC3-targeting portions disclosed herein.
The effects and technical advantages achieved by using these oligomeric compounds for inhibiting AGT expression will become apparent in more detail in the detailed description and the examples. Brief Description of the Figures
Figure 1 shows single dose curves of certain AGT mxRNA compounds and their activity in inhibiting AGT gene expression (primary screening), selected from Table 3c, SEQ ID Nos. 501-600 and 3604- 3605.
Figures 2a to 2h show dose curves of 30 AGT mxRNA compounds and their activity in inhibiting AGT gene expression (secondary screening). See Example 2.
Figure 2a: AGT_27, AGT_44, AGT_41 , AGT_97 (SEQ ID Nos. 527, 544 541 & 597); Figure 2b: AGT_90, AGT_62, AGT_52, AGT_93 (SEQ ID Nos. 590, 562, 552 & 593); Figure 2c: AGT_49, AGT_73, AGT_18, AGT_37 (SEQ ID Nos. 549, 573, 518 & 537); Figure 2d: AGT_56, AGT_100, AGT_40, AGT_75 (SEQ ID Nos. 556, 5100, 540 & 575); Figure 2e: AGT_30, AGT_42, AGT_81 , AGT_17 (SEQ ID Nos. 530, 542, 581 & 517); Figure 2f: AGT_34, AGT_53, AGT_29, AGT_26 (SEQ ID Nos. 534, 553, 529 & 526);
Figure 2g: AGT_74, AGT_94, AGT_14, AGT_3 (SEQ ID Nos. 574, 594, 514 & 503); and Figure 2h: AGT_7, AGT_2, TMPRSS, M4K4 (SEQ ID Nos. 507 & 502; two: controls).
Figure 3a shows dose curves of APOC3 leads for candidates in primary human hepatocytes at various doses; and Figure 3b shows dose curves of APOC3 leads for the humanized mouse study in primary human hepatocytes, as described in Examples 3-5.
Figure 4 shows a schematic overview of a study including the time point of applying the dose to the mice and time points for taking samples, as described in Examples 6 and 7
Figure 5 shows a mean percent of remaining APOC3 mRNA in liver tissues and APOC3 protein levels in plasma for the animals treated with APOC3-targeting mxRNA constructs (A28(14-4)mF mF (SEQ ID Nos. 2176 & 2188) and A277(12-5) mF (SEQ ID Nos. 2169 & 2181 versus controls, as further described in Example 6.
Figure 6 shows a mean percent of triglycerides (TG) and total cholesterol (TC) in the serum of the animals treated with APOC3-targeting mxRNA constructs (A28(14-4)mF mF (SEQ ID Nos. 2176 & 2188) and A277(12-5) mF (SEQ ID Nos. 2169 & 2181 versus controls, as further described in Example 6.
Figures 7a and 7b show a mean percent of remaining APOC3 mRNA in liver tissues (Fig. 7a) and APOC3 protein levels in the plasma measured using ELISA (Fig. 7b) for the animals treated with APOC3-targeting mxRNA constructs (A28(14-4)mF mF (SEQ ID Nos. 2176 & 2188) and A277(12-5) mF (SEQ ID Nos. 2169 & 2181 (10mg/kg) at weeks 2 and 6 versus controls, as further described in Example 6.
Figures 8a and 8b show mean percent of triglycerides (Fig. 8a) and total cholesterol (Fig. 8b) in the serum of the animals treated with APOC-3 targeting mxRNA constructs (A28(14-4)mF mF (SEQ ID Nos. 2176 & 2188) and A277(12-5) mF (SEQ ID Nos. 2169 8> 2181) as versus controls at weeks 2 and 6, as further described in Example 6.
Figure 9 presents a schematic overview of the extended study (See also Fig. 4 and Example 6) performed with compound A28(14-4)mF (also designated STP125G) (SEQ ID Nos. 2176 & 2188) in mice with a humanized liver, as described in Example 7. A humanized liver mouse model (n=4) was used to test STP125G at 10 mg/kg administered subcutaneously; Terminal endpoints were 2, 4, 6, 8 and 10 weeks. qPCR (mRNA - human AGT), plasma ELISA (protein - human AGT) and triglyceride concentration assays were run.
Figures 10a and b show APOC3 mRNA in liver and protein knockdown in plasma through week 12, as described in Example 7.
Figures 11 a and b show serum triglyceride (TG) and total cholesterol (TC) through week 8, as described in Example 7.
Figure 12 is a diagram illustrating the development of a humanized liver in mice used in the study described in Example 7. From M. Grompe and S. Strom (2013) Gastroenterology, 145:1209-1214. Figure 13 shows a table of PCSK9 knockdown values as compared to negative control in hepatoma cell line. Nucleobase sequences together with backbone (sugar, phosphate) modifications as selected from Tables 7a, SEQ ID Nos. 2189-2215, without ligand attached, and Table 7b, with ligand, SEQ ID Nos. 2216-2242). Asymmetrical 15-19 configuration with alternating chemical modification pattern.
Cell seeding: 10,000 HepG2 cells/well; lipofectamine RNAiMax mediated transfection; Transfection: 20 nM compounds, antibiotic-free EMEM medium 10% FBS, 72 h incubation; gene expression measured by qPCR (Taqman chemistry), adjusted to the standard curve, and normalized ot the reference gene GAPDH; data expressed as percent of gene expression in nontreated cells (NT). Figure 14 shows IC50 concentrations for PCSK9 knockdown using a variety of PCSK9 constructs. Nucleobase sequences together with backbone (sugar, phosphate) modifications selected from Tables 7a and 7b, without and with ligand attached (SEQ ID Nos. 2189-2242 and in sequences identified in Tables 8a-11 a, as shown in Table 19). See Examples 8-9.
Figure 15 shows a concentration dependency of PCSK9 knockdown by particularly advantageous double-stranded constructs (antisense strand: 19 nt; sense strand: 14 nt) carrying a GalNAc ligand (constructs P29 (SEQ ID Nos. 3588-3589), P57 (SEQ ID Nos. 3590-3591), P53 (SEQ ID Nos. 3592- 3593), P44 (SEQ ID Nos. 3594-3595), as well as controls: TMPRSS6 and M4K4 G8, all at various concentrations The nucleobase sequence of the 14 nt sense strand differs from that given in the sequence listing (15 nt) in that the 5'-terminal nucleotides is removed. Backbone (sugar, phosphate) modifications as given in Table 20, as described in Example 10, optimized double stranded constructs.. M4K4 and TMPRSS6 were used as negative controls (unrelated targets).
Figure 16 shows a comparison of two types of double-stranded constructs, as described in Example 10. Antisense strand: 19 nt; sense strand: 15 nt when indicated ("(15)"; nucleobase sequence as given in the sequence listing), otherwise 14 nt., (constructs P29 (SEQ ID Nos. 3588-3589), P52 (SEQ ID Nos. 2194, 2221), P29(15) (SEQ ID Nos. 3596-3597), P52(15), as well as controls: M4K4 and PC1 a). Backbone (sugar, phosphate) modifications as given in Table 20 (SEQ ID Nos. 3588-3597). PC1 a: positive control. An inclisiran-type molecule has been used which differs from inclisiran in that the ligand is 3xGalNAc. This is for reasons of consistency with constructs which carry a 3xGalNAc ligand. M4K4 was usedas a negative control.
Figure 17 shows a concentration dependency of PCSK9 knockdown by selected hairpin molecules (mxRNAs). "14-5-14" stands for a 19 nt antisense region connected to a 14 nt sense region (shortened by 1 nt as for Figure 15), where the 5 3'-terminal nucleotides of the antisense region for the loop of the hairpin and the molecules contains a 14 bp duplex region formed by base pairing between the 14 5'-terminal nucleotides ofthe antisense region with a nucleotides of the sense region. Corresponding nucleobase sequences of the entire hairpin molecules are those set forth in the Tables including the experimental labels. Backbone (sugar, phosphate) modifications are given in Table 21 (SEQ ID Nos. 3598-3601 . TMPRSS6 was used as a negative control. See Example 11 .
Figure 18 shows a schematic overview of a study performed in mice with humanized liver for the purpose of selection of candidate molecules. A humanized liver mouse model (n=4 or 5 per group) was used to test AGT27A mxRNA (SEQ ID No. 3604) and AGT-52A mxRNA (SEQ ID No. 3605) at 5, 10 and 30 mg/kg administered subcutaneously; Terminal endpoint was 2 weeks. qPCR (mRNA - human AGT) and plasma ELISA (protein - human AGT) were run. See Example 14.
Figures 19a and b show knockdown (KD) liver (Fig. 19a) and plasma protein (Fig. 19b) data after two weeks obtained in the study (design depicted in Figure 18).
Figure 20 shows a schematic overview of a study performed in mice with humanized liver designed to determine the duration of response to GalNAc conjugated mxRNA targeting human AGT mRNA AGT27A mxRNA (SEQ ID Nos. 3604) and AGT-52A mxRNA (SEQ ID Nos. 3605) of the disclosed embodiments, as described in Example 15. A humanized liver mouse model (n=5) was used to test AGT27A at 30 mg/kg administered subcutaneously; Terminal endpoints were 2, 4, 6, 8, and 12 weeks. qPCR (mRNA - human AGT) and plasma ELISA (protein - human AGT) were run. Figures 21a and b show time dependent data (duration response) in liver (Fig .21 a) and plasma protein (Fig. 21 b) acquired in the study as described in the study of Example 15.
Detailed Description and Embodiments
Further embodiments (items) are described below by way of example only.
It will be understood that the benefits and advantages described herein may relate to one embodiment or may relate to several embodiments. The embodiments are not limited to those that solve any or all of the stated problems or those that have any or all of the stated benefits and advantages..
Features of different aspects and embodiments may be combined as appropriate, as would be apparent to a skilled person, and may be combined with any of the aspects as described below.
Definitions
The following definitions pertain throughout. In many instances, the definitions, in addition to the respective definition as such, provide non-exhaustive listings of possible implementations. Unless specific definitions are provided, the nomenclature used in connection with, and the procedures and techniques of, analytical chemistry, synthetic organic chemistry, and medicinal and pharmaceutical chemistry described herein are those well-known and commonly used in the art. Standard techniques may be used for chemical synthesis, and chemical analysis. Certain such techniques and procedures may be found for example in "Carbohydrate Modifications in Antisense Research" Edited by Sangvi and Cook, American Chemical Society , Washington D.C., 1994; "Remington's Pharmaceutical Sciences," Mack Publishing Co., Easton, Pa., 21st edition, 2005; and "Antisense Drug Technology, Principles, Strategies, and Applications" Edited by Stanley T. Crooke, CRC Press, Boca Raton, Florida; and Sambrook et al., "Molecular Cloning, A laboratory Manual," 2nd Edition, Cold Spring Harbor Laboratory Press, 1989, which are hereby incorporated by reference for any purpose. Where permitted, all patents, applications, published applications and other publications and other data referred to throughout in the disclosure are incorporated by reference herein in their entirety.
Unless otherwise indicated, the following terms have the following meanings:
As used herein, "excipient" means any compound or mixture of compounds that is added to a composition as provided herein that is suitable for delivery of an oligomeric compound.
As used herein, "nucleoside" means a compound containing a nucleobase moiety and a sugar moiety. Nucleosides include, but are not limited to, naturally occurring nucleosides (as found in DNA and RNA) and modified nucleosides. Nucleosides may be linked to a phosphate moiety, phosphate-linked
nucleosides also being referred to as "nucleotides". The structural features and/or the lengths of oligomeric compounds or nucleic acid constructs disclosed herein is expressed in terms of "nucleosides" or "nucleotides".
As used herein, "chemical modification" or "chemically modified" means a chemical difference in a compound when compared to a naturally occurring counterpart. Chemical modifications of oligonucleotides include nucleoside modifications (including sugar moiety modifications and nucleobase modifications) and internucleoside linkage modifications. In reference to an oligonucleotide, chemical modification does not include differences only in nucleobase sequence. As used herein, "furanosyl" means a structure having a 5-membered ring having four carbon atoms and one oxygen atom.
As used herein, "naturally occurring sugar moiety" means a ribofuranosyl as found in naturally occurring RNA or a deoxyribofuranosyl as found in naturally occurring DNA. A "naturally occurring sugar moiety" as referred to herein is also termed as an "unmodified sugar moiety". In particular, such a "naturally occurring sugar moiety" or an "unmodified sugar moiety" as referred to herein has a -H (DNA sugar moiety) or -OH (RNA sugar moiety) at the 2'-position of the sugar moiety, especially a -H (DNA sugar moiety) at the 2'-position of the sugar moiety.
As used herein, "sugar moiety" means a naturally occurring sugar moiety or a modified sugar moiety of a nucleoside. As used herein, "modified sugar moiety," means a substituted sugar moiety or a sugar surrogate.
As used herein, "substituted sugar moiety" means a furanosyl that has been substituted. Substituted sugar moieties include, but are not limited to furanosyls having substituents at the 2 -position, the 3'- position, the 5'-position and I or the 4'-position. Certain substituted sugar moieties are bicyclic sugar moieties.
As used herein, "2'-substituted sugar moiety" means a furanosyl having a substituent at the 2'- position other than H or OH. Unless otherwise indicated, a 2'-substituted sugar moiety is not a bicyclic sugar moiety (i.e., the 2' -substituent of a 2'-substituted sugar moiety does not form a bridge to another atom of the furanosyl ring).
As used herein, "MOE" means -OCH2CH2OCH3.
As used herein, "2'-F nucleoside" refers to a nucleoside having a sugar having fluorine at the 2' position. Unless otherwise indicated, the fluorine in a 2'-F nucleoside is in the ribo position (replacing the OH of a natural ribose). Duplexes of uniformly modified 2'-fluorinated (ribo) oligonucleotides hybridized to RNA strands are not RNase H substrates while the analogues retain RNase H activity. As used herein the term "sugar surrogate" means a structure that does not contain a furanosyl and that is capable of replacing the naturally occurring sugar moiety of a nucleoside, such that the resulting nucleoside sub-units are capable of linking together and I or linking to other nucleosides to form an oligomeric compound which is capable of hybridizing to a complementary oligomeric compound. Such structures include rings having a different number of atoms than furanosyl (e.g., 4, 6, or 7-membered rings); replacement of the oxygen of a furanosyl with a non-oxygen atom (e.g, carbon, sulfur, or nitrogen); or both a change in the number of atoms and a replacement of the oxygen. Such structures may also contain substitutions corresponding to those described for
substituted sugar moieties (e.g., 6-membered carbocyclic bicyclic sugar surrogates optionally having additional substituents). Sugar surrogates also include more complex sugar replacements (e.g., the non-ring systems of peptide nucleic acid). Sugar surrogates include without limitation morpholinos, cyclohexenyls and cyclohexitols.
As used herein, "bicyclic sugar moiety" means a modified sugar moiety having a 4 to 7 membered ring (including but not limited to a furanosyl) having a bridge connecting two atoms of the 4 to 7 membered ring to form a second ring, resulting in a bicyclic structure. In certain embodiments, the 4 to 7 membered ring is a sugar ring. In certain embodiments, the 4 to 7 membered ring is a furanosyl. In certain such embodiments, the bridge connects the 2 '-carbon and the 4 '-carbon of the furanosyl. As used herein, "nucleotide" means a nucleoside further having a phosphate linking group. As used herein, "linked nucleosides" may or may not be linked by phosphate linkages and thus includes, but is not limited to "linked nucleotides." As used herein, "linked nucleosides" are nucleosides that are connected in a continuous sequence (i.e. no additional nucleosides are present between those that are linked).
As used herein, "nucleobase" means a group of atoms that can be linked to a sugar moiety to create a nucleoside that is capable of incorporation into an oligonucleotide, and where the group of atoms is capable of bonding, more specifically hydrogen bonding, with a complementary naturally occurring nucleobase of another oligonucleotide or nucleic acid. Nucleobases may be naturally occurring or may be modified.
As used herein the terms, "unmodified nucleobase" or "naturally occurring nucleobase" means the naturally occurring heterocyclic nucleobases of RNA or DNA: the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) (including 5-methyl C), and uracil (U). As used herein, "modified nucleobase," means any nucleobase that is not a naturally occurring nucleobase.
As used herein, "modified nucleoside" means a nucleoside having at least one chemical modification compared to naturally occurring RNA or DNA nucleosides. Modified nucleosides can contain a modified sugar moiety and / or a modified nucleobase.
As used herein, "bicyclic nucleoside" or "BNA" means a nucleoside having a bicyclic sugar moiety.
As used herein, "locked nucleic acid nucleoside" or "LNA" means a nucleoside having a bicyclic sugar moiety having a 4'-CH2-O-2'bridge.
As used herein, "2 '-substituted nucleoside" means a nucleoside having a substituent at the 2'- position of the sugar moiety other than H or OH. Unless otherwise indicated, a 2 '-substituted nucleoside is not a bicyclic nucleoside.
As used herein, "deoxynucleoside" means a nucleoside having 2'-H furanosyl sugar moiety, as found in naturally occurring deoxyribonucleosides (DNA). In certain embodiments, a 2'-deoxynucleoside may contain a modified nucleobase or may contain an RNA nucleobase (e.g., uracil).
As used herein, "oligonucleotide" means a compound having a plurality of linked nucleosides. In certain embodiments, an oligonucleotide contains one or more unmodified ribonucleosides (RNA) and / or unmodified deoxyribonucleosides (DNA) and / or one or more modified nucleosides.
As used herein, "modified oligonucleotide" means an oligonucleotide having at least one modified nucleoside and / or at least one modified internucleoside linkage.
Advantageous modified internucleoside linkages are those, which confer increased stability as compared to the naturally occurring phosphodiesters. "Stability" refers in particular to stability against hydrolysis including enzyme-catalyzed hydrolysis, enzymes including exonucleases and endonucleases.
Advantageous positions for such modified internucleoside linkages include the termini and the hairpin loop of single-stranded oligomeric compounds. For example, the internucleoside linkages connecting first and second nucleoside and second and third nucleoside counting from the 5' terminus, and/or the internucleoside linkages connecting first and second nucleoside and second and third nucleoside counting from the 3' terminus are modified. In addition, a linkage connecting the terminal nucleoside of the 3' terminus with a ligand, such as GalNAc, may be modified.
As discussed above, advantageous positions are in the hairpin loop of the single-stranded oligomeric compounds. In particular, all linkages, all but one linkages or the majority of linkages in the hairpin loop are modified. As used herein, "linkages in the hairpin loop" designates the linkages between nucleosides, which are not engaged in base pairing. For example, in a hairpin loop consisting of five nucleosides, there are four linkages between nucleosides which are not engaged in base pairing. Advantageously, the term "linkages in the hairpin loop” also extends to the linkages connecting the stem to the loop, i.e., those linkages which connect a base-paired nucleoside to a non-based paired nucleoside. Generally, there are two such positions in hairpins and mxRNAs.
Most advantageous is that modified internucleoside linkages are at both termini and in the hairpin loop.
As used herein, "linkage” or "linking group" means a group of atoms that link together two or more other groups of atoms.
As used herein "internucleoside linkage" means a covalent linkage between adjacent nucleosides in an oligonucleotide.
As used herein "naturally occurring internucleoside linkage" means a 3' to 5' phosphodiester linkage. As used herein, "modified internucleoside linkage," means any internucleoside linkage other than a naturally occurring internucleoside linkage. In particular, a "modified internucleoside linkage" as referred to herein can include a modified phosphorous linking group such as a phosphorothioate or phosphorodithioate internucleoside linkage.
As used herein, "terminal internucleoside linkage" means the linkage between the last two nucleosides of an oligonucleotide or defined region thereof.
As used herein, "phosphorus linking group" means a linking group having a phosphorus atom and can include naturally occurring phosphorous linking groups as present in naturally occurring RNA or DNA, such as phosphodiester linking groups, or modified phosphorous linking groups that are not generally present in naturally occurring RNA or DNA, such as phosphorothioate or phosphorodithioate linking groups. Phosphorus linking groups can therefore include without limitation, phosphodiester, phosphorothioate, phosphorodithioate, phosphonate, methylphosphonate, phosphoramidate,
phosphorothioamidate, thionoalkylphosphonate, phosphotriesters, thionoalkylphosphotriester and boranophosphate.
As used herein, "internucleoside phosphorus linking group" means a phosphorus linking group that directly links two nucleosides.
As used herein, "oligomeric compound" means a polymeric structure having two or more substructures. In certain embodiments, an oligomeric compound contains an oligonucleotide, such as a modified oligonucleotide. In certain embodiments, an oligomeric compound further contains one or more conjugate groups and I or terminal groups and I or ligands. In certain embodiments, an oligomeric compound consists of an oligonucleotide. In certain embodiments, an oligomeric compound contains a backbone of one or more linked monomeric sugar moieties, where each linked monomeric sugar moiety is directly or indirectly attached to a heterocyclic base moiety. In certain embodiments, oligomeric compounds may also include monomeric sugar moieties that are not linked to a heterocyclic base moiety, thereby providing abasic sites. Oligomeric compounds may be defined in terms of a nucleobase sequence only, i.e., by specifying the sequence of A, G, C, U (or T). In such a case, the structure of the sugar-phosphate backbone is not particularly limited and may or may not contain modified sugars and/or modified phosphates. On the other hand, oligomeric compounds may be more comprehensively defined, i.e., by specifying not only the nucleobase sequence, but also the structure of the backbone, in particular the modification status of the sugars (unmodified, 2'-OMe modified, 2'-F modified etc.) and/or of the phosphates. An mxRNA is one non-limiting example for an oligomeric compound.
As used herein, "nucleic acid construct" or "construct" refers to an assembly of two or more, such as four oligomeric compounds. The oligomeric compounds may be connected to each other by covalent bonds such phosphodiester bonds as they occur in naturally occurring nucleic acids or modified versions thereof as disclosed herein, or by non-covalent bonds such as hydrogen bonds, advantageously hydrogen bonds between nucleobases such as Watson-Crick base pairing. In certain embodiments, advantageous is that a construct contains four oligomeric compounds, two of which are connected covalently, thereby giving rise to two nucleic acid strands which nucleic acid strands are bound to each other by hydrogen bonds. Complementarity between the strand may be throughout, but is not necessarily so. In particular, exemplary embodiments provide for an antisense strand targeting a first region of AGT mRNA to be connected covalently with a sense strand of another AGT- targeting double stranded RNA molecule, and of the antisense strand of the AGT mRNA-targeting double stranded RNA molecule to be connected covalently to a sense strand of the other AGT mRNA-targeting double stranded RNA molecule. Since antisense and sense strands of the parent single-target-directed RNA molecules do not need to have the same length and advantageously do not have the same length with antisense portions being longer than sense portions, one construct contains a central region where the 3' regions of the antisense portions of the parent single-target- directed RNA molecules face each other. In that region generally no or only partial base pairing will occur, while full complementarity is not excluded. Otherwise, where antisense and sense portions of the respective parent RNA molecules face each other; there is complementarity, advantageously full
complementarity or 1 or 2 mismatches. An muRNA is non-limiting example for a nucleic acid construct.
The term "strand" has its art-established meaning and refers to a plurality of linked nucleosides, the linker not being particularly limited, but including phosphodiesters and variants thereof as disclosed herein. A strand may also be viewed as a plurality of linked nucleotides in which case the linker would be a covalent bond.
As used herein, "terminal group" means one or more atom attached to either, or both, the 3 ' end or the 5' end, also called "terminus" of an oligonucleotide. In certain embodiments, a terminal group contains one or more terminal group nucleosides, whereas a "terminal nucleoside" is only one nucleotide at the respective end (5' end or 3' end).
As used herein, "conjugate" or "conjugate group" means an atom or group of atoms bound to an oligonucleotide or oligomeric compound. In certain embodiments, a conjugate group links a ligand to a modified oligonucleotide or oligomeric compound. In general, conjugate groups can modify one or more properties of the compound to which they are attached, including, but not limited to pharmacodynamic, pharmacokinetic, binding, absorption, cellular distribution, cellular uptake, charge and I or clearance properties.
As used herein, "conjugate linker" or "linker" in the context of a conjugate group means a portion of a conjugate group having any atom or group of atoms and which covalently link an oligonucleotide to another portion of the conjugate group. In certain embodiments, the point of attachment on the oligomeric compound is the 3 '-oxygen atom of the 3'-hydroxyl group of the 3' terminal nucleoside of the oligonucleotide. In certain embodiments, the point of attachment on the oligomeric compound is the 5'-oxygen atom of the 5'-hydroxyl group of the 5' terminal nucleoside of the oligonucleotide. In certain embodiments, the bond for forming attachment to the oligomeric compound is a cleavable bond. In certain such embodiments, such cleavable bond constitutes all or part of a cleavable moiety. In certain embodiments, conjugate groups contain a cleavable moiety (e.g., a cleavable bond or cleavable nucleoside) and ligand portion that can contain one or more ligands, such as a carbohydrate cluster portion, such as an N-Acetyl-Galactosamine, also referred to as "GalNAc", cluster portion. In certain embodiments, the carbohydrate cluster portion is identified by the number and identity of the ligand. For example, in certain embodiments, the carbohydrate cluster portion contains 2 GalNAc groups. For example, in certain embodiments, the carbohydrate cluster portion contains 3 GalNAc groups and this is particularly advantageous. In certain embodiments, the carbohydrate cluster portion contains 4 GalNAc groups. Such ligand portions are attached to an oligomeric compound via a cleavable moiety, such as a cleavable bond or cleavable nucleoside. The ligands can be arranged in a linear or branched configuration, such as a biantennary or triantennary configurations. An advantageous carbohydrate cluster has the following formula:
, where in the structural formula one, two, or three phosphodiester linkages can also be substituted by phosphorothioate linkages.
As used herein, "cleavable moiety" means a bond or group that is capable of being cleaved under physiological conditions. In certain embodiments, a cleavable moiety is cleaved inside a cell or sub- cellular compartments, such as an endosome or lysosome. In certain embodiments, a cleavable moiety is cleaved by endogenous enzymes, such as nucleases. In certain embodiments, a cleavable moiety contains a group of atoms having one, two, three, four, or more than four cleavable bonds. In certain embodiments, a cleavable moiety is a phosphodiester linkage.
As used herein, "cleavable bond" means any chemical bond capable of being broken.
As used herein, "carbohydrate cluster" means a compound having one or more carbohydrate residues attached to a linker group.
As used herein, "modified carbohydrate" means any carbohydrate having one or more chemical modifications relative to naturally occurring carbohydrates.
As used herein, "carbohydrate derivative" means any compound which may be synthesized using a carbohydrate as a starting material or intermediate.
As used herein, "carbohydrate" means a naturally occurring carbohydrate, a modified carbohydrate, or a carbohydrate derivative. A carbohydrate is a biomolecule including carbon (C), hydrogen (H) and oxygen (O) atoms. Carbohydrates can include monosaccharide, disaccharides, trisaccharides, tetrasaccharides, oligosaccharides or polysaccharides, such as one or more galactose moieties, one or more lactose moieties, one or more N-Acetyl-Galactosamine moieties, and I or one or more mannose moieties. A particularly advantageous carbohydrate is N-Acetyl-Galactosamine.
As used herein, "strand" means an oligomeric compound having linked nucleosides.
As used herein, "single strand" or "single-stranded" means an oligomeric compound having linked nucleosides that are connected in a continuous sequence without a break there between. Such
single strands may include regions of sufficient self-complementarity so as to be capable of forming a stable self-duplex in a hairpin structure.
As used herein, "hairpin" means a single stranded oligomeric compound that includes a duplex formed by base pairing between sequences in the strand that are self-complementary and opposite in directionality.
As used herein, "hairpin loop" means an unpaired loop of linked nucleosides in a hairpin that is created as a result of hybridization of the self-complementary sequences. The resulting structure looks like a loop or a U-shape.
In particular, short hairpin RNA, also denoted as shRNA, contains a duplex region and a loop connecting the regions forming the duplex. The end of the duplex region, which does not carry the loop, may be blunt-ended or carry (a) 3' and/or (a) 5' overhang(s). Blunt-ended constructs are particularly advantageous. The term "shRNA" is more generic than "mxRNA", as defined below, and may include compounds in which the loop is not or not exclusively formed out of an antisense strand. In particular, shRNA includes an antisense strand, also called guide strand, being complementary to a region of a target RNA, and a sense strand, i.e. a passenger strand, being substantially complementary to the antisense strand. More particularly, the antisense strand and the sense strand within the shRNA are directly linked, e.g. by a phosphate or a phosphorothioate, or linked by a third portion of linked nucleosides forming the loop, which means that the 3' end of the antisense strand is linked to the 5' end of the sense strand via covalent bonding over several other groups. Such direct linkage does not include a gap or nick.
As used herein, "directionality" means the end-to-end chemical orientation of an oligonucleotide based on the chemical convention of numbering of carbon atoms in the sugar moiety meaning that there will be a 5'-end defined by the 5' carbon of the sugar moiety, and a 3'-end defined by the 3' carbon of the sugar moiety. In a duplex or double stranded oligonucleotide, the respective strands run in opposite 5' to 3' directions to permit base pairing between them.
As used herein, "duplex", or also abbreviated as "dup", means two or more complementary strand regions, or strands, of an oligonucleotide or oligonucleotides, hybridized together by way of non- covalent, sequence-specific interaction there between. Most commonly, the hybridization in the duplex will be between nucleobases adenine (A) and thymine (T), and / or (A) adenine and uracil (U), and I or guanine (G) and cytosine (C). The duplex may be part of a single stranded structure, where self-complementarity leads to hybridization, or as a result of hybridization between respective strands in a double stranded construct.
As used herein, "double strand" or "double stranded" means a pair of oligomeric compounds that are hybridized to one another. In certain embodiments, a double-stranded oligomeric compound contains a first and a second oligomeric compound.
As used herein, "expression" means the process by which a gene ultimately results in a protein. Expression includes, but is not limited to, transcription, post-transcriptional modification (e.g., splicing, polyadenylation, addition of 5 '-cap), and translation.
As used herein, "transcription" or "transcribed" refers to the first of several steps of DNA based gene expression in which a target sequence of DNA is copied into RNA (especially mRNA) by the enzyme
RNA polymerase. During transcription, a DNA sequence is read by an RNA polymerase, which produces a complementary, antiparallel RNA sequence called a primary transcript.
As used herein, "target sequence" means a sequence to which an oligomeric compound is intended to hybridize to result in a desired activity with respect to AGT expression. Oligonucleotides have sufficient complementarity to their target sequences to allow hybridization under physiological conditions.
As used herein, "nucleobase complementarity" or "complementarity" when in reference to nucleobases means a nucleobase that is capable of base pairing with another nucleobase. For example, in DNA, adenine (A) is complementary to thymine (T). For example, in RNA, adenine (A) is complementary to uracil (U). In both DNA and RNA, guanine (G) is complementary to cytosine (C). In certain embodiments, complementary nucleobase means a nucleobase of an oligomeric compound that is capable of base pairing with a nucleobase of its target sequence. For example, if a nucleobase at a certain position of an oligomeric compound is capable of hydrogen bonding with a nucleobase at a certain position of a target sequence, then the position of hydrogen bonding between the oligomeric compound and the target sequence is considered complementary at that nucleobase pair.
Nucleobases having certain modifications may maintain the ability to pair with a counterpart nucleobase and thus, are still capable of nucleobase complementarity.
As used herein, "non-complementary" in reference to nucleobases means a pair of nucleobases that do not form hydrogen bonds with one another.
As used herein, "complementary" in reference to oligomeric compounds (e.g., linked nucleosides, oligonucleotides) means the capacity of such oligomeric compounds or regions thereof to hybridize to a target sequence, or to a region of the oligomeric compound itself, through nucleobase complementarity.
Complementary oligomeric compounds need not have nucleobase complementarity at each nucleoside. Rather, some mismatches are tolerated. In certain embodiments, complementary oligomeric compounds or regions are complementary at 70% of the nucleobases (70% complementary). In certain embodiments, complementary oligomeric compounds or regions are 80%> complementary. In certain embodiments, complementary oligomeric compounds or regions are 90%> complementary. In certain embodiments, complementary oligomeric compounds or regions are at least 95% complementary. In certain embodiments, complementary oligomeric compounds or regions are 100% complementary.
As used herein, "self-complementarity" in reference to oligomeric compounds means a compound that may fold back on itself, creating a duplex as a result of nucleobase hybridization of internal complementary strand regions. Depending on how close together and I or how long the strand regions are, then the compound may form hairpin loops, junctions, bulges or internal loops.
As used herein, "mismatch" means a nucleobase of an oligomeric compound that is not capable of pairing with a nucleobase at a corresponding position of a target sequence, or at a corresponding position of the oligomeric compound itself when the oligomeric compound hybridizes as a result of self-complementarity, when the oligomeric compound and the target sequence and I or self- complementary regions of the oligomeric compound, are aligned.
As used herein, "hybridization" means the pairing of complementary oligomeric compounds (e.g., an oligomeric compound and its target sequence). While not limited to a particular mechanism, the most common mechanism of pairing involves hydrogen bonding, which may be Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding, between complementary nucleobases.
As used herein, "specifically hybridizes" means the ability of an oligomeric compound to hybridize to one nucleic acid site with greater affinity than it hybridizes to another nucleic acid site.
As used herein, "fully complementary" in reference to an oligomeric compound or region thereof means that each nucleobase of the oligomeric compound or region thereof is capable of pairing with a nucleobase of a complementary nucleic acid target sequence or a self-complementary region of the oligomeric compound. Thus, a fully complementary oligomeric compound or region thereof contains no mismatches or unhybridized nucleobases with respect to its target sequence or a self- complementary region of the oligomeric compound.
As used herein, "percent complementarity" means the percentage of nucleobases of an oligomeric compound that are complementary to an equal-length portion of a target nucleic acid. Percent complementarity is calculated by dividing the number of nucleobases of the oligomeric compound that are complementary to nucleobases at corresponding positions in the target nucleic acid by the total length of the oligomeric compound.
As used herein, "percent identity" means the number of nucleobases in a first nucleic acid that are the same type (independent of chemical modification) as nucleobases at corresponding positions in a second nucleic acid, divided by the total number of nucleobases in the first nucleic acid.
As used herein, "modulation" means a change of amount or quality of a molecule, function, or activity when compared to the amount or quality of a molecule, function, or activity prior to modulation. For example, modulation includes the change, either an increase (stimulation or induction) or a decrease (inhibition or reduction) in gene expression.
As used herein, "type of modification" in reference to a nucleoside or a nucleoside of a "type" means the chemical modification of a nucleoside and includes modified and unmodified nucleosides. Accordingly, unless otherwise indicated, a "nucleoside having a modification of a first type" may be an unmodified nucleoside.
As used herein, "differently modified" mean chemical modifications or chemical substituents that are different from one another, including absence of modifications. Thus, for example, a MOE nucleoside and an unmodified naturally occurring RNA nucleoside are "differently modified," even though the naturally occurring nucleoside is unmodified. Likewise, DNA and RNA oligonucleotides are "differently modified," even though both are naturally occurring unmodified nucleosides. Nucleosides that are the same but for the presence of different nucleobases are not differently modified. For example, a nucleoside having a 2'-OMe modified sugar moiety and an unmodified adenine nucleobase and a nucleoside having a 2'-OMe modified sugar moiety and an unmodified thymine nucleobase are not differently modified.
As used herein, "the same type of modifications" refers to modifications that are the same as one another, including absence of modifications. Thus, for example, two unmodified RNA nucleosides
have "the same type of modification," even though the RNA nucleosides are unmodified. Such nucleosides having the same type modification may contain different nucleobases.
As used herein, "region" or "regions", or "portion" or "portions", mean a plurality of linked nucleosides that have a function or character as defined herein, in particular with reference to the claims and definitions as provided herein. Typically, such regions or portions contain at least 10, at least 11 , at least 12 or at least 13 linked nucleosides. For example, such regions can contain 13 to 20 linked nucleosides, such as 13 to 16 or 18 to 20 linked nucleosides. Typically a first region as defined herein consists essentially of 18 to 20 nucleosides and a second region as defined herein consists essentially of 13 to 16 linked nucleosides.
As used herein, "pharmaceutically acceptable carrier or diluent" means any substance suitable for use in administering to an animal. In certain embodiments, a pharmaceutically acceptable carrier or diluent is sterile saline. In certain embodiments, such sterile saline is pharmaceutical grade saline.
As used herein, "substituent" and "substituent group," means an atom or group that replaces the atom or group of a named parent compound. For example a substituent of a modified nucleoside is any atom or group that differs from the atom or group found in a naturally occurring nucleoside (e.g., a modified 2'- substituent is any atom or group at the 2 '-position of a nucleoside other than H or OH). Substituent groups can be protected or unprotected. In certain embodiments, compounds of the present disclosure have substituents at one or at more than one position of the parent compound. Substituents may also be further substituted with other substituent groups and may be attached directly or via a linking group such as oxygen or an alkyl or hydrocarbyl group to a parent compound. Such substituents can be present as the modification on the sugar moiety, in particular a substituent present at the 2'-position of the sugar moiety. Unless otherwise indicated, groups amenable for use as substituents include without limitation, one or more of halo, hydroxyl, alkyl, alkenyl, alkynyl, acyl, carboxyl, alkoxy, alkoxyalkylene and amino substituents. Certain substituents as described herein can represent modifications directly attached to a ring of a sugar moiety (such as a halo, such as fluoro, directly attached to a sugar ring), or a modification indirectly linked to a ring of a sugar moiety by way of an oxygen linking atom that itself is directly linked to the sugar moiety (such as an alkoxyalkylene, such as methoxyethylene, linked to an oxygen atom, overall providing an MOE substituent as described herein attached to the 2'-position of the sugar moiety).
As used herein, "alkyl,” as used herein, means a saturated straight or branched monovalent C1-6 hydrocarbon radical, with methyl being a typical alkyl as a substituent at the 2'-position of the sugar moiety. The alkyl group typically attaches to an oxygen linking atom at the 2' position of the sugar, therefore, overall providing a -Oalkyl substituent, such as an -OCH3 substituent, on a sugar moiety of an oligomeric compound as described herein.
As used herein, "alkylene" means a saturated straight or branched divalent hydrocarbon radical of the general formula -CnHzn- where n is 1 -6. Methylene or ethylene are typical alkylenes.
As used herein, "alkenyl" means a straight or branched unsaturated monovalent C2-6 hydrocarbon radical, with ethenyl or propenyl being most typical alkenyls as a substituent at the 2'-position of the sugar moiety. As will be well understood in the art, the degree of unsaturation that is present in an alkenyl radical is the presence of at least one carbon to carbon double bond. The alkenyl group
typically attaches to an oxygen linking atom at the 2'-position of the sugar, therefore, overall providing a -Oalkenyl substituent, such as an -OCH2CH=CH2 substituent, on a sugar moiety of an oligomeric compound as described herein.
As used herein, "alkynyl" means a straight or branched unsaturated C2-6 hydrocarbon radical, with ethynyl being a typical alkynyl as a substituent at the 2'-position of the sugar moiety. As will be well understood in the art, the degree of unsaturation that is present in an alkynyl radical is the presence of at least one carbon to carbon triple bond. The alkynyl group typically attaches to an oxygen linking atom at the 2'-position of the sugar, therefore, overall providing a -Oalkynyl substituent on a sugar moiety of an oligomeric compound as described herein.
As used herein, "carboxyl" is a radical having a general formula -CO2H.
As used herein, "acyl" means a radical formed by removal of a hydroxyl group from a carboxyl radical as defined herein and has the general Formula -C(O)-X where X is typically C1 -6 alkyl.
As used herein, "alkoxy" means a radical formed between an alkyl group, such as a C1-6 alkyl group, and an oxygen atom where the oxygen atom is used to attach the alkoxy group either to a parent molecule (such as at the 2'-position of a sugar moiety), or to another group such as an alkylene group as defined herein. Examples of alkoxy groups include without limitation, methoxy, ethoxy, propoxy, isopropoxy, n-butoxy, sec-butoxy and tert-butoxy. Alkoxy groups as used herein may optionally include further substituent groups.
As used herein, alkoxyalkylene means an alkoxy group as defined herein that is attached to an alkylene group also as defined herein, and where the oxygen atom of the alkoxy group attaches to the alkylene group and the alkylene attaches to a parent molecule. The alkylene group typically attaches to an oxygen linking atom at the 2'-position of the sugar, therefore, overall providing a - Oalkylenealkoxy substituent, such as an -OCH2CH2OCH3 substituent, on a sugar moiety of an oligomeric compound as described herein. This is generally referred to as an MOE substituent as defined herein and as known in the art.
As used herein, "amino" includes primary, secondary and tertiary amino groups.
As used herein, "halo" and "halogen," mean an atom selected from fluorine, chlorine, bromine and iodine.
As used herein, the term "mxRNA" is in particular understood as defined in WO 2020/044186 A2, which is incorporated by reference herein in its entirety. In particular, an mxRNA is a hairpin-shaped RNA molecule consisting of an antisense portion (also referred to as the guide strand) and a sense portion (also referred to the passenger strand). The mxRNA contains duplex region and a hairpin loop, where the mxRNA has approximate length of about 34 nucleotides. The duplex region contains a region in which parts of the antisense portion and substantially the entire sense portion, typically 14 or 15 nucleotides of each strand, are base-paired. The hairpin loop connects both regions, i.e. antisense region and sense region, of that duplex via e.g. a phosphate or a phosphorothioate linker, i.e. covalently, while the antisense portion typically has a length of about 18 to 20 nucleotides and, therefore, forms the antisense duplex region and the loop. The loop, of which the antisense portion is part, furthermore connects the sense, forming the second strand of the loop, and the antisense portion.
The term "angiotensinogen" or abbreviated "AGT", also known as SERPINA 8 or ANHU, is used in its common sense and denotes a protein produced in the liver which is a component of the renin- angiotensin-aldosterone-system (RAAS), and which is converted to angiotensin I by renin when released in circulation. Angiotensinogen is expressed and produced in the liver by the angiotensin gene or "AGT gene".
As used herein, the term "muRNA" or "multi RNA" includes nucleic acid constructs having more than one, typically two, RNA sequences, i.e. first and second nucleic acid portions, targeting different regions of AGT mRNA; or one region of AGT mRNA and an mRNA region of another target molecule. The targeting RNA sequences are also referred to as "antisense" or "guide" strands, while the respective passenger strands, i.e. third and fourth nucleic acid portions being complementary to the first and second portion, respectively, are also included in the nucleic acid construct. In particular, such muRNA are designed such that subsequent to in vivo administration, they are disassembled and the first and second nucleic acid portions are released. A particular example for such muRNA is shown below, where (1) is the first nucleic acid portion, (2) is the third nucleic acid portion being complementary to (1), (3) is the second nucleic acid portion being complementary to the fourth nucleic acid portion, while (5) is a labile linker while (6) is a ligand, which will both be explained below.
It will also be understood that oligomeric compounds as described herein may have one or more nonhybridizing nucleosides at one or both ends of one or both strands (overhangs) and I or one or more internal non-hybridizing nucleosides (mismatches) provided there is sufficient complementarity to maintain hybridization under physiologically relevant conditions. Alternatively, oligomeric compounds as described herein may be blunt ended at least one end.
As used herein, proprotein convertase subtilkisin/kexin type 9 (PCSK9) is a serine protease involved in lipid metabolism. PCSK9 reduces the number of LDL receptors on the surface of liver cells. As a consequence, elevated amounts and/or activity of PCSK9 entail higher blood levels of "bad" LDL cholesterol. This molecular and cellular function of PCSK9 has led to its recognition as a therapeutic target molecule.
As used herein, APOC3 is referred to apolipoprotein C3 which is secreted by the liver and the small intestine. It can be found on triglyceride-rich lipoproteins including very low density lipoproteins (VLDL) and chylomicrons. It is involved in the negative regulation of lipid catabolism, especially triglyceride catabolism, and of the clearance of VLDL, LDL and HDL lipoproteins. A molecular function of APOC3 is the inhibition of lipoprotein lipase and of hepatic lipase.
The terms "includes" or "including” is used herein to mean including the method steps or elements identified, but that such steps or elements are not an exclusive list and as such, there may be present additional steps or elements.
Small hairpin (shRNA) and mxRNA oligomeric compounds
In a first aspect, oligomeric compounds are provided that are capable of inhibiting expression of angiotensinogen (AGT), where the compound contains at least a first region of linked nucleosides having at least a first nucleobase sequence that is at least partially complementary to at least a portion of RNA transcribed from an AGT gene, where the first nucleobase sequence is selected from the following sequences, or a portion thereof: sequences of Table 1 a (SEQ ID NOs: 1 to 100), where the portion advantageously has a length of at least 18 nucleosides. In particular, the 5' terminal nucleoside of the first nucleobase sequence can contain U instead of A; or U instead of G; or U instead of C, respectively.
In certain embodiments, the oligomeric compound further may contain at least a second region of linked nucleosides having at least a second nucleobase sequence that is at least partially complementary to the first nucleobase sequence and is selected from the following sequences, or a portion thereof: sequences of Table 1 b (SEQ ID NOs: 101 to 200), where the portion advantageously has a length of at least 8, 9, 10 or 11 , advantageously at least 10, nucleosides. In particular, the 3' terminal nucleoside of the second nucleobase sequence may contain an A instead of U, G or C, respectively; and more particularly the nucleobase A as a complementary nucleobase to the 5' terminal nucleoside of the first nucleobase sequence.
The first region of linked nucleosides is also referred to as antisense region or guide region/strand, and the second region of linked nucleosides is referred to as sense region or passenger region/strand. As disclosed in some embodiments below, the two regions may be located on the same RNA strand, advantageously in an adjacent manner. This gives rise to hairpin molecules, also referred to as mxRNAs. On the other hand, the two regions may be located on separate strands, which gives rise to double-stranded RNAs (dsRNAs), where advantageously each strand consists of the respective region.
Without wishing to be bound by theory, it is assumed that the oligomeric compounds set forth above including the first region of linked nucleosides and the second region of linked nucleosides are, during the process of RNA interference, incorporated into the RNA-induced silencing complex (RISC). The RISC assembly then binds and degrades the target mRNA. Specifically, this is accomplished when the guide strand pairs with a complementary sequence in an AGT mRNA molecule and induces cleavage by Ago2, a catalytic component of the RISC. Forthat reason, as the expression of AGT is inhibited, it is believed effects correlating with overregulation of angiotensin II by the pathway described above, is inhibited too.
In certain embodiments the first nucleobase sequence is selected from the following sequences, or a portion thereof: SEQ ID NOs: 27, 44, 41 , 97, 90, 62, 52, 93, 49, 73, 18, 37, 56, 100, 40, 75, 30, 42, 81 , 17, 34, 53, 29, 26, 74, 94, 14, 3, 7 and 2. Advantageously the first nucleobase sequence is selected from the following sequences, or a portion thereof: SEQ ID NOs: 27, 52, 56, 62, 75, and 93, in particular from SEQ ID NO: 27 and 52.
The second nucleobase sequence may, for example, be selected from the following sequences, or a portion thereof: SEQ ID NOs: 127, 144, 141 , 197, 190, 162, 152, 193, 149, 173, 118, 137, 156, 200, 140, 175, 130, 142, 181 , 117, 134, 153, 129, 126, 174, 194, 114, 103, 107 and 102. Advantageously the second nucleobase sequence is selected from the following sequences, or a portion thereof: SEQ ID NOs: 127, 152, 156, 162, 175, and 193.
Lengths and molecular features of the oligomeric compounds according to the first aspect
The first region of linked nucleosides may essentially consist of 18 to 35, advantageously 18 to 20, more advantageously 18 or 19, and yet more advantageously 19 linked nucleosides. In addition, the second region of linked nucleosides may consist essentially of 10 to 35, 10 to 20, 10 to 16, 10 to 15, or 13, 14 or 15 linked nucleosides.
The oligomeric compound including the first and second regions of linked nucleosides may contain at least one complementary duplex region that contains at least a portion of the first region of linked nucleosides directly or indirectly linked to at least a portion of the second region of linked nucleosides, where advantageously the duplex region has a length of 10 to 19, 12 to 19, 12 to 15, or 14 or 15, base pairs, where optionally there is one mismatch within the duplex region.
In certain embodiments, each of the first and second regions of linked nucleosides has a 5’ to 3’ directionality thereby defining 5’ and 3’ regions respectively thereof.
In the oligomeric compound having the first and second regions of linked nucleosides having a 5' to 3' directionality, the 5’ region of the first region of linked nucleosides may be directly or indirectly linked to the 3’ region of the second region of linked nucleosides, for example by complementary base pairing, where advantageously the 5' terminal nucleoside of the first nucleoside region base pairs with the 3' terminal nucleoside of the second nucleoside region.
In the aforementioned embodiments, the 3’ region of the first region of linked nucleosides may be directly or indirectly linked to the 5’ region of the second region of linked nucleosides, where advantageously the first nucleoside region is directly and covalently linked to the second nucleoside region such as by a phosphate, a phosphorothioate, or a phosphorodithioate, where more advantageously a 3' terminal nucleoside of the first region of linked nucleosides is directly and covalently linked to a 5' terminal nucleoside of the second region of linked nucleosides by a phosphate, a phosphorothioate, or a phosphorodithioate. It is particularly advantageous that the 3' terminal nucleoside of the first region is directly linked to the 5' terminal nucleoside of the second region via a phosphorothioate internucleoside linkage.
This amounts to the formation of a single oligonucleotide having or consisting of the two regions being directly fused to each other. Owing to the base pairing as defined in the previous embodiment, such oligonucleotide will assume a hairpin configuration. Optimized hairpins, especially in terms of size, are the subject of further embodiments below.
In certain embodiments, the oligomeric compound may consist of the first region of linked nucleosides and the second region of linked nucleosides.
Each ofthe regions may constitute a separate strand, thereby giving rise to a double-stranded RNA (dsRNA). Particularly advantageous dsRNAs are those with a length of the first strand of 19 nucleosides and a length of the second region of 14 or 15, advantageously 14 nucleosides. When
used for defining the length of a region or strand, the terms "nucleoside" and "nucleotide" (sometimes abbreviated "nt") are used equivalently.
In the alternative, and as stated above, the two regions may be fused together, giving rise to a hairpin. In certain embodiments, there may be an intervening third region of linked nucleosides between the first and the second region.
The oligomeric compound may contain or consist of a single strand having or consisting of the first, the third, and the second nucleoside regions, where at least a portion of the first nucleoside region is directly or indirectly linked to at least a portion of the second nucleoside region so as to form the at least partially complementary duplex region.
In other words, the oligomeric compound contains a single strand having the first and second nucleoside regions, where at least a portion of the first nucleoside region is directly or indirectly linked to at least a portion of the second nucleoside region so as to form the at least partially complementary duplex region. As noted above, the third region is optional.
In certain embodiments, the oligomeric compound may contain or may consist of a single strand having or consisting of the first and second regions of linked nucleosides, where at least a portion of the first region of linked nucleosides is directly or indirectly linked to at least a portion of the second region of linked nucleosides so as to form the at least partially complementary duplex region.
In the oligomeric compound, which may contain or may consist of a single strand, the first and the second nucleoside regions are directly adjacent on the single strand.
In certain embodiments, the first nucleoside region may have a greater number of linked nucleosides compared to the second nucleoside region.
Optionally, a ratio between a total number of linked nucleosides of the first nucleoside region and a total number of linked nucleosides of the second nucleoside region ranges from about 19/15 to about 19/8 or from about 18/15 to about 18/8. In particularly advantageous embodiments, the ratio is 19/15, 19/14, 19/13, 18/15, 18/14 or 18/13.
Alternatively or in addition, a percentage of the total number of linked nucleosides of the first nucleoside region relative to the total number of nucleosides of the oligomeric compound may range from about to about 55% to about 60%. The percentage may range from 57% to about 59.5%, most advantageously the percentage is about 57.6% or about 59.4%.
Without wishing to be bound by theory, it is assumed that the ratio and/or percentages as mentioned above provides a suitable ratio/percentage of the number of nucleotides in the mxRNA strand to be processed by the RISC complex as mentioned above, and therefore, for being effective in AGT knockdown.
In the oligomeric compound having a greater number of linked nucleotides in the first region than in the second region, the additional number of linked nucleosides of the first nucleoside region form a hairpin loop linking the first and second regions of linked nucleosides, where advantageously a part of the first nucleobase sequence of the first nucleobase sequence being complementary RNA transcribed from an AGT gene forms the hairpin loop, where the loop contains 2 to 5, advantageously 4 or 5, nucleosides.
Such compounds are also referred to as hairpins or mxRNAs herein. Owing to the second region being shorter as compared to the first region, the compound is optimized in terms of size (or miniaturized) as compared to a conventional siRNA which has two regions of comparable length. Advantageously, the loop has 4 or 5 linked nucleosides. Particularly advantageous is a length of the first region of 19 nucleosides, of the second region of 14 nucleosides, and of the hairpin loop of 5 nucleosides, where the 5 nucleosides in the hairpin are the 5 3'-terminal nucleosides of the first region. Such molecular architecture of a hairpin or mxRNA is also designated "14-5-14" herein.
In certain embodiments, an oligomeric single strand as disclosed earlier herein, can be selected from Table 2, in particular selected from the group consisting of SEQ IDs NO: 227, 252, 256, 262, 275, 293 and 3602-3603, where advantageously the 5' terminal nucleoside of the first region of linked nucleosides is substituted by an U as the nucleobase, and the 5' terminal nucleoside of the second region of linked nucleosides is substituted by an A as the nucleobase.
In particular embodiments, the single strand is selected from Table 3c, in particular from Construct ID NOs: 527, 552, 556, 562, 575, 593 and 3604-3605, where advantageously the 5' terminal nucleoside of the first region of linked nucleosides is substituted by an U as the nucleobase, and the 5' terminal nucleoside of the second region of linked nucleosides is substituted by an A as the nucleobase.
In certain embodiments a hairpin loop as described earlier herein may be present at the 3' region of the first region of linked nucleosides, where optionally one, two or more 3' terminal nucleosides of the first nucleobase sequence, to the extent the nucleobases of the one, two or more 3' terminal nucleosides permit, fold back and form or contribute to the second region of linked nucleoside.
This is a structural design also referred to as "spill-over". It is only possible in those cases where there is self-complementarity between the nucleobases at the 3'-terminal end of the region of the guide sequence contained in the duplex and the very 3'-terminal nucleobases of the same guide sequence. For example, this could implemented as a 13-5-13 design, thereby allowing for further miniaturization. The first "13" refers to the region of the guide sequence involved in the duplex, 5 is the length of the loop which is also formed by the guide sequence, and the second 13 refers to the second region of the duplex and is formed by one nucleobase of the guide sequence and 12 nucleobases of the passenger region in 5' to 3' direction. As such, a length of the guide sequence of 19 nucleosides is maintained, but the passenger sequence is shortened to 12 nucleosides.
In certain embodiments, in case a third nucleoside region as described earlier herein, the third nucleoside region and optionally a 3'-terminal portion, advantageously consisting of 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 linked nucleosides, of the first nucleoside region and/or a 5'-terminal portion, advantageously consisting of 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 linked nucleosides, of the second nucleoside region may form a hairpin loop.
In certain embodiments where the hairpin loop contains 1 to 8, 2 to 7, 3 to 6, advantageously 4 or 5 linked nucleosides.
The oligomeric compounds according to the first aspect disclosed herein may be blunt ended.
In the oligomeric compounds according to the first aspect disclosed herein, either the first or second nucleoside region may have an overhang.
In the oligomeric compounds according to the first aspect disclosed herein, the first region may be selected from the sequences of Table 3a, or a portion thereof, in particular from Construct ID NOs: 327, 352, 356, 362, 375 and 393.
In the oligomeric compounds according to the first aspect disclosed herein the second region may be selected from the sequences of Table 3b, or a portion thereof, especially a portion having a length of 14 nucleosides, in particular from Construct ID NOs: 427, 452, 456, 462, 475 and 493.
The oligomeric compound may have a total length of about 25 to about 35 nucleosides, in particular about 33 or about 34 nucleosides.
In certain embodiments, a terminal nucleoside at a 5' position of the first region has a nucleobase selected from the group consisting of A, U, G and C, advantageously U, and, where optionally, a terminal nucleoside at a 3' position of the second region is substituted by a base being complementary to the base at the 5' position of the first region, advantageously A.
Ligands
The oligomeric compounds may contain one or more ligands.
The one or more ligands, in particular two or more or three ligands, may be conjugated to the second region of linked nucleosides and/or the first region of linked nucleosides.
The one or more ligands may be conjugated at the 3' region, advantageously at the 3' terminal nucleoside of the second region of linked nucleosides and/or of the first region of linked nucleosides, and/or to the 5' terminal nucleoside of the second region of linked nucleosides. In particular, the ligands may be conjugated to the 3' terminal nucleoside.
The one or more ligands are any cell directing moiety, such as lipids, carbohydrates, aptamers, vitamins and / or peptides that bind cellular membrane or a specific target on cellular surface. The one or more ligands may contain one or more, in particular three, carbohydrates.
The one or more, in particular three, carbohydrates can be a monosaccharide, disaccharide, trisaccharide, tetrasaccharide, oligosaccharide or polysaccharide.
The one or more carbohydrates may contain or consist of one or more, in particular three, hexose moieties.
The one or more, in particular three, hexose moieties are one or more galactose moieties, one or more lactose moieties, one or more, in particular three, N-Acetyl-Galactosamine moieties, and I or one or more mannose moieties.
The one or more carbohydrates may contain one or more, in particular three, N-Acetyl-Galactosamine moieties.
Alternatively, the one or more carbohydrates may contain two or more N-Acetyl-Galactosamine moieties, advantageously three.
The one or more ligands are attached to the oligomeric compound, advantageously to the second region of linked nucleosides thereof, in a linear configuration, or in a branched configuration.
A particularly advantageous ligand is the following, also referred to as a "toothbrush":
Without wishing to be bound by a particular theory, it is assumed that due to such ligand the target tissue, i.e. the liver where AGT is produced, can be selectively targeted so the oligomeric compounds can exhibit their inhibition of AGT gene more efficiently.
The one or more, in particular three, ligands may be attached to the oligomeric compound as a biantennary or triantennary configuration.
The one or more ligands as discussed above are advantageously attached to the 3' terminal nucleoside of the second region of linked nucleosides.
Internucleoside linkages
The oligomeric compound according to the first aspect disclosed herein may contain internucleoside linkages and where at least one internucleoside linkage is a modified internucleoside linkage.
The modified internucleoside linkage may be a phosphorothioate or phosphorodithioate internucleoside linkage.
The oligomeric compound according to the first aspect disclosed herein may contain 1 to 16 phosphorothioate or phosphorodithioate internucleoside linkages.
Specific modified internucleoside linkages are the subject of some of the embodiments which follow. Certain modified internucleoside linkages are known in the art and described in, for example, Hu et al., Signal Transduction and Targeted Therapy (2020)5:101 .
The oligomeric compound may contain 7, 8, 9 or 10 phosphorothioate or phosphorodithioate internucleoside linkages. The one or more phosphorothioate or phosphorodithioate internucleoside linkages may present at the 5’ region of the first region of linked nucleosides, where advantageously, the oligomeric compound contains three phosphorothioate internucleoside linkages at three adjacent nucleosides at the 5' region.
In addition, the oligomeric compound may contain phosphorothioate or phosphorodithioate internucleoside linkages between at least two, at least three, at least four, or at least five, adjacent nucleosides of the hairpin loop, dependent on the number of nucleosides present in the hairpin loop. Particularly, the oligomeric compound may contain a phosphorothioate or phosphorodithioate internucleoside linkage between each adjacent nucleoside that is present in the hairpin loop.
Modifications
In the oligomeric compound according to the first aspect described above, at least one nucleoside may contain a modified sugar.
The modified sugar may be selected from 2' modified sugars, a conformationally restricted nucleoside (CRN) sugar such as locked nucleic acid (LNA) sugar, (S)-constrained ethyl bicyclic nucleic acid, and constrained ethyl (cEt) sugar, tricyclo-DNA, morpholino, unlocked nucleic acid (UNA) sugar, glycol nucleic acid (GNA), D-hexitol nucleic acid (HNA), and cyclohexene nucleic acid (CeNA).
Specific modified sugars are the subject of some exemplary embodiments, which follow. Certain modified sugars are known in the art and described in, for example, Hu et al., Signal Transduction and Targeted Therapy (2020)5:101 .
The 2' modified sugar may be selected from 2'-O-alkyl modified sugar, 2'-O-methyl modified sugar, 2'- O-methoxyethyl modified sugar, 2'-O-allyl modified sugar, 2'-C-allyl modified sugar, 2'-deoxy modified sugar such as 2'-deoxy ribose, 2'-F modified sugar, 2'-arabino-fluoro modified sugar, 2'-O-benzyl modified sugar, and 2'-O-methyl-4-pyridine modified sugar. At least one modified sugar may be a 2'- O-methyl modified sugar.
At least one modified sugar may be a 2'-F modified sugar and, advantageously, at most 16 or 17 sugars are 2'-F modified sugars. Advantageously, the sugar is ribose.
In the oligomeric compound according to the first aspect disclosed herein, sugars of the nucleosides at any of positions 2 and 14 downstream from the first nucleoside of the 5’ region ofthe first region of linked nucleosides, do not contain 2'-O-methyl modifications.
In certain embodiments, the 3' terminal position ofthe second region of linked nucleosides does not contain a 2'-O-methyl modification.
In certain embodiments, sugars of the nucleosides at any of positions 2 and 14 downstream from the first nucleoside of the 5’ region of the first region of linked nucleosides contain 2'-F modifications. In certain embodiments, sugars of the nucleosides of the second region of linked nucleosides that correspond in position to any of the nucleosides of the first region of linked nucleosides at any of positions 11 to 13 downstream from the first nucleoside of the 5’ region of the first region of linked nucleosides contain 2'-F modifications.
In certain embodiments, the 3' terminal nucleoside of the second region of linked nucleosides contains a 2'-F modification.
In certain embodiments, one or more of the odd numbered nucleosides starting from the 5’ region of the first region of linked nucleosides may be modified, and I or where one or more of the even numbered nucleosides starting from the 5’ region of the first region of linked nucleosides may be modified, where typically the modification of the even numbered nucleosides is a second modification that is different from the modification of odd numbered nucleosides.
In certain embodiments, one or more of the odd numbered nucleosides starting from the 3’ region of the second region of linked nucleosides may be modified by a modification that is different from the modification of odd numbered nucleosides of the first region of linked nucleosides.
In certain embodiments, one or more of the even numbered nucleosides starting from the 3’ region of the second region of linked nucleosides are modified by a modification that is different from the modification of even numbered nucleosides of the first region of linked nucleoside.
In certain embodiments, at least one or more of the modified even numbered nucleosides ofthe first region of linked nucleosides is adjacent to at least one or more of the differently modified odd numbered nucleosides of the first nucleoside region.
In certain embodiments, at least one or more of the modified even numbered nucleosides ofthe second nucleoside region is adjacent to at least one or more of the differently modified odd numbered nucleosides of the second region of linked nucleosides.
In certain embodiments, sugars of one or more of the odd numbered nucleosides starting from the 5’ region of the first region of nucleosides may be 2'-O-methyl modified sugars.
In certain embodiments, one or more of the even numbered nucleosides starting from the 3’ region of the first region of linked nucleosides may be 2'-F modified sugars.
In certain embodiments, sugars of one or more of the odd numbered nucleosides starting from the 5’ region of the second region of linked nucleosides may be 2'-O methyl modified sugars.
In certain embodiments, one or more of the even numbered nucleosides starting from the 5’ region of the second region of linked nucleosides may be 2'-F modified sugars.
In certain embodiments, sugars of a plurality of adjacent nucleosides of the first nucleoside region may be modified by a common or different modification.
In certain embodiments, sugars of a plurality of adjacent nucleosides of the second nucleoside region may be modified by a common or different modification.
In certain embodiments, sugars of a plurality of adjacent nucleosides of the hairpin loop may be modified by a common or different modification. The common modification may be a 2'-F modified sugar.
Alternatively, the common modification may be a 2'-O-methyl modified sugar.
The plurality of adjacent 2'-O-methyl modified sugars may be present in at least eight adjacent nucleosides of the first and / or second nucleoside regions. The plurality of adjacent 2'-O-methyl modified sugars may be present in three or four adjacent nucleosides of the hairpin loop.
In certain embodiments, where the hairpin loop, as disclosed earlier herein, may contain at least one nucleoside having a modified sugar.
In certain embodiments, the at least one nucleoside is adjacent to a nucleoside with a differently modified sugar, where advantageously all adjacent nucleosides in the hairpin loop have a differently modified sugar.
In certain embodiments, the modified sugar is a 2'-O-methyl modified sugar, and the differently modified sugar is a 2'-F modified sugar.
In certain embodiments one or more nucleosides of the first region of linked nucleosides and / or the second region of linked nucleosides may be an inverted nucleoside and is attached to an adjacent nucleoside via the 3' carbon of its sugar and the 3' carbon of the sugar of the adjacent nucleoside, and / or one or more nucleosides of the first region of linked nucleosides and / or the second region
of linked nucleosides is an inverted nucleoside and is attached to an adjacent nucleoside via the 5' carbon of its sugar and the 5' carbon of the sugar of the adjacent nucleoside. muRNA nucleic acid constructs
In a second aspect, a nucleic acid construct is provided having at least:
(a) a first nucleic acid portion that is at least partially complementary to at least a first portion of an RNA, which is transcribed from an AGT gene;
(b) a second nucleic acid portion that is at least partially complementary to at least a second portion of an RNA, which is transcribed from an AGT gene, the second portion being different from the first portion;
(c) a third nucleic acid portion that is at least partially complementary to the first nucleic acid portion of (a), so as to form a first nucleic acid duplex region therewith;
(d) a fourth nucleic acid portion that is at least partially complementary to the second nucleic acid portion of (b), so as to form a second nucleic acid duplex region therewith.
The construct may be designed such that subsequent to in vivo administration the construct disassembles to yield at least first and second discrete nucleic acid targeting molecules that respectively target the RNA portions transcribed from the target genes of (a) and (b); whereby (i) the first nucleic acid targeting molecule is capable of modulating expression of the target gene of (a), and contains, or is derived from, at least the first nucleic acid portion of (a), and (ii) the second nucleic acid targeting molecule is capable of modulating expression of the target gene of (b), and contains, or is derived from, the second nucleic acid portion of (b).
The construct may be designed to disassemble such that the first and second discrete nucleic acid targeting molecules are respectively processed by independent RNAi-induced silencing complexes. Sequence features, labile functionality and structural features of the RNA molecules
The construct according to the second aspect and its aforementioned embodiments may at least contain one labile functionality such that subsequent to in vivo administration the construct is cleaved so as to yield the at least first and second discrete nucleic acid targeting molecules.
The labile functionality may contain one or more unmodified nucleotides. In particular the one or more unmodified nucleotides of the labile functionality represent one or more cleavage positions within the construct whereby subsequent to in vivo administration the construct is cleaved at the one or more cleavage positions so as to yield the at least first and second discrete nucleic acid targeting molecules. Especially the cleavage positions may be respectively located within the construct so that subsequent to cleavage the first discrete nucleic acid targeting molecule contains, or is derived from, the first nucleic acid duplex region, and the second discrete nucleic acid targeting molecule contains, or is derived from, the second nucleic acid duplex region. Advantageously, the first discrete nucleic acid targeting molecule contains or consists of the first nucleic acid portion of (a) and the third nucleic acid portion of (c), and/or the second discrete nucleic acid targeting molecule contains or consists of the second nucleic acid portion of (b) and the fourth nucleic acid portion of (d).
In certain embodiments
(a) the first nucleic acid portion has a nucleobase sequence selected from SEQ ID NOs: 1 to 100 in Table 1a;
(b) the second nucleic acid portion has a nucleobase sequence selected from Table 1a (SEQ ID NOs: 1 to 100);
(c) the third nucleic acid portion has a nucleobase sequence selected from Table 1 b SEQ ID NOs: 101 to 200; and/or
(d) the fourth nucleic acid portion has a nucleobase sequence selected from Table 1 b (SEQ ID NOs: 101 to 200). where the third and fourth nucleobase sequences, to the extent they have a length of 14 nucleobases, may be shorter by one, two or three nucleobases, where advantageously the 5'-terminal nucleobase(s) is/are absent.
In certain such embodiments, the first nucleic acid portion of (a) may be directly or indirectly linked to the fourth nucleic acid portion of (d) as a primary structure.
In certain embodiments, the first and the fourth nucleic acid portions may have the nucleobase sequences of SEQ ID NOs: 27 and 127, 44 and 144, 41 and 141 , 97 and 197, 90 and 190, 62 and 162, 52 and 152, 93 and 193, 49 and 149, 73 and 173, 18 and 118, 37 and 137, 56 and 156, 100 and
200, 40 and 140, 75 and 175, 30 and 130, 42 and 142, 81 and 181 , 17 and 117, 34 and 134, 53 and
153, 29 and 129, 26 and 126, 74 and 174, 94 and 194, 14 and 114, 3 and 103, 7 and 107, as well as
2 and 102, respectively, advantageously, where the sequences of SEQ ID NOs: 27, 52, 56, 62, 75, and 93 may be shorter by one, two, three or four nucleobases, where advantageously the 5'-terminal nucleobase(s) is/are absent.
In certain embodiments, the second nucleic acid portion of (b) may be directly or indirectly linked to the third nucleic acid portion of (c) as a primary structure.
In certain embodiments, the second and third nucleic acid portions may have the nucleobase sequences of SEQ ID NOs: 27 and 127, 44 and 144, 41 and 141 , 97 and 197, 90 and 190, 62 and 162, 52 and 152, 93 and 193, 49 and 149, 73 and 173, 18 and 118, 37 and 137, 56 and 156, 100 and
200, 40 and 140, 75 and 175, 30 and 130, 42 and 142, 81 and 181 , 17 and 117, 34 and 134, 53 and
153, 29 and 129, 26 and 126, 74 and 174, 94 and 194, 14 and 114, 3 and 103, 7 and 107, as well as
2 and 102, respectively, advantageously, where the sequences of SEQ ID NOs: 27, 52, 56, 62, 75, and 93 may be shorter by one, two, three or four nucleobases, where advantageously the 5'-terminal nucleobase(s) is/are absent.
In certain embodiments, the construct may further contain 1 to 8 additional nucleic acid portions that are respectively at least partially complementary to an additional 1 to 8 portions of RNA transcribed from one or more target genes, which target genes may be the same or different to each other, and / or the same or different to the target genes defined in (a) and I or (b), and where each of the 1 to 8 additional nucleic acid portions respectively form additional duplex regions with respective passenger nucleic acid portions that are respectively at least partially complementary therewith. In particular, the second nucleic acid portion of (b), and the 1 to 8 additional nucleic acid portions, may be directly or indirectly linked to selected passenger nucleic acid portions as respective primary structures.
In certain embodiments the direct or indirect linking may represent either (i) an internucleotide bond, (ii) an internucleotide nick, or (iii) a nucleic acid linker portion of 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10
nucleotides, the nucleic acid linker advantageously being single stranded. Advantageously, the linking may be direct, thereby giving rise to (a) contiguous strand(s).
In certain embodiments, there may exist some complementarity between the first nucleic acid portion of (a) and the second nucleic acid portion of (b), or the third nucleic acid portion of (c) and the fourth nucleic acid portion of (d). Advantageously the complementarity
(i) may be 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10, advantageously 2, 3, 4 or 5 base pairs; and/or
(ii) may be between the first nucleic acid portion of (a) and the second nucleic acid portion of (b). In certain embodiments, the internucleotide bond may involve at least one of the one or more unmodified nucleotides, where advantageously cleavage may occur at the 3' position of (at least one of) the unmodified nucleotide(s).
In certain embodiments, the first nucleic acid portion of (a), and / or the second nucleic acid portion of (b), and I orthe third nucleic acid portion of (c), and I or the fourth nucleic acid portion of (d), may be respectively 7 to 25 nucleotides in length. Optionally, the first nucleic acid portion of (a) and/or the second nucleic acid portion of (b) may have a length of 18 to 21 , 18 to 20, or 19 nucleotides. In specific embodiments, the first nucleic acid portion of (a) and the second nucleic acid portion of (b) have a length of 19 nucleotides. The third nucleic acid portion of (c), and / or the fourth nucleic acid portion of (d) may have a length of 11 to 20, 13 to 16, 14 or 15, or 14 nucleotides.
In certain embodiments, the first nucleic portion of (a) and the second nucleic acid portion of (b) may have a length of 19 nucleotides and the third nucleic acid portion of (c) as well as the fourth nucleic acid portion of (b) may have a length of 14 nucleotides.
In certain embodiments, the unmodified nucleotide(s) is / are at any of position 18 to 25, positions 18 to 21 , and/or the 3' terminal position of the first nucleic acid portion of (a) and I or of the third nucleic acid portion of (c).
In certain embodiments, the unmodified nucleotide is at position 19.
In certain embodiments, the first nucleic portion of (a) and the second nucleic acid portion of (b) may have a length of 19 nucleotides and the third nucleic acid portion of (c) as well as the fourth nucleic acid portion of (b) may have a length of 14 nucleotides and the unmodified nucleoside is at position 19 of the first nucleic acid portion of (a) and the second nucleic acid portion of (b).
In certain embodiments, the nucleic acid linker portion may be 1 to 8 nucleotides in length, 2 to 7 or 3 to 6 nucleotides in length, 4 or 5, or 4 nucleotides in length.
In certain embodiments, one, more of all of the duplex regions independently may have a length of 10 to 19, 13 to 19, 13, 14 or 15 base pairs, where optionally there is one mismatch within the duplex region.
In certain embodiments, the nucleic acid construct may be blunt ended.
In certain embodiments, the first nucleic acid portion of ( the second nucleic acid portion the third nucleic acid portion of the fourth nucleic acid portion o
to the extent present, the 1 to 8 additional nucleic acid portions as defined previously herein; and / or
to the extent present, the passenger nucleic acid portions as defined previously herein; may have an overhang.
In certain embodiments, the target RNA may be an mRNA or another RNA molecule.
Ligands
The nucleic acid construct according to the second aspect and the aforementioned embodiments may further contain one or more ligands.
In certain embodiments, the first nucleic acid portion of (a), and / or the second nucleic acid portion of (b), and / orthe third nucleic acid portion of (c), and / or the fourth nucleic acid portion of (d), and / or, to the extent present, the 1 to 8 additional nucleic acid portions as defined previously herein, and / or the passenger nucleic acid portions as defined previously herein, respectively may have a 5’ to 3’ directionality thereby defining 5’ and 3’ regions thereof.
In certain embodiments, one or more ligands are conjugated at the 3 ' region, advantageously the 3' end, of any of (I) the third nucleic acid portion of (c), and / or (ii) the fourth nucleic acid portion of (d), and / or, to the extent present, the (ill) passenger nucleic acid portions as defined previously herein. In certain embodiments, one or more ligands may be conjugated at one or more regions intermediate of the 5’ and 3’ regions of any of the nucleic acid portions, advantageously of the third nucleic acid portion of (c), and I or the fourth nucleic acid portion of (d), and / orthe passenger nucleic acid portions as defined previously herein.
In certain embodiments, one or more ligands may be conjugated at the 5' region, advantageously the 5' end, of any of the nucleic acid portions.
In certain embodiments, the one or more ligands may be any cell directing moiety, such as lipids, carbohydrates, aptamers, vitamins and I or peptides that bind cellular membrane or a specific target on cellular surface. The one or more carbohydrates can be a monosaccharide, disaccharide, trisaccharide, tetrasaccharide, oligosaccharide or polysaccharide. In one embodiment, the one or more carbohydrates may contain one or more hexose moieties, such as one or more galactose moieties, one or more lactose moieties, one or more N-Acetyl-Galactosamine moieties, and I or one or more mannose moieties. The hexose moiety may contain two or three N-Acetyl-Galactosamine moieties. In particular, the hexose moiety may contain three N-Acetyl-Galactosamine moieties. In certain embodiments, the one or more ligands may be attached in a linear configuration, or in a branched configuration. Advantageously, where the one or more ligands may be attached as a biantennary or triantennary configuration, or as a configuration based on single ligands at different positions.
Advantageously, the ligand may have the following structure:
Intemucleoside linkages
The nucleotide construct according to the second aspect as described above or its aforementioned embodiments may contain one or more phosphorothioate or phosphorodithioate internucleotide linkages.
In certain embodiments, the nucleic acid construct may contain 1 to 15 phosphorothioate or phosphorodithioate internucleotide linkages.
In certain embodiments, the nucleic acid construct may contain one or more phosphorothioate or phosphorodithioate internucleotide linkages at one or more of the 5’ and / or 3’ regions of the first nucleic acid portion of (a), and I or the second nucleic acid portion of (b), and ! or the third nucleic acid portion of (c), and I orthe fourth nucleic acid portion of (d), and / orthe 1 to 8 additional nucleic acid portions as defined previously herein, and / or the passenger nucleic acid portions as defined in previously herein.
In certain embodiments, the nucleic acid construct may contain phosphorothioate or phosphorodithioate internucleotide linkages between at least two adjacent nucleotides of the nucleic acid linker portion as defined in previously herein.
In certain embodiments, the nucleic acid construct may contain a phosphorothioate or phosphorodithioate internucleotide linkage between each adjacent nucleotide that is present in the nucleic acid linker portion.
In certain embodiments, the nucleic acid construct may contain a phosphorothioate or phosphorodithioate internucleotide linkage linking: the first nucleic acid portion of (a) to the nucleic acid linker portion as defined in previously herein; and I or the second nucleic acid portion of (b) to the nucleic acid linker portion as defined previously herein; and / or the third nucleic acid portion of (c) to the nucleic acid linker portion as defined previously herein and / or the fourth nucleic acid portion of (d) to the nucleic acid linker portion as defined previously herein ; and / or
the 1 to 8 additional nucleic acid portions as defined previously herein to the nucleic acid linker portion as further defined previously herein; and I or the passenger nucleic acid portions as defined previously herein to the nucleic acid linker portion as further defined previously herein.
Modifications
In the nucleic acid construct according to the second aspect as described above and its aforementioned embodiments, at least one nucleotide of at least one of the following may be modified: the first nucleic acid portion of (a); and / or the second nucleic acid portion of (b); and / or the third nucleic acid portion of (c); and I or the fourth nucleic acid portion of (d); and I or to the extent present, the 1 to 8 additional nucleic acid portions as defined previously herein; and I or to the extent present, the passenger nucleic acid portions as defined previously herein; and / or to the extent present, the nucleic acid linker portion as further defined previously herein.
In some embodiments one or more of the odd numbered nucleotides starting from the 5’ region of one of the following may be modified, and / or where one or more of the even numbered nucleotides starting from the 5' region of one of the following are modified, where typically the modification of the even numbered nucleotides is a second modification that is different from the modification of odd numbered nucleotides: the first nucleic acid portion of (a); and / or the second nucleic acid portion of (b); and / or the third nucleic acid portion of (c); and I or the fourth nucleic acid portion of (d); and I or to the extent present, the 1 to 8 additional nucleic acid portions as defined previously herein; and / or to the extent present, the passenger nucleic acid portions as defined previously herein.
In certain embodiments, one or more of the odd numbered nucleotides starting from the 3’ region of the third nucleic acid portion of (c) may be modified by a modification that is different from the modification of odd numbered nucleotides starting from the 5’ region of the first nucleic acid portion of (a); and I or one or more of the odd numbered nucleotides starting from the 3’ region of the fourth nucleic acid portion of (d) may be modified by a modification that is different from the modification of odd numbered nucleotides starting from the 5’ region of the second nucleic acid portion of (b); and / or one or more of the odd numbered nucleotides starting from the 3’ region of the passenger nucleic acid portions as defined previously herein, to the extent present, may be modified by a modification that is different from the modification of odd numbered nucleotides starting from the 5’ region of the 1 to 8 additional nucleic acid portions as defined previously herein; and I or where one or more of the nucleotides of a nucleic acid linker portion as further defined previously herein, to the extent present, may be modified by a modification that (i) is different from the modification of an adjacent nucleotide of the 3’ region of the first nucleic acid portion of (a); and / or (ii)
is different from the modification of an adjacent nucleotide of the 3’ region of the second nucleic acid portion of (b); and I or is different from the modification of an adjacent nucleotide of the 3’ region of the 1 to 8 additional nucleic acid portions, to the extent present, as defined previously herein.
In certain embodiments, one or more of the even numbered nucleotides starting from the 3’ region of: (i) the third nucleic acid portion of (c), and I or (ii) the fourth nucleic acid portion of (d), and I or (iii) the passenger nucleic acid portions as defined previously herein, to the extent present, may be modified by a modification that is different from the modification of odd numbered nucleotides starting from the 3’ region of these respective portions.
In certain embodiments, at least one or more of the modified even numbered nucleotides of (I) the first nucleic acid portion of (a), and I or (ii) the second nucleic acid portion of (b), and I or (iii), to the extent present, the 1 to 8 additional nucleic acid portions as defined previously herein, may be adjacent to at least one or more differently modified odd numbered nucleotides of these respective portions.
In certain embodiments, at least one or more of the modified even numbered nucleotides of (I) the third nucleic acid portion of (c), and I or (ii) the fourth nucleic acid portion of (d), and I or (iii), to the extent present, the passenger nucleic acid portions as defined previously herein, may be adjacent to at least one or more differently modified odd numbered nucleotides of these respective portions.
In certain embodiments, a plurality of adjacent nucleotides of (i) the first nucleic acid portion of (a), and / or (ii) the second nucleic acid portion of (b), and I or (iii), to the extent present, the 1 to 8 additional nucleic acid portions as defined previously herein, may be modified by a common modification.
In certain embodiments, a plurality of adjacent nucleotides of (i) the third nucleic acid portion of (c), and I or (ii) the fourth nucleic acid portion of (d), and I or (iii), to the extent present, the passenger nucleic acid portions as defined previously herein, may be modified by a common modification.
In certain embodiments, the plurality of adjacent commonly modified nucleotides may be 2 to 4 adjacent nucleotides, advantageously 3 or 4 adjacent nucleotides.
In certain embodiments, the plurality of adjacent commonly modified nucleotides may be located in the 5’ region of (i) the third nucleic acid portion of (c), and I or (ii) the fourth nucleic acid portion of (d), and I or (iii), to the extent present, the passenger nucleic acid portions previously herein.
In certain embodiments, a plurality of adjacent commonly modified nucleotides may be located in the nucleic acid linker portion as further defined previously herein.
In certain embodiments, the one or more of the modified nucleotides of first nucleic acid portion of (a) may not have a common modification present in the corresponding nucleotide of the third nucleic acid portion of (c) of the first duplex region; and I or one or more of the modified nucleotides of second nucleic acid portion of (b) may not have a common modification present in the corresponding nucleotide of the fourth nucleic acid portion of (d) of the second duplex region; and I or one or more of the modified nucleotides of the 1 to 8 additional nucleic acid portions, to the extent present, as defined previously herein, may not have a common modification present in the corresponding nucleotide of the corresponding passenger nucleic acid portions of the respective duplex regions.
In certain embodiments, the one or more of the modified nucleotides ofthe first nucleic acid portion of (a) may be shifted by at least one nucleotide relative to a commonly modified nucleotide of the third
nucleic acid portion of (c); and / or one or more of the modified nucleotides of the second nucleic acid portion of (b) may be shifted by at least one nucleotide relative to a commonly modified nucleotide of the fourth nucleic acid portion of (d); and / or one or more of the modified nucleotides of the 1 to 8 additional nucleic acid portions, to the extent present, as defined previously herein may be shifted by at least one nucleotide relative to a commonly modified nucleotide of the passenger nucleic acid portions, to the extent present, as defined previously herein.
In certain embodiments, the modification and I or modifications may be each and individually sugar, phosphate, or base modifications.
In certain embodiments, the modification may be selected from nucleotides with 2' modified sugars; conformationally restricted nucleotides (CRN) sugar such as locked nucleic acid (LNA), (S)- constrained ethyl bicyclic nucleic acid, and constrained ethyl (cEt), tricyclo-DNA; morpholino, unlocked nucleic acid (UNA), glycol nucleic acid (GNA), D-hexitol nucleic acid (HNA), and cyclohexene nucleic acid (CeNA). The 2' modified sugar may be selected from 2'-O-alkyl modified sugar, 2'-O-methyl modified sugar, 2'-0-methoxyethyl modified sugar, 2'-O-allyl modified sugar, 2'-C- allyl modified sugar, 2'-deoxy modified sugar such as 2'-deoxy ribose, 2'-F modified sugar, 2'-arabino- fluoro modified sugar, 2'-O-benzyl modified sugar, 2'-amino modified sugar, and 2'-O-methyl-4- pyridine modified sugar.
In certain embodiments, the base modification may be any one of an abasic nucleotide and a nonnatural base containing nucleotide.
In certain embodiments, at least one modification may be a 2'-O-methyl modification in a ribose moiety.
In certain embodiments, at least one modification may be a 2'-F modification in a ribose moiety.
In certain embodiments, the nucleotides at any of positions 2 and 14 downstream from the first nucleotide of the 5’ region of (i) the first nucleic acid portion of (a); and I or (ii) the second nucleic acid portion of (b); and I or (iii), to the extent present, the 1 to 8 additional nucleic acid portions as defined previously herein; may not contain 2'-O-methyl modifications in ribose moieties.
In certain embodiments, one, two or all three nucleotides of (i) the third nucleic acid portion of (c); and I or (ii) the fourth nucleic acid portion of (d); and I or (iii), to the extent present, the passenger nucleic acid portions as defined previously herein; that respectively correspond in position to any of the nucleotides at any of positions 11 to 13 downstream from the first nucleotide of the 5’ region of (i) the first nucleic acid portion of (a); and I or (ii) the second nucleic acid portion of (b); and I or (iii) the 1 to 8 additional nucleic acid portions, to the extent present, as defined previously herein; may not contain 2'-O-methyl modifications in ribose moieties.
In certain embodiments, the nucleotides at any of positions 2 and 14 downstream from the first of (i) the first nucleic acid portion of (a); and / or (ii) the second nucleic acid portion of (b); and I or (iii), to the extent present, the 1 to 8 additional nucleic acid portions as defined previously herein; may contain 2'-F modifications in ribose moieties.
In certain embodiments, one, two or all three nucleotides of (i) the third nucleic acid portion of (c); and or (ii) the fourth nucleic acid portion of (d); and / or (iii), to the extent present, the passenger nucleic acid portions as defined previously herein; that respectively correspond in position to any of the
nucleotides at any of positions 11 to 13 downstream from the first nucleotide of the 5’ region of (i) the first nucleic acid portion of (a); and I or (ii) the second nucleic acid portion of (b); and I or (ill), to the extent present, the 1 to 8 additional nucleic acid portions as defined previously herein; may contain 2'- F modifications in ribose moieties.
In certain embodiments, all remaining nucleotides may contain either 2'-O-methyl modifications or 2'-F modifications in ribose moieties, advantageously with the exception of the unmodified nucleotide(s) in accordance with the labile linkage defined herein. Advantageously, the remaining nucleotides may contain 2'-O-methyl modifications in ribose moieties.
In certain embodiments, the one or more, advantageously one, unmodified nucleotide represents any of the nucleotides of the nucleic acid linker portion as further defined previously herein, advantageously the nucleotide of the nucleic acid linker portion as further defined previously herein that is adjacent to (i) the third nucleic acid portion of (c); and or (ii) the fourth nucleic acid portion of (d); and I or (iii), to the extent present, the passenger nucleic acid portions as defined previously herein.
In certain embodiments,
(a) the first nucleic acid portion may be selected from Table 3a;
(b) the second nucleic acid portion may be selected from Table 3a;
(c) the third nucleic acid portion may be selected from Table 3b; and/or
(d) the fourth nucleic acid portion may be selected from Table 3b.
The first nucleic acid portion and the second nucleic acid portion may be selected from Table 3a, where the first and second nucleic acid portions are different; and the third and fourth nucleic acid portions may be selected from Table 3b.
In certain embodiments, the 3' terminal positions of the first and the third nucleic acid portions may be replaced with an unmodified nucleotide.
In certain embodiments, the nucleic acid construct may contain at least one vinylphosphonate modification, such as at least one vinylphosphonate modification in the 5’ region of (i) the first nucleic acid portion of (a); and I or (ii) the second nucleic acid portion of (b); and I or (iii), to the extent present, the 1 to 8 additional nucleic acid portions as defined previously herein.
In certain embodiments, one or more nucleotides of the first nucleic acid portion of ( the second nucleic acid portion the third nucleic acid portion of the fourth nucleic acid portion o
to the extent present, the 1 to 8 additional nucleic acid portions as defined previously herein; and / or to the extent present, the passenger nucleic acid portions as defined previously herein; may be an inverted an inverted nucleotide and may be attached to the adjacent nucleotide via the 3' carbon of the nucleotide and the 3' carbon of the adjacent nucleotide, and / or may be an inverted nucleotide and may be attached to the adjacent nucleotide via the 5' carbon of the nucleotide and the 5' carbon of the adjacent nucleotide.
In certain embodiments, the inverted nucleotide may be attached to the adjacent nucleotide via a phosphate group by way of a phosphodiester linkage; or may be attached to the adjacent nucleotide via a phosphorothioate group; or may be attached to the adjacent nucleotide via a phosphorodithioate group.
Different targets
The (b) second nucleic acid portion that is at least partially complementary to at least a second portion of an RNA, which is transcribed from a target gene which is different from the AGT gene. This in particular enables the simultaneous treatment of AGT-associated diseases or disorders and further disorders associated with different targets as described below.
The target gene different from the AGT gene can, therefore, be selected from the group consisting of genes encoding ApoB-containing atherogenic Lipoproteins, genes encoding proteins related to inflammatory-signalling pathways, such as IL-6, CRP and IL-11 , genes encoding further hypertension-related proteins, genes encoding proteins related to platelet-aggregation and coagulation pathways, genes encoding proteins related to diabetes, genes encoding proteins related to obesity and metabolic syndrome, and genes encoding proteins related to further pro-atherogenic factors and modifiable risk factors for cardiovascular diseases.
In particular, the target gene different from the AGT gene is selected from the group consisting of: an APOC3 gene, a PCSK9 gene, an ANGPTL3 gene, an ANGPTL4 gene, an Lp(a) gene, an ANGPTL 8 gene, and an ASGR1/2 gene, advantageously an APOC3 gene or PCSK9 gene.
AGT and AP0C3 muRNA
Therefore, in certain embodiments, the target gene different from the AGT gene can be an APOC3 gene. In this particular case, the (b) second nucleic acid portion is an APOC3 antisense strand and (d) the fourth nucleic portion a strand at least partially complementary thereto.
In particular,
(a) the first nucleic acid portion is selected from Table 1 a;
(b) the second nucleic acid portion is selected from Table 4a;
(c) the third nucleic acid portion is selected from Table 1b; and
(d) the fourth nucleic acid portion is selected from Table 4c.
Additionally or alternatively,
(a) the first nucleic acid portion is selected from Table 3a;
(b) the second nucleic acid portion is selected from Table 4b;
(c) the third nucleic acid portion is selected from Table 3b; and
(d) the fourth nucleic acid portion is selected from Table 4d.
Additionally or alternatively,
(a) the first nucleic acid portion is selected from Table 1 a;
(b) the second nucleic acid portion is selected from Table 5a;
(c) the third nucleic acid portion is selected from Table 1b; and
(d) the fourth nucleic acid portion is selected from Table 5c.
Additionally or alternatively,
(a) the first nucleic acid portion is selected from Table 3a;
(b) the second nucleic acid portion is selected from Table 5b;
(c) the third nucleic acid portion is selected from Table 3b; and
(d) the fourth nucleic acid portion is selected from Table 5d.
Additionally or alternatively,
(a) the first nucleic acid portion is selected from Table 1 a, in particular Table 3a;
(b) the second nucleic acid portion is selected from Table 10b, in particular Table 12b;
(c) the third nucleic acid portion is selected from Table 1 b, in particular Table 3b; and
(d) the fourth nucleic acid portion is selected from Table 11 b, in particular Table 13b.
It is particularly advantageous that the (a) first nucleic acid portion, no matter if selected from Table 1a in its unmodified form or from Table 3a in its modified form, is selected from group consisting of the constructs denoted AGT_27, AGT_62, AGT_52, AGT_56, AGT_93 and AGT_75. In this embodiment, the corresponding (c) third nucleic acid portion has the corresponding denotation in Table 1 b or 3b. Furthermore, it is particularly advantageous that (b) the second nucleic acid portion is selected from the group consisting of A28(14-4)mF and A277(12-5) in Table 6a, in particular in Table 6b, where the second portion consists of the first 19 nucleotides of these entries. The corresponding (d) fourth portion contains the remaining nucleotides from the corresponding entries in Table 6a, in particular Table 6b.
The nucleic acid portions targeting the AGT gene can be arbitrarily combined with the nucleic acid portions targeting the APOC3 gene as mentioned above, such as AGT_27+A28(14-4)mF, AGT_27+A277(12-5), AGT_62+A28(14-4)mF etc. in orderto arrive at a muRNA molecule targeting both, AGT and APOC3. Such combination is also plausible due to the activity of the respective compounds as set forth in the Examples.
Therefore, it is possible to treat AGT-associated diseases or disorders simultaneously with APOC3- related diseases or disorders.
AGT and PCSK9 muRNA
In certain embodiments, the target gene different from the AGT gene may be a PCSK9 gene. In this particular case, the (b) second nucleic acid portion is e.g. an PCSK9 antisense strand and (d) the fourth nucleic portion a strand at least partially complementary thereto.
Alternatively or additionally,
(a) the first nucleic acid portion is selected from Table 3a;
(b) the second nucleic acid portion is selected from Table 7a,
(c) the third nucleic acid portion is selected from Table 3b; and
(d) the fourth nucleic acid portion is selected from 7b.
Alternatively or additonally,
(a) the first nucleic acid portion is selected from Table 1 a, in particular Table 3a;
(b) the second nucleic acid portion is selected from Table 8a, in particular Table 8b;
(c) the third nucleic acid portion is selected from Table 1 b, in particular Table 3b; and
(d) the fourth nucleic acid portion is selected from Table 8c, in particular Table 8d. Alternatively or additionally,
(a) the first nucleic acid portion is selected from Table 1 a, in particular Table 3a;
(b) the second nucleic acid portion is selected from Table 9a, in particular Table 9b;
(c) the third nucleic acid portion is selected from Table 1 b, in particular Table 3b; and
(d) the fourth nucleic acid portion is selected from Table 9c, in particular Table 9d. Alternatively or additionally,
(a) the first nucleic acid portion is selected from Table 1 a, in particular Table 3a;
(b) the second nucleic acid portion is selected from Table 10a, in particular Table 11 a;
(c) the third nucleic acid portion is selected from Table 1 b, in particular Table 3b; and
(d) the fourth nucleic acid portion is selected from Table 12a, in particular Table 13a.
It is particularly advantageous that the (a) first nucleic acid portion, no matter if selected from Table 1a in its unmodified form or from Table 3a in its modified form, is selected from group consisting of the constructs denoted AGT_27, AGT_62, AGT_52, AGT_56, AGT_93 and AGT_75. In this particularly advantageous embodiment, the corresponding (c) third nucleic acid portion has the corresponding denotation in Table 1 b or 3b.
Furthermore, it is particularly advantageous that (b) the second nucleic acid portion is selected from the group consisting of PCS29, PCS44 and PCS53 in Table 22, where the second portion consists of the first 19 nucleotides of these entries. The corresponding (d) fourth portion contains the remaining nucleotides from the corresponding entries in Table 22.
The nucleic acid portions targeting the AGT gene can be arbitrarily combined with the nucleic acid portions targeting the APOC3 gene as mentioned above, such as AGT_27+PCS29, AGT_27+PCS44, AGT_27+PCS53, AGT_62+PCS29 etc. in order to arrive at a muRNA molecule targeting both, AGT and PCSK9. Such combination is also plausible due to the activity of the respective compounds as set forth in the Examples.
Therefore, it is possible to treat AGT-associated diseases or disorders simultaneously with PCSK9 associated diseases or disorders.
AGT/APOC3 and PCSK9 muRNA
In certain embodiments, the construct further contains 1 to 8 additional nucleic acid portions that are respectively at least partially complementary to an additional 1 to 8 portions of RNA transcribed from one or more target genes, which target genes different to each other, and / or the same or different to the target genes defined in (a) and (b), and where each of the 1 to 8 additional nucleic acid portions respectively form additional duplex regions with respective passenger nucleic acid portions that are
respectively at least partially complementary therewith. Advantageously, the construct contains 1 additional nucleic acid portion.
In certain embodiment, the construct targets the target genes selected from the group consisting of:
(a) AGT gene, (b) APOC3 gene and (e) PCSK9 gene,
(a) AGT gene, (b) ANGPTL3 gene and (e) Lp(a) gene, and
(a) AGT gene, (b) APOC3 gene and (e) Lp(a) gene, where (a) is the first nucleic acid portion that is at least partially complementary to at least a first portion of an RNA, which is transcribed from an AGT gene, (b) is the second nucleic acid portion that is at least partially complementary to a first portion of an RNA which is transcribed from the second gene and (e) is a fifth nucleic acid portion that is at least partially complementary to a third portion of RNA which is transcribed from the third gene and (f) is a sixth nucleic acid portion that is at least partially complementary to (e), where advantageously the target genes are (a) AGT gene, (b) APOC3 gene and (e) PCSK9 gene.
In certain embodiments, the target genes are (a) an AGT gene, (b) an APOC3 gene and (e) a PCSK9 gene.
Accordingly,
(a) the first nucleic acid portion is selected from Table 1 a, in particular Table 3a;
(b) the second nucleic acid portion is selected from Table 4a;
(c) the third nucleic acid portion is selected from Table 1b, in particular Table 3b;
(d) the fourth nucleic acid portion is selected from Table 4c;
(e) the fifth nucleic acid portion is selected from Table 7a; and
(d) the sixth nucleic acid portion is selected from Table 7b.
Additionally or alternatively,
(a) the first nucleic acid portion is selected from Table 1 a, in particular Table 3a;
(b) the second nucleic acid portion is selected from Table 4a, in particular Table 4b;
(c) the third nucleic acid portion is selected from Table 1 b, in particular Table 3b;
(d) the fourth nucleic acid portion is selected from Table 4c, in particular Table 4d;
(e) the fifth nucleic acid portion is selected from Table 8a, in particular Table 8b; and (d) the sixth nucleic acid portion is selected from Table 8c, in particular Table 8d.
Alternatively or additionally,
(a) the first nucleic acid portion is selected from Table 1 a, in particular Table 3a;
(b) the second nucleic acid portion is selected from Table 4a, in particular Table 4b;
(c) the third nucleic acid portion is selected from Table 1b, in particular Table 3b;
(d) the fourth nucleic acid portion is selected from Table 4c, in particular Table 4d;
(e) the fifth nucleic acid portion is selected from Table 8a, in particular Table 8b; and
(f) the sixth nucleic acid portion is selected from Table 8c, in particular Table 8d.
Alternatively or additionally
(a) the first nucleic acid portion is selected from Table 1 a;
(b) the second nucleic acid portion is selected from Table 5a;
(c) the third nucleic acid portion is selected from Table 1b;
(d) the fourth nucleic acid portion is selected from Table 5c;
(e) the fifth nucleic acid portion is selected from Table 9a, in particular Table 9b; and
(f) the sixth nucleic acid portion is selected from Table 9c, in particular Table 9d.
Alternatively or additionally,
(a) the first nucleic acid portion is selected from Table 3a;
(b) the second nucleic acid portion is selected from Table 5b;
(c) the third nucleic acid portion is selected from Table 3b;
(d) the fourth nucleic acid portion is selected from Table 5d;
(e) the fifth nucleic acid portion is selected from Table 9a, in particular Table 9b; and
(f) the sixth nucleic acid portion is selected from Table 9c, in particular Table 9d.
Alternatively or additionally,
(a) the first nucleic acid portion is selected from Table 1 a, in particular Table 3a;
(b) the second nucleic acid portion is selected from Table 10b, in particular Table 12b;
(c) the third nucleic acid portion is selected from Table 1 b, in particular Table 3b; and
(d) the fourth nucleic acid portion is selected from Table 11 b, in particular Table 13b;
(e) the fifth nucleic acid portion is selected from Table 10b, in particular Table 11 b; and
(f) the sixth nucleic acid portion is selected from Table 12b, in particular Table 12b.
Certain advantageous nucleic acid portions to be used are set forth under the headings "AGT and APOC3 muRNA” and "AGT and PCSK9 muRNA" above. Among these nucleic acid portions, all combinations are possible, such as AGT_27+A28(14-4)mF+PCS44, AGT_62+277(12-5)+PCS29, as long as it contains or consists of one AGT-targeting construct, one APCO3-targeting construct and one PCSK9-targeting construct among these specific constructs. Such combinations are also possible due to the activity of the respective compounds as set forth in the Examples.
Therefore, it is possible to treat AGT-associated diseases or disorders simultaneously with APOC3- associated diseases or disorders and PCSK9-associated diseases or disorders.
Compositions and pharmaceutical compositions including shRNA, mxRNA and/or muRNA oligomeric constructs
In a a third aspect, the composition contains an oligomeric compound according to the first aspect and/or a nucleic acid construct according the second aspect as described above, and a physiologically acceptable excipient.
According to a fourth aspect, a pharmaceutical composition is provided containing an oligomeric compound according to the first aspect and/or a nucleic acid construct according to the second aspect as described above.
The pharmaceutical composition may further contain a pharmaceutically acceptable excipient, diluent, antioxidant, and/or preservative.
The oligomeric compound according to the first aspect and/or the construct according to the second aspect may be the only pharmaceutically active agent(s).
Alternatively, the pharmaceutical composition furthermore contains one or more further pharmaceutically active agents. The further pharmaceutically active agent(s) may be (an) agent(s)
which decrease hypertension, where the further pharmaceutically active agent(s) is/are optionally selected from the group consisting of a diuretic, an angiotensin converting enzyme (ACE) inhibitor, an angiotensin II receptor antagonist, a beta-blocker, a vasodilator, a calcium channel blocker, an aldosterone antagonist, an alpha2-agonist, a renin inhibitor, an alpha-blocker, a peripheral acting adrenergic agent, a selective D1 receptor partial agonist, a nonselective alpha-adrenergic antagonist, a synthetic, a steroidal antimineralocorticoid agent; a combination of any of the foregoing; and a hypertension therapeutic agent formulated as a combination of agents, more optionally an angiotensin II receptor antagonist selected from the group consisting of losartan, valsartan, olmesartan, eprosartan, and azilsartan. Advantageously the oligomeric compound and/or the nucleic acid construct; and the further pharmaceutically active agent(s) are to be administered concomitantly or in any order.
Diseases to be treated by shRNA, mxRNA and/or muRNA oligomeric compounds and further uses
According to a fifth aspect, an oligomeric compound is provided according to the first aspect and/or a nucleic acid construct according to the second aspect as described above, for use in human or veterinary medicine or therapy.
In a sixth aspect, an oligomeric compound according to the first aspect and/or a nucleic acid construct according to the second aspect as described above may be used to treat, ameliorate and/or prevent a disease or disorder.
One of the diseases may be an AGT-associated disease or disorder as discussed below. However, more diseases may be treated simultaneously by using muRNA constructs as described herein. Such diseases may be, for example, ApoB containing atherogenic Lipoprotein-associated diseases or disorders; Inflammatory signalling pathway-related diseases, such as related to IL-6, CRP and IL-11 ; Platelet aggregation and coagulation pathway-associated diseases; Diabetes; Obesity and metabolic syndrome; and/or other pro-atherogenic factor and modifiable risk factors for CVD-related diseases. Corresponding targets, in particular in terms of dyslipidaemia, may be selected from the group consisting of APOC3, PCSK9, ANGPTL3, ANGPTL4, Lp(a), ANGPTL8 and ASGR1/2. AGT-associated disease or disorder
The disease or disorder may be a disease or disorder associated AGT or a disease or disorder requiring reduction of AGT expression.
In particular, the disease or disorder is selected from the group consisting of high blood pressure, hypertension, borderline hypertension, primary hypertension, secondary hypertension isolated systolic or diastolic hypertension, pregnancy-associated hypertension, diabetic hypertension, resistant hypertension, refractory hypertension, paroxysmal hypertension, renovascular hypertension, Goldblatt hypertension, ocular hypertension, glaucoma, pulmonary hypertension, portal hypertension, systemic venous hypertension, systolic hypertension, labile hypertension; hypertensive heart disease, hypertensive nephropathy, atherosclerosis, arteriosclerosis, vasculopathy, diabetic nephropathy, diabetic retinopathy, chronic heart failure, cardiomyopathy, diabetic cardiac myopathy, nocturnal hypotension, glomerulosclerosis, coarctation of the aorta, aortic aneurism, ventricular fibrosis, heart failure, myocardial infarction, angina, stroke, renal disease, renal failure, systemic sclerosis,
intrauterine growth restriction (IUGR) , fetal growth restriction, obesity, liver steatosis/ fatty liver, nonalcoholic Steatohepatitis (NASH), non-alcoholic fatty liver disease (NAFLD); glucose intolerance, type 2 diabetes, and metabolic syndrome.
APOC3-associated disease or disorder
In addition to the diseases or disorders discussed before, the disease or disorder is further an APOC3-associated disease or disorder, or a disease or disorder requiring reduction of APOC3 expression levels, the disease or disorder advantageously being selected from dyslipidaemia including mixed dyslipidaemia; hyperchylomicronaemia including familial hyperchylomicronaemia; hypertriglyceridemia, advantageously severe hypertriglyceridemia and/or hypertriglyceridemia with blood triglyceride levels above 500 mg/dl; inflammation including low-grade inflammation; atherosclerosis; atherosclerotic cardiovascular diseases (ASCVD) including major adverse cardiovascular events (MACE) such as myocardial infarction, stroke and peripheral arterial disease; and pancreatitis including acute pancreatitis.
PCSK9-associated disease or disorder
In addition to the diseases or disorders discussed before, the disease or disorder is further a PCSK9- associated disease or disorder, or a disease or disorder requiring reduction of low-density lipoprotein (LDL) cholesterol, the disease or disorder advantageously being selected from dyslipidaemia including mixed dyslipidaemia, hypercholesterolemia, heterozygous familial hypercholesterolemia, non-familial hypercholesterolemia; atherosclerosis; and atherosclerotic cardiovascular disease (ASCVD) including myocardial infarction, stroke and peripheral arterial disease.
In a seventh aspect, methods are provided for treating a disease or disorder by administering an oligomeric compound according the first aspect and/or a nucleic acid construct according to the second aspect, to an individual in need of treatment.
The oligomeric compound and/or the nucleic acid construct may be administered subcutaneously or intravenously to the individual.
According to an eighth aspect, an oligomeric compound according to the first aspect or a nucleic acid construct according to the second aspect, may be used in research as a gene function analysis tool. According to a ninth aspect, an oligomeric compound according to the first aspect and/or a nucleic acid construct according to the second aspect may be used in the manufacture of a medicament for a treatment of a disease or disorder.
Constructs and sequences of the oligomeric compounds
The following Tables show nucleobase sequences of antisense and sense strands of the oligomeric compounds as well as of nucleobase sequences of single-stranded oligomeric compounds, and definitions of modified oligomeric compounds. The notation includes nucleobase sequence, sugar modifications, and, where applicable, modified phosphates.
The notation used is common in the art and as the following meaning:
A represents adenine;
U represents uracil;
C represents cytosine;
G represents guanine.
5Phos represents a 5’ terminal phosphate group which is advantageous but not indispensable; m represents a methyl modification at the 2' position of the sugar of the underlying nucleoside; f represents a fluoro modification at the 2' position of the sugar of the underlying nucleoside; r indicates an unmodified (2'-OH) ribonucleotide; [Ps] or # represents a phosphorothioate inter-nucleoside linkage;
I represents an inverted inter-nucleoside linkage, which can be either 3'-3', or 5'-5';
3xGalNAc represents a trivalent GalNAc.
Tables 1 a and 1 b below show nucleobase sequences of antisense and sense strands of 100 oligomeric compounds in accordance with the Examples. Table 1a: Nucleobase sequences of the antisense strands of 100 constructs
Table 1b: Nucleobase sequences of the sense strands of 100 constructs
Note = In particular, the nucleobase of the 3' terminal nucleotide of each of the sense strands presented within the table can be replaced by A.
Table 2 below shows the nucleobase sequences of the 100 hairpin constructs as selected in accordance with the Examples. The nucleobase sequences are a direct fusion of the antisense sequences of Table 1 a with the corresponding sense sequences of Table 1 b.
Table 2: Nucleobase sequences of the 100 constructs in which the sense and the antisense sequences of tables 1a and 1b are combined.
Note = In particular, the nucleobase of the 3' terminal nucleotide of each of the sense strands presented within the table can be replaced by A.
Tables 3a to c below shows 100 antisense sequences, sense sequences and hairpins, respectively, with full modification information (modified sugars and, where applicable, modified phosphates).
Table 3a: Modified antisense constructs
Note = each of the above constructs may or may not have a phosphate modification at the 5' end group.
Table 3b: Modified sense constructs
Note = each of the above constructs may or may not have a "3x GalNAc" coupled to the 3' end group. Advantageously the constructs have a 3x GalNAc ligand, in particular a toothbrush ligand as defined herein.
Table 3c: Modified hairpin constructs
Note = each of the above constructs may or may not have a phosphate modification at the 5' end group. Furthermore, and independently, each of the above constructs may or may not have a "3x GalNAc" coupled to the 3' end group. Advantageously the constructs have a 3x GalNAc ligand, in particular a toothbrush ligand as defined herein. Particularly advantageous are constructs which in addition have a 5' phosphate, even though this is not a strict requirement, given that in the absence thereof, mammalian cells will add such phosphate in case it is absent from the molecule as administered.
Specific notes about the nomenclature in tables 3a to 3c: fN: 2'-Fluoro residues mN: 2'-O-methyl residues Ps: phosphorothioate p, Phos: phosphate
(GalNAc): Sirnaomics mono-GalNAc building block
Furthermore when a notation like "A277(12-5)mF" is used, the term "A277" designates the sequence suitable for RNAi with APOC3, where the first number in the round brackets, i.e. 12 in the present case, designates the number of base pairs within a duplex region within a shRNA, and the second number in the round brackets, in this case 5, designates the number of nucleotides present in the hairpin loop of the shRNA. If there is no designation after the hyphen in the round brackets, it means that the loop consists of 5 nucleotides.
Tables 4a to 4d below show nucleobase sequences and sugar-phosphate backbone modifications of antisense and sense strands of the 376 APOC3 constructs selected in accordance with the Examples. The disclosed 30 specific oligomeric compounds have been selected from these 376 constructs.
Table 4a: Nucleobase sequences of the APOC3 antisense strands of 376 constructs
Table 4b: Nucleobase sequences and sugar-phosphate backbone modifications of the
APOC3 antisense strands of 376 constructs
Table 4c: Nucleobase sequences of the APOC3 sense strands of 376 constructs
Table 4d: Nucleobase sequences and sugar-phosphate backbone modifications of the
APOC3 sense strands of 376 constructs
Tables 5a to 5d below show nucleobase sequences and sugar-phosphate backbone modifications of antisense and sense strands of a further 15 constructs .
Table 5a: Nucleobase sequences of the APOC3 antisense strands of 15 further constructs
Table 5b: Nucleobase sequences and sugar-phosphate backbone modifications of the APOC3 antisense strands of 15 further constructs
Table 5c: Nucleobase sequences of the APOC3 sense strands of 15 further constructs
Table 5d: Nucleobase sequences and sugar-phosphate backbone modifications of the sense strands of 15 further constructs
Tables 6a to 6b below show nucleobase sequences and sugar-phosphate backbone modifications of 12 further APOC3 constructs.
Table 6a: Nucleobase sequences of the strands of 12 further APOC3 constructs
Table 6b: APOC3 Nucleobase sequences and sugar-phosphate backbone modifications of the strands of 12 further constructs
In Example 9 below, the nucleobase sequences of antisense and sense strands of 27 specific oligomeric PCSK9-targeting compounds are given. These are also subject of specific embodiments disclosed further herein. Tables 7a and 7b below shows specific sugar-phosphate backbone modifications of PCSK9 antisense and sense strands of the 27 constructs.
Table 7a: Exemplary sugar-phosphate backbone modifications of PCSK9 antisense strands of the 27 constructs.
Table 7b: Exemplary sugar-phosphate backbone modifications of PCSK9 sense strands of the 27 constructs.
Tables 8a to 8d below show nucleobase sequences and sugar-phosphate backbone modifications of PCSK9 antisense and sense strands of the 250 constructs selected in accordance with Example 8 below. The above disclosed 27 oligomeric PCSK9 compounds have been selected from these 250 constructs.
Table 8a: 250 unmodified PCSK9 antisense nucleobase sequences
Table 8b: 250 modified PCSK9 antisense nucleobase sequences corresponding to Table 8a.
Table 8c: 250 PCSK9 unmodified sense nucleobase sequences corresponding to Table 8a.
Table 8d: 250 modified PCSK9 sense strands corresponding to the antisense strands of
Table 8a.
Tables 9a to 9d below show nucleobase sequences and sugar-phosphate backbone modifications of PCSK9 antisense and sense strands of a further 43 constructs.
Table 9a: 43 unmodified PCSK9 antisense nucleobase sequences.
Table 9b: 43 modified PCSK9 antisense nucleobase sequences
Table 9c: 43 unmodified PCSK9 sense nucleobase sequences corresponding to Table 9a.
Table 9d: 43 modified PSCK9 modified sense strands corresponding to the strands of Table 9a.
Table 10a below shows the nucleobase sequences of PCSK9-targeting antisense portions (e.g. second nucleic acid portions).
Table 10b below shows the nucleobase sequences of APOC3-targeting antisense portions
(e.g. second or fifth acid portions).
Table 11a below shows the nucleobase sequences of PCSK9-targeting sense portions (third nucleic acid portions).
Table 11b below shows the nucleobase sequences of APOC3-targeting sense portions (fourth or sixth nucleic acid portions).
Table 12a shows PCSK9-targeting antisense portions including modification information.
Table 12b shows APOC3-targeting antisense portions including modification information.
Table 13a shows PCSK9-targeting sense portions including modification information.
Table 13b shows APOC3-targeting sense portions including modification information.
Table 14a shows combination (APOC3 + PSCK9) linked first and fourth nucleic acid portions. Linking is direct to give rise to a single contiguous strand.
Table 14b shows (combination (APOC3 + PCSK9) linked second and third nucleic acid portions. Linking is direct to give rise to a single contiguous strand.
The 5' terminal nucleoside of the antisense (guide) strand (first region as defined in the claims herein) can include any nucleobase that can be present in an RNA molecule, i.e., can be any of adenine (A), uracil (U), guanine (G) or cytosine (C). Additionally, the 3' terminal nucleoside of the sense (passenger) strand (second region as defined herein) can include any nucleobase that can be present in an RNA molecule, i.e., can be any of adenine (A), uracil (U), guanine (G) or cytosine (C), advantageously, however, the 3’ terminal residue is a nucleobase that is complementary to the 5' nucleobase of the antisense (guide) strand (first region as defined herein).
While the methods are shown and described as being a series of acts that are performed in a particular sequence, it is to be understood and appreciated that the methods are not limited by the order of the sequence. For example, some acts can occur in a different order than what is described herein. In addition, an act can occur concurrently with another act. Further, in some instances, not all acts may be required to implement a method described herein.
The order of the steps of the methods described herein is exemplary, but the steps may be carried out in any suitable order, or simultaneously where appropriate. Additionally, steps may be added or substituted in, or individual steps may be deleted from any of the methods without departing
from the scope of the subject matter described herein. Aspects of any of the Examples described above may be combined with aspects of any of the other Examples described to form further Examples.
It will be understood that the above description of a specific embodiment is given by way of example only and that various modifications may be made by those skilled in the art. What has been described above includes Examples of one or more embodiments. It is, of course, not possible to describe every conceivable modification and alteration of the above compounds, compositions or methods for purposes of describing the aforementioned aspects, but one of ordinary skill in the art can recognize that many further modifications and permutations of various aspects are possible. Accordingly, the described aspects are intended to embrace all such alterations, modifications, and variations that fall within the scope of the appended claims.
Examples
The following Examples illustrate certain embodiments of the present disclosure and are not limiting. Moreover, where specific embodiments are provided, the inventors have contemplated generic application of those specific embodiments. For example, disclosure of an oligonucleotide having a particular motif or modification patterns provides reasonable support for additional oligonucleotides having the same or similar motif or modification patterns.
The syntheses of the RNAi constructs disclosed herein have been carried out using synthesis methods known to the person skilled in the art, such as synthesis methods disclosed in https://en.wikipedia.org/wiki/Oligonucleotide_synthesis {retrieved on 16 February 2022}, where the methods disclosed on this website are incorporated by reference herein in their entirety . The only difference to the synthesis method disclosed in this reference is that GalNAc phosphoramidite immobilized on a support is used in the synthesis method during the first synthesis step.
Example 1
Materials and Methods
AGT Target identification and duplex preparation:
Oligomeric compounds targeting AGT were identified by bioinformatics analysis on human AGT mRNA sequence as given in RefSeq sequence ID NM_000029.3 100 compounds were selected for synthesis as mxRNA hairpins. Compounds were dissolved to 50uM in molecular biology grade water. Duplexes were annealed by heating at 95 °C for 5 minutes followed by gradual cooling to room temperature. mxRNAs were annealed by heating at 95 °C for 5 minutes followed by rapid cooling on ice.
Cell culture:
Human primary hepatocytes (5 donor pooled - Sekisui XenoTech, HPCH05+) were thawed immediately prior to experimentation and cultured in 1x complete Williams medium (Gibco, A1217601) supplemented with Hepatocytes plating supplement pack (Gibco, CM3000). FBS concentration was modified from manufacture recipe to a final 2.5% (as opposed to 5%) for compound stability.
AGT - Primary Screen:
Human primary hepatocytes (5 donor pooled - Sekisui XenoTech, HPCH05+; 2 vials) of cells were thawed by pouring Hepatocyte pellets to warm, 45 ml of Sekisui OptiThaw Hepatocyte Media (K8000), spun at 250xg for 5 min, resuspended in 40 ml of complete 2X WEM 1x Complete WEM: 2.5% FBS, 1 pM Dexamethasone, Pen/Strep (100 U/mL /100 pg/mL), 4 pg/ml Human Insulin, 2 mM GlutaMAX, 15 mM HEPES, pH 7.4.) and counted.Cells were then plated in 50 pL of 2x complete WEM at 25,000 cells per well on 96 well type 1 rat tail Collagen plates and allowed to rest and attach for 5 hours before transfection. After rest, the compounds were diluted further to 2 pM in basal WEM. 50 pL of each 2 pM AGT targeting oligonucleoside compound (AGT_1 to AGT_100 of Table 3c) was added to respective plated hepatocytes for a final concentration of 1 pM in a volume of 100uL 1x complete WEM.
72 hours post transfection, cells were harvested and RNA isolated using the PureLink Pro 96 total RNA Purification Kit (ThermoFisher, 12173011 A) according to the manufacturer protocol.
Harvested RNA was assayed for AGT expression via Taqman qPCR using the Luna Universal Probe One-Step RT-qPCR Kit (NEB, E3006). A qPCR assay was performed for each sample using a AGT TaqMan probe set (Hs01586213_m-FAM) multiplexed with a common GAPDH VIC probe (ThermoFisher, 4326317E). Thermocycling and data acquisition was performed with an Applied Biosystems Quantstudio 3/5 Real-Time PCR System.
Fig. 1 shows results of the primary screening of selected oligomeric compounds targeting AGT (selected from Table 3c SEQ ID Nos. 501-600 and 3604-3605) and their activity in inhibiting AGT expression.
Example 2 Table 15 below shows IC50 values (in nM) for 30 selected constructs (from Table 3c) selected in accordance with the Examples. Seven serials of 5-fold dilution of these constructs starting at 10OOnM were prepared in basal WEM. Effect of different concentration of constructs on inhibition of AGT mRNA was determined using the protocol described above for the primary screen. Max % KD indicates the maximally achieved knock-down at 1000 nM with 0% being no knock-down and 100% full knock-down. M4K4 was used as reference. Percentage inhibition of construct at different concentration was calculated and the IC50 was determined using GraphPad Prism 9.0.
Table 15:
Figs. 2a to 2h show the results for inhibiting AGT gene expression for fivefold dilution series for various oligomeric nucleoside compounds targeting AGT (from Table 3c).
The TMPRSS6 construct, used as a positive control, has the following modified structure: 5'vP[mA][fA][mC][fC][mA][fG][mA][fA][mG][fA][mA][fG][mC][fA][mG][fG][mU][fG][iN][fC][mU][fG][fC][ fU][mU][fC][mU][fU][mC][fU][mG][fG][mU][fU]#[3XGalNAc] (SEQ ID NO: 3587).
Example 3
Materials and Methods
Cell Culture:
HepG2 (ATCC cat. 85011430) cells were maintained by biweekly passing in EMEM supplemented with 10% FBS, 20 mM L-glutamine, 10 mM HEPES pH 7.2, 1 mM sodium pyruvate, 1x MEM non- essential amino acids, and 1x Pen/Strep (EMEM complete).
APOC3 Target identification and duplex preparation:
Targets to APOC3 were identified by bioinformatic analysis on human APOC3 mRNA sequence as given in RefSeq sequence ID NM_000040, where inter alia it has been taken into consideration that constructs should target APOC3 mRNA irrespective of splice variants and isoforms. 376 targets were selected for synthesis as asymmetric duplexes (14 nucleotide sense strand, 19 nucleotide antisense strand). Compounds were dissolved to 50uM in molecular biology grade water and annealed by heating at 95C for 5 minutes followed by gradual cooling to room temperature.
APOC3 - Primary Screen:
On the day of transfection, HepG2 cells were collected by trypsinization, counted, and seeded in 96 well tissue culture treated plates at 10,000 cells per well in 50uL complete EMEM with 20% FBS. Cells were allowed to rest for 4 hours before transfection with 2 pmoles of each respective APOC3 duplex in triplicate via RNAiMax (ThermoFisher). In brief, 8 pmoles of each duplex were diluted in 100 uL OptiMEM and mixed gently with 0.8 uL of RNAiMax in 100 uL OptiMEM to make 200 uL total complex. 50 uL of each RNAiMax complexed duplex was added to each respective triplicate well of HepG2 cells for a final mixture of 20 nM duplex in a volume of 10OuL, 50/50 EMEM/OptiMEM at 10% FBS.
72 hours post transfection, cells were harvested and RNA isolated using the PureLink Pro 96 total RNA Purification Kit (ThermoFisher, 12173011 A) according to the manufacturer protocol. Harvested RNA was assayed for APOC3 expression via Taqman qPCR using the Luna Universal Probe One-Step RT-qPCR Kit (NEB, E3006). Two separate qPCR assays were performed for
each sample using two separate APOC3 Taqman probe sets multiplexed with a common GAPDH VIC probe (ThermoFisher, 4326317E). Thermocycling and data acquisition was performed with an Applied Biosystems Quantstudio 3 Real-Time PCR System. Based on the results of the primary screen, a subset of 77 oligomeric compounds was selected which exhibit at least 70% target knockdown when assessed with either probe. These 77 compounds are selected from SEQ ID Nos. 601-1352 above in Tables 4a and 4b.
APOC3 - Secondary Screen:
Based on data from the primary screen, a yet narrower set of the best performing 30 APOC3 duplexes were tested in dose curves. As before, HepG2 cells were collected by trypsinization and seeded in 96 well tissue culture plates at 10,000 cells per well in 50uL complete EMEM with 20% FBS and allowed to rest for 4 hours. Transfection complexes were formed by gently mixing 36 pmoles of each duplex in 180 uL OptiMEM with 2.16 uL RNAiMax in 180 uL OptiMEM to make 360 uL total complex. A two fold dilution series was then performed with basal OptiMEM. 50 uL of each dilution was added to respective triplicates of HepG2 cells to make a final dilution series of 50 nM down to 0.32 nM in a volume of 100uL, 50/50 EMEM/OptiMEM at 10% FBS.
72 hours post transfection, cells were harvested and RNA isolated using the PureLink Pro 96 total RNA Purification Kit (ThermoFisher, 12173011 A) according to the manufacturer protocol.
Harvested RNA was assayed for APOC3 expression via Taqman qPCR using the Luna Universal Probe One-Step RT-qPCR Kit (NEB, E3006). A single qPCR assay was performed for each sample using APOC3 Taqman probe set multiplexed with a common GAPDH VIC probe (ThermoFisher, 4326317E). Thermocycling and data acquisition was performed with an Applied Biosystems Quantstudio 3 Real-Time PCR System.
Example 4
Results
Table 16 below shows IC50 values (in nM) for the 30 constructs selected in accordance with the Examples.
The IC50 data in the single- to double-digit nanomolar range demonstrate outstanding performance of numerous constructs as described herein.
Example 5 Materials and Methods
Cell culture:
Human primary hepatocytes (5 donor pooled - Sekisui XenoTech, HPCH05+) were thawed immediately prior to experimentation and cultured in 1x complete Williams medium (Gibco, A1217601) supplemented with Hepatocytes plating supplement pack (Gibco, CM3000). FBS concentration was modified from manufacture recipe to a final 2.5% (as opposed to 5%) for compound stability.
1x Complete WEM: 2.5% FBS, 1 pM Dexamethasone, Pen/Strep (100 U/mL /100 pg/mL), 4 pg/ml Human Insulin, 2 mM GlutaMAX, 15 mM HEPES, pH 7.4).
Hepatocytes were plated on Collagen I (rat tail) coated 96 well tissue culture plates (Gibco, A1142803).
APOC3 compound preparation:
Compounds were dissolved to 10 mg/mL in PBS and annealed by heating at 95C for 5 minutes followed by rapid cooling on ice.
APOC3 compound transfections:
On the day of transfection, primary human hepatocytes were thawed in 45mL of human OptiThaw (Sekisui Xenotech, K8000) and centrifuged down at 200g for 5 minutes. Cells were resuspended in 2x complete WEM and counted. Cell were then plated in 50 uL of 2x complete WEM at 25,000 cells per well on 96 well type 1 rat tail Collagen plates and allowed to rest and attach for four hours before transfection.
Compounds were diluted further to 2 uM in basal WEM. A seven step, five-fold dilution series was prepared in basal WEM from 2 uM to 0.000128 uM. 50 uL of each dilution was added to respective triplicates of the plated hepatocytes for a final dilution series of 1 uM down to 0.000064 uM in a volume of 100uL 1x complete WEM.
72 hours post transfection, cells were harvested and RNA isolated using the PureLink Pro 96 total RNA Purification Kit (ThermoFisher, 12173011 A) according to the manufacturer protocol. Harvested RNA was assayed for APOC3 expression via Taqman qPCR using the Luna Universal Probe One-Step RT-qPCR Kit (NEB, E3006). A single qPCR assay was performed for each sample using an APOC3 Taqman probe set (Hs00906501_g1-FAM) multiplexed with a common GAPDH VIC probe (ThermoFisher, 4326317E). Thermocycling and data acquisition was performed with an Applied Biosystems Quantstudio 3/5 Real-Time PCR System.
Table 17: Constructs used as positive control
Note: vP = vinyl-phosphonate; iN = inverted with 2'OH
Results
As can be seen from Figure 3a, several variations of both A28 and A277 structures demonstrated excellent activities. As can be seen from Figure 3b, all molecules produced excellent activities. See also SEQ ID Nos. 2165-2188 in Tables 6a-6b.
Example 6
STUDY PROTOCOL
The following study protocol for the study entitled "mxRNA Leads for Candidate Screening Study in Male human liver-uPA-SCID mice, non-GLP" has been drafted before the animal experiments and studies have been completed and therefore uses the future tense. However, as the study has already been completely carried out, each usage of "future tense" shall be considered as the "past tense" in the following description of the study protocol. See Figure 4.
STUDY OBJECTIVE(S) The objective of this non-GLP study is to evaluate the dose and duration response effect of two selected mxRNA leads for candidate GalNAc-siRNA constructs targeting APOC3 using the human
liver-uPA-SCID mice models. The compounds will be administered subcutaneously and the mice were kept alive for 14-days and 42-days, corresponding to each of the two lead mxRNAs.
Prior to necropsy, plasma and serum will be collected. At necropsy, 3 liver biopsies (2 mm) per animal will be preserved in separate vials in RNAIater, flash frozen, and stored at -80°C. Three more liver biopsies (2mm) will be taken, flash frozen in the same vial, and stored at -80°C. REGULATORY COMPLIANCE
This non-GLP study will not be conducted in accordance with the Food and Drug Administration’s Good Laboratory Practice (GLP) regulations (21 CFR Part 58).
ANIMAL WELFARE COMPLIANCE
The procedures described and performed below will be conducted in accordance with the Guide for the Care and Use of Laboratory Animals, USDA APHIS, Animal Welfare Act and/or in accordance with the Standard Operating Procedures.
This protocol has been reviewed and approved by the Test Facility IACUC Committee.
STUDY SCHEDULE
Acclimatization/Quarantine End Date: > 5 days
Baseline Procedure Date: No baseline procedures Procedure Start Day 0 Date: Tentative: December Waiting on test material.
Necropsy Start: On Day 14- and 42-days post treatment.
In-Life Study Completion: 6 weeks post treatment
Preliminary Report: None required by Sponsor, Data only
Final Report Issued: None required
TEST SYSTEM INFORMATION
Animal Test
Common Name: Mouse
Breed/Class: Rodent - human liver- uPA-SCID mouse
Number of Animals (by gender): 36 Male, all naive
Age Range: 14-19 weeks
Weight Range: Approx. 20 grams
The mice used in this study were human liver-uPA-SCID mice. About 80% of the hepatocytes of each mouse have been replaced by human hepatocytes. The skilled person is aware of ways of producing such mice; where at least some of these ways are shown and referenced in P. Meuleman and G. Leroux-Roels in Antiviral Res. 2008 Dec;80(3):231-8 which is incorporated herein by reference in its entirety.
Acclimation Period:
Duration:
All animals will be acclimated for a minimum period of five (5) days prior to release by the Attending veterinarian, at which time the overall health of the animals will be evaluated. Animals which are not released from acclimation will be treated accordingly and further evaluation will be performed prior to release. All records from the acclimation period will remain in the study file. Animal Identification Method and Location:
Animals will be assigned sequential numbers. The animals will be ear notched to permanently identify each animal. This method involves punching holes or notches in the ear pinna while anesthetized. Alternatively, the animals may have a tattoo placed on their tail. A cage card will also be affixed to each animal cage denoting the animal number, gender, vendor, strain, study director, and study number
STUDY DESIGN
Design Details
This study will have one type of mice, 36 human liver-uPA-SCID mice. Animals will be grouped by treatment type, dosage, and survival period. Each animal will be treated by subcutaneous injection of test material. Groups 1A and 1 B will have four animals receive a control dose of PBS. Groups
2A, 2B, 2C, 3A, 3B, and 3C will receive one dose (10 or 30 mg/kg) with four animals for each dose amount. All animals will be kept alive for 14 or 42 days. See study Table 18 below for details.
Table 18: Study Table
Prior to necropsy, the animals will be deeply anesthetized and a terminal blood draw will be performed through the vena cava. The target blood volume to be collected per animal is as much blood as possible with a minimum of 1 .2 mL which will be split equally between a serum and plasma separation tube. After separation (see section 14.10) the serum will be split equally in two separate vials and plasma will also be separated in two separate vials, see example below.
• 1 .2 mL of blood= 0.6 mL for serum and 0.6 mL for plasma separation tubes
• Serum (0.3 mL after separation)^ 0.15 mL x 2 vials • Plasma (0.3 mL after separation^ 0.15 mL x 2 vials.
Above serum and plasma samples will be labelled, flash frozen and stored at -80°C.
Additional blood collected over the minimum 1 .2 mL volume will be placed in a serum separation tube, processed, serum transferred to a labeled vial, refrigerated at 4°C for rodent lipid analysis.
Note: serum and plasma will be used to measure protein, caution should be taken to avoid hemolysis or clot formation.
At necropsy, three 2 mm biopsy punches will be taken from the left, middle and right liver lobes, placed in separate vials, soaked in RNAIater for 15 minutes, flash frozen and stored at -80°C. Another three 2mm liver biopsies from the left, middle and right liver lobes will be placed into one vial, flash frozen and stored at -80°C. The rest of the liver will be flash frozen and stored in 10mL conical tubes at -80°C.
Alteration of Study Design
Alterations of this protocol may be made as the study progresses. Changes (to the protocol) that have the potential to negatively impact the study or the safety of the study subjects would require IACUC approval.
Animal Inclusion and Exclusion Criteria
Any animals that are deemed unhealthy during veterinary pre-screen will be excluded from the study and replaced with a spare animal if available. For survival animals found dead or moribund after treatment may be replaced via study protocol amendment by a spare animal if available. Animal Disposition
At the end of the study, the animals will be euthanized.
Route of Administration
Subcutaneous injection in the scruff. An injection volume of 200 uL.
RESULTS
Figure 5 highlights the dose-response effect on the percent reduction of APOC3 mRNA in the liver tissues and APOC3 protein levels in the plasma of the animals treated with the different mxRNA constructs (A28(14-4)mF, SEQ ID Nos. 2176, 2188, and A277(12-5), SEQ ID Nos. 2169, 2181) at Day 14 as compared to the control animals.
In addition, the following notes apply to Figure 5:
A28(14-4)mF-10 - A28(14-4)mF 10mg/kg dose group
A28(14-4)mF-30 = A28(14-4)mF 30mg/kg dose group
A277(12-5)-10 = A277(12-5) 10mg/kg dose group
A277(12-5)-30 = A277(12-5) 30mg/kg dose group
Figure 6 highlights the dose -response effect on the mean percent reduction of Triglycerides and Total Cholesterol in the serum of the animals treated with the different APOC-3 targeting mxRNA constructs (A28(14-4)mF, SEQ ID Nos. 2176, 2188, and A277(12-5), SEQ ID Nos. 2169, 2181) at 10 and 30 mg. kg doses at Day 14 as compared to the control animals.
Figures 7a and 7b highlight the duration effect on the mean percent reduction of APOC3 mRNA in liver tissues and APOC3 protein levels in the plasma of the animals treated with the different APOC3-targeting mxRNA (10mg/kg) constructs A28(14-4)mF, SEQ ID Nos. 2176, 2188, and A277(12-5), SEQ ID Nos. 2169, 2181) at Day 14 (Week 2) and at Week 6 as compared to the control animals. Moreover, it is noted with respect to these figures that an outlier from the A277(12-5) group is excluded.
Figures 8a and 8b highlight the duration effect on the mean percent reduction of triglycerides (TGs) and total cholesterol (TC) in the serum of the animals treated with the different APOC3- targeting mxRNA (10mg/kg) constructs (A28(14-4)mF, SEQ ID Nos. 2176, 2188, and A277(12-5), SEQ ID Nos. 2169, 2181) at Day 14 (Week 2) and at Week 6 as compared to the control animals. With respect to these Figures it is noted, that an outlier from the A277(12-5) group is excluded. Summary of Results
A28(14-4)mF APOC3-targeting mxRNA construct (SEQ ID Nos. 2176, 2188):
• 88% suppression of APOC3 mRNA as compared to control group at week 2 that was maintained at 78% on Week 6.
• 90% reduction in plasma APOC3 levels as compared to control group at week 6 that was sustained at 85% on Week 6.
• 32% reduction in serum triglycerides levels as compared to control group at week 2 that increased to 41% reduction on Week 6.
• 43% reduction in serum total cholesterol levels as compared to control group at week 2 that was maintained at 33% on Week 6.
A277(12-5) APOC3-targeting mxRNA construct: (SEQ ID Nos. 2169, 2181)
• 56% suppression of APOC3 mRNA as compared to control group at week 2 that was maintained at 42% on Week 6.
• 83% reduction in plasma APOC3 levels as compared to control group at week 6 that was sustained at 84% on Week 6.
• 8% reduction in serum triglycerides levels as compared to control group at week 2that increased to 52% reduction on Week 6.
• 36% reduction in serum total cholesterol levels as compared to control group at week 2 that was lost on Week 6.
CONCLUSIONS
Construct A28(14-4)mF produced outstanding activity, with 98% of the targeted protein downregulation at 2-week timepoint at 30 mg/kg dosing. Furthermore, construct A28(14-4)mF sustained excellent (protein knockdown) activity at 10 mg/kg dosing both on week 2 and week 6
Example 7
Following the protocol described in detail in Example 6, the effects of compound A28(14-4)mF (also designated STP125G) have been observed over a longer period of time. See Figure 9 for an overview of this extended study, ssss
The corresponding results are displayed in Figure 10 (APOC3 mRNA and protein knockdown) and Figure 11 (triglyceride and total cholesterol).
Several aspects are noteworthy:
• A single dose of 10 mg/kg is sufficient for knockdown of mRNA and protein for a period of six weeks with a rebound becoming slowly apparent towards the end of the study.
• Not only triglycerides, the blood fat primarily considered to be associated with APOC3, is downregulated, but surprisingly also total cholesterol.
• In the assessment of the latter findings, the properties of the mice used for the study have to be properly considered. As shown in Figure 12, an estimated fraction of 20 to 25% of the cells of the humanized liver are sill murine. A28(14-4)mF does not target murine APOC3. As a consequence, the non-silenced murine APOC3 contributes to the observed levels of triglycerides and total cholesterol. In other words, the downregulation of these two blood fats in a (purely) human system is expected to exceed what has been observed in this study.
Example 8
Materials and Methods
Cell Culture:
HepG2 (ATCC cat. 85011430) cells were maintained by biweekly passing in EMEM supplemented with 10% FBS, 20 mM L-glutamine, 10 mM HEPES pH 7.2, 1 mM sodium pyruvate, 1x MEM non- essential amino acids, and 1x Pen/Strep (EMEM complete).
PCSK9 Target identification and duplex preparation:
Targets to PCSK9 were identified by bioinformatic analysis on human PCSK9 mRNA sequence (refseq NM_174936.3). 250 targets were selected for synthesis as asymmetric duplexes (15 sense, 19 antisense). Compounds were dissolved to 50uM in molecular biology grade water and annealed by heating at 95C for 5 minutes followed by gradual cooling to room temperature.
PCSK9 - Primary Screen:
On the day of transfection, HepG2 cells were collected by trypsinization, counted, and seeded in 96 well tissue culture treated plates at 10,000 cells per well in 50uL complete EMEM with 20% FBS. Cells were allowed to rest for 4 hours before transfection with 2 pmoles of each respective PCSK9 duplex in triplicate via RNAIMax (ThermoFisher). In brief, 8 pmoles of each duplex were diluted in 100 uL OptiMEM and mixed gently with 0.8 uL of RNAIMax in 100 uL OptiMEM to make 200 uL total complex. 50 uL of each RNAiMax complexed duplex was added to each respective triplicate well of HepG2 cells for a final mixture of 20 nM duplex in a volume of 10OuL, 50/50 EMEM/OptiMEM at 10% FBS.
72 hours post transfection, cells were harvested and RNA isolated using the PureLink Pro 96 total RNA Purification Kit (ThermoFisher, 12173011 A) according to the manufacturer protocol. Harvested RNA was assayed for PCSK9 expression via Taqman qPCR using the Luna Universal Probe One-Step RT-qPCR Kit (NEB, E3006). Two separate qPCR assays were performed for each sample using two separate PCSK9 Taqman probe sets (Hs00545399_m1-FAM and Hs03037355_m1-FAM) multiplexed with a common GAPDH VIC probe (ThermoFisher, 4326317E). Thermocycling and data acquisition was performed with an Applied Biosystems Quantstudio 3 Real-Time PCR System.
PCSK9 - Secondary Screen:
Based on data from the primary screen, the best performing 27 PCSK9 duplexes were tested in dose curves and IC50 values have been determined. As before, HepG2 cells were collected by
trypsinization and seeded in 96 well tissue culture plates at 10,000 cells per well in 50uL complete EMEM with 20% FBS and allowed to rest for 4 hours. Transfection complexes were formed by gently mixing 36 pmoles of each duplex in 180 uL OptiMEM with 2.16 uL RNAiMax in 180 uL OptiMEM to make 360 uL total complex. A two fold dilution series was then performed with basal OptiMEM. 50 uL of each dilution was added to respective triplicates of HepG2 cells to make a final dilution series of 50 nM down to 0.32 nM in a volume of 100uL, 50/50 EMEM/OptiMEM at 10% FBS.
72 hours post transfection, cells were harvested and RNA isolated using the PureLink Pro 96 total RNA Purification Kit (ThermoFisher, 12173011 A) according to the manufacturer protocol. Harvested RNA was assayed for PCSK9 expression via Taqman qPCR using the Luna Universal Probe One-Step RT-qPCR Kit (NEB, E3006). A single qPCR assay was performed for each sample using PCSK9 Taqman probe set Hs00545399_m1-FAM multiplexed with a common GAPDH VIC probe (ThermoFisher, 4326317E). Thermocycling and data acquisition was performed with an Applied Biosystems Quantstudio 3 Real-Time PCR System. Example s
Results obtained by performing methods of Example 8
Figure 13 shows the results (% knockdown) of the primary screen.
Table 19 below and Figure 14 show IC50 values (in nM) for the 27 constructs selected in accordance with Example 8.
The ICso data in the single- to double-digit nanomolar range demonstrate outstanding performance of numerous constructs as described herein.
Example 10
Optimized double stranded constructs Full definitions of the constructs are given in Table 20 below. AS = antisense strand (also referred as first region herein); SS = sense strand (also referred to as second region herein). Notations are explained further above.
TABLE 20
Performance data are shown in Figures 15 and 16. Comparison with an inclisiran-type molecule (Figure 16) shows outstanding performance of the constructs. Indeed, performance of two constructs is very similar to a 3xGalNAc (toothbrush) derivative of inclisiran.
Example 11 Optimized hairpin molecules (mxRNAs)
Full definitions of the molecules are given in Table 21 below.
Performance data are shown in Figure 17.
Example 12
Materials and Methods
Cell Culture:
HepG2 (ATCC cat. 85011430) cells were maintained by biweekly passing in EMEM supplemented with 10% FBS, 20 mM L-glutamine, 10 mM HEPES pH 7.2, 1 mM sodium pyruvate, 1 x MEM non- essential amino acids, and 1x Pen/Strep (EMEM complete).
PCSK9 and APOC3 Combo identification and compound preparation:
Combination compounds with the best performing PCSK9 and APOC3 sequences were designed and synthesized as 49 candidates selected from Tables 14a-14b above, and shown in Tables 22a and 22b belows. Compounds were dissolved to 50uM in molecular biology grade water and annealed by heating at 95C for 5 minutes followed by gradual cooling to room temperature. APOC3/PCSK9 Combo - Screen:
Based on data from screens with PCSK9 and APOC3 duplexes, the best performing APOC3 and PCSK9 sequences were combined into 49 candidates and tested in dose curves. HepG2 cells were collected by trypsinization and seeded in 96 well tissue culture plates at 10,000 cells per well in 50uL complete EMEM with 20% FBS and allowed to rest for 4 hours. Transfection complexes were formed by gently mixing 36 pmoles of each duplex in 180 uL OptiMEM with 2.16 uL RNAiMax in 180 uL OptiMEM to make 360 uL total complex. A two fold dilution series was then performed with basal OptiMEM. 50 uL of each dilution was added to respective triplicates of HepG2 cells to make a final dilution series of 50 nM down to 0.32 nM in a volume of 10OuL, 50/50 EMEM/OptiMEM at 10% FBS.
72 hours post transfection, cells were harvested and RNA isolated using the PureLink Pro 96 total RNA Purification Kit (ThermoFisher, 1217301 1 A) according to the manufacturer protocol.
Harvested RNA was assayed for both PCSK9 and APOC3 expression via Taqman qPCR using the Luna Universal Probe One-Step RT-qPCR Kit (NEB, E3006). Two separate qPCR assays were performed for each sample using an either an APOC3 Taqman probe (Hs00906501_g1- FAM) or PCSK9 probe (Hs00906501_g1-FAM) multiplexed with a common GAPDH VIC probe (ThermoFisher, 4326317E). Thermocycling and data acquisition was performed with an Applied Biosystems Quantstudio 3 Real-Time PCR System.
Example 13
Results
Tables 22a and 22b below show IC50 values (in nM) for specific constructs selected in accordance with the Examples. Table 22a shows PCSK9 knock-down, and Table 22b shows APOC3 knockdown. The numbers after "SR1-" in the first column correspond to the construct numbering in Tables 14a and 14b above.
Table 22a:
Table 22b:
The ICso data in the single- to double-digit nanomolar range demonstrate outstanding performance of numerous constructs. Of note, either target of the double-targeting constructs is knocked down by each of a multitude of constructs.
Example 14
Dose Response Study evaluating Leads for Candidate targeting human Anqiotensinoqen (mxRNA) in humanized liver-uPA-SCID mice (PXB) model. non-GLP
Materials and Methods
1. STUDY OBJECTIVE(S)
The objective of this non-GLP study is to evaluate, in humanized liver-uPA-SCID (PXB) mice, the dose response of GalNAc conjugated human Angiotensinogen (AGT) targeting mxRNA constructs. The compound(s) will be administered subcutaneously, and the mice will be kept alive for up to 14 days.
2. TEST SYSTEM INFORMATION
2.1. Animal Test
2.1.1. Common Name: Mouse
2.1.2. Breed/Class: Rodent - Mouse PXB
2.1.3. Number of Animals (by gender): 32 Male PXB all naive
2.1.4. Age Range: 14-19 weeks for PXB mice,
2.1 .5. Weight Range: Approx. 20 grams for all mice
2.2. Acclimation Period:
2.2.1. Duration:
All animals will be acclimated for a minimum period of five (5) days prior to release by the Attending veterinarian, at which time the overall health of the animals will be evaluated.
3. STUDY DESIGN
This study will have one type of mice, 32 PXB. Animals will be grouped by treatment type, dosage, and survival period. Each animal will be treated by subcutaneous injection of test material.
• Group 1 A will have four animals and receive a control dose of PBS. • Group 2A, 2B and 2C will have four/five animals and receive a single dose of
(AGT_27) at 5mg/kg, 10mg/kg and 30mg/kg, respectively.
• Group 3A, 3B and 3C will have four/five animals and receive a single dose of (AGT_52) at 5mg/kg, 10mg/kg, and 30mg/kg, respectively. Animals will be kept alive for 14 days. See Study Table 23 for details.
At necropsy, three 2 mm biopsy punches will be taken from the left, middle and right liver lobes, placed in separate vials, soaked in RNA/afer for 15 minutes, flash frozen and stored at -80°C. Another three 2mm liver biopsies from the left, middle and right liver lobes will be placed into one vial, flash frozen and stored at -80°C. The rest of the liver will be flash frozen and stored in 10mL conical tubes at -80°C.
Table 23: Study Table
3.1. Test Drug 1 :
3.1.1. Identification: AGT_27
3.1.2. Manufacturer: Sirnaomics
3.1.3. Description: GalNAc-mxRNA targeting human angiotensinogen
(AGT) mRNA
3.1.4. Lot/Bat ch Number: Will be recorded on study materials form.
3.1.5. Expiration Date: Will be recorded on study materials form.
3.1.6. Storage Temperature: 4°C
3.1.7. Bio-Hazard Status: None
3.1.8. MSDS*: TBD
3.1.9. Appearance: Clear Liquid
3.1.10. Dose Information: See Table 1
3.1.11. Residual Test Article Storage: None
3.2. Test Drug 2:
3.2.1. Identification: AGT_52
3.2.2. Manufacturer: Sirnaomics
3.2.3. Description: GalNAc-mxRNA targeting human angiotensinogen
(AGT) mRNA
3.2.4. Lot/Batch Number: Will be recorded on study materials form.
3.2.5. Expiration Date: Will be recorded on study materials form.
3.2.6. Storage Temperature: 4°C
3.2.7. Bio-Hazard Status: None
3.2.8. MSDS*: TBD
3.2.9. Appearance: Clear Liquid
3.2.10. Dose Information: See Table 1
3.2.11. Residual Test Article Storage: None
Reference is made to Figure 18 for a schematic overview of this study.
Results
Results are shown in Figure 19. In particular, Figure 19 demonstrates that both molecules tested cause significant and dose-dependent knockdown of both mRNA as well as protein levels. In view of the better performance of AGT-27, this molecule is further investigated in the following Example.
Example 15
Evaluation of Duration Effect of Human AGT targeting mxRNA, in the humanized liver-uPA-SCID mice (PXB) model. non-GLP
Materials and Methods
1. STUDY OBJECTIVE(S)
The objective of this non-GLP study is to evaluate, in humanized liver-uPA-SCID (PXB) mice, the duration effect of AGT-27A (SEQ ID No. 3604), human AGT (Angiotensin) targeting mxRNA. The compound(s) will be administered subcutaneously, and the mice will be kept alive for up to 84 days.
2. TEST SYSTEM INFORMATION
2.1. Animal Test
2.1.1. Common Name: Mouse
2.1.2. Breed/Class: Rodent - Mouse PXB
2.1.3. Number of Animals (by gender): 40 Male PXB all naive
2.1.4. Age Range: 14-19 weeks for PXB mice,
2.1 .5. Weight Range: Approx. 20 grams for all mice
2.2. Acclimation Period:
2.2.1. Duration:
All animals will be acclimated for a minimum period of seven (7) days prior to release by the Attending veterinarian, at which time the overall health of the animals will be evaluated.
3. STUDY DESIGN
3.1. Design Details
This study will have one type of mice, 40 PXB. Animals will be grouped by treatment type, dosage, and survival period. Each animal will be treated by subcutaneous injection of test material.
• Group 1A, 1 B, 1 C, and 1 D will have five animals and receive a single control dose of PBS.
• Group 2A, 2B, 2C, and 2D will have five animals and receive a single dose of AGT-27A at 30 mg/kg.
Animals will be kept alive for 14, 28, 56, and 84 days. See Table 24 for details.
Prior to necropsy, the animals will be deeply anesthetized, and a terminal blood draw will be performed through the vena cava. Blood volume will be collected in a plasma separation tube.
Note: plasma will be used to measure protein, caution should be taken to avoid hemolysis or clot formation.
At necropsy, three 2 mm biopsy punches will be taken from the left, middle and right liver lobes, placed in separate vials, soaked in RNA/ater for 15 minutes, flash frozen and stored at -80°C. Another three 2mm liver biopsies from the left, middle and right liver lobes will be placed into one vial, flash frozen and stored at -80°C. The rest of the liver will be flash frozen and stored in 10mL conical tubes at -80°C.
Table 24: Study Table
3.2. Test Drug 1 :
3.2.1. Identification: AGT-27A
3.2.2. Manufacturer: Sirnaomics
3.2.3. Description: GalNAc-mxRNA targeting human AGT (angiotensin) mRNA
3.2.4. Lot/Batch Number: Will be recorded on study materials form.
3.2.5. Expiration Date: Will be recorded on study materials form.
3.2.6. Storage Temperature: 4°C
3.2.7. Bio-Hazard Status: None
3.2.8. SDS*: TBD 3.2.9. Appearance: Clear Liquid
3.2.10. Dose Information: See Table t
3.2.11. Residual Test Article Storage: None
Reference is also made to Figure 20 which provides a schematic overview of the study.
Results Results are shown in Figure 21 . It is apparent that after a single administration a long-lasting effect on both mRNA levels in liver and protein levels in plasma ensues.
Claims
1 . An oligomeric compound capable of inhibiting expression of angiotensinogen (AGT), comprising at least a first region of linked nucleosides having at least a first nucleobase sequence that is at least partially complementary to at least a portion of RNA transcribed from an AGT gene, wherein said first nucleobase sequence is selected from the following sequences, or a portion thereof: sequences of Table 1a (SEQ ID NOs: 1 to 100), wherein said portion optionally has a length of at least 18 nucleosides.
2. The oligomeric compound according to claim 1 , further comprising at least a second region of linked nucleosides having at least a second nucleobase sequence that is at least partially complementary to said first nucleobase sequence and is selected from the following sequences, or a portion thereof: sequences of Table 1 b (SEQ ID NOs: 101 to 200), wherein said portion optionally has a length of at least 8, 9, 10 or 11 nucleosides.
3. The oligomeric compound according to claim 1 or 2, wherein said first nucleobase sequence is selected from the following sequences, or a portion thereof: SEQ ID NOs: 27, 44, 41 , 97, 90, 62, 52, 93, 49, 73, 18, 37, 56, 100, 40, 75, 30, 42, 81 , 17, 34, 53, 29, 26, 74, 94, 14, 3, 7 and 2.
4. The oligomeric compound according to claim 3, wherein said second nucleobase sequence is selected from the following sequences, or a portion thereof: SEQ ID NOs: 127, 144, 141 , 197, 190, 162, 152, 193, 149, 173, 118, 137, 156, 200, 140, 175, 130, 142, 181 , 117, 134, 153, 129, 126, 174, 194, 114, 103, 107 and 102.
5. The oligomeric compound according to any of claims 1 to 4, wherein said first nucleobase sequence is selected from the following sequences, or a portion thereof: SEQ ID NOs: 27, 52, 56, 62, 75, and 93.
6. The oligomeric compound according to claim 5, wherein said second nucleobase sequence is selected from the following sequences, or a portion thereof: SEQ ID NOs: 127, 152, 156, 162, 175, and 193.
7. The oligomeric compound according to any of claims 1 to 6, wherein said first region of linked nucleosides consists essentially of 18 to 35, 18 to 20, 18 or 19, or 19 linked nucleosides.
8. The oligomeric compound according to any of claims 2 to 7, wherein said second region of linked nucleosides consists essentially of 10 to 35, 10 to 20, 10 to 16, 10 to 15, or 13, 14 or 15 linked nucleosides.
9. The oligomeric compound according to any of claims 2 to 8, comprising at least one complementary duplex region that comprises at least a portion of said first region of linked nucleosides directly or indirectly linked to at least a portion of said second region of linked nucleosides, wherein optionally said duplex region has a length of 10 to 19, 12 to 19, 12 to 15, or 14 or 15, base pairs, wherein optionally there is one mismatch within said duplex region.
10. The oligomeric compound according to claim 9, wherein each of said first and second regions of linked nucleosides has a 5’ to 3’ directionality thereby defining 5’ and 3’ regions respectively thereof.
11 . The oligomeric compound according to claim 10, wherein the 5’ region of said first region of linked nucleosides is directly or indirectly linked to the 3’ region of said second region of linked nucleosides, optionally by complementary base pairing, wherein optionally the 5' terminal nucleoside of said first nucleoside region base pairs with the 3' terminal nucleoside of said second nucleoside region.
12. The oligomeric compound according to claim 10 or 11 , wherein the 3’ region of said first region of linked nucleosides is directly or indirectly linked to the 5’ region of said second region of linked nucleosides, wherein optionally said first nucleoside region is directly and covalently linked to said second nucleoside region such as by a phosphate, a phosphorothioate, or a phosphorodithioate, and wherein optionally a 3' terminal nucleoside of the first region of linked nucleosides is directly and covalently linked to a 5' terminal nucleoside of said second region of linked nucleosides by a phosphate, a phosphorothioate, or a phosphorodithioate.
13. The oligomeric compound according to any of claims 1 to 12, further comprising one or more ligands.
14. The oligomeric compound according to claim 13, wherein said one or more ligands, in particular two or more or three ligands, are conjugated to said second region of linked nucleosides and/or said first region of linked nucleosides.
15. The oligomeric compound according to claim 14, as dependent on claim 10, wherein said one or more ligands are conjugated at the 3' region, optionally at the 3' terminal nucleoside of the second region of linked nucleosides and/or of the first region of linked nucleosides, and/or to the 5' terminal nucleoside of said second region of linked nucleosides.
16. The oligomeric compound according to any of claims 13 to 15, wherein said one or more ligands are any cell directing moiety, such as lipids, carbohydrates, aptamers, vitamins and I or peptides that bind cellular membrane or a specific target on cellular surface.
17. The oligomeric compound according to claim 16, wherein said one or more ligands comprise one or more carbohydrates.
18. The oligomeric compound according to claim 17, wherein said one or more carbohydrates can be a monosaccharide, disaccharide, trisaccharide, tetrasaccharide, oligosaccharide or polysaccharide.
19. The oligomeric compound according to claim 18, wherein said one or more carbohydrates comprise or consist of one or more hexose moieties.
20. The oligomeric compound according to claim 19, wherein said one or more hexose moieties are one or more galactose moieties, one or more lactose moieties, one or more N-Acetyl- Galactosamine moieties, and I or one or more mannose moieties.
21 . The oligomeric compound according to claim 20, wherein said one or more carbohydrates comprise one or more N-Acetyl-Galactosamine moieties.
22. The oligomeric compound according to claim 21 , comprising two or more N-Acetyl- Galactosamine moieties, optionally three.
23. The oligomeric compound according to any of claims 13 to 22, wherein said one or more ligands are attached to said oligomeric compound, optionally to the second region of linked nucleosides thereof, in a linear configuration, or in a branched configuration.
24. The oligomeric compound according to claim 23, wherein said one or more ligands are attached to said oligomeric compound as a biantennary or triantennary configuration.
25. The oligomeric compound according to any one of claims 1 to 24, wherein said compound consists of said first region of linked nucleosides and said second region of linked nucleosides.
26. The oligomeric compound according to any one of claims 1 to 24, wherein there is an intervening third region of linked nucleosides between said first and said second region.
27. The oligomeric compound according to claim 26, wherein said oligomeric compound comprises or consists of a single strand having or consisting of said first, said third, and said second nucleoside regions, wherein at least a portion of said first nucleoside region is directly or indirectly linked to at least a portion of said second nucleoside region so as to form said at least partially complementary duplex region.
28. The oligomeric compound according to any one of claim 9 to 25, wherein said oligomeric compound comprises or consists of a single strand having or consisting of said first and second regions of linked nucleosides, wherein at least a portion of said first region of linked nucleosides is directly or indirectly linked to at least a portion of said second region of linked nucleosides so as to form said at least partially complementary duplex region.
29. The oligomeric compound according to claim 28, wherein said first and said second nucleoside regions are directly adjacent on said single strand.
30. The oligomeric compound according to claim 28 or 29, wherein said first nucleoside region has a greater number of linked nucleosides compared to the second nucleoside region, wherein optionally a ratio between a total number of linked nucleosides of the first nucleoside region and a total number of linked nucleosides of the second nucleoside region ranges from about 19/15 to about 19/8, or from about 18/15 to about 18/8; and/or a percentage of the total number of linked nucleosides of the first nucleoside region relative to the total number of nucleosides of the oligomeric compound ranges from about to about 55% to about 60%.
31 . The oligomeric compound of claim 30, whereby the additional number of linked nucleosides of the first nucleoside region form a hairpin loop linking the first and second regions of linked nucleosides, wherein optionally a part of the first nucleobase sequence being complementary RNA transcribed from an AGT gene forms the hairpin loop, wherein the loop comprises 2 to 5, or 4 or 5, nucleosides.
32. The oligomeric compound according to any one of the preceding claims, wherein said single strand is selected from Table 2, in particular selected from the group consisting of SEQ IDs NO: 227, 252, 256, 262, 275 and 293, wherein optionally the 5' terminal nucleoside of the first region of linked nucleosides is substituted by a U as the nucleobase, and the 5' terminal nucleoside of the second region of linked nucleosides is substituted by an A as the nucleobase.
33. The oligomeric compound according to claim 32, wherein said single strand is selected from the group consisting of SEQ ID NOs: 527, 552, 556, 562, 575, 593, 3604 and 3605 wherein optionally the 5' terminal nucleoside of the first region of linked nucleosides is substituted by an U as the nucleobase, and the 5' terminal nucleoside of the second region of linked nucleosides is substituted by an A as the nucleobase.
34. The oligomeric compound according to claim 33, as dependent on claim 10, whereby said hairpin loop is present at the 3' region of said first region of linked nucleosides, wherein optionally one, two or more 3' terminal nucleosides of the first nucleobase sequence, to the extent the nucleobases of said one, two or more 3' terminal nucleosides permit, fold back and form or contribute to the second region of linked nucleoside.
35. The oligomeric compound of claim 26 or 27, wherein said third nucleoside region and optionally a 3'-terminal portion, optionally consisting of 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 linked nucleosides, of said first nucleoside region and/or a 5'-terminal portion, optionally consisting of 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 linked nucleosides, of said second nucleoside region form a hairpin loop.
36. The oligomeric compound according to any one of claims 29 to 31 , wherein said hairpin loop comprises 1 to 8, 2 to 7, 3 to 6, or 4 or 5 linked nucleosides.
37. The oligomeric compound according to any of claims 1 to 36, comprising internucleoside linkages and wherein at least one internucleoside linkage is a modified internucleoside linkage.
38. The oligomeric compound according to claim 37, wherein said modified internucleoside linkage is a phosphorothioate or phosphorodithioate internucleoside linkage.
39. The oligomeric compound according to claim 38, comprising 1 to 16 phosphorothioate or phosphorodithioate internucleoside linkages.
40. The oligomeric compound according to claim 39, comprising 7, 8, 9 or 10 phosphorothioate or phosphorodithioate internucleoside linkages.
41 . The oligomeric compound according to any of claims 38 to 40, as dependent on claim 10, comprising one or more phosphorothioate or phosphorodithioate internucleoside linkages at the 5’ region of the first region of linked nucleosides.
42. The oligomeric compound according to any of claims 38 to 41 , as dependent on claim 10, comprising one or more phosphorothioate or phosphorodithioate internucleoside linkages at the 5’ region of the second region of linked nucleosides, wherein optionally, the oligomeric compound comprises three phosphorothioate internucleoside linkages at three adjacent nucleosides at said 5' region.
43. The oligomeric compound according to any of claims 38 to 42, as dependent on any one of claims 30 to 32, comprising phosphorothioate or phosphorodithioate internucleoside linkages between at least two, at least three, at least four, or at least five, adjacent nucleosides of the hairpin loop, dependent on the number of nucleosides present in the hairpin loop.
44. The oligomeric compound according to claim 43, comprising a phosphorothioate or phosphorodithioate internucleoside linkage between each adjacent nucleoside that is present in said hairpin loop.
45. The oligomeric compound according to any of claims 1 to 44, wherein at least one nucleoside comprises a modified sugar.
46. The oligomeric compound according to claim 45, wherein said modified sugar is selected from 2' modified sugars, a conformationally restricted nucleoside (CRN) sugar such as locked nucleic acid (LNA) sugar, (S)-constrained ethyl bicyclic nucleic acid, and constrained ethyl (cEt) sugar, tricyclo-DNA, morpholino, unlocked nucleic acid (UNA) sugar, glycol nucleic acid (GNA), D- hexitol nucleic acid (HNA), and cyclohexene nucleic acid (CeNA).
47. The oligomeric compound according to claim 46, wherein said 2' modified sugar is selected from 2'-O-alkyl modified sugar, 2'-O-methyl modified sugar, 2'-0-methoxyethyl modified sugar, 2'-O-allyl modified sugar, 2'-C-allyl modified sugar, 2'-deoxy modified sugar such as 2'- deoxy ribose, 2'-F modified sugar, 2'-arabino-fluoro modified sugar, 2'-O-benzyl modified sugar, and 2'-O-methyl-4-pyridine modified sugar.
48. The oligomeric compound according to claim 47, wherein at least one modified sugar is a 2'-O-methyl modified sugar.
49. The oligomeric compound according to claim 47 or 48, wherein at least one modified sugar is a 2'-F modified sugar and, optionally, at most 16 or 17 sugars are 2'-F modified sugars.
50. The oligomeric compound of claim 48 or 49, wherein the sugar is ribose.
51 . The oligomeric compound according to any of claims 48 to 50, as dependent on claim 10, wherein sugars of the nucleosides at any of positions 2 and 14 downstream from the first nucleoside of the 5’ region of the first region of linked nucleosides, do not contain 2'-O-methyl modifications.
52. The oligomeric compound of any one of claims 48 to 51 , wherein the 3' terminal position of the second region of linked nucleosides does not contain a 2'-O-methyl modification.
53. The oligomeric compound according to any one of claims 48 to 52, wherein sugars of the nucleosides at any of positions 2 and 14 downstream from the first nucleoside of the 5’ region of the first region of linked nucleosides, contain 2'-F modifications.
54. The oligomeric compound according to any of claims 52 to 53, wherein sugars of the nucleosides of the second region of linked nucleosides, that correspond in position to any of the nucleosides of the first region of linked nucleosides at any of positions 11 to 13 downstream from the first nucleoside of the 5’ region of the first region of linked nucleosides, contain 2'-F modifications.
55. The oligomeric compound of claim 53 or 54, wherein the 3' terminal nucleoside of the second region of linked nucleosides contains a 2'-F modification.
56. The oligomeric compound according to any of claims 52 to 55, as dependent on claim 10, wherein one or more of the odd numbered nucleosides starting from the 5’ region of the first region of linked nucleosides are modified, and / or wherein one or more of the even numbered nucleosides starting from the 5’ region of the first region of linked nucleosides are modified, wherein typically the modification of the even numbered nucleosides is a second modification that is different from the modification of odd numbered nucleosides.
57. The oligomeric compound according to claim 56, wherein one or more of the odd numbered nucleosides starting from the 3’ region of the second region of linked nucleosides are modified by a modification that is different from the modification of odd numbered nucleosides of the first region of linked nucleosides.
58. The oligomeric compound according to claim 56 or 57, wherein one or more of the even numbered nucleosides starting from the 3’ region of the second region of linked nucleosides are modified by a modification that is different from the modification of even numbered nucleosides of the first region of linked nucleoside according to claim 51 .
59. The oligomeric compound according to any of claims 56 to 58, wherein at least one or more of the modified even numbered nucleosides of the first region of linked nucleosides is adjacent to at least one or more of the differently modified odd numbered nucleosides of the first nucleoside region.
60. The oligomeric compound according to any of claims 56 to 59, wherein at least one or more of the modified even numbered nucleosides of the second nucleoside region is adjacent to at least one or more of the differently modified odd numbered nucleosides of the second region of linked nucleosides.
61 . The oligomeric compound according to any of claims 56 to 60, wherein sugars of one or more of the odd numbered nucleosides starting from the 5’ region of the first region of nucleosides are 2'-O-methyl modified sugars.
62. The oligomeric compound according to any of claims 56 to 61 , wherein one or more of the even numbered nucleosides starting from the 3’ region of the first region of linked nucleosides are 2'-F modified sugars.
63. The oligomeric compound according to any of claims 56 to 62, wherein sugars of one or more of the odd numbered nucleosides starting from the 5’ region of the second region of linked nucleosides are 2'-0 methyl modified sugars.
64. The oligomeric compound according to any of claims 56 to 63, wherein one or more of the even numbered nucleosides starting from the 5’ region of the second region of linked nucleosides are 2'-F modified sugars.
65. The oligomeric compound according to any of claims 45 to 64, wherein sugars of a plurality of adjacent nucleosides of the first nucleoside region are modified by a common or different modification.
66. The oligomeric compound according to any of claims 45 to 65, wherein sugars of a plurality of adjacent nucleosides of the second nucleoside region are modified by a common or different modification.
67. The oligomeric compound according to any of claims 56 to 66, as dependent on any one of claims 30 to 33, wherein sugars of a plurality of adjacent nucleosides of the hairpin loop are modified by a common or different modification.
68. The oligomeric compound according to any of claims 65 to 67, wherein said common modification is a 2'-F modified sugar.
69. The oligomeric compound according to any of claims 65 to 67, wherein said common modification is a 2'-O-methyl modified sugar.
70. The oligomeric compound according to claim 69, wherein said plurality of adjacent 2'-O- methyl modified sugars are present in at least eight adjacent nucleosides of said first and / or second nucleoside regions.
71 . The oligomeric compound according to claim 70, wherein said plurality of adjacent 2'-O- methyl modified sugars are present in three or four adjacent nucleosides of said hairpin loop.
72. The oligomeric compound according to claim 46, as dependent on any one of claims 31 to 35, wherein said hairpin loop comprises at least one nucleoside having a modified sugar.
73. The oligomeric compound according to claim 72, wherein said at least one nucleoside is adjacent to a nucleoside with a differently modified sugar, wherein optionally all adjacent nucleosides in the hairpin loop have a differently modified sugar.
74. The oligomeric compound according to claim 73, wherein said modified sugar is a 2'-O- methyl modified sugar, and said differently modified sugar is a 2'-F modified sugar.
75. The oligomeric compound according to any of claims 1 to 74, wherein one or more nucleosides of the first region of linked nucleosides and I or the second region of linked nucleosides is an inverted nucleoside and is attached to an adjacent nucleoside via the 3' carbon of its sugar and the 3' carbon of the sugar of the adjacent nucleoside, and I or one or more nucleosides of the first region of linked nucleosides and I or the second region of linked nucleosides is an inverted nucleoside and is attached to an adjacent nucleoside via the 5' carbon of its sugar and the 5' carbon of the sugar of the adjacent nucleoside.
76. The oligomeric compound according to any of claims 1 to 75, which is blunt ended.
77. The oligomeric compound according to any of claims 1 to 76, wherein either the first or second nucleoside region has an overhang.
78. The oligomeric compound according to any one of claims 1 to 77, wherein said first region is selected from the group consisting of SEQ ID NOs: 327, 352, 356, 362, 375, 393, and a portion thereof.
79. The oligomeric compound according to any one of claims 1 to 79, wherein said second region is selected from the group consisting of, SEQ ID NOs: 427, 452, 456, 462, 475, 493, and a portion thereof, wherein said second region optionally has a length of 14 nucleosides.
80. The oligomeric compound according to any one of claims 1 to 80, wherein the oligomeric compound has a total length of about 25 to about 37 nucleosides, in particular about 33 or about 34 nucleosides.
81 . The oligomeric compound according to any one of claims 10 to 80, wherein a terminal nucleoside at a 5' position of said first region has a nucleobase selected from the group consisting of A, U, G and C, optionally U, and, wherein optionally, a terminal nucleoside at a 3' position of said second region is substituted by a base being complementary to the base at the 5' position of said first region, optionally A.
82. A nucleic acid construct comprising at least:
(a) a first nucleic acid portion that is at least partially complementary to at least a first portion of an RNA, which is transcribed from an AGT gene;
(b) a second nucleic acid portion that is at least partially complementary to at least a second portion of an RNA, which is transcribed from an AGT gene or a different target gene, the second portion being different from the first portion;
(c) a third nucleic acid portion that is at least partially complementary to said first nucleic acid portion of (a), so as to form a first nucleic acid duplex region therewith;
(d) a fourth nucleic acid portion that is at least partially complementary to said second nucleic acid portion of (b), so as to form a second nucleic acid duplex region therewith.
83. The construct according to claim 82, wherein said construct is designed such that subsequent to in vivo administration said construct disassembles to yield at least first and second discrete nucleic acid targeting molecules that respectively target said RNA portions transcribed from said target genes of (a) and (b); whereby (I) said first nucleic acid targeting molecule is capable of modulating expression of said target gene of (a), and comprises, or is derived from, at least said first nucleic acid portion of (a), and (ii) said second nucleic acid targeting molecule is capable of modulating expression of said target gene of (b), and comprises, or is derived from, said second nucleic acid portion of (b).
84. The construct according to claim 82 or 83, wherein said construct is designed to disassemble such that said first and second discrete nucleic acid targeting molecules are respectively processed by independent RNAi-induced silencing complexes.
85. The construct according to any one of claims 82 to 84, further comprising at least one labile functionality such that subsequent to in vivo administration said construct is cleaved so as to yield said at least first and second discrete nucleic acid targeting molecules.
86. The construct according to claim 85, wherein said labile functionality comprises one or more unmodified nucleotides.
87. The construct according to claim 86, wherein said one or more unmodified nucleotides of said labile functionality represent one or more cleavage positions within said construct whereby subsequent to in vivo administration said construct is cleaved at said one or more cleavage positions so as to yield said at least first and second discrete nucleic acid targeting molecules.
88. The construct according to claim 87, wherein said cleavage positions are respectively located within the construct so that subsequent to cleavage said first discrete nucleic acid targeting molecule comprises, or is derived from, said first nucleic acid duplex region, and said second discrete nucleic acid targeting molecule comprises, or is derived from, said second nucleic acid duplex region.
89. The construct according to claim 88, wherein said first discrete nucleic acid targeting molecule comprises or consists of said first nucleic acid portion of (a) and said third nucleic acid portion of (c), and/or said second discrete nucleic acid targeting molecule comprises or consists of said second nucleic acid portion of (b) and said fourth nucleic acid portion of (d).
90. The construct according to any one of claims 82 to 89, wherein
(a) said first nucleic acid portion has a nucleobase sequence selected from the group consisting of SEQ ID NOs: 1 to 100;
(b) said second nucleic acid portion has a nucleobase sequence selected from the group consisting of SEQ ID NOs: 1 to 100;
(c) said third nucleic acid portion has a nucleobase sequence selected from the group consisting of SEQ ID NOs: 101 to 200; and/or
(d) said fourth nucleic acid portion has a nucleobase sequence selected from the group consisting of SEQ ID NOs: 101 to 200. wherein said third and fourth nucleobase sequences, to the extent they have a length of 14 nucleobases, may be shorter by one, two or three nucleobases, wherein optionally the 5'-terminal nucleobase(s) is/are absent.
91 . The construct according to any of claims 82 to 90, wherein said first nucleic acid portion of (a) is directly or indirectly linked to said fourth nucleic acid portion of (d) as a primary structure.
92. The construct according to claim 91 , wherein said first and said fourth nucleic acid portions have the nucleobase sequences selected from the group consisting of SEQ ID NOs: 27 and 127, 44 and 144, 41 and 141 , 97 and 197, 90 and 190, 62 and 162, 52 and 152, 93 and 193, 49 and
149, 73 and 173, 18 and 118, 37 and 137, 56 and 156, 100 and 200, 40 and 140, 75 and 175, 30 and 130, 42 and 142, 81 and 181 , 17 and 117, 34 and 134, 53 and 153, 29 and 129, 26 and 126, 74 and 174, 94 and 194, 14 and 114, 3 and 103, 7 and 107, and 2 and 102, respectively, wherein optionally said sequences of SEQ ID NOs: 27, 52, 56, 62, 75, and 93 may be shorter by one, two, three or four nucleobases, and wherein optionally the 5'-terminal nucleobase(s) is/are absent.
93. The construct according to any of claims 82 to 92, wherein said second nucleic acid portion of (b) is directly or indirectly linked to said third nucleic acid portion of (c) as a primary structure.
94. The construct according to claim 92 or 93, wherein said second and third nucleic acid portions have the nucleobase sequences selected from the group consisting of SEQ ID NOs: 27 and 127, 44 and 144, 41 and 141 , 97 and 197, 90 and 190, 62 and 162, 52 and 152, 93 and 193, 49 and 149, 73 and 173, 18 and 118, 37 and 137, 56 and 156, 100 and 200, 40 and 140, 75 and 175, 30 and 130, 42 and 142, 81 and 181 , 17 and 117, 34 and 134, 53 and 153, 29 and 129, 26 and 126, 74 and 174, 94 and 194, 14 and 114, 3 and 103, 7 and 107, and 2 and 102, respectively, wherein optionally said sequences of SEQ ID NOs: 27, 52, 56, 62, 75, and 93 may be shorter by one, two, three or four nucleobases, and wherein optionally the 5'-terminal nucleobase(s) is/are absent.
95. The construct according to any of claims 82 to 90, 91 or 93, that further comprises 1 to 8 additional nucleic acid portions that are respectively at least partially complementary to an additional 1 to 8 portions of RNA transcribed from one or more target genes, which target genes may be the same or different to each other, and I or the same or different to the target genes defined in (a) and / or (b), and wherein each of the 1 to 8 additional nucleic acid portions
respectively form additional duplex regions with respective passenger nucleic acid portions that are respectively at least partially complementary therewith.
96. The construct according to claim 95, wherein said second nucleic acid portion of (b), and said 1 to 8 additional nucleic acid portions, are directly or indirectly linked to selected passenger nucleic acid portions as respective primary structures.
97. The construct according to any of claims 91 , 93 or 96, wherein said direct or indirect linking represents either (i) an internucleotide bond, (ii) an internucleotide nick, or (iii) a nucleic acid linker portion of 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides, said nucleic acid linker optionally being single stranded.
98. The construct according to claim 97 (i), wherein said linking is direct, thereby giving rise to (a) contiguous strand(s).
99. The construct of any one of claims 82 to 99, especially of claim 97 (i), wherein there exists some complementarity between the first nucleic acid portion of (a) and the second nucleic acid portion of (b), or the third nucleic acid portion of (c) and the fourth nucleic acid portion of (d).
100. The construct according to claim 99, wherein said complementarity
(i) is/are 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10, or 2, 3, 4 or 5 base pairs; and/or
(ii) is between the first nucleic acid portion of (a) and the second nucleic acid portion of (b).
101 . The construct according to claim 97 (i) to 100, as dependent on claim 86, wherein said internucleotide bond involves at least one of said one or more unmodified nucleotides, wherein optionally cleavage occurs at the 3' position of (at least one of) said unmodified nucleotide(s).
102. The construct according to any of claims 82 to 101 , wherein said first nucleic acid portion of (a), and I or said second nucleic acid portion of (b), and I or said third nucleic acid portion of (c), and I or said fourth nucleic acid portion of (d), are respectively 7 to 25 nucleotides in length.
103. The construct according to claim 102, wherein said first nucleic acid portion of (a) and/or said second nucleic acid portion of (b) have a length of 18 to 21 , 18 to 20, or 19 nucleotides.
104. The construct according to claim 102 or 103, wherein said third nucleic acid portion of (c), and / or said fourth nucleic acid portion of (d) have a length of 11 to 20, 13 to 16, 14 or 15, or 14 nucleotides.
105. The construct according to any one of claims 102 to 104, wherein said unmodified nucleotide(s) is I are at any of position 18 to 25, at any of positions 18 to 21 , and/or the 3' terminal position of said first nucleic acid portion of (a) and / or of said third nucleic acid portion of (c).
106. The construct according to claim 105, wherein said unmodified nucleotide is at position 19.
107. The construct according to any of claims 99 to 100 or 102 to 105 as dependent on claim 87(iii), wherein said nucleic acid linker portion is 1 to 8 nucleotides in length, 2 to 7 or 3 to 6 nucleotides in length, 4 or 5 nucleotides in length.
108. The construct according to any one of claims 103 to 107, wherein one or more of all of the duplex regions independently have a length of 10 to 19, 13 to 19, 13, 14 or 15 base pairs, or 14 base pairs, wherein optionally there is one mismatch within said duplex region.
109. The construct according to any of claims 82 to 108, further comprising one or more ligands.
110. The construct according to any one of claims 82 to 109, wherein said first nucleic acid portion of (a), and I or said second nucleic acid portion of (b), and I or said third nucleic acid portion of (c), and / or said fourth nucleic acid portion of (d), and / or, to the extent present, said 1 to 8 additional nucleic acid portions as defined in claims 14 and 15, and I or said passenger nucleic acid portions as defined in claims 95 or 96, respectively have a 5’ to 3’ directionality thereby defining 5’ and 3’ regions thereof.
111. The construct according to any one of claims 109 or 110, wherein one or more ligands are conjugated at the 3 ' region, optionally the 3' end, of any of (I) said third nucleic acid portion of (c), and I or (ii) said fourth nucleic acid portion of (d), and I or, to the extent present, said (iii) passenger nucleic acid portions as defined in claims 95 or 96.
112. The construct according to any one of claims 109 to 111 , wherein one or more ligands are conjugated at one or more regions intermediate of the 5’ and 3’ regions of any of said nucleic acid portions, optionally of said third nucleic acid portion of (c), and / or said fourth nucleic acid portion of (d), and I or said passenger nucleic acid portions as defined in claims 95 or 96.
113. The construct of any one of claims 109 to 112, wherein one or more ligands are conjugated at the 5' region, optionally the 5' end, of any of said nucleic acid portions.
114. The construct according to any of claims 109 to 113, wherein said one or more ligands are any cell directing moiety, such as lipids, carbohydrates, aptamers, vitamins and I or peptides that bind cellular membrane or a specific target on cellular surface.
115. The construct according to claim 114, wherein said one or more carbohydrates can be a monosaccharide, disaccharide, trisaccharide, tetrasaccharide, oligosaccharide or polysaccharide.
116. The construct according to claim 115, wherein said one or more carbohydrates comprise one or more hexose moieties.
117. The construct of claim 116, wherein said one or more hexose moieties are one or more galactose moieties, one or more lactose moieties, one or more N-Acetyl-Galactosamine moieties, and I or one or more mannose moieties.
118. The construct according to claim 117, comprising two or three N-Acetyl-Galactosamine moieties.
119. The construct according to any of claims 109 to 118, wherein said one or more ligands are attached in a linear configuration, or in a branched configuration.
120. The construct according to claim 119, wherein said one or more ligands are attached as a biantennary or triantennary configuration, or as a configuration based on single ligands at different positions.
121 . The construct according to claim 118 or 119, wherein said ligand has the following structure:
122. The construct according to any of claims 82 to 121 , further comprising one or more phosphorothioate or phosphorodithioate internucleotide linkages.
123. The construct according claim 122, comprising 1 to 15 phosphorothioate or phosphorodithioate internucleotide linkages.
124. The construct according to claim 122 or 123, comprising one or more phosphorothioate or phosphorodithioate internucleotide linkages at one or more of the 5’ and / or 3’ regions of said first nucleic acid portion of (a), and / or said second nucleic acid portion of (b), and / or said third nucleic acid portion of (c), and I or said fourth nucleic acid portion of (d), and I or said 1 to 8 additional nucleic acid portions as defined in claims 95 or 96, and I or said passenger nucleic acid portions as defined in claims 95 or 96.
125. The construct according to any of claims 122 to 124, comprising phosphorothioate or phosphorodithioate internucleotide linkages between at least two adjacent nucleotides of the nucleic acid linker portion as defined in claim 97 (iii).
126. The construct according to any of claim 125, comprising a phosphorothioate or phosphorodithioate internucleotide linkage between each adjacent nucleotide that is present in said nucleic acid linker portion.
127. The construct according to any of claims 122 to 126, comprising a phosphorothioate or phosphorodithioate internucleotide linkage linking: the first nucleic acid portion of (a) to the nucleic acid linker portion as defined in claims 97 (iii); and I or the second nucleic acid portion of (b) to the nucleic acid linker portion as defined in claims 97 (iii); and / or the third nucleic acid portion of (c) to the nucleic acid linker portion as defined in claims 97 (iii) and I or the fourth nucleic acid portion of (d) to the nucleic acid linker portion as defined in claims 97 (iii); and / or
the 1 to 8 additional nucleic acid portions as defined in claims 95 or 96 to the nucleic acid linker portion as defined in claims 97 (ill); and / or the passenger nucleic acid portions as defined in claims 95 or 96 to the nucleic acid linker portion as defined in claims 97 (iii).
128. The construct according to any of claims 82 to 127, wherein at least one nucleotide of at least one of the following is modified: the first nucleic acid portion of ( the second nucleic acid portion the third nucleic acid portion of the fourth nucleic acid portion o
to the extent present, the 1 to 8 additional nucleic acid portions as defined in claims 95 or 96; and I or to the extent present, the passenger nucleic acid portions as defined in claims 95 or 96; and I or to the extent present, the nucleic acid linker portion as defined in claims 97 (iii).
129. The construct according to claim 128, wherein one or more of the odd numbered nucleotides starting from the 5’ region of one of the following are modified, and I or wherein one or more of the even numbered nucleotides starting from the 5’ region of one of the following are modified, wherein typically the modification of the even numbered nucleotides is a second modification that is different from the modification of odd numbered nucleotides: the first nucleic acid portion of ( the second nucleic acid portion the third nucleic acid portion of the fourth nucleic acid portion o
to the extent present, the 1 to 8 additional nucleic acid portions as defined in claims 95 or 96; and / or to the extent present, the passenger nucleic acid portions as defined in claims 95 or 96.
130. The construct according to claim 128 or 129, wherein one or more of the odd numbered nucleotides starting from the 3’ region of the third nucleic acid portion of (c) are modified by a modification that is different from the modification of odd numbered nucleotides starting from the 5’ region of the first nucleic acid portion of (a); and / or wherein one or more of the odd numbered nucleotides starting from the 3’ region of the fourth nucleic acid portion of (d) are modified by a modification that is different from the modification of odd numbered nucleotides starting from the 5’ region of the second nucleic acid portion of (b); and I or wherein one or more of the odd numbered nucleotides starting from the 3’ region of the passenger nucleic acid portions as defined in claims 95 or 96, to the extent present, are modified by a modification that is different from the modification of odd numbered nucleotides starting from the 5’ region of the 1 to 8 additional nucleic acid portions as defined in claims 95 or 96; and / or wherein one or more of the nucleotides of a nucleic acid linker portion as defined in claims 97 (iii), to the extent present, are modified by a modification that (i) is different from the modification of an
adjacent nucleotide of the 3' region of the first nucleic acid portion of (a); and I or (ii) is different from the modification of an adjacent nucleotide of the 3’ region of the second nucleic acid portion of (b); and I or is different from the modification of an adjacent nucleotide of the 3’ region of the 1 to 8 additional nucleic acid portions, to the extent present, as defined in claims 95 or 96.
131. The construct according to any of claims 128 to 130, wherein one or more of the even numbered nucleotides starting from the 3’ region of: (i) the third nucleic acid portion of (c), and / or (ii) the fourth nucleic acid portion of (d), and / or (ill) said passenger nucleic acid portions as defined in claims 95 or 96, to the extent present, are modified by a modification that is different from the modification of odd numbered nucleotides starting from the 3’ region of these respective portions.
132. The construct according to any of claims 128 to 131 , wherein at least one or more of the modified even numbered nucleotides of (i) the first nucleic acid portion of (a), and I or (ii) the second nucleic acid portion of (b), and I or (iii), to the extent present, the 1 to 8 additional nucleic acid portions as defined in claims 95 or 96, is adjacent to at least one or more differently modified odd numbered nucleotides of these respective portions.
133. The construct according to any of claims 128 to 132, wherein at least one or more of the modified even numbered nucleotides of (i) the third nucleic acid portion of (c), and I or (ii) the fourth nucleic acid portion of (d), and / or (iii), to the extent present, the passenger nucleic acid portions as defined in claims 95 or 96, is adjacent to at least one or more differently modified odd numbered nucleotides of these respective portions.
134. The construct according to any of claims 128 to 133, wherein a plurality of adjacent nucleotides of (I) the first nucleic acid portion of (a), and I or (ii) the second nucleic acid portion of (b), and / or (iii), to the extent present, the 1 to 8 additional nucleic acid portions as defined in claims 95 or 96, are modified by a common modification.
135. The construct according to any of claims 128 to 134, wherein a plurality of adjacent nucleotides of (i) the third nucleic acid portion of (c), and I or (ii) the fourth nucleic acid portion of (d), and / or (iii), to the extent present, the passenger nucleic acid portions as defined in claims 95 or 96, are modified by a common modification.
136. The construct according to claim 134 or 135, wherein said plurality of adjacent commonly modified nucleotides are 2 to 4 adjacent nucleotides, or 3 or 4 adjacent nucleotides.
137. The construct according to claim 136, wherein said plurality of adjacent commonly modified nucleotides are located in the 5’ region of (i) the third nucleic acid portion of (c), and I or
(ii) the fourth nucleic acid portion of (d), and / or (iii), to the extent present, the passenger nucleic acid portions as defined in claims 95 or 96.
138. The construct according to any one of claims 134 to 137, wherein a plurality of adjacent commonly modified nucleotides are located in the nucleic acid linker portion as defined in claim 97
(iii).
139. The construct according to any of claims 128 to 138, wherein the one or more of the modified nucleotides of first nucleic acid portion of (a) do not have a common modification present in the corresponding nucleotide of the third nucleic acid portion of (c) of the first duplex region; and
I or one or more of the modified nucleotides of second nucleic acid portion of (b) do not have a common modification present in the corresponding nucleotide of the fourth nucleic acid portion of (d) of the second duplex region; and / or one or more of the modified nucleotides of the 1 to 8 additional nucleic acid portions, to the extent present, as defined in claim 95 or 96, do not have a common modification present in the corresponding nucleotide of the corresponding passenger nucleic acid portions of the respective duplex regions.
140. The construct according to any of claims 128 to 139, wherein the one or more of the modified nucleotides of the first nucleic acid portion of (a) are shifted by at least one nucleotide relative to a commonly modified nucleotide of the third nucleic acid portion of (c); and I or one or more of the modified nucleotides of the second nucleic acid portion of (b) are shifted by at least one nucleotide relative to a commonly modified nucleotide of the fourth nucleic acid portion of (d); and I or one or more of the modified nucleotides of the 1 to 8 additional nucleic acid portions, to the extent present, as defined in claim 95 or 96 are shifted by at least one nucleotide relative to a commonly modified nucleotide of the passenger nucleic acid portions, to the extent present, as defined in claim 95 or 96.
141 . The construct according to any of claims 128 to 140, wherein the modification and I or modifications are each and individually sugar, phosphate, or base modifications.
142. The construct according to claim 141 , where the modification is selected from nucleotides with 2' modified sugars; conformationally restricted nucleotides (CRN) sugar such as locked nucleic acid (LNA), (S)-constrained ethyl bicyclic nucleic acid, and constrained ethyl (cEt), tricyclo- DNA; morpholino, unlocked nucleic acid (UNA), glycol nucleic acid (GNA), D-hexitol nucleic acid (HNA), and cyclohexene nucleic acid (CeNA).
143. The construct according to claim 142, wherein said 2' modified sugar is selected from 2'- O-alkyl modified sugar, 2'-O-methyl modified sugar, 2'-O- methoxyethyl modified sugar, 2'-O-allyl modified sugar, 2'-C-allyl modified sugar, 2'-deoxy modified sugar such as 2'-deoxy ribose, 2'-F modified sugar, 2'-arabino-fluoro modified sugar, 2'-O-benzyl modified sugar, 2'-amino modified sugar, and 2'-O-methyl-4-pyridine modified sugar.
144. The construct according to any of claims 141 to 143, wherein the base modification is any one of an abasic nucleotide and a non-natural base comprising nucleotide.
145. The construct according to any of claims 138 to 144, wherein at least one modification is a 2'-O-methyl modification in a ribose moiety.
146. The construct according to any of claims 138 to 145, wherein at least one modification is a 2'-F modification in a ribose moiety.
147. The construct according to any of claims 138 to 146 wherein the nucleotides at any of positions 2 and 14 downstream from the first nucleotide of the 5’ region of (i) the first nucleic acid portion of (a); and I or (ii) the second nucleic acid portion of (b); and I or (iii), to the extent present, the 1 to 8 additional nucleic acid portions as defined in claim 95 or 96; do not contain 2'-O-methyl modifications in ribose moieties.
148. The construct according to any of claims 138 to 147, wherein one, two or all three nucleotides of (i) the third nucleic acid portion of (c); and / or (ii) the fourth nucleic acid portion of
(d); and / or (iii), to the extent present, said passenger nucleic acid portions as defined in claim 95 or 96; that respectively correspond in position to any of the nucleotides at any of positions 11 to 13 downstream from the first nucleotide of the 5’ region of (i) the first nucleic acid portion of (a); and I or (ii) the second nucleic acid portion of (b); and I or (iii) the 1 to 8 additional nucleic acid portions, to the extent present, as defined in claim 95 or 96; do not contain 2'-O-methyl modifications in ribose moieties.
149. The construct according to claim 147 or 148, wherein the nucleotides at any of positions 2 and 14 downstream from the first of (I) the first nucleic acid portion of (a); and / or (ii) the second nucleic acid portion of (b); and I or (iii), to the extent present, the 1 to 8 additional nucleic acid portions as defined in claim 95 or 96; contain 2'-F modifications in ribose moieties.
150. The construct according to any of claims 147 to 149, wherein one, two or all three nucleotides of (i) the third nucleic acid portion of (c); and or (ii) the fourth nucleic acid portion of (d); and / or (iii), to the extent present, said passenger nucleic acid portions as defined in claims 95 or 96; that respectively correspond in position to any of the nucleotides at any of positions 11 to 13 downstream from the first nucleotide of the 5’ region of (I) the first nucleic acid portion of (a); and / or (ii) the second nucleic acid portion of (b); and / or (iii), to the extent present, the 1 to 8 additional nucleic acid portions as defined in claim 95 or 96; contain 2'-F modifications in ribose moieties.
151 . The construct according to any one of claims 146 to 150, wherein all remaining nucleotides contain either 2'-O-methyl modifications or 2'-F modifications in ribose moieties, optionally with the exception of the unmodified nucleotide(s) in accordance with claim 86.
152. The construct according to claim 151 , wherein said remaining nucleotides contain 2'-O- methyl modifications in ribose moieties.
153. The construct according to claim 151 or 152, wherein said one or more, optionally one, unmodified nucleotide represents any of the nucleotides of the nucleic acid linker portion as defined in claim 97 (iii), optionally the nucleotide of the nucleic acid linker portion as defined in claim 97 (iii) that is adjacent to (i) the third nucleic acid portion of (c); and or (ii) the fourth nucleic acid portion of (d); and / or (iii), to the extent present, said passenger nucleic acid portions as defined in claim 95 or 96.
154. The construct of any one of the preceding claims, wherein
(a) said first nucleic acid portion is selected from the group consisting of SEQ ID Nos. 501- 600 and 3604-3605;
(b) said second nucleic acid portion is selected from the group consisting of SEQ ID Nos. 501 - 600 and 3604-3605;
(c) said third nucleic acid portion is selected from the group consisting of SEQ ID Nos. 401- 500; and/or
(d) said fourth nucleic acid portion is selected from the group consisting of SEQ ID Nos. 401 - 500.
155. The construct according to claim 154, wherein the 3' terminal positions of said first and said third nucleic acid portions are replaced with an unmodified nucleotide.
156. The construct according to any of claims 82 to 155, comprising at least one vinylphosphonate modification, such as at least one vinylphosphonate modification in the 5’ region of (i) the first nucleic acid portion of (a); and I or (ii) the second nucleic acid portion of (b); and I or (iii), to the extent present, the 1 to 8 additional nucleic acid portions as defined in claim 95 or 96.
157. The construct according to any of claims 82 to 156, wherein one or more nucleotides of the first nucleic acid portion of (a); and I or the second nucleic acid portion of (b); and I or the third nucleic acid portion of (c); and I or the fourth nucleic acid portion of (d); and I or to the extent present, the 1 to 8 additional nucleic acid portions as defined in claim 95 or 96; and I or to the extent present, the passenger nucleic acid portions as defined in claim 95 or 96; is an inverted nucleotide and is attached to the adjacent nucleotide via the 3' carbon of the nucleotide and the 3' carbon of the adjacent nucleotide, and I or is an inverted nucleotide and is attached to the adjacent nucleotide via the 5' carbon of the nucleotide and the 5' carbon of the adjacent nucleotide.
158. The construct according to claim 157, wherein the inverted nucleotide is attached to the adjacent nucleotide via a phosphate group by way of a phosphodiester linkage; or is attached to the adjacent nucleotide via a phosphorothioate group; or is attached to the adjacent nucleotide via a phosphorodithioate group.
159. The construct according to any of claims 82 to 158, which is blunt ended.
160. The construct according to any of claims 82 to 158, wherein the first nucleic acid portion of (a); and I or the second nucleic acid portion of (b); and / or the third nucleic acid portion of (c); and / or the fourth nucleic acid portion of (d); and I or to the extent present, the 1 to 8 additional nucleic acid portions as defined in claim 95 or 96; and / or to the extent present, the passenger nucleic acid portions as defined in claim 95 or 96; has an overhang.
161 . The construct according to any of claims 82 to 160, wherein the target RNA is an mRNA or another RNA molecule.
162. The construct according to any one of claims 82 to 160, wherein (b) the second nucleic acid portion that is at least partially complementary to at least a second portion of an RNA, which is transcribed from a target gene which is different from the AGT gene.
163. The construct according to any one of claims 82 to 162, wherein the target gene different from the AGT gene is selected from the group consisting of genes encoding ApoB-containing atherogenic Lipoproteins, genes encoding proteins related to inflammatory-signaling pathways, such as IL-6, CRP and IL-11 ,
genes encoding further hypertension-related proteins, genes encoding proteins related to platelet-aggregation and coagulation pathways, genes encoding proteins related to diabetes, genes encoding proteins related to obesity and metabolic syndrome, and genes encoding proteins related to further pro-atherogenic factors and modifiable risk factors for cardiovascular diseases.
164. The construct according to claim 82 or 163, wherein the target gene different from the
AGT gene is selected from the group consisting of: an APOC3 gene, a PCSK9 gene, an ANGPTL3 gene, an ANGPTL4 gene, an Lp(a) gene, an ANGPTL 8 gene, and an ASGR1/2 gene.
165. The construct according to claim 164, wherein the target gene different from the AGT gene is an APOC3 gene, wherein
(a) the first nucleic acid portion is selected from the group consisting of SEQ ID Nos. 1 -100
(b) the second nucleic acid portion is selected from the group consisting of SEQ ID Nos. 601- 976;
(c) the third nucleic acid portion is selected from the group consisting of SEQ ID Nos. 101- 200; and
(d) the fourth nucleic acid portion is selected from the group consisting of SEQ ID Nos.1353- 1728.
166. The construct according to claim 164 or 165, wherein
(a) the first nucleic acid portion is selected from the group consisting of SEQ ID Nos.301-400;
(b) the second nucleic acid portion is selected from the group consisting of SEQ ID Nos. the group consisting of SEQ ID Nos. 977-1352 ;
(c) the third nucleic acid portion is selected from the group consisting of SEQ ID Nos. 401- 500; and
(d) the fourth nucleic acid portion is selected from the group consisting of SEQ ID Nos:.1729- 2104.
167. The construct according to any one of claims 164 to 166, wherein
(a) the first nucleic acid portion is selected from the group consisting of SEQ ID Nos.1 -100;
(b) the second nucleic acid portion is selected from the group consisting of SEQ ID Nos: 2105-2119;
(c) the third nucleic acid portion is selected from the group consisting of SEQ ID Nos.101-200; and
(d) the fourth nucleic acid portion is selected from the group consisting of SEQ ID Nos. 2135- 2149.
168. The construct according to any one of claims 164 to 167, wherein
(a) the first nucleic acid portion is selected from the group consisting of SEQ ID Nos.301-400;
(b) the second nucleic acid portion is selected from the group consisting of SEQ ID Nos2120- 2134;
(c) the third nucleic acid portion is selected from the group consisting of SEQ ID Nos401-500; and
(d) the fourth nucleic acid portion is selected from the group consisting of SEQ ID Nos. 2150- 2164.
169. The construct according to any one of claims 164 to 168, wherein
(a) the first nucleic acid portion is selected from the group consisting of SEQ ID Nos.301-400;
(b) the second nucleic acid portion is selected from the group consisting of SEQ ID Nos.3450- 3456;
(c) the third nucleic acid portion is selected from the group consisting of SEQ ID Nos.401-500; and
(d) the fourth nucleic acid portion is selected from the group consisting of SEQ ID Nos.3464- 3470.
170. The construct according to claim 164, wherein the target gene different from the AGT gene is a PCSK9 gene, wherein
(a) the first nucleic acid portion is selected from the group consisting of SEQ ID Nos.301-400;
(b) the second nucleic acid portion is selected from the group consisting of SEQ ID Nos. 2189-2215,
(c) the third nucleic acid portion is selected from the group consisting of SEQ ID Nos.401-500; and
(d) the fourth nucleic acid portion is selected from the group consisting of SEQ ID Nos.2216- 2242.
171. The construct according to claim 164 or claim 170, wherein
(a) the first nucleic acid portion is selected from the group consisting of SEQ ID Nos.1 -100 and 301-400;
(b) the second nucleic acid portion is selected from from the group consisting of SEQ ID Nos. 2493-2742;
(c) the third nucleic acid portion is selected from the group consisting of SEQ ID Nos.101-200 and 401-500; and
(d) the fourth nucleic acid portion is selected from the group consisting of SEQ ID Nos.2993- 3242.
172. The construct according to claim 164, 170 or 171 , wherein,
(a) the first nucleic acid portion is selected from the group consisting of SEQ ID Nos.1 -100 and 301-400;
(b) the second nucleic acid portion is selected from the group consisting of SEQ ID Nos.3243- 3328;
(c) the third nucleic acid portion is selected from the group consisting of SEQ ID Nos. 101-200 and 401-500; and
(d) the fourth nucleic acid portion is selected from the group consisting of SEQ ID Nos.3329- 3414.
173. The construct according to claim 164 or 170 to 172, wherein
(a) the first nucleic acid portion is selected from the group consisting of SEQ ID Nos.1 -100 and 301-400;
(b) the second nucleic acid portion is selected from the group consisting of SEQ ID Nos. 341—3421 and 3429-3435;
(c) the third nucleic acid portion is selected from the group consisting of SEQ ID Nos.101-200 and 401-500; and
(d) the fourth nucleic acid portion is selected from the group consisting of SEQ ID Nos.3443- 3456.
174. The construct according to claims 82 to 173 that further comprises 1 to 8 additional nucleic acid portions that are respectively at least partially complementary to an additional 1 to 8 portions of RNA transcribed from one or more target genes, which target genes different to each other, and I or the same or different to the target genes defined in (a) and (b), and wherein each of the 1 to 8 additional nucleic acid portions respectively form additional duplex regions with respective passenger nucleic acid portions that are respectively at least partially complementary therewith.
175. The construct according to claim 174, that further comprises 1 additional nucleic acid portion.
176. The construct according to claim 175, that targets the target genes selected from the group consisting of:
(a) AGT gene, (b) APOC3 gene and (e) PCSK9 gene,
(a) AGT gene, (b) ANGPTL3 gene and (e) Lp(a) gene, and
(a) AGT gene, (b) APOC3 gene and (e) Lp(a) gene, wherein (a) is the first nucleic acid portion that is at least partially complementary to at least a first portion of an RNA, which is transcribed from an AGT gene, (b) is the second nucleic acid portion that is at least partially complementary to a first portion of an RNA which is transcribed from the second gene and (e) is a fifth nucleic acid portion that is at least partially complementary to a third portion of RNA which is transcribed from the third gene and (f) is a sixth nucleic acid portion that is at least partially complementary to (e), wherein optionally the target genes are (a) AGT gene, (b) APOC3 gene and (e) PCSK9 gene.
177. A composition comprising an oligomeric compound according to any of claims 1 to 81 and/or a nucleic acid construct according to any of claims 82 to 176, and a physiologically acceptable excipient.
178. A pharmaceutical composition comprising an oligomeric compound according to any of claims 1 to 81 and/or a nucleic acid construct according to any of claims 82 to 176.
179. The pharmaceutical composition of claim 178, further comprising a pharmaceutically acceptable excipient, diluent, antioxidant, and/or preservative.
180. The pharmaceutical composition of claim 178 or 179, wherein said oligomeric compound according to any one of claims 1 to 81 and/or the construct according to any one of claims 82 to 176 is/are the only pharmaceutically active agent(s).
181 . The pharmaceutical composition of claim 178 or 179, wherein said pharmaceutical composition furthermore comprises one or more further pharmaceutically active agents.
182. The pharmaceutical composition of claim 181 , wherein said further pharmaceutically active agent(s) is/are (an) agent(s) which decrease hypertension, wherein said further pharmaceutically active agent(s) is/are optionally selected from the group consisting of a diuretic, an angiotensin converting enzyme (ACE) inhibitor, an angiotensin II receptor antagonist, a beta-blocker, a vasodilator, a calcium channel blocker, an aldosterone antagonist, an alpha2-agonist, a renin inhibitor, an alpha-blocker, a peripheral acting adrenergic agent, a selective D1 receptor partial agonist, a nonselective alpha-adrenergic antagonist, a synthetic, a steroidal antimineralocorticoid agent; a combination of any of the foregoing; and a hypertension therapeutic agent formulated as a combination of agents, more optionally an angiotensin II receptor antagonist selected from the group consisting of losartan, valsartan, olmesartan, eprosartan, and azilsartan.
183. The pharmaceutical composition of claim 181 or 182, wherein said further pharmaceutically active agent(s) is/are a further oligomeric compound which is directed to a target different from APOC3, optionally PCSK9; Vascepa; Vupanorsen; statins such as Rosuvastatin and Simvastatin; fibrates such fenofibrate; and/or LDL-cholesterol lowering compounds such as statins and ezetimib.
184. The pharmaceutical composition of any one of claims 181 or 182, wherein said further pharmaceutically active agent(s) is/are a further oligomeric compound which is directed to a target different from PCSK9 and/or a lipid-lowering agent distinct from said oligomeric compound, wherein said lipid-lowering agent is optionally a statin or ezetimib.
185. The pharmaceutical composition of claim 181 to 184, wherein said oligomeric compound and/or said nucleic acid construct; and said further pharmaceutically active agent(s) are to be administered concomitantly or in any order.
186. An oligomeric compound according to any of claims 1 to 81 and/or a nucleic acid construct according to any of claims 82 to 176, for use in human or veterinary medicine or therapy.
187. An oligomeric compound according to any of claims 1 to 81 and/or a nucleic acid construct according to any of claims 82 to 176, for use in a method of treating, ameliorating and/or preventing a disease or disorder.
188. The compound and/or the construct for use of claim 187, wherein said disease or disorder is a disease or disorder associated AGT or a disease or disorder requiring reduction of AGT expression.
189. The compound and/or the construct for use of claim 188, wherein said disease or disorder is selected from the group consisting of high blood pressure, hypertension, borderline hypertension, primary hypertension, secondary hypertension isolated systolic or diastolic hypertension, pregnancy-associated hypertension, diabetic hypertension, resistant hypertension, refractory hypertension, paroxysmal hypertension, renovascular hypertension, Goldblatt
hypertension, ocular hypertension, glaucoma, pulmonary hypertension, portal hypertension, systemic venous hypertension, systolic hypertension, labile hypertension; hypertensive heart disease, hypertensive nephropathy, atherosclerosis, arteriosclerosis, vasculopathy, diabetic nephropathy, diabetic retinopathy, chronic heart failure, cardiomyopathy, diabetic cardiac myopathy, nocturnal hypotension, glomerulosclerosis, coarctation of the aorta, aortic aneurism, ventricular fibrosis, heart failure, myocardial infarction, angina, stroke, renal disease, renal failure, systemic sclerosis, intrauterine growth restriction (IUGR) , fetal growth restriction, obesity, liver steatosis/ fatty liver, non-alcoholic Steatohepatitis (NASH), non-alcoholic fatty liver disease (NAFLD); glucose intolerance, type 2 diabetes, and metabolic syndrome..
190. The compound and/or the construct for use according to claims 188 or 189.wherein said disease or disorder is further an APOC3-associated disease or disorder, or a disease or disorder requiring reduction of APOC3 expression levels, said disease or disorder optionally being selected from dyslipidemia including mixed dyslipidemia; hyperchylomicronemia including familial hyperchylomicronemia; hypertriglyceridemia, optionally severe hypertriglyceridemia and/or hypertriglyceridemia with blood triglyceride levels above 500 mg/dl; inflammation including low- grade inflammation; atherosclerosis; atherosclerotic cardiovascular diseases (ASCVD) including major adverse cardiovascular events (MACE) such as myocardial infarction, stroke and peripheral arterial disease; and pancreatitis including acute pancreatitis.
191 . The compound and/or the construct for use according to claims 188 to 190, wherein said disease or disorder is further a PCSK9-associated disease or disorder, or a disease or disorder requiring reduction of low-density lipoprotein (LDL) cholesterol, said disease or disorder optionally being selected from dyslipidemia including mixed dyslipidemia, hypercholesterolemia, heterozygous familial hypercholesterolemia, non-familial hypercholesterolemia; atherosclerosis; and atherosclerotic cardiovascular disease (ASCVD) including myocardial infarction, stroke and peripheral arterial disease.
192. A method of treating a disease or disorder comprising administration of an oligomeric compound according to any of claims 1 to 81 and/or a nucleic acid construct according to any one of claims 82 to 176, to an individual in need of treatment.
193. The method according to claim 192, wherein the oligomeric compound and/or the nucleic acid construct is administered subcutaneously or intravenously to the individual.
194. Use of an oligomeric compound according to any of claims 1 to 81 or a nucleic acid construct according to any of claims 82 to 176, for use in research as a gene function analysis tool.
195. Use of an oligomeric compound according to any of claims 1 to 81 and/or a nucleic acid construct according to any of claims 82 to 176 in the manufacture of a medicament for a treatment of a disease or disorder.
Applications Claiming Priority (2)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US202263407353P | 2022-09-16 | 2022-09-16 | |
| PCT/US2023/074512 WO2024059881A2 (en) | 2022-09-16 | 2023-09-18 | Products and compositions |
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| Publication Number | Publication Date |
|---|---|
| EP4587573A2 true EP4587573A2 (en) | 2025-07-23 |
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| Application Number | Title | Priority Date | Filing Date |
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| EP23866589.7A Pending EP4587573A2 (en) | 2022-09-16 | 2023-09-18 | Products and compositions |
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| EP (1) | EP4587573A2 (en) |
| CN (1) | CN120303402A (en) |
| WO (1) | WO2024059881A2 (en) |
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| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US9187746B2 (en) * | 2009-09-22 | 2015-11-17 | Alnylam Pharmaceuticals, Inc. | Dual targeting siRNA agents |
| AU2015264038B2 (en) * | 2014-05-22 | 2021-02-11 | Alnylam Pharmaceuticals, Inc. | Angiotensinogen (AGT) iRNA compositions and methods of use thereof |
| CN113817735A (en) * | 2015-10-08 | 2021-12-21 | Ionis制药公司 | Compounds and methods for modulating angiotensinogen expression |
| LT4136092T (en) * | 2020-11-18 | 2024-09-25 | Ionis Pharmaceuticals, Inc. | Compounds and methods for modulating angiotensinogen expression |
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2023
- 2023-09-18 EP EP23866589.7A patent/EP4587573A2/en active Pending
- 2023-09-18 WO PCT/US2023/074512 patent/WO2024059881A2/en not_active Ceased
- 2023-09-18 CN CN202380066528.6A patent/CN120303402A/en active Pending
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| Publication number | Publication date |
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| WO2024059881A3 (en) | 2024-05-16 |
| WO2024059881A2 (en) | 2024-03-21 |
| CN120303402A (en) | 2025-07-11 |
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