Patent Application
20230089502
The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Oct. 4, 2022, is named 4690_0049 C_SequenceListing and is 288 kilobytes in size.
Compositions are provided that modulate, interfere with, or inhibit, proprotein convertase subtilkisin/kexin type 9 (PCSK9) gene expression, together with methods of using the compositions for the treatment, prevention or amelioration of PCSK9-associated disorders such as dyslipidemia, including hypercholesterolemia.
Cholesterol has multiple vital functions, including the maintenance of integrity and fluidity of cell membranes. It furthermore serves a precursor for biosynthetic pathways, including those leading to steroid hormones and vitamin D. Cholesterol is present in the blood, where it occurs mainly in two forms: as component in high density lipoproteins (HDL) and in low density lipoproteins (LDL). Often the HDL cholesterol is referred as “good” or beneficial, while LDL cholesterol, in particular when present in elevated levels, presents a health risk and lead to disease.
Regulation of LDL Cholesterol
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 result in higher blood levels of “bad” LDL cholesterol. This molecular and cellular function of PCSK9 has led to its recognition as a therapeutic target molecule.
Disease
Abnormal amounts of circulating cholesterol, in particular of LDL cholesterol, also referred to as hypercholesterolemia, is a recognized disorder in itself which is inter alia owed to the fact that such abnormal amounts, in particular if they persist over extended periods of time, may result in disorder of the cardiovascular system. More specifically, excess amounts of cholesterol may be deposited on the inner walls of blood vessel which in turn may lead to clogging, wherein the clinical manifestations of such clogging include myocardial infarction, stroke and peripheral artery disease.
Treatment
Established treatments for hypercholestorolemia include the administration of statins. Statins may, however, cause side effects, and certain patients are statin-intolerant. Compounds, methods, and pharmaceutical compositions for the treatment of dyslipidemia are provided.
Double-stranded RNA (dsRNA) able to complementarily bind expressed mRNA has been shown to be able to block gene expression (Fire et al., 1998, Nature. 1998 Feb. 19;391 (6669):806-1 1 and Elbashir et al., 2001, Nature. 2001 May 24;41 1 (6836):494-8) by a mechanism that has been termed RNA interference (RNAi). Short dsRNAs direct gene-specific, post-transcriptional silencing in many organisms, including vertebrates, and have become a useful tool for studying gene function. RNAi is mediated by the RNA-induced silencing complex (RISC), a sequence-specific, multi-component nuclease that destroys messenger RNAs homologous to the silencing trigger loaded into the RISC complex. Interfering RNA (iRNA) such as siRNAs, antisense RNA, and micro-RNA are oligonucleotides that prevent the formation of proteins by gene-silencing i.e. inhibiting gene translation of the protein through degradation of mRNA molecules. Gene-silencing agents are becoming increasingly important for therapeutic applications in medicine.
According to Watts and Corey in the Journal of Pathology (2012; Vol 226, p 365-379) algorithms may be used to design nucleic acid silencing triggers, but these suffer from severe limitations. Further experimentation is needed to identify potent siRNAs, since algorithms do not take into account factors such as tertiary structure of the target mRNA or the involvement of RNA binding proteins. Accordingly, discovery of a potent nucleic acid silencing trigger with minimal off-target effects is a complex process. For the pharmaceutical development of these highly charged molecules it is necessary that they be synthesised economically, distributed to and taken up by target tissues, enter cells and function within acceptable limits of toxicity. We provide herein compounds, methods, and pharmaceutical compositions for the treatment of thromboembolic diseases as described herein, which compounds, methods and compositions comprise oligomeric compounds that modulate, in particular inhibit, gene expression by RNAi.
Nucleic acid products are provided that modulate and, in particular, interfere with or inhibit, proprotein convertase subtilkisin/kexin type 9 (PCSK9) gene expression, and associated therapeutic uses. Specific oligomeric compounds and sequences according to the disclosed embodiments are described herein. This summary is not intended to identify key features or essential features of the claimed subject matter, nor is it intended to be used to determine the scope of the claimed subject matter.
PCSK9-targeting constructs are labelled as P, p, PCS or PCSK9, followed by a two- or three-digit construct number, wherein numbering adheres to the numbering of the nucleobase sequences shown in the sequence listing as follows: SEQ ID NO of the nucleobase sequence of the antisense region=construct number; SEQ ID NO of the nucleobase sequence of the sense region=250+ construct number. In certain instances, such designation of PCSK9-targeting constructs is followed by information in brackets about the architecture of the construct (dsRNA vs. mxRNA; lengths of regions).
The following aspects are non-limiting.
Aspect 1. An oligomeric compound capable of inhibiting expression of PCSK9, wherein this compound comprises 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 a PCSK9 gene, wherein the first nucleobase sequence is selected from the following sequences, or a portion thereof: sequences of Table 2a (SEQ ID NOs 1 to 250), or sequences of Table 3a (SEQ ID NOs 501 to 543), wherein the portion advantageously has a length of at least 18 nucleotides.
Particularly advantageous embodiments relate to dsRNAs on the one hand and mxRNAs on the other hand; for further details see the embodiments and their discussion further below. In addition, the antisense and sense regions disclosed herein may serve as building blocks for compounds (muRNAs) which are directed to multiple targets. The general architecture of such compounds is described in WO 2020/065602.
Aspect 2. A composition comprising an oligomeric compound according to aspect 1, and a physiologically acceptable excipient.
Aspect 3. A pharmaceutical composition comprising an oligomeric compound according to aspect 1.
Aspect 4. An oligomeric compound according to aspect 1, for use in human or veterinary medicine or therapy.
Aspect 5. An oligomeric compound according to aspect 1, for use in a method of treating a disease or disorder.
Aspect 6. A method of treating a disease or disorder comprising administration of an oligomeric compound according to aspect 1, to an individual in need of treatment.
Aspect 7. Use of an oligomeric compound according to aspect 1, for use in research as a gene function analysis tool.
Further embodiments (items) are described below by way of example only. These examples represent ways in which the disclosed compositions and methods are put into practice but the skilled artisan will recognize that they are not the only ways in which this could be achieved. 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 herein.
In many instances, the definitions, in addition to the respective definition as such, provide non-exhaustive listings of possible implementations which amount to specific embodiments. Unless specific definitions are provided, the nomenclature used in connection with, and the procedures and techniques of, analytical chemistry, synthetic organic chemistry, and medicinal and pharmaceutical chemistry described herein are those well known and commonly used in the art. Standard techniques may be used for chemical synthesis, and chemical analysis. Certain such techniques and procedures may be found for example in “Carbohydrate Modifications in Antisense Research” Edited by Sangvi and Cook, American Chemical Society, Washington D.C., 1994; “Remington's Pharmaceutical Sciences,” Mack Publishing Co., Easton, Pa., 21st edition, 2005; and “Antisense Drug Technology, Principles, Strategies, and Applications” Edited by Stanley T. Crooke, CRC Press, Boca Raton, Fla.; and Sambrook et al., “Molecular Cloning, A laboratory Manual,” 2nd Edition, Cold Spring Harbor Laboratory Press, 1989.
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 comprising a nucleobase moiety and a sugar moiety. Nucleosides include, but are not limited to, naturally occurring nucleosides (as found in DNA and RNA) and modified nucleosides. Nucleosides may be linked to a phosphate moiety, phosphate-linked nucleosides also being referred to as “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 comprising a 5-membered ring comprising 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 comprising substituents at the 2′-position, the 3′-position, the 5′-position and/or the 4′-position. Certain substituted sugar moieties are bicyclic sugar moieties.
As used herein, “2′-substituted sugar moiety” means a furanosyl comprising a substituent at the 2′-position other than H or OH. Unless otherwise indicated, a 2′-substituted sugar moiety is not a bicyclic sugar moiety (i.e., the 2′-substituent of a 2′-substituted sugar moiety does not form a bridge to another atom of the furanosyl ring).
As used herein, “MOE” means —OCH2CH2OCH3.
As used herein, “2′-F nucleoside” refers to a nucleoside comprising a sugar comprising fluorine at the 2′ position. Unless otherwise indicated, the fluorine in a 2′-F nucleoside is in the ribo position (replacing the OH of a natural ribose). Duplexes of uniformly modified 2′-fluorinated (ribo) oligonucleotides hybridized to RNA strands are not RNase H substrates while the ara analogs retain RNase H activity.
As used herein the term “sugar surrogate” means a structure that does not comprise a furanosyl and that is capable of replacing the naturally occurring sugar moiety of a nucleoside, such that the resulting nucleoside sub-units are capable of linking together and/or linking to other nucleosides to form an oligomeric compound which is capable of hybridizing to a complementary oligomeric compound. Such structures include rings comprising a different number of atoms than furanosyl (e.g., 4, 6, or 7-membered rings); replacement of the oxygen of a furanosyl with a non-oxygen atom (e.g., carbon, sulfur, or nitrogen); or both a change in the number of atoms and a replacement of the oxygen. Such structures may also comprise substitutions corresponding to those described for substituted sugar moieties (e.g., 6-membered carbocyclic bicyclic sugar surrogates optionally comprising additional substituents). Sugar surrogates also include more complex sugar replacements (e.g., the non-ring systems of peptide nucleic acid). Sugar surrogates include without limitation morpholinos, cyclohexenyls and cyclohexitols.
As used herein, “bicyclic sugar moiety” means a modified sugar moiety comprising a 4 to 7 membered ring (including but not limited to a furanosyl) comprising a bridge connecting two atoms of the 4 to 7 membered ring to form a second ring, resulting in a bicyclic structure. In certain embodiments, the 4 to 7 membered ring is a sugar ring. In certain embodiments the 4 to 7 membered ring is a furanosyl. In certain such embodiments, the bridge connects the 2 ‘-carbon and the 4’-carbon of the furanosyl.
As used herein, “nucleotide” means a nucleoside further comprising a phosphate linking group. As used herein, “linked nucleosides” may or may not be linked by phosphate linkages and thus includes, but is not limited to “linked nucleotides.” As used herein, “linked nucleosides” are nucleosides that are connected in a continuous sequence (i.e. no additional nucleosides are present between those that are linked).
As used herein, “nucleobase” means a group of atoms that can be linked to a sugar moiety to create a nucleoside that is capable of incorporation into an oligonucleotide, and wherein the group of atoms is capable of bonding, 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 comprising at least one chemical modification compared to naturally occurring RNA or DNA nucleosides. Modified nucleosides can comprise a modified sugar moiety and/or a modified nucleobase.
As used herein, “bicyclic nucleoside” or “BNA” means a nucleoside comprising a bicyclic sugar moiety.
As used herein, “locked nucleic acid nucleoside” or “LNA” means a nucleoside comprising a bicyclic sugar moiety comprising a 4′-CH2—O-2′bridge.
As used herein, “2 ‘-substituted nucleoside” means a nucleoside comprising 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 comprising 2’—H furanosyl sugar moiety, as found in naturally occurring deoxyribonucleosides (DNA). In certain embodiments, a 2′-deoxynucleoside may comprise a modified nucleobase or may comprise an RNA nucleobase (e.g., uracil).
As used herein, “oligonucleotide” means a compound comprising a plurality of linked nucleosides. In certain embodiments, an oligonucleotide comprises one or more un-modified ribonucleosides (RNA) and/or unmodified deoxyribonucleosides (DNA) and/or one or more modified nucleosides.
As used herein, “modified oligonucleotide” means an oligonucleotide comprising 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 as described herein. 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 GaINAc, 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 as described herein.
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 comprising 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 comprising two or more substructures. In certain embodiments, an oligomeric compound comprises an oligonucleotide, such as a modified oligonucletide. In certain embodiments, an oligomeric compound further comprises one or more conjugate groups and/or terminal groups and/or ligands. In certain embodiments, an oligomeric compound consists of an oligonucleotide. In certain embodiments, an oligomeric compound comprises 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 partictularly limited and may or may not comprise 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.
As used herein, “terminal group” means one or more atom attached to either, or both, the 3′ end or the 5′ end of an oligonucleotide. In certain embodiments, a terminal group comprises one or more terminal group nucleosides.
As used herein, “conjugate” or “conjugate group” means an atom or group of atoms bound to an oligonucleotide or oligomeric compound. In 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/or clearance properties.
As used herein, “conjugate linker” or “linker” in the context of a conjugate group means a portion of a conjugate group comprising any atom or group of atoms and which covalently link 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 comprise a cleavable moiety (e.g., a cleavable bond or cleavable nucleoside) and ligand portion that can comprise one or more ligands, such as a carbohydrate cluster portion, such as an N-Acetyl-Galactosamine, also referred to as “GaINAc”, 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 comprises 2 GaINAc groups. For example, in certain embodiments, the carbohydrate cluster portion comprises 3 GaINAc groups and this is particularly advantageous. In certain embodiments, the carbohydrate cluster portion comprises 4 GaINAc 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. A particular carbohydrate cluster has the following formula:
wherein in this structural formula one, two, or three phosphodiester linkages can also be substituted by phosphothionate 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 comprises 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/or one or more mannose moieties. A particularly advantageous carbohydrate is N-Acetyl-Galactosamine.
As used herein, “strand” means an oligomeric compound comprising linked nucleosides.
As used herein, “single strand” or “single-stranded” means an oligomeric compound comprising linked nucleosides that are connected in a continuous sequence without a break therebetween. 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.
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” means two or more complementary strand regions, or strands, of an oligonucleotide or oligonucleotides, hybridized together by way of non-covalent, sequence-specific interaction therebetween. Most commonly, the hybridization in the duplex will be between nucleobases adenine (A) and thymine (T), and/or (A) adenine and uracil (U), and/or guanine (G) and cytosine (C). The duplex may be part of a single stranded structure, wherein 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 comprises 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, polyadenlyation, 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 PCSK9 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 to be complementary at that nucleobase pair. Nucleobases comprising certain modifications may maintain the ability to pair with a counterpart nucleobase and thus, are still capable of nucleobase complementarity.
As used herein, “non-complementary” in reference to nucleobases means a pair of nucleobases that do not form hydrogen bonds with one another.
As used herein, “complementary” in reference to oligomeric compounds (e.g., linked nucleosides, oligonucleotides) 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/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/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 comprises 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 un-modified 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 comprising different nucleobases are not differently modified. For example, a nucleoside comprising a 2′-OMe modified sugar moiety and an unmodified adenine nucleobase and a nucleoside comprising 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 comprise 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 comprise at least 10, at least 11, at least 12 or at least 13 linked nucleosides. For example, such regions can comprise 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 most advantageous 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′poisition 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. This will be well understood be a person skilled in the art.
As used herein, “alkylene” means a saturated straight or branched divalent hydrocarbon radical of the general formula —CnH2n— where n is 1-6. Advantageously the alkylenes are methylene or ethylene.
As used herein, “alkenyl” means a straight or branched unsaturated monovalent C2-6 hydrocarbon radical, with ethenyl or propenyl being most advantageous 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. This will be well understood be a person skilled in the art.
As used herein, “alkynyl” means a straight or branched unsaturated C2-6 hydrocarbon radical, with ethynyl being a most advantageous 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. This will be well understood be a person skilled in the art.
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 wherein 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 wherein 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 will be well understood by a person skilled in the art and 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.
It will also be understood that oligomeric compounds as described herein may have one or more non-hybridizing nucleosides at one or both ends of one or both strands (overhangs) and/or one or more internal non-hybridizing nucleosides (mismatches) provided there is sufficient complementarity to maintain hybridization under physiologically relevant conditions.
Alternatively, oligomeric compounds as described herein may be blunt ended at at least one end.
The term “comprising” is used herein to mean including the method steps or elements identified, but that such steps or elements do not comprise an exclusive list and as such there may be present additional steps or elements.
Further, to the extent that the term “includes” is used in either the detailed description or the claims, such term is intended to be inclusive in a manner similar to the term “comprising” as “comprising” is interpreted when employed as a transitional word in a claim.
The following items are provided:
1. An oligomeric compound capable of inhibiting expression of PCSK9, wherein the compound comprises 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 a PCSK9 gene, wherein the first nucleobase sequence is selected from the following sequences, or a portion thereof: SEQ ID NOs 1 to 250, or SEQ ID NOs 501 to 543, wherein the portion advantageously has a length of at least 18 nucleotides.
The first region is also referred to as antisense region, and the second region is also referred to as sense region. As disclosed in specific embodiments below, the two regions may be located on the same 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), wherein advantageously each strand consists of the respective region.
Moreover, the regions may serve as building blocks for muRNAs (see above). In other words, the first and the second region as defined herein may be used, in accordance with the following definition of muRNAs, as first and third regions, respectively:
A nucleic acid construct (muRNA) comprising at least:
Specific embodiments of and further aspects relating to muRNAs are disclosed in WO 2020/065602.
2. The oligomeric compound according to item 1, which further comprises 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: SEQ ID NOs 251 to 500, or SEQ ID NOs 544 to 586, wherein the portion advantageously has a length of at least 11 nucleotides.
3. The oligomeric compound according to item 1 or 2, wherein the first nucleobase sequence is selected from the following sequences, or a portion thereof: SEQ ID NOs 13, 31, 76, 127, 55, 29, 28, 53, 44, 49, 58, 94, 52, 57, 43, 36, 21, 35, 232, 87, 48, 139, 46, 233, 34, 100, and 77.
4. The oligomeric compound according to item 3, wherein the second nucleobase sequence is selected from the following sequences, or a portion thereof: SEQ ID NOs 263, 281, 326, 377, 305, 279, 278, 303, 294, 299, 308, 344, 302, 307, 293, 286, 271, 285, 482, 337, 298, 389, 296, 483, 284, 350, and 327, and wherein the portion is advantageously 14 nucleosides long and lacks the 5′-terminal nucleobase as set forth in the SEQ ID NOs.
5. The oligomeric compound according to any of items 1 to 4, wherein the first nucleobase sequence is selected from the following sequences, or a portion thereof: SEQ ID NOs 29, 44, 46, 52, 53, 55, and 57; advantageously SEQ ID NOs: 29, 44, 53 and 57, more advantageously SEQ ID NO: 29.
This embodiments defines antisense nucleobase sequences which provide for surprisingly outstanding performance. For evidence, reference is made to the Examples.
6. The oligomeric compound according to item 5, wherein the second nucleobase sequence is selected from the following sequences, or a portion thereof: SEQ ID NOs 279, 294, 296, 302, 303, 305, and 307, advantageously SEQ ID NOs: 279, 294, 303 and 307, more advantageously SEQ ID NO: 279, and wherein the portion is advantageously 14 nucleosides long and lacks the 5′-terminal nucleobase as set forth in the SEQ ID NOs.
7. The oligomeric compound according to any of items 1 to 6, wherein the first region of linked nucleosides consists essentially of 18 to 35, advantageously 18 to 20, more advantageously 18 or 19, and yet more advantageously 19 linked nucleosides.
8. The oligomeric compound according to any of items 2 to 7, wherein the second region of linked nucleosides consists essentially of 11 to 35, advantageously 11 to 20, more advantageously 13 to 16, and yet more advantageously 14 or 15, most advantageously 14 linked nucleosides.
9. The oligomeric compound according to any of items 2 to 8, which comprises at least one complementary duplex region that comprises at least a portion of the first nucleoside region directly or indirectly linked to at least a portion of the second nucleoside region, wherein advantageously the duplex region has a length of 11 to 19, more advantageously 14 to 19, and yet more advantageously 14 or 15 base pairs, most advantageously 14 base pairs, wherein optionally there is one mismatch within the duplex region.
10. The oligomeric compound according to item 9, wherein each of the first and second nucleoside regions has a 5′ to 3′ directionality thereby defining 5′ and 3′ regions respectively thereof.
11. The oligomeric compound according to item 10, wherein the 5′ region of the first nucleoside region is directly or indirectly linked to the 3′ region of the second nucleoside region, for example by complementary base pairing, and/or wherein the 3′ region of the first nucleoside region is directly or indirectly linked to the 5′ region of the second nucleoside region, wherein advantageously the 5′ terminal nucleoside of the first nucleoside region base pairs with the 3′ terminal nucleoside of the second nucleoside region.
12. The oligomeric compound according to any of items 1 to 11, which further comprises one or more ligands.
13. The oligomeric compound according to item 12, wherein the one or more ligands are conjugated to the second nucleoside region and/or the first nucleoside region.
14. The oligomeric compound according to item 13, as dependent on item 10, wherein the one or more ligands are conjugated at the 3′ region, advantageously to the 3′ end of the second nucleoside region and/or of the first nucleoside region, and/or to the 5′ end of the second nucleoside region.
15. The oligomeric compound according to any of items 12 to 14, wherein 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.
16. The oligomeric compound according to item 15, wherein the one or more ligands comprise one or more carbohydrates.
17. The oligomeric compound according to item 16, wherein the one or more carbohydrates can be a monosaccharide, disaccharide, trisaccharide, tetrasaccharide, oligosaccharide or polysaccharide.
18. The oligomeric compound according to item 17, wherein the one or more carbohydrates comprise or consist of one or more hexose moieties.
19. The oligomeric compound according to item 18, wherein the one or more hexose moieties are one or more galactose moieties, one or more lactose moieties, one or more N-Acetyl-Galactosamine moieties, and/or one or more mannose moieties.
20. The oligomeric compound according to item 19, wherein the one or more carbohydrates comprise one or more N-Acetyl-Galactosamine moieties.
21. The oligomeric compound according to item 20, which comprises two or three N-Acetyl-Galactosamine moieties, advantageously three.
22. The oligomeric compound according to any of items 12 to 21, wherein the one or more ligands are attached to the oligomeric compound, advantageously to the second nucleoside region thereof, in a linear configuration, or in a branched configuration.
23. The oligomeric compound according to item 22, wherein the one or more ligands are attached to the oligomeric compound as a biantennary or triantennary configuration.
24. The oligomeric compound according to any one of items 1 to 23, wherein the compound consists of the first region of linked nucleosides and the second region of linked nucleosides. Each of the 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.
25. The oligomeric compound according to any one of items 9 to 24, wherein the oligomeric compound comprises a single strand comprising the first and second nucleoside regions, wherein the single strand dimerises whereby 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 term “dimerise” in relation to the embodiment above refers to the formation of intramolecular base pairs between first and second region.
26. The oligomeric compound according to item 25, wherein the first nucleoside region has a greater number of linked nucleosides compared to the second nucleoside region, whereby the additional number of linked nucleosides of the first nucleoside region form a hairpin loop linking the first and second nucleoside regions.
Such compounds are also referred to as hairpins or mxRNAs herein.
27. The oligomeric compound according to item 26, as dependent on claim 10, whereby the hairpin loop is present at the 3′ region of the first nucleoside region, and/or wherein the hairpin loop comprises 4 or 5 linked nucleosides.
Particularly advantageous is a length of the first region of 19 nucleosides, of the second region of 14 nucleotides, and of the hairpin loop of 5 nucleotides, wherein the 5 nucleotides 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.
28. The oligomeric compound according to item 26 or 27, the compound has a nucleobase sequence selected from SEQ ID NOs: 587 to 590, and advantageously is selected from Table 6.
29. The oligomeric compound according to any of items 1 to 28, which comprises internucleoside linkages and wherein at least one internucleoside linkage is a modified internucleoside linkage.
Specific modified internucleoside linkages are the subject of the specific 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.
30. The oligomeric compound according to item 29, wherein the modified inter-nucleoside linkage is a phosphorothioate or phosphorodithioate internucleoside linkage.
31. The oligomeric compound according to item 30, which comprises 1 to 15 phosphorothioate or phosphorodithioate internucleoside linkages.
32. The oligomeric compound according to item 31, which comprises 7, 8, 9 or 10 phosphorothioate or phosphorodithioate internucleoside linkages.
33. The oligomeric compound according to any of items 30 to 32, as dependent on item 10, which comprises one or more phosphorothioate or phosphorodithioate internucleoside linkages at the 5′ region of the first nucleoside region.
34. The oligomeric compound according to any of items 30 to 33, as dependent on item 10, which comprises one or more phosphorothioate or phosphorodithioate internucleoside linkages at the 5′ region of the second nucleoside region.
35. The oligomeric compound according to any of items 30 to 34, as dependent on item 26, which comprises phosphorothioate or phosphorodithioate internucleoside linkages between at least two, advantageously at least three, advantageously at least four, advantageously at least five, adjacent nucleosides of the hairpin loop, dependent on the number of nucleotides present in the hairpin loop.
36. The oligomeric compound according to item 35, which comprises a phosphorothioate or phosphorodithioate internucleoside linkage between each adjacent nucleoside that is present in the hairpin loop.
37. The oligomeric compound according to any of items 1 to 36, wherein at least one nucleoside comprises a modified sugar.
Specific modified sugars are subject of the 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.
38. The oligomeric compound according to item 37, wherein the modified sugar is selected from 2′ modified sugars, locked nucleic acid (LNA) sugar, (S)-constrained ethyl bicyclic nucleic acid sugar, tricyclo-DNA sugar, morpholino, unlocked nucleic acid (UNA) sugar, and glycol nucleic acid (GNA) sugar.
39. The oligomeric compound according to item 38, wherein the 2′ modified sugar is selected from 2′-O-methyl modified sugar, 2′-O-methoxyethyl modified sugar, 2′-F modified sugar, 2′-arabino-fluoro modified sugar, 2′-O-benzyl modified sugar, and 2′-O-methyl-4-pyridine modified sugar.
40. The oligomeric compound according to item 39, wherein at least one modified sugar is a 2′-O-methyl modified sugar.
41. The oligomeric compound according to item 39 or 40, wherein at least one modified sugar is a 2′-F modified sugar.
42. The oligomeric compound of item 40 or 41, wherein the sugar is ribose.
43. The oligomeric compound according to any of items 40 to 42, as dependent on item 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 nucleoside region, do not contain 2′-O-methyl modifications.
44. The oligomeric compound according to any of items 40 to 43, as dependent on item 10, wherein sugars of the nucleosides of the second nucleoside region, that correspond in position to any of the nucleosides of the first nucleoside region at any of positions 9 to 11 downstream from the first nucleotide of the 5′ region of the first nucleoside region, do not contain 2′-O-methyl modifications.
45. The oligomeric compound of any one of items 40 to 44, wherein the 3′ terminal position of the second nucleoside region does not contain a 2′-O-methyl modification.
46. The oligomeric compound according to item 44 or 45, wherein sugars of the nucleosides at any of positions 2 and 14 downstream from the first nucleoside of the 5′ region of the first nucleoside region, contain 2′-F modifications.
47. The oligomeric compound according to any of items 44 to 46, wherein sugars of the nucleosides of the second nucleoside region, that correspond in position to any of the nucleosides of the first nucleoside region at any of positions 9 to 11 downstream from the first nucleoside of the 5′ region of the first nucleoside region, contain 2′-F modifications.
48. The oligomeric compound of item 46 or 47, wherein the 3′ terminal position of the second nucleoside region contains a 2′-F modification.
49. The oligomeric compound according to any of items 42 to 48, as dependent on item 10, wherein one or more of the odd numbered nucleosides starting from the 5′ region of the first nucleoside region are modified, and/or wherein one or more of the even numbered nucleotides starting from the 5′ region of the first nucleoside region 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.
50. The oligomeric compound according to item 49, wherein one or more of the odd numbered nucleosides starting from the 3′ region of the second nucleoside region are modified by a modification that is different from the modification of odd numbered nucleosides of the first nucleoside region.
51. The oligomeric compound according to item 49 or 50, wherein one or more of the even numbered nucleosides starting from the 3′ region of the second nucleoside region are modified by a modification that is different from the modification of even numbered nucleosides of the first nucleoside region according to item 53.
52. The oligomeric compound according to any of items 49 to 51, wherein at least one or more of the modified even numbered nucleosides of the first nucleoside region is adjacent to at least one or more of the differently modified odd numbered nucleosides of the first nucleoside region.
53. The oligomeric compound according to any of items 49 to 52, 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 nucleoside region.
54. The oligomeric compound according to any of items 49 to 53, wherein sugars of one or more of the odd numbered nucleosides starting from the 5′ region of the first nucleoside region are 2′-O-methyl modified sugars.
55. The oligomeric compound according to any of items 49 to 54, wherein one or more of the even numbered nucleosides starting from the 5′ region of the first nucleoside region are 2′-F modified sugars.
56. The oligomeric compound according to any of items 49 to 55, wherein sugars of one or more of the odd numbered nucleosides starting from the 3′ region of the second nucleoside region are 2′-F modified sugars.
57. The oligomeric compound according to any of items 49 to 56, wherein one or more of the even numbered nucleosides starting from the 3′ region of the second nucleoside region are 2′-O-methyl modified sugars.
58. The oligomeric compound according to any of items 37 to 57, wherein sugars of a plurality of adjacent nucleosides of the first nucleoside region are modified by a common modification.
59. The oligomeric compound according to any of items 37 to 58, wherein sugars of a plurality of adjacent nucleosides of the second nucleoside region are modified by a common modification.
60. The oligomeric compound according to any of items 49 to 59, as dependent on item 26, wherein sugars of a plurality of adjacent nucleosides of the hairpin loop are modified by a common modification.
61. The oligomeric compound according to any of items 58 to 60, wherein the common modification is a 2′-F modified sugar.
62. The oligomeric compound according to any of items 58 to 60, wherein the common modification is a 2′-O-methyl modified sugar.
63. The oligomeric compound according to item 62, wherein the plurality of adjacent 2′-O-methyl modified sugars are present in at least eight adjacent nucleosides of the first and/or second nucleoside regions.
64. The oligomeric compound according to item 62, wherein the plurality of adjacent 2′-O-methyl modified sugars are present in three or four adjacent nucleosides of the hairpin loop.
65. The oligomeric compound according to item 37, as dependent on item 26, wherein the hairpin loop comprises at least one nucleoside having a modified sugar.
66. The oligomeric compound according to item 66, wherein the at least one nucleoside is adjacent a nucleoside with a differently modified sugar.
67. The oligomeric compound according to item 66, wherein the modified sugar is a 2′-O-methyl modified sugar, and the differently modified sugar is a 2′-F modified sugar.
68. The oligomeric compound according to any of items 1 to 67, which comprises one or more nucleosides having an un-modified sugar moiety.
69. The oligomeric compound according to item 68, wherein the unmodified sugar is present in the 5′ region of the second nucleoside region.
70. The oligomeric compound according to item 68 or 69, as dependent on item 26, wherein the unmodified sugar is present in the hairpin loop.
71. The oligomeric compound according to any of items 1 to 70, wherein one or more nucleosides of the first nucleoside region and/or the second nucleoside region 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/or one or more nucleosides of the first nucleoside region and/or the second nucleoside region 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.
72. The oligomeric compound according to any of items 1 to 71, which is blunt ended.
73. The oligomeric compound according to any of items 1 to 71, wherein either the first or second nucleoside region has an overhang.
74. The oligomeric compound according to any one of the preceding items, wherein the first region of linked nucleotides is selected from Table 2b or Table 3b, advantageously from Table 1a, more advantageously from Table 5.
75. The oligomeric compound according to any one of the preceding items, wherein the second region of linked nucleotides is selected from Table 2d or Table 3d, advantageously from Table 1 b, more advantageously from Table 5.
76. A composition comprising an oligomeric compound according to any of items 1 to 75, and a physiologically acceptable excipient.
77. A pharmaceutical composition comprising an oligomeric compound according to any of items 1 to 75.
78. The pharmaceutical composition of item 77, further comprising a pharmaceutically acceptable excipient, diluent, antioxidant, and/or preservative.
79. The pharmaceutical composition of item 77 or 78, wherein the oligomeric compound is the only pharmaceutically active agent.
80. The pharmaceutical composition of item 79, wherein the pharmaceutical composition is to be administered to patients or individuals which are statin-intolerant and/or for whom statins are contraindicated.
81. The pharmaceutical composition of item 77 or 78, wherein the pharmaceutical composition furthermore comprises one or more further pharmaceutically active agents.
82. The pharmaceutical composition of item 81, wherein the 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 the oligomeric compound, wherein the lipid-lowering agent is advantageously a statin or ezetimib.
83. The pharmaceutical composition of item 81 or 82, wherein the oligomeric compound and the further pharmaceutically active agent(s) are to be administered concomitantly or in any order.
84. An oligomeric compound according to any of items 1 to 75, for use in human or veterinary medicine or therapy.
85. An oligomeric compound according to any of items 1 to 75, for use in a method of treating a disease or disorder.
86. The compound for use of item 85, wherein the disease or disorder is 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 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.
87. A method of treating a disease or disorder comprising administration of an oligomeric compound according to any of items 1 to 75, to an individual in need of treatment.
88. The method according to item 87, wherein the oligomeric compound is administered subcutaneously or intravenously to the individual.
89. Use of an oligomeric compound according to any of items 1 to 75, for use in research as a gene function analysis tool.
The following Tables show nucleobase sequences of antisense and sense strands of oligomeric compounds as described herein, and definitions of antisense and sense strands of modified oligomeric compounds (the notation including 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.
P represents a terminal phosphate group;
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 # or * represents a phosphorothioate inter-nucleoside linkage;
i represents an inverted inter-nucleoside linkage, which can be either 3′-3′, or 5′-5′;
vp represents vinyl phosphonate;
mvp represents methyl vinyl phosphonate;
3xGaINAc or Mono-Galnac-PAHMono-Galnac-PAHMono-Galnac-PA/ represents a trivalent GaINAc, advantageously a “toothbrush” moiety as disclosed herein.
Sometimes, nucleoside are in square brackets for better reading. They do not indicate structural elements or modifications.
To the extent displayed, the presence of a 5′-terminal phosphate (“P”) is optional. On the other hand, to the extent a 5′-terminal phosphate is not displayed, its presence is optional as well. Generally, there is no requirement for a 5′-terminal phosphate in compounds to be administered to mammalian cells, since a mammalian kinase would add a 5′-terminal phosphate in case of its absence.
In Example 2, the nucleobase sequences of antisense and sense strands of 27 specific oligomeric compounds as described herein are given. These are also the subject of specific embodiments disclosed further above. For antisense sequences, the construct number coincides with the SEQ ID NO in the attached sequence listing. For sense sequences, the number of the corresponding entry in the sequence listing is construct number ±250.
Tables 1a and 1 b below shows the sugar-phosphate backbone modifications of the antisense and sense strands of the 27 constructs.
Tables 2a to 2d below show nucleobase sequences and sugar-phosphate backbone modifications of antisense and sense strands of the 250 constructs selected in accordance with Example 1. The above-disclosed 27 oligomeric compounds have been selected from these 250 constructs. The numbering in Table 2a coincides with the number of the corresponding entry in the sequence listing. For Table 2c the following applies: entry number in the sequence listing=entry number in the Table+250.
Tables 3a to 3d below show nucleobase sequences and sugar-phosphate backbone modifications of antisense and sense strands of further 43 constructs as described herein. For corresponding entries in the sequence listing, the following applies: entry number in Table 3a+500=entry number in the sequence listing; entry number in Table 3c+543=entry number in the sequence listing.
It should also be noted that the scope of the disclosed embodiments extends to sequences that correspond to those in the Tables above, and wherein the 5′ 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, in other words can be any of adenine (A), uracil (U), guanine (G) or cytosine (C). Additionally, the scope of the present embodiments extends to sequences that correspond to those in Table 1a or Table 1 b, and wherein the 3′ nucleoside of the sense (passenger) strand (second region as defined in the claims herein) can include any nucleobase that can be present in an RNA molecule, in other words can be any of adenine (A), uracil (U), guanine (G) or cytosine (C), advantageously however a nucleobase that is complementary to the 5′ nucleobase of the antisense (guide) strand (first region as defined in the claims 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 particular 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.
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.
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, 1xMEM non-essential amino acids, and 1xPen/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 50 uM in molecular biology grade water and annealed by heating at 95 C 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 50 uL 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 100 uL, 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, 12173011A) 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 50 uL 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 100 uL, 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, 12173011A) 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.
Results obtained by performing methods of Example 1
Table 4 below and
The IC50 data in the single- to double-digit nanomolar range demonstrate outstanding performance of numerous constructs as described herein.
Optimized Double Stranded Constructs
Full definitions of the constructs are given in Table 5 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.
Performance data are shown in
Optimized hairpin molecules (mxRNAs)
Full definitions of the molecules are given in Table 6 below.
Performance data are shown in
This application claims priority to U.S. Provisional application Ser. No. 63/211,861, filed Jun. 17, 2021, the contents of which are hereby incorporated by reference in their entirety.
| Number | Date | Country | |
|---|---|---|---|
| 63211861 | Jun 2021 | US |
