Patent Application
20210332358
The present invention relates to novel RNAi triggers that can be chemically synthesized and used to modulate gene expression inside animal cells to study various genes function in laboratories or as an active ingredient for agricultural, veterinary, cosmetic and/or therapeutic applications
RNA interference or RNAi is a biologic phenomenon characterized by ability of double-stranded RNA molecules to specifically down-regulate individual genes in animals, it was discovered in 1998 by Craig Mello and Andrew Fire, and received a 2006 Nobel Prize for Physiology or Medicine due to its promise to offer novel type of therapeutics. Since 2001, when chemically synthesized RNAi triggers (short interfering RNAs or siRNAs) were shown to work in mammalian cell culture, siRNAs have been extensively used to study various genes functions in research labs around the world. The first RNAi drug Onpattro™ was approved by FDA in August 2018 to help patients with hereditary ATTR amyloidosis. Numerous other RNAi drugs are been currently developed and tested in pre-clinical and clinical studies.
While RNAi promises to become one of the major new drug modality, there are certain challenges associated with it. One of those is the high cost of production of the active ingredient. The conventional RNAi trigger the short interfering RNA (or siRNA) is composed of two 19-25 nt long oligonucleotides (totaling about 40-50 nucleotides) annealed to each other. Production of such molecules requires sophisticated multi-step synthesis, followed, in some cases, by extensive purification procedures, resulting in relatively high production costs. The first RNAi drug Onpattro™ will go for $450,000 per treatment annually, and one of the contributing factors for such a high price is likely to be the drug's cost of production.
The terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting of the invention. As used herein, the term “and/or” includes any and all combinations of one or more of the associated items. As used herein, the singular forms “a”, “an” and “the” are intended to include the plural forms as well as the singular forms, unless the context clearly indicates otherwise. It will be further understood that the terms “comprises” and/or “comprising” when used in this specification, specify the presence of stated features, steps, operations, elements and/or components, but do not preclude the presence or addition of one or more other features, steps, operations, elements, components, and/or groups thereof.
Unless otherwise defined, all terms (including technical and scientific terms) used herein have the same meaning as commonly understood by one having ordinary skill in the art, to which this invention belongs. It will be further understood that terms, such as those defined in commonly used dictionaries, should be interpreted as having a meaning that is consistent with their meaning in the context of the relevant art and the present disclosure and will not be interpreted in an idealized or overly formal sense unless expressly so defined herein.
In describing the invention, it will be understood that a number of features, steps, operations, elements and/or components are disclosed. Each of these has individual benefit and each can also be used in conjunction with one or more, or in some cases all, of the other disclosed features, steps, operations, elements and/or components. Accordingly, for the sake of clarity, this description will refrain from repeating every possible combination of the individual features, steps, operations, elements and/or components in an unnecessary fashion. Nevertheless, the specifications should be read with the understanding that such combinations are entirely within the scope of the invention.
The new miniaturized hairpin RNAi triggers (mxRNA) and methods of uses thereof are discussed herein. In the following description, for the purposes of explanation, numerous specific details are set forth in order to provide a thorough understanding of the present invention. It will be evident, however, to one skilled in the art that the present invention may be practiced without theses specific details.
The present disclosure is to be considered as an exemplification of the invention, and is not intended to limit the invention to the specific embodiments illustrated by the figures or described below.
The current invention will now be described by referencing the appended figures representing certain embodiments. It introduces miniaturized hairpin RNAi trigger molecules (mxRNA) comprising the following components:
According to the present invention, there is also provided a conjugate for modulating, preferably inhibiting, expression of a target gene in a cell, said conjugate comprising a nucleic acid attached to one or more ligands, wherein said nucleic acid is preferably not a substrate for dicer, and comprises:
first, second and third nucleic acid portions;
wherein said first portion (i) is at least partially complementary to at least a portion of RNA transcribed from said target gene, and (ii) has a 5′ to 3′ directionality thereby defining 5′ and 3′ regions of said first portion;
wherein said second portion (i) is at least partially complementary to said first portion, and (ii) has a 5′ to 3′ directionality thereby defining 5′ and 3′ regions of said second portion;
wherein said first and second portions dimerise to form an at least partially complementary duplex;
wherein the third nucleic acid portion links the 3′ region of said first portion to the 5′ region of said second portion.
A conjugate according to the present invention comprises a third nucleic acid portion that is at least partially complementary to at least a portion of RNA transcribed from said target gene. Still further, a conjugate according to the present invention can comprise a second nucleic acid portion that is at least partially complementary to at least a portion of RNA transcribed from said target gene.
Preferably, a conjugate according to the present invention comprises one or more ligands that are conjugated to the second nucleic acid portion. Suitably, the one or more ligands are conjugated at the 3 ‘ region of the second nucleic acid portion. Alternatively, the one or more ligands are conjugated at the 3’ region of the first nucleic acid portion and/or at the 5′ region of the second nucleic acid portion. A still further alternative is where the one or more ligands are conjugated at one or more regions intermediate of the 5′ and 3′ regions of the first nucleic acid portion, and/or are conjugated at one or more regions intermediate of the 5′ and 3′ regions of the second nucleic acid portion. As a still further alternative, the one or more ligands are conjugated at one or more regions of the third nucleic acid portion.
Typically, 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. In a preferred embodiment, the one or more ligands comprise one or more carbohydrates, such as a monosaccharide, disaccharide, trisaccharide, tetrasaccharide, oligosaccharide or polysaccharide. Even more preferably, the one or more carbohydrates comprise one or more galactose moieties, one or more lactose moieties, one or more N-Acetyl-Galactosamine moieties, and/or one or more mannose moieties, such as one or more N-Acetyl-Galactosamine moieties, preferably two or three N-Acetyl-Galactosamine moieties.
The one or more ligands can be attached to the nucleic acid in a linear configuration, or in a branched configuration, such that for example the one or more ligands are attached to the nucleic acid as a biantennary or triantennary configuration, or as a configuration based on single ligands at different positions.
A conjugate according to the present invention comprises a nucleic acid that is a single strand that dimerises whereby the first and second portions form an at least partially complementary duplex. Typically, the nucleic acid is 17 to 40 nucleotides in length, preferably at least 20 nucleotides in length, or more preferably is at least 25 nucleotides in length.
In a conjugate according to the present invention, the first nucleic acid portion is 7 to 20 nucleotides in length, preferably 10 to 18 nucleotides in length, more preferably less than 18 nucleotides in length. Similarly, in a conjugate according to the present invention the second nucleic acid portion is 7 to 20 nucleotides in length, preferably 10 to 18 nucleotides in length, more preferably less than 18 nucleotides in length. Still further, it is preferred that in a conjugate according to the present invention the third nucleic acid portion is 1 to 10 nucleotides in length, such as 4 to 9 nucleotides in length, such as 4, 5, 7 or 9 nucleotides in length.
A conjugate according to the present invention further comprises one or more phosphorothioate or phosphorodithioate internucleotide linkages, such as 1 to 15 phosphorothioate or phosphorodithioate internucleotide linkages. Typically, the one or more phosphorothioate or phosphorodithioate internucleotide linkages at one or more of the 5′ and/or 3′ regions of the first and/or second nucleic acid portions. In a preferred embodiment, a conjugate according to the present invention comprises phosphorothioate or phosphorodithioate internucleotide linkages between at least two, preferably at least three, preferably at least four, preferably at least five, preferably at least six, preferably at least seven, preferably at least eight, preferably at least nine, preferably ten, adjacent nucleotides of the third nucleic acid portion, dependent on the number of nucleotides present in the third nucleic acid portion. Still further, a conjugate according to the present invention can comprise a phosphorothioate or phosphorodithioate internucleotide linkage between each adjacent nucleotide that is present in the third nucleic acid portion. Furthermore, a conjugate according to the present invention can comprise a phosphorothioate or phosphorodithioate internucleotide linkage linking the first nucleic acid portion to the third nucleic acid portion and/or the second nucleic acid portion to the third nucleic acid portion.
A conjugate according to the present invention according to the present invention further comprises at least one nucleotide of the first and/or second and/or third nucleic acid portion that is modified. For example, in a conjugate according to the present invention the one or more of the odd numbered nucleotides starting from the 5′ region of the first nucleic acid portion are modified, and/or wherein one or more of the even numbered nucleotides starting from the 5′ region of the first nucleic acid portion 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. Typically, the one or more of the odd numbered nucleotides starting from the 3′ region of the second nucleic acid portion are modified by a modification that is different from the modification of odd numbered nucleotides of the first nucleic acid portion.
Further characteristics of the modification pattern can be as follows, but for the avoidance of doubt the following statements are not limiting on the scope of the invention as described herein:
Typically, in a conjugate according to the present invention the modification and/or modifications are each and individually sugar, backbone or base modifications, and are suitably selected from the group consisting of 3′-terminal deoxy-thymine, 2′-O-methyl, a 2′-deoxy-modification, a 2′-amino-modification, a 2′-alkyl-modification, a morpholino modification, a phosphoramidate modification, phosphorothioate or phosphorodithioate group modification, a 5′ phosphate or 5′ phosphate mimic modification and a cholesteryl derivative or a dodecanoic acid bisdecylamide group modification.
The modification can be any one of a locked nucleotide; an abasic nucleotide or a non-natural base comprising nucleotide.
In a preferred embodiment, at least one modification is 7-O-methyl. In a further preferred embodiment, at least one modification is 2′-F.
In a further preferred embodiment, the nucleotides at any of positions 2 and 14 downstream from the first nucleotide of the 5′ region of the first nucleic acid portion do not contain 2′-O-methyl modifications in ribose moieties, and/or the nucleotides of the second nucleic acid portion, that correspond in position to any of the nucleotides of the first nucleic acid portion at any of positions 9 to 11 downstream from the first nucleotide of the 5′ region of the first nucleic acid portion, do not contain 2′-O-methyl modifications in ribose moieties.
A conjugate according to the present invention preferably further comprises one or more unmodified nucleotides, which can typically replace any modified nucleotide as hereinbefore described. Such one or more unmodified nucleotides can be positioned in the 5′ region of the second nucleic acid portion and/or can be positioned in the third nucleic acid portion at positions proximal to the second nucleic acid portion.
Preferably, the one or more, preferably one, unmodified nucleotide represent the nucleotide or nucleotides of the 5′ region of the second nucleic acid portion, typically the nucleotide of the second nucleic acid portion that is directly linked to the third nucleic acid portion, and; or the nucleotide or nucleotides of the third nucleic acid portion proximal the 5′ region of the second nucleic acid portion, typically the nucleotide of the third nucleic acid portion that is directly linked to the second nucleic acid portion, and preferably represent any of the nucleotides at any of positions 17, 18, 19, 20, 21, 22, 23, 24 and/or 25 downstream from the first nucleotide of the 5′ region of the first nucleic acid portion, preferably positions 18, 19, 20 and/or 21.
In a conjugate according to the present invention, typically all nucleotides other than the unmodified nucleotides, and f or the nucleotides at any of positions 2 and 14 downstream from the first nucleotide of the 5′ region of the first nucleic acid portion, and/or the nucleotides of the second nucleic acid portion, that correspond in position to any of the nucleotides of the first nucleic acid portion at any of positions 9 to 11 downstream from the first nucleotide of the 5′ region of the first nucleic acid portion, contain 2′-O-methyl modifications in ribose moieties
In a preferred embodiment, all odd numbered nucleotides of the first nucleic acid region, starting from the 5′ region of the first nucleic acid portion, are 2′-0-methyl modified, and all even numbered nucleotides of the first nucleic acid region, starting from the 5′ region of the first nucleic acid portion, are 2′-F modified.
In a particular embodiment, other than the unmodified nucleotide or nucleotides of the second nucleic acid portion, all odd numbered nucleotides of the second nucleic acid region, starting from the 3′ region of the second nucleic acid portion, are 2′-F modified, and all even numbered nucleotides of the second nucleic acid region, starting from the 3′ region of the second nucleic acid portion, are 2′-0-methyl modified. For example, a plurality of adjacent commonly modified nucleotides of 2 to 4 adjacent nucleotides; preferably 3 or 4 adjacent nucleotides, are located downstream of the unmodified nucleotide or nucleotides of the second nucleic acid portion, and for the remaining nucleotides of the second nucleic acid portion all odd numbered nucleotides of the second nucleic acid region, starting from the 3′ region of the second nucleic acid portion, are 2′-F modified, and all even numbered nucleotides of the second nucleic acid region, starting from the 3′ region of the second nucleic acid portion, are 2′-0-methyl modified.
In a further embodiment of the present invention, in a conjugate as described herein the nucleotides in the third nucleic acid portion are modified in an alternating 2′-0-methyl, 2′-F, pattern, starting with a 2′-0-methyl modification adjacent to the 3′ region of the first nucleic acid portion.
A conjugate according to the present invention can further comprise at least one vinylphosphonate modification, such as at least one vinylphosphonate modification in the 5′ region of the first nucleic acid portion.
In a conjugate according to the present invention, one or more nucleotides of at least one of the first nucleic acid portion and the second nucleic acid portion 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 or one or more nucleotides of at least one of the first nucleic acid portion and the second nucleic acid portion 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
A conjugate according to the present invention can further comprise one or more nucleotides at the 3′ region of at least one of the first nucleic acid portion and the second nucleic acid portion is an inverted nucleotide and is attached to the adjacent nucleotide via the 3′ carbon of the terminal nucleotide and the 3′ carbon of the adjacent nucleotide, and/or one or more nucleotides at the 5′ region of at least one of the first nucleic acid portion and the second nucleic acid portion is an inverted nucleotide and is attached to the adjacent nucleotide via the 5′ carbon of the terminal nucleotide and the 5′ carbon of the adjacent nucleotide, and or one or more nucleotides intermediate the 3′ and 5′ regions of at least one of the first nucleic acid portion and the second nucleic acid portion is an inverted nucleotide and is attached to the adjacent nucleotide via the 3′ carbon of the terminal nucleotide and the 3′ carbon of the adjacent nucleotide and/or one or more nucleotides intermediate the 3′ and 5′ regions of at least one of the first nucleic acid portion and the second nucleic acid portion is an inverted nucleotide and is attached to the adjacent nucleotide via the 5′ carbon of the terminal nucleotide and the 5′ carbon of the adjacent nucleotide, and/or one or more nucleotides of at least one of the third nucleic acid portion is an inverted nucleotide and is attached to the adjacent nucleotide via the 3′ carbon of the terminal nucleotide and the 3′ carbon of the adjacent nucleotide and/or one or more nucleotides of at least one of the third nucleic acid portion is an inverted nucleotide and is attached to the adjacent nucleotide via the 5′ carbon of the terminal nucleotide and the 5′ carbon of the adjacent nucleotide. Typically, the 3′ and/or 5′ inverted nucleotide of the first and/or second strand is attached to the adjacent nucleotide via a phosphate group by way of a phosphodiester linkage; or the 3′ and/or 5′ inverted nucleotide of the first and/or second strand is attached to the adjacent nucleotide via a phosphorothioate group; or the 3′ and/or 5′ inverted nucleotide of the first and/or second strand is attached to the adjacent nucleotide via a phosphorodithioate group.
A conjugate according to the present invention can be blunt ended at one end. Alternatively, a conjugate according to the present invention can comprise a first or second nucleic acid portion that has an overhang.
According to the present invention, there is further provided a homo-dimer RNA molecule comprising two nucleic acid molecules as hereinbefore described, wherein the nucleic acid molecules are bound together through complementary interactions, where the first portion of the first molecule interacts with the second portion of the second molecule and there is a third portion in each molecule that generates a bulge structure intermediate of the first and second portions of the respective nucleic acid molecules.
A conjugate or homo-dimer RNA molecule and/or conjugate as described herein is directed at a target RNA that is selected from at least one of: mRNA, IncRNA, and/or other RNA molecules.
The present invention further comprises:
There is also provided by the present invention a conjugate as hereinbefore described wherein the conjugate comprises a sequence selected from the group consisting of SEQ ID NOs: 14, 15, 16, 17 and 18, the linker and the tri-valent GaINAc moiety being at the 3′-end of the nucleic acid moiety. For each of sequences of SEQ ID NOs: 14, 15, 16, 17 and 18, these comprise first, second and third nucleic acid portions as follows:
For the sequences as set out above, the first and second portions dimerise to form an at least partially complementary duplex as hereinbefore described.
Typically such sequences comprise phosphorothioate or phosphorodithioate internucleotide linkages between each of the nucleotides of the third nucleic acid portion thereof and or unmodified nucleotides in positions 17, 18, 19, 20, 21, 22, 23, 24 and/or 25 from the 5′ region of the first portion.
Example 1 of
Example 2 of
Example 3 of
mxRNA molecules can be chemically synthesized using conventional and/or advanced approaches, and be used as research tools to study various genes functions in the labs, and/or as active ingredients for agricultural, veterinary, cosmetic and/or therapeutic applications.
Aspects of the invention are demonstrated by the following non-limiting examples.
Activity tests for mxRNAs versus conventional double stranded siRNA constructs that were directed against MAP4K4 were conducted. Hep3B cells were incubated in 96-well plates at a density of 15,000 cells per each well. The compounds tested with this study were at a final concentration of 50 nM. Reverse transfection was carried out using RNAiMax at 0.3 μL per well. In addition to the test compounds two controls ((TTR PC) TTR-directed siRNA and (INT PC) aha-1 directed siRNA) were also used (Tables 3 & 4). The duration of incubation was 24 hours. Subsequently mRNA was isolated and quantified using a bDNA assay (Quantigene 1.0/2.0). The readouts were normalised to GAPDH transcript, and the mean of quadruplicates was determined. The values from mock treated cells was set at 1.
A summary of the results obtained from this experiment are presented in Table 1 and
Primary mouse hepatocytes (Lot#MC830; ThermoFisher Scientific) were incubated in a 96-well plate at a density of 60,000 cells per well. The compounds tested with this study were added at a final concentration of 500 nM. In addition to the test compounds two controls ((XD-12171) TTR-directed siRNA and (XD-00033) aha-1 directed siRNA as a negative control) were also used (Tables 3 & 4). A direct incubation transfection (without transfection lipid) method was used. The duration of incubation was 72 hours. Subsequently mRNA was isolated and quantified using a bDNA assay (Quantigene 1.0/2.0). The readouts were normalised to GAPDH, and the mean of quadruplicates was determined. The values from mock treated cells was set at 1.
A summary of the results obtained from this experiment are presented in Table 2 and
Summary of Results from Examples 1 and 2
The results confirm that the single-oligo miniaturized hairpin structures (mxRNA) can elicit target gene knock-down, if used with transfection reagent and unobstructed with conjugate moieties, as was previously demonstrated in Lapierre et al, 2011.
We demonstrated that mxRNA molecules conjugated with a bulky chemical moiety (GaINAc in this case) can still elicit target gene knock-down, when used with a transfection reagent. This is a new and non-trivial finding since adding a conjugate to the 3′ end of the active strand could have affected the mxRNAs' ability to be recognized by the RNAi machinery, to enter an RNA-induced silencing complex (RISC) and/or to remain active within the RISC.
Next, mxRNA-conjugates (conjugated with GaINAc in this case) were demonstrated to enter cells via receptor-mediated uptake and to yield activities higher than those of conventional siRNA targeting exactly the same portion of mRNA (e.g. mxRNA C24, C25, C26 constructs compared with conventional C16, C17 constructs). This is a new finding and without wishing to be bound to a particular theory, such improvement could be due to the smaller size of the mxRNA-conjugate molecules (approximately 32 nucleotides in total), if compared with conventional siRNAs (approximately 42 nucleotides in total).
Finally the results showed that the use of diverse chemical modification patterns comprising phosphodiester linkage modifications (e.g. phosphorothioate modifications) and/or sugar modifications (e.g. 2′OH positions) can further improved the performance of mxRNAs.
| Number | Date | Country | |
|---|---|---|---|
| 62765454 | Aug 2018 | US | |
| 62726619 | Sep 2018 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | PCT/IB2019/057110 | Aug 2019 | US |
| Child | 17187309 | US |
