NZ624471B2 - Modified rnai agents - Google Patents
Modified rnai agents Download PDFInfo
- Publication number
- NZ624471B2 NZ624471B2 NZ624471A NZ62447112A NZ624471B2 NZ 624471 B2 NZ624471 B2 NZ 624471B2 NZ 624471 A NZ624471 A NZ 624471A NZ 62447112 A NZ62447112 A NZ 62447112A NZ 624471 B2 NZ624471 B2 NZ 624471B2
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- New Zealand
- Prior art keywords
- kjm
- annotation
- nucleotides
- strand
- double
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Classifications
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- C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
- C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
- C07H21/02—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with ribosyl as saccharide radical
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- C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
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- C12N2310/14—Type of nucleic acid interfering N.A.
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- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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- C12N2310/321—2'-O-R Modification
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N2320/00—Applications; Uses
- C12N2320/30—Special therapeutic applications
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N2320/00—Applications; Uses
- C12N2320/50—Methods for regulating/modulating their activity
- C12N2320/51—Methods for regulating/modulating their activity modulating the chemical stability, e.g. nuclease-resistance
Abstract
Disclosed is a double-stranded RNAi (dsRNA) duplex agent capable of inhibiting the expression of a target gene. The dsRNA duplex comprises one or more motifs of three identical modifications on three consecutive nucleotides in one or both strand, particularly at or near the cleavage site of the strand. Other aspects of the invention relates to pharmaceutical compositions comprising these dsRNA agents and the use of such dsRNA agents in the manufacture of a medicament for delivering a polynucleotide to a specific target in a subject. nd. Other aspects of the invention relates to pharmaceutical compositions comprising these dsRNA agents and the use of such dsRNA agents in the manufacture of a medicament for delivering a polynucleotide to a specific target in a subject.
Description
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Modified RNAi Agents
RELATED APPLICATION
This application claims priority to U.S. Provisional Application No. 61/561,710,
filed on November 18, 201 1, the entire contents of which are hereby incorporated herein
by reference.
FIELD OF THE INVENTION
The ion relates to RNAi duplex agents having particular motifs that are
advantageous for tion of target gene expression, as well as RNAi compositions
suitable for therapeutic use. Additionally, the invention provides methods of ting
the expression of a target gene by administering these RNAi duplex agents, e.g., for the
treatment of various diseases.
BACKGROUND
RNA interference or "RNAi" is a term initially coined by Fire and co-workers to
describe the observation that double-stranded RNAi (dsRNA) can block gene expression
(Fire et al. (1998) Nature 391, 806-81 1; Elbashir et al. (2001) Genes Dev. 15, 188-200).
Short dsRNA s gene-specific, post-transcriptional silencing in many organisms,
including vertebrates, and has provided a new tool for studying gene function. RNAi is
mediated by duced silencing complex (RISC), a sequence-specific, multicomponent
se that destroys messenger RNAs homologous to the silencing r.
RISC is known to contain short RNAs (approximately 22 nucleotides) derived from the
-stranded RNA r, but the protein components of this activity remained
unknown.
Double-stranded RNA (dsRNA) molecules with good gene-silencing properties
are needed for drug development based on RNA interference (RNAi). An initial step in
RNAi is the activation of the RNA induced silencing x (RISC), which requires
degradation of the sense strand of the dsRNA duplex. Sense strand was known to act as
the first RISC substrate that is cleaved by Argonaute 2 in the middle of the duplex region
Immediately after the d 5'-end and 3'-end fragments of the sense strand are
removed from the endonuclease Ago2, the RISC becomes ted by the nse
strand (Rand et al. (2005) Cell 123, 621).
It was believed that when the cleavage of the sense strand is inhibited, the
endonucleo lytic cleavage of target mRNA is impaired (Leuschner et al. (2006) EMBO
Rep., 7, 314; Rand et al. (2005) Cell 123, 621; Schwarz et al. (2004) Curr. Biol. 14, 787).
Leuschner et al. showed that incorporation of a 2'Me ribose to the Ago2 cleavage site
in the sense strand inhibits RNAi in HeLa cells (Leuschner et al. (2006) EMBO Rep., 7,
314). A similar effect was observed with phosphorothioate modifications, showing that
cleavage of the sense strand was required for efficient RNAi also in mammals.
Morrissey et al. used a siRNA duplex containing 2'-F modified residues, among
other sites and modifications, also at the Ago2 cleavage site, and obtained compatible
silencing compared to the unmodified siRNAs (Morrissey et al. (2005) Hepatology 41,
1349). However, Morrissey's modification is not motif specific, e.g., one modification
includes 2'-F modifications on all pyrimidines on both sense and antisense strands as
long as pyrimidine residue is present, without any selectivity; and hence it is uncertain,
based on these teachings, if specific motif cation at the cleavage site of sense
strand can have any actual effect on gene ing acitivity.
Muhonen et al. used a siRNA duplex containing two 2'-F modified residues at the
Ago2 cleavage site on the sense or antisense strand and found it was ted (Muhonen
et al. (2007) Chemistry & Biodiversity 4, 858-873). r, Muhonen's modification
is also sequence specific, e.g., for each particular strand, Muhonen only modifies either
all pyrimidines or all purines, without any selectivity.
Choung et al. used a siRNA duplex containing ative modifications by 2'-
OMe or various combinations of 2'-F, 2'-OMe and phosphorothioate modifications to
stabilize siRNA in serum to Surl0058 (Choung et al. (2006) Biochemical and
Biophysical Research Communications 342, 7). Choung suggested that the
residues at the ge site of the antisense strand should not be modified with 2'-OMe
in order to increase the stability of the siRNA.
There is thus an g need for iRNA duplex agents to improve the gene
ing efficacy of siRNA gene therapeutics. This invention is directed to that need.
SUMMARY
In one aspect, the invention provides a -stranded RNAi agent capable of inhibiting the
expression of a target gene, comprising a sense strand and an antisense strand, each strand having
14 to 30 nucleotides, wherein the duplex is represented by formula (III):
sense: 5' np -Na -(X X X)i-Nb -Y Y Y -Nb -(Z Z Z)j -Na - nq 3'
antisense: 3' np’-Na’-(X’X′X′)k-Nb’-Y′Y′Y′-Nb’-(Z′Z′Z′)l-Na’- nq’ 5'
(III)
wherein:
i, j, k, and l are each ndently 0 or 1;
p and q are each independently 0-6;
each Na and Na’independently represents an oligonucleotide sequence comprising 0-25 nucleotides
which are either modified or unmodified or combinations thereof, each ce comprising at least two
differently modified nucleotides, each Nb and Nb’independently ents an oligonucleotide ce
comprising 1-10 modified nucleotides;
each np, np’, nq and nq’ independently represents an overhang tide sequence comprising 0-6
nucleotides; and
XXX, YYY, ZZZ, X′X′X′, Y′Y′Y′, and Z′Z′Z′ each independently represent one motif of three
identical modifications on three consecutive nucleotides;
wherein the modification on Nb is different than the modification on Y and the cation on
Nb’is different than the modification on Y’; and
n the Y’Y’Y’ motif occurs at the 11, 12 and 13 positions of the antisense strand from the 5’-
end.
In another aspect, the present invention provides a double-stranded RNAi agent capable of
inhibiting the expression of a target gene, comprising a sense strand and an antisense strand, each
strand having 14 to 30 nucleotides,
wherein the sense strand contains at least two motifs of three identical modifications on
three consecutive nucleotides, one of said motifs ing at the cleavage site in the strand and at
least one of said motifs occurring at another portion of the strand that is separated from the motif at
the cleavage site by at least one ed nucleotide, wherein the modification on the at least one
modified nucleotide is different than the modification on the three consecutive modified
nucleotides;
and wherein the antisense strand contains at least a first motif of three identical
modifications on three consecutive nucleotides, one of said motifs occurring at or near the cleavage
site in the strand and a second motif occurring at another portion of the strand that is separated from
the first motif by at least one modified nucleotide, wherein the modification on the at least one
modified nucleotide is different than the modification on the three consecutive modified
nucleotides;
wherein the modification in the motif occurring at the cleavage site in the sense strand is
different than the modification in the motif occurring at or near the cleavage site in the antisense
strand; and wherein the first or the second motif in the antisense strand occurs at the 11, 12 and 13
positions of the antisense strand from the 5’-end.
In another aspect, the present invention provides a double-stranded RNAi agent capable of
inhibiting the sion of a target gene, comprising a sense strand and an antisense strand, each
strand having 14 to 30 nucleotides,
wherein the sense strand contains at least one motif of three 2’-F modifications on three
utive nucleotides, one of said motifs occurring at or near the cleavage site in the strand, and
wherein a polynucleotide adjacent to the three consecutive nucleotides is a modified nucleotide
having a modification other than a 2’-F modification; and
wherein the nse strand contains at least one motif of three 2’-O-methyl modifications
on three consecutive nucleotides, one of said motifs occurring at or near the cleavage site, and
wherein a cleotide adjacent to the three consecutive nucleotides is a modified nucleotide
having a modification other than a 2’-O-methyl modification; and wherein one of the at least one
motif in the antisense strand occurs at the 11, 12 and 13 positions of the nse strand from the
’-end.
In another , the present invention provides a pharmaceutical composition sing
the -stranded RNAi agent according to the invention alone or in combination with a
pharmaceutically acceptable carrier or excipient.
In another aspect, the present invention provides the use of the double-stranded RNAi agent
ing to the invention in the manufacture of a medicament for inhibiting the expression of a
target gene.
In r aspect, the present invention provides the use of a dsRNA agent represented by
formula (III):
sense: 5' np -Na -(X X X) i-Nb -Y Y Y -Nb -(Z Z Z)j -Na - nq 3'
antisense: 3' np’-Na’-(X’X′X′)k-Nb’-Y′Y′Y′-Nb’-(Z′Z′Z′)l-Na’- nq’ 5'
(III)
i, j, k, and l are each independently 0 or 1;
p and q are each independently 0-6;
each Na and Na′ independently represents an oligonucleotide sequence comprising 0-25
nucleotides which are either modified or unmodified or combinations thereof, each sequence
comprising at least two differently modified tides;
each Nb and Nb′ ndently represents an oligonucleotide sequence comprising 1-10
modified nucleotides;
each np, np’, nq and nq’ independently represents an overhang tide sequence
comprising 0-6 nucleotide sequence; and
XXX, YYY, ZZZ, X′X′X′, Y′Y′Y′, and Z′Z′Z′ each independently represent one motif of
three identical modifications on three consecutive nucleotides; and
n the modifications on Nb is different than the modification on Y and the
modification on Nb’ is different than the modification on Y’; and
wherein the Y’Y’Y’ motif occurs at the 11, 12 and 13 positions of the antisense strand from
the 5’-end
in the manufacture of a medicament for delivering a cleotide to a ic target in a
subject.
In r aspect, the present invention provides the use of the dsRNAi agent of the
invention in the manufacture of a medicament for delivering a cleotide to a specific target of
a subject, wherein the ment is provided for subcutaneous administration.
This invention provides effective nucleotide or chemical motifs for dsRNA agents optionally
conjugated to at least one ligand, which are advantageous for inhibition of target gene sion,
as well as RNAi compositions suitable for therapeutic use.
The inventors surprisingly discovered that introducing one or more motifs of three identical
modifications on three consecutive nucleotides at or near the cleavage site of a dsRNA agent that is
comprised of ed sense and antisense strands enhances the gene silencing activity of the
dsRNA agent.
In one aspect, the invention relates to a double-stranded RNAi (dsRNA) agent capable of
inhibiting the sion of a target gene. The dsRNA agent comprises a sense strand and an
antisense strand, each strand having 14 to 30 nucleotides. The dsRNA duplex is represented by
formula (III):
sense: 5' np -Na -(X X X) i-Nb -Y Y Y -Nb -(Z Z Z)j -Na - nq 3'
antisense: 3' np’-Na’-(X’X′X′)k-Nb’-Y′Y′Y′-Nb’-(Z′Z′Z′)l-Na’- nq’ 5'
(III),
In a (III), i, j, k, and l are each independently 0 or 1; p and q are each independently 0-6; n
represents a nucleotide; each Na and Na′ independently represents an oligonucleotide sequence
comprising 0-25 nucleotides which are either modified or unmodified or combinations thereof, each
sequence comprising at least two differently modified nucleotides; each Nb and Nb′ independently
represents an ucleotide sequence comprising 0-10 nucleotides which are either modified or
unmodified or combinations thereof; each np and nq independently represents an overhang
nucleotide sequence comprising 0-6 nucleotides; and XXX, YYY, ZZZ, X′X′X′, Y′Y′Y′, and Z′Z′Z′
each independently represent one motif of three identical modifications on three consecutive
nucleotides; wherein the modifications on Nb is ent than the modification on Y and the
modifications on Nb’ is different than the modification on Y’. At least one of the Y nucleotides
forms a base pair with its complementary Y’ nucleotides, and wherein the modification on the Y
tide is ent than the modification on the Y’ nucleotide.
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Each np and nq independently represents an overhang nucleotide sequence
comprising 0-6 nucleotides; each n and n ' represents an overhang nucleotide; and p and q
are each independently 0-6.
In another aspect, the invention relates to a dsRNA agent capable of inhibiting the
expression of a target gene. The dsRNA agent ses a sense strand and an nse
strand, each strand having 14 to 30 nucleotides. The sense strand contains at least two
motifs of three identical modifications on three consecutive nucleotides, where at least
one of the motifs occurs at or near the cleavage site within the strand and at least one of
the motifs occurs at another portion of the strand that is separated from the motif at the
cleavage site by at least one nucleotide. The antisense strand contains at least one motif
of three cal modifications on three consecutive nucleotides, where at least one of
the motifs occurs at or near the cleavage site within the strand and at least one of the
motifs occurs at another portion of the strand that is ted from the motif at or near
cleavage site by at least one nucleotide. The cation in the motif occurring at or
near the cleavage site in the sense strand is different than the modification in the motif
occurring at or near the cleavage site in the antisense strand.
In another , the invention relates to a dsRNA agent capable of inhibiting the
expression of a target gene. The dsRNA agent comprises a sense strand and an antisense
strand, each strand having 14 to 30 nucleotides. The sense strand ns at least one
motif of three 2'-F modifications on three consecutive nucleotides, where at least one of
the motifs occurs at or near the cleavage site in the strand. The antisense strand contains
at least one motif of three 2'methyl cations on three consecutive nucleotides at
or near the cleavage site.
In r aspect, the invention relates to a dsRNA agent capable of inhibiting the
expression of a target gene. The dsRNA agent comprises a sense strand and an antisense
, each strand having 14 to 30 nucleotides. The sense strand contains at least one
motif of three 2'-F modifications on three consecutive nucleotides at positions 9,10,1 1
from the 5'end. The antisense strand contains at least one motif of three 2'methyl
modifications on three consecutive tides at positions 11,12,13 from the 5'end.
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In another , the invention further provides a method for delivering
dsRNA to a ic target in a t by subcutaneous or intravenenuous
administration.
DETAILED DESCRIPTION
A superior result may be obtained by introducing one or more motifs of three
identical modifications on three consecutive nucleotides into a sense strand and/or
antisense strand of a dsRNA agent, particularly at or near the ge site. The sense
strand and antisense strand of the dsRNA agent may otherwise be completely modified.
The introduction of these motifs interrupts the modification pattern, if present, of the
sense and/or antisense strand. The dsRNA agent optionally conjugates with a GalNAc
derivative ligand, for instance on the sense strand. The resulting dsRNA agents present
superior gene ing activity.
The inventors surprisingly discovered that having one or more motifs of three
identical modifications on three consecutive nucleotides at or near the ge site of at
least one strand of a dsRNA agent superiorly ed the gene silencing acitivity of the
dsRNA agent.
Accordingly, the invention provides a double-stranded RNAi (dsRNA) agent
capable of inhibiting the expression of a target gene. The dsRNA agent comprises a
sense strand and an antisense strand. Each strand of the dsRNA agent can range from 12-
nucleotides in length. For example, each strand can be between 14-30 nucleotides in
length, 17-30 nucleotides in length, 25-30 nucleotides in length, 27-30 nucleotides in
length, 17-23 nucleotides in length, 17-21 nucleotides in length, 17-19 nucleotides in
, 19-25 nucleotides in length, 19-23 nucleotides in length, 19-21 nucleotides in
length, 21-25 nucleotides in length, or 21-23 nucleotides in length.
The sense strand and antisense strand typically form a duplex dsRNA. The
duplex region of a dsRNA agent may be 12-30 nucleotide pairs in length. For example,
the duplex region can be between 14-30 nucleotide pairs in length, 17-30 nucleotide pairs
in length, 25-30 nucleotides in , 27-30 nucleotide pairs in , 17 - 23 nucleotide
pairs in length, 17-21 nucleotide pairs in length, 17-19 tide pairs in length, 19-25
nucleotide pairs in , 19-23 nucleotide pairs in length, 19- 2 1 nucleotide pairs in
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length, 21-25 nucleotide pairs in length, or 21-23 nucleotide pairs in length. In another
e, the duplex region is selected from 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,
and 27.
In one embodiment, the dsRNA agent of the invention comprises may contain one
or more overhang regions and/or capping groups of dsRNA agent at the 3'-end, or 5'-end
or both ends of a . The ng can be 1-6 nucleotides in length, for ce 2-6
nucleotides in length, 1-5 nucleotides in length, 2-5 nucleotides in , 1-4 nucleotides
in length, 2-4 nucleotides in length, 1-3 nucleotides in length, 2-3 nucleotides in length,
or 1-2 nucleotides in length. The overhangs can be the result of one strand being longer
than the other, or the result of two strands of the same length being staggered. The
overhang can form a mismatch with the target mR A or it can be mentary to the
gene ces being targeted or can be other sequence. The first and second strands can
also be joined, e.g., by additional bases to form a hairpin, or by other non-base linkers.
In one embodiment, the nucleotides in the overhang region of the dsRNA agent of
the invention can each independently be a modified or unmodified nucleotide including,
but no limited to 2'-sugar modified, such as, 2-F 2'-Omethyl, thymidine (T), 2'
methoxyethylmethyluridine (Teo), 2'methoxyethyladenosine (Aeo), 2'
methoxyethylmethylcytidine (m5Ceo), and any combinations thereof. For example,
TT can be an overhang sequence for either end on either strand. The overhang can form
a mismatch with the target mRNA or it can be complementary to the gene sequences
being ed or can be other ce.
The 5'- or 3'- overhangs at the sense , antisense strand or both strands of the
dsRNA agent of the invention may be phosphorylated. In some embodiments, the
overhang region contains two tides having a phosphorothioate between the two
nucleotides, where the two nucleotides can be the same or different. In one embodiment,
the overhang is present at the 3'-end of the sense strand, antisense strand or both strands.
In one embodiment, this 3'-overhang is present in the antisense strand. In one
embodiment, this 3'-overhang is present in the sense strand.
The dsRNA agent of the invention comprises only single overhang, which can
strengthen the interference activity of the dsRNA, without affecting its overall ity.
For example, the -stranded overhang is located at the 3'-terminal end ofthe sense
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strand or, alternatively, at the 3'-terminal end of the antisense strand. The dsRNA may
also have a blunt end, d at the 5'-end of the antisense strand (or the 3'-end of the
sense strand) or vice versa. Generally, the antisense strand of the dsRNA has a
nucleotide overhang at the 3'-end, and the 5'-endis blunt. While not bound by theory,
the asymmetric blunt end at the 5'-end of the antisense strand and 3'-end overhang of the
antisense strand favor the guide strand loading into RISC process.
In one embodiment, the dsRNA agent of the invention may also have two blunt
ends, at both ends of the dsRNA duplex.
In one embodiment, the dsRNA agent of the ion is a double ended er
of 19 nt in length, wherein the sense strand contains at least one motif of three 2'-F
cations on three consecutive nucleotides at ons 7,8,9 from the 5'end. The
antisense strand ns at least one motif of three 2'methyl modifications on three
consecutive tides at positions 11,12,13 from the 5'end.
In one embodiment, the dsRNA agent of the invention is a double ended bluntmer
of 20 nt in length, wherein the sense strand contains at least one motif of three 2'-F
modifications on three consecutive nucleotides at positions 8,9,10 from the 5'end. The
antisense strand contains at least one motif of three 2'methyl modifications on three
consecutive nucleotides at positions 11,12,13 from the 5'end.
In one embodiment, the dsRNA agent of the ion is a double ended bluntmer
of 2 1 nt in length, wherein the sense strand contains at least one motif of three 2'-F
modifications on three consecutive nucleotides at positions 9,10,1 1 from the 5'end. The
antisense strand contains at least one motif of three 2'methyl modifications on three
consecutive nucleotides at positions 11,12,13 from the 5'end.
In one embodiment, the dsRNA agent of the invention comprises a 2 1 nucleotides
(nt) sense strand and a 23 nucleotides (nt) antisense, wherein the sense strand contains at
least one motif of three 2'-F cations on three consecutive nucleotides at positions
9,10,1 1 from the 5'end; the antisense strand contains at least one motif of three 2'
methyl modifications on three consecutive nucleotides at positions 11,12,13 from the
'end, wherein one end of the dsRNA is blunt, while the other end is comprises a 2 nt
overhang. Preferably, the 2 nt overhang is at the 3'-end of the antisense. Optionally, the
dsRNA further comprises a ligand (preferably GalNAc ) .
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In one embodiment, the dsR A agent of the ion comprising a sense and
antisense strands, wherein: the sense strand is 25-30 nucleotide residues in length,
wherein starting from the 5'terminal nucleotide (position 1) positions 1 to 23 of said first
strand comprise at least 8 ribonucleotides; antisense strand is 36-66 nucleotide residues in
length and, starting from the 3'terminal nucleotide, comprises at least 8 cleotides
in the positions paired with positions 1- 23 of sense strand to form a duplex; wherein at
least the 3 ' terminal nucleotide of antisense strand is unpaired with sense , and up
to 6 consecutive 3'terminal nucleotides are ed with sense strand, thereby forming a
3' single stranded overhang of 1-6 nucleotides; wherein the inus of antisense strand
comprises from 10-30 consecutive nucleotides which are unpaired with sense strand,
thereby forming a 10-30 nucleotide single stranded 5'overhang; wherein at least the
sense strand 5'terminal and 3'terminal nucleotides are base paired with nucleotides of
antisense strand when sense and antisense strands are aligned for maximum
mentarity, thereby forming a substantially duplexed region between sense and
antisense strands; and antisense strand is sufficiently mentary to a target R A
along at least 19 ribonucleotides of antisense strand length to reduce target gene
expression when said double stranded nucleic acid is uced into a ian cell;
and wherein the sense strand contains at least one motif of three 2'-F cations on
three consecutive nucleotides, where at least one of the motifs occurs at or near the
cleavage site. The antisense strand contains at least one motif of three 2'methyl
modifications on three consecutive nucleotides at or near the cleavage site.
In one embodiment, the dsRNA agent of the invention sing a sense and
antisense s, wherein said dsRNA agent comprises a first strand having a length
which is at least 25 and at most 29 nucleotides and a second strand having a length
which is at most 30 nucleotides with at least one motif of three 2'methyl
modifications on three consecutive nucleotides at position 11,12,13 from the 5' end;
wherein said 3' end of said first strand and said 5' end of said second strand form a blunt
end and said second strand is 1-4 nucleotides longer at its 3' end than the first strand,
wherein the duplex region region which is at least 25 nucleotides in length, and said
second strand is sufficiently complemenatary to a target mR A along at least 19 nt of
said second strand length to reduce target gene expression when said dsRNA agent is
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introduced into a mammalian cell, and wherein dicer cleavage of said dsR A
preferentially s in an siR A comprising said 3' end of said second strand, thereby
reducing expression of the target gene in the mammal. ally, the dsRNA agent
further comprises a ligand.
In one embodiment, the sense strand of the dsRNA agent contains at least one
motif of three identical modifications on three consecutive nucleotides, where one of the
motifs occurs at the cleavage site in the sense strand.
In one embodiment, the antisense strand of the dsRNA agent can also contain at
least one motif of three identical modifications on three consecutive nucleotides, where
one of the motifs occurs at or near the ge site in the antisense strand.
For dsRNA agent having a duplex region of 17-23 nt in length, the cleavage site
of the nse strand is typically around the 10, 11 and 12 positions from the 5'-end.
Thus the motifs of three identical modifications may occur at the 9, 10, 11 positions; 10,
11, 12 positions; 11, 12, 13 positions; 12, 13, 14 positions; or 13, 14, 15 positions of the
antisense strand, the count starting from the 1st nucleotide from the 5'-end of the
nse strand, or, the count starting from the 1st paired nucleotide within the duplex
region from the 5'- end of the antisense strand. The cleavage site in the antisense strand
may also change according to the length of the duplex region of the dsRNA from the 5'-
end.
The sense strand of the dsRNA agent comprises at least one motif of three
cal modifications on three consecutive nucleotides at the cleavage site of the ;
and the antisense strand may have at least one motif of three identical modifications on
three consecutive nucleotides at or near the ge site of the strand. When the sense
strand and the antisense strand form a dsRNA duplex, the sense strand and the nse
strand can be so aligned that one motif of the three nucleotides on the sense strand and
one motif of the three nucleotides on the antisense strand have at least one nucleotide
overlap, i.e., at least one of the three nucleotides of the motif in the sense strand forms a
base pair with at least one of the three nucleotides of the motif in the antisense strand.
Alternatively, at least two nucleotides of the motifs from both strands may overlap, or all
three nucleotides may overlap.
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In one embodiment, the sense strand of the dsR A agent comprises more than
one motif of three identical modifications on three consecutive tides. The first
motif should occur at or near the cleavage site of the strand and the other motifs may be a
wing modifications. The term "wing modification" herein refers to a motif occurring at
r portion of the strand that is separated from the motif at or near the cleavage site
of the same strand. The wing modification is either adajacent to the first motif or is
separated by at least one or more nucleotides. When the motifs are immediately adjacent
to each other the chemistry of the motifs are distinct from each other and when the motifs
are separated by one or more nucleotide the chemistries of the motifs can be the same or
different. Two or more wing modifications may be present. For instance, when two
wing modifications are present, the wing modifications may both occur at one end of the
duplex region relative to the first motif which is at or near the cleavage site or each of the
wing cations may occur on either side of the first motif.
Like the sense strand, the antisense strand of the dsRNA agent comprises at least
two motifs of three cal modifications on three consecutive nucleotides, with at least
one of the motifs occurring at or near the cleavage site of the strand. This antisense
strand may also contain one or more wing modifications in an alignment similar to the
wing modifications that is present on the sense .
In one embodiment, the wing modification on the sense strand, antisense strand,
or both strands of the dsRNA agent typically does not include the first one or two
terminal nucleotides at the 3'-end, 5'-end or bothends of the .
In r embodiment, the wing modification on the sense strand, nse
strand, or both strands of the dsRNA agent typically does not include the first one or two
paired nucleotides within the duplex region at the 3'-end, 5'-end or bothends of the
strand.
When the sense strand and the antisense strand of the dsRNA agent each n
at least one wing modification, the wing modifications may fall on the same end of the
duplex region, and have an overlap of one, two or three nucleotides.
When the sense strand and the antisense strand of the dsRNA agent each contain
at least two wing modifications, the sense strand and the antisense strand can be aligned
so that two wing modifications each from one strand fall on one end of the duplex region,
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having an overlap of one, two or three nucleotides; two modifications each from one
strand fall on the other end of the duplex , having an overlap of one, two or three
nucleotides.
In one ment, every nucleotide in the sense strand and antisense strand of
the dsRNA agent, including the tides that are part of the motifs, may be modified.
Each nucleotide may be modified with the same or different modification which can
include one or more tion of one or both of the non-linking phosphate oxygens
and/or of one or more of the linking phosphate oxygens; alteration of a constituent of the
ribose sugar, e.g., of the 2' hydroxyl onthe ribose sugar; wholesale replacement of the
phosphate moiety with "dephospho" linkers; modification or ement of a naturally
occurring base; and replacement or modification of the ribose-phosphate backbone.
As nucleic acids are polymers of subunits, many of the modifications occur at a
position which is repeated within a nucleic acid, e.g., a modification of a base, or a
phosphate moiety, or a non-linking O of a phosphate moiety. In some cases the
modification will occur at all of the t positions in the nucleic acid but in many
cases it will not. By way of example, a modification may only occur at a 3' or 5'
terminal position, may only occur in a terminal region, e.g., at a position on a terminal
tide or in the last 2, 3, 4, 5, or 10 nucleotides of a strand. A modification may
occur in a double strand region, a single strand region, or in both. A modification may
occur only in the double strand region of a R A or may only occur in a single strand
region of a RNA. E.g., a phosphorothioate modification at a nking O position may
only occur at one or both termini, may only occur in a terminal , e.g., at a position
on a terminal nucleotide or in the last 2, 3, 4, 5, or 10 nucleotides of a strand, or may
occur in double strand and single strand regions, particularly at i. The 5' end or
ends can be phosphorylated.
It may be possible, e.g., to enhance stability, to include particular bases in
overhangs, or to include modified nucleotides or nucleotide surrogates, in single strand
overhangs, e.g., in a 5' or 3' overhang, or in both. E.g., it can be desirable to include
purine nucleotides in overhangs. In some embodiments all or some of the bases in a 3' or
' overhang may be modified, e.g., with a modification described herein. Modifications
can include, e.g., the use of cations at the 2' position of the ribose sugar with
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modifications that are known in the art, e.g., the use of deoxyribonucleotides, 2'-deoxy-
2'-fluoro (2'-F) or 2'methyl modified instead of the ribosugar of the nucleobase, and
modifications in the phosphate group, e.g., orothioate modifications. Overhangs
need not be homologous with the target sequence.
In one ment, each residue of the sense strand and antisense strand is
independently modified with LNA, HNA, CeNA, 2'-methoxyethyl, 2'- O-methyl, 2'
allyl, 2'-C- allyl, 2'-deoxy, or 2'-fluoro. The strands can contain more than one
modification. In one embodiment, each residue of the sense strand and antisense strand is
independently modified with 2'- O-methyl or 2'-fluoro.
At least two different modifications are lly present on the sense strand and
nse strand. Those two modifications may be the 2'- O-methyl or 2'-fluoro
modifications, or others.
In one embodiment, the sense strand and antisense strand each contains two
differently modified nucleotides selected from 2'methyl or 2'-fluoro.
In one embodiment, each residue of the sense strand and antisense strand is
independently modified with 2'methyl nucleotide, xyfluoro tide, 2 -O-N-
methylacetamido (2'NMA) nucleotide, a 2'dimethylaminoethoxyethyl (2'
DMAEOE) nucleotide, 2'aminopropyl (2'AP) nucleotide, or 2'-ara-Fnucleotide.
In one embodiment, the Na and/or b comprise modifications of an alternating
pattern. The term "alternating motif or "alternative pattern" as used herein refers to a
motif having one or more modifications, each modification occurring on ating
nucleotides of one strand. The ating nucleotide may refer to one per every other
tide or one per every three nucleotides, or a similar pattern. For example, if A, B
and C each represent one type of modification to the nucleotide, the alternating motif can
be "ABABABABABAB...," "AABBAABBAABB ...," "AABAABAABAAB
"AAABAAABAAAB ...," "AAABBBAAABBB ...," or "ABCABCABC ABC ...," etc.
In one embodiment, the Na' and/or Nb' se modifications of an alternating
pattern. The term "alternating motif or "alternative pattern" as used herein refers to a
motif having one or more modifications, each modification occurring on alternating
nucleotides of one strand. The alternating nucleotide may refer to one per every other
tide or one per every three tides, or a similar pattern. For example, if A, B
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and C each represent one type of cation to the nucleotide, the alternating motif can
be "ABABABABABAB ...," "AABBAABB AABB ...," BAABAAB
"AAABAAABAAAB ...," "AAABBBAAABBB ...," or "ABCABCABC ABC ...." etc.
The type of cations contained in the alternating motif may be the same or
ent. For example, if A, B, C, D each represent one type of modification on the
nucleotide, the alternating pattern, i.e., modifications on every other nucleotide, may be
the same, but each of the sense strand or antisense strand can be selected from several
possibilities of modifications within the ating motif such as "ABABAB. ..",
"ACACAC..." "BDBDBD ..." or "CDCDCD ...," etc.
In one embodiment, the dsR A agent of the invnetion comprises the modification
pattern for the alternating motif on the sense strand relative to the modification pattern for
the alternating motif on the nse strand is shifted.The shift may be such that the
modified group of nucleotides of the sense strand corresponds to a differently modified
group of nucleotides of the antisense strand and vice versa. For example, the sense strand
when paired with the antisense strand in the dsRNA duplex, the alternating motif in the
sense strand may start with "ABABAB" from 5'-3' of the strand and the alternating motif
in the antisense strand may start with "BABABA" from 3'-5 f the strand within the
duplex region. As r example, the alternating motif in the sense strand may start
with "AABBAABB" from 5'-3' of the strand and the alternating motif in the antisenese
strand may start with "BBAABBAA" from 3'-5 f the strand within the duplex region, so
that there is a complete or partial shift of the modification patterns between the sense
strand and the nse strand.
In one embodiment, the dsRNA agent of the invention comprises the pattern of
the alternating motif of 2'methyl modification and 2'-F modification on the sense
strand initially has a shift relative to the pattern of the alternating motif of 2'methyl
modification and 2'-F modification on the antisense strand initially, i.e., the 2'methyl
modified nucleotide on the sense strand base pairs with a 2'-F ed tide on the
antisense strand and vice versa. The 1 position of the sense strand may start with the 2'-F
modification, and the 1 position of the antisense strand may start with the 2'- O-methyl
modification.
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The introduction of one or more motifs of three identical modifications on three
utive nucleotides to the sense strand and/or antisense strand interrupts the initial
modification n present in the sense strand and/or nse . This interruption
of the modification pattern of the sense and/or antisense strand by introducing one or
more motifs of three cal modifications on three consecutive nucleotides to the sense
and/or antisense strand singly enhances the gene silencing acitivty to the target
gene.
In one embodiment, when the motif of three identical modifications on three
consecutive nucleotides is introduced to any of the strands, the modification of the
nucleotide next to the motif is a different modification than the modification of the motif.
For example, the portion of the sequence containing the motif is " . ..NaYYYNb. ..," where
"Y" represents the modification of the motif of three identical modifications on three
consecutive nucleotide, and "Na" and "Nb" represent a modification to the nucleotide next
to the motif "YYY" that is different than the modification of Y, and where Na and b can
be the same or different modifications. Altnernatively, Na and/or b may be present or
absent when there is a wing modification present.
The dsRNA agent of the invention may further comprise at least one
phosphorothioate or methylphosphonate internucleotide linkage. The phosphorothioate
or methylphosphonate internucleotide linkage modification may occur on any nucleotide
of the sense strand or nse strand or both in any position of the strand. For instance,
the internucleotide linkage modification may occur on every nucleotide on the sense
strand and/or nse strand; each internucleotide linkage modification may occur in an
alternating pattern on the sense strand or antisense ; or the sense strand or nse
strand comprises both internucleotide linkage modifications in an alternating pattern.
The alternating pattern of the internucleotide linkage modification on the sense strand
may be the same or different from the antisense strand, and the alternating n of the
internucleotide linkage modification on the sense strand may have a shift relative to the
alternating pattern of the internucleotide linkage modification on the nse strand.
In one ment, the dsRNA comprises the phosphorothioate or
methylphosphonate internucleotide linkage modification in the overhang region. For
example, the overhang region comprises two nucleotides having a phosphorothioate or
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phosphonate intemucleotide linkage between the two nucleotides. Intemucleotide
linkage modifications also may be made to link the overhang nucleotides with the
terminal paired nucleotides within duplex region. For example, at least 2, 3, 4, or all the
overhang nucleotides may be linked through phosphorothioate or methylphosphonate
intemucleotide linkage, and optionally, there may be additional phosphorothioate or
methylphosphonate intemucleotide linkages linking the overhang nucleotide with a
paired nucleotide that is next to the overhang nucleotide. For instance, there may be at
least two phosphorothioate intemucleotide es between the terminal three
nucleotides, in which two of the three nucleotides are overhang tides, and the third
is a paried nucleotide next to the overhang nucleotide. ably, these terminal three
nucleotides may be at the 3'-end of the antisense strand.
In one embodiment the sense strand of the dsR A comprises 1-10 blocks of two
to ten phosphorothioate or methylphosphonate intemucleotide linkages separated by 1, 2,
3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 16 phosphate cleotide es, wherein
one of the phosphorothioate or methylphosphonate intemucleotide es is placed at
any position in the oligonucleotide sequence and the said sense strand is paired with an
antisense strand comprising any combination of phosphorothioate, methylphosphonate
and ate intemucleotide linkages or an antisense strand comprising either
phosphorothioate or methylphophonate or ate linkage.
In one embodiment the antisense strand of the dsRNA comprises two blocks of
two phosphorothioate or methylphosphonate cleotide linkages separated by 1, 2, 3,
4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, or 18 phosphate intemucleotide linkages,
wherein one of the phosphorothioate or methylphosphonate intemucleotide linkages is
placed at any position in the oligonucleotide sequence and the said nse strand is
paired with a sense strand comprising any combination of phosphorothioate,
methylphosphonate and phosphate intemucleotide linkages or an antisense strand
comprising either phosphorothioate or methylphophonate or phosphate linkage.
In one embodiment the antisense strand of the dsRNA comprises two blocks of
three phosphorothioate or phosphonate intemucleotide linkages separated by 1, 2,
3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or 16 phosphate intemucleotide linkages, wherein
one of the phosphorothioate or methylphosphonate intemucleotide linkages is placed at
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any position in the oligonucleotide sequence and the said antisense strand is paired with a
sense strand comprising any combination of phosphorothioate, methylphosphonate and
phosphate internucleotide linkages or an antisense strand comprising either
phosphorothioate or methylphophonate or phosphate linkage.
In one embodiment the nse strand of the dsR A comprises two blocks of
four phosphorothioate or methylphosphonate internucleotide es separated by 1, 2,
3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 phosphate internucleotide linkages, wherein one of
the phosphorothioate or methylphosphonate internucleotide linkages is placed at any
position in the oligonucleotide sequence and the said antisense strand is paired with a
sense strand comprising any combination of phosphorothioate, methylphosphonate and
phosphate internucleotide linkages or an nse strand comprising either
phosphorothioate or methylphophonate or phosphate linkage.
In one embodiment the antisense strand of the dsRNA comprises two blocks of
five phosphorothioate or methylphosphonate ucleotide linkages separated by 1, 2,
3, 4, 5, 6, 7, 8, 9, 10, 11 or 12 phosphate internucleotide linkages, wherein one of the
phosphorothioate or methylphosphonate internucleotide linkages is placed at any position
in the oligonucleotide sequence and the said nse strand is paired with a sense strand
comprising any combination of phosphorothioate, methylphosphonate and phosphate
internucleotide linkages or an nse strand comprising either phosphorothioate or
methylphophonate or phosphate e.
In one embodiment the antisense strand of the dsRNA comprises two blocks of
six orothioate or methylphosphonate internucleotide es separated by 1, 2, 3,
4, 5, 6, 7, 8, 9 or 10 phosphate internucleotide linkages, wherein one of the
phosphorothioate or methylphosphonate internucleotide linkages is placed at any position
in the oligonucleotide sequence and the said antisense strand is paired with a sense strand
comprising any combination of phosphorothioate, methylphosphonate and phosphate
ucleotide es or an antisense strand comprising either phosphorothioate or
phophonate or phosphate linkage.
In one embodiment the antisense strand of the dsRNA comprises two blocks of
seven phosphorothioate or methylphosphonate internucleotide linkages separated by 1, 2,
3, 4, 5, 6, 7 or 8 phosphate internucleotide linkages, wherein one of the phosphorothioate
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or methylphosphonate internucleotide linkages is placed at any position in the
oligonucleotide sequence and the said antisense strand is paired with a sense strand
comprising any ation of orothioate, methylphosphonate and phosphate
internucleotide es or an antisense strand comprising either phosphorothioate or
methylphophonate or phosphate linkage.
In one embodiment the antisense strand of the dsR A comprises two blocks of
eight phosphorothioate or methylphosphonate internucleotide linkages separated by 1, 2,
3, 4, 5 or 6 phosphate internucleotide es, wherein one of the phosphorothioate or
methylphosphonate internucleotide linkages is placed at any position in the
oligonucleotide sequence and the said antisense strand is paired with a sense strand
comprising any combination of phosphorothioate, methylphosphonate and phosphate
internucleotide linkages or an antisense strand comprising either phosphorothioate or
methylphophonate or phosphate linkage.
In one embodiment the antisense strand of the dsRNA ses two blocks of
nine phosphorothioate or methylphosphonate internucleotide linkages separated by 1, 2, 3
or 4 phosphate internucleotide linkages, wherein one of the phosphorothioate or
methylphosphonate internucleotide linkages is placed at any on in the
oligonucleotide sequence and the said antisense strand is paired with a sense strand
comprising any combination of phosphorothioate, methylphosphonate and phosphate
internucleotide linkages or an nse strand comprising either phosphorothioate or
methylphophonate or phosphate linkage.
In one ment, the dsRNA of the invention further comprises one or more
orothioate or methylphosphonate internucleotide linkage modification within 1-10
of the termini position(s) of the sense and/or antisense strand. For e, at least 2, 3,
4, 5, 6, 7, 8, 9 or 10 nucleotides may be linked through phosphorothioate or
methylphosphonate internucleotide linkage at one end or both ends of the sense and/or
antisense strand.
In one embodiment, the dsRNA of the invention r comprises one or more
orothioate or methylphosphonate internucleotide linkage modification within 1-10
of the internal region of the duplex of each of the sense and/or antisense strand. For
e, at least 2, 3, 4, 5, 6, 7, 8, 9 or 10 nucleotides may be linked through
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phosphorothioate methylphosphonate cleotide linkage at position 8-16 of the
duplex region counting from the 5'-end of the sense strand; the dsR A can optionally
further comprise one or more phosphorothioate or methylphosphonate intemucleotide
linkage modification within 1-10 of the termini position(s).
In one embodiment, the dsRNA of the invention further comprises one to five
phosphorothioate or methylphosphonate intemucleotide linkage modification(s) within
position 1-5 and one to five phosphorothioate or phosphonate intemucleotide
linkage modification(s) within position 18-23 of the sense strand (counting from the 5'-
end), and one to five phosphorothioate or methylphosphonate intemucleotide linkage
modification at positions 1 and 2 and one to five within positions 18-23 of the antisense
strand ing from the 5'-end).
In one embodiment, the dsRNA of the invention further comprises one
orothioate intemucleotide linkage modification within on 1-5 and one
phosphorothioate or methylphosphonate intemucleotide linkage modification within
position 18-23 of the sense strand (counting from the ), and one phosphorothioate
intemucleotide e modification at positions 1 and 2 and two phosphorothioate or
methylphosphonate intemucleotide linkage modifications within positions 18-23 of the
antisense strand (counting from the 5'-end).
In one embodiment, the dsRNA of the invention further comprises two
orothioate intemucleotide linkage modifications within position 1-5 and one
phosphorothioate intemucleotide linkage modification within position 18-23 of the sense
strand (counting from the 5'-end), and one phosphorothioate intemucleotide linkage
modification at positions 1 and 2 and two phosphorothioate intemucleotide linkage
modifications within positions 18-23 of the antisense strand (counting from the ).
In one embodiment, the dsRNA of the invention further comprises two
orothioate intemucleotide linkage modifications within on 1-5 and two
phosphorothioate intemucleotide linkage modifications within position 18-23 of the sense
strand ing from the 5'-end), and one phosphorothioate intemucleotide linkage
modification at positions 1 and 2 and two phosphorothioate intemucleotide linkage
modifications within positions 18-23 of the antisense strand (counting from the 5'-end).
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In one embodiment, the dsR A of the invention further comprises two
phosphorothioate intemucleotide e modifications within position 1-5 and two
phosphorothioate intemucleotide linkage cations within on 18-23 of the sense
strand (counting from the 5'-end), and one phosphorothioate intemucleotide linkage
modification at positions 1 and 2 and one phosphorothioate intemucleotide linkage
modification within ons 18-23 of the antisense strand (counting from the 5'-end).
In one embodiment, the dsRNA of the invention further comprises one
phosphorothioate intemucleotide linkage modification within position 1-5 and one
phosphorothioate cleotide linkage modification within position 18-23 of the sense
strand (counting from the 5'-end), and two orothioate intemucleotide linkage
modifications at positions 1 and 2 and two phosphorothioate intemucleotide linkage
modifications within positions 18-23 of the antisense strand (counting from the 5'-end).
In one embodiment, the dsRNA of the ion further comprises one
orothioate intemucleotide e modification within position 1-5 and one within
position 18-23 of the sense strand ing from the 5'-end), and two phosphorothioate
intemucleotide linkage modification at positions 1 and 2 and one phosphorothioate
intemucleotide linkage modification within positions 18-23 of the antisense strand
(counting from the 5'-end).
In one embodiment, the dsRNA of the ion further comprises one
phosphorothioate intemucleotide linkage modification within position 1-5 (counting from
the 5'-end), and two phosphorothioateintemucleotide linkage modifications at positions 1
and 2 and one phosphorothioate intemucleotide linkage modification within positions 18-
23 of the antisense strand (counting from the 5'-end).
In one ment, the dsRNA of the ion further comprises two
phosphorothioate intemucleotide linkage modifications within position 1-5 (counting
from the 5'-end), and one phosphorothioateintemucleotide linkage modification at
positions 1 and 2 and two phosphorothioate intemucleotide linkage modifications within
positions 18-23 of the antisense strand (counting from the 5'-end).
In one embodiment, the dsRNA of the ion further ses two
phosphorothioate intemucleotide linkage modifications within position 1-5 and one
within position 18-23 of the sense strand (counting from the 5'-end), and two
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phosphorothioate intemucleotide linkage modifications at positions 1 and 2 and one
phosphorothioate intemucleotide linkage modification within positions 18-23 of the
antisense strand (counting from the 5'-end).
In one embodiment, the dsR A of the invention further comprises two
phosphorothioate intemucleotide linkage cations within position 1-5 and one
phosphorothioate intemucleotide linkage modification within position 18-23 of the sense
strand (counting from the 5'-end), and two orothioate intemucleotide linkage
modifications at positions 1 and 2 and two phosphorothioate intemucleotide e
modifications within positions 18-23 of the nse strand (counting from the 5'-end).
In one embodiment, the dsRNA of the invention further comprises two
phosphorothioate intemucleotide e modifications within position 1-5 and one
phosphorothioate intemucleotide linkage modification within position 18-23 of the sense
strand (counting from the 5'-end), and one orothioate intemucleotide linkage
cation at positions 1 and 2 and two phosphorothioate intemucleotide e
modifications within positions 18-23 of the antisense strand (counting from the 5'-end).
In one embodiment, the dsRNA of the invention further comprises two
orothioate intemucleotide linkage modifications at position 1 and 2, and two
phosphorothioate intemucleotide linkage modifications at position 20 and 2 1 of the sense
strand (counting from the 5'-end), and one phosphorothioate intemucleotide linkage
modification at positions 1 and one at position 2 1 of the antisense strand (counting from
the 5'-end).
In one embodiment, the dsRNA of the ion further comprises one
phosphorothioate intemucleotide linkage modification at on 1, and one
phosphorothioate intemucleotide linkage modification at position 2 1 of the sense strand
(counting from the 5'-end), and two phosphorothioate intemucleotide linkage
modifications at ons 1 and 2 and two phosphorothioate intemucleotide linkage
modifications at ons 20 and 2 1 the antisense strand (counting from the 5'-end).
In one ment, the dsRNA of the invention further comprises two
phosphorothioate cleotide linkage modifications at position 1 and 2, and two
phosphorothioate intemucleotide linkage modifications at position 2 1 and 22 of the sense
strand (counting from the 5'-end), and one phosphorothioate intemucleotide linkage
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modification at positions 1 and one phosphorothioate internucleotide e
modification at position 2 1 of the antisense strand (counting from the 5'-end).
In one ment, the dsR A of the invention further comprises one
orothioate internucleotide linkage cation at on 1, and one
phosphorothioate internucleotide linkage modification at position 1 of the sense strand
(counting from the 5'-end), and two phosphorothioate internucleotide linkage
modifications at positions 1 and 2 and two phosphorothioate internucleotide linkage
modifications at positions 2 1 and 22 the antisense strand (counting from the 5'-end).
In one embodiment, the dsRNA of the invention further comprises two
phosphorothioate internucleotide linkage modifications at position 1 and 2, and two
phosphorothioate internucleotide e modifications at position 22 and 23 of the sense
strand ing from the 5'-end), and one phosphorothioate internucleotide linkage
modification at positions 1 and one phosphorothioate internucleotide linkage
modification at position 2 1 of the antisense strand (counting from the 5'-end).
In one embodiment, the dsRNA of the invention further comprises one
phosphorothioate ucleotide linkage modification at position 1, and one
phosphorothioate internucleotide linkage modification at position 2 1 of the sense strand
(counting from the 5'-end), and two phosphorothioate internucleotide linkage
modifications at positions 1 and 2 and two phosphorothioate internucleotide linkage
modifications at positions 23 and 23 the antisense strand (counting from the 5'-end).
In one embodiment, the dsRNA agent of the invention ses mismatch(es)
with the target, within the duplex, or combinations thereof. The mistmatch can occur in
the overhang region or the duplex region. The base pair can be ranked on the basis of
their propensity to promote iation or melting (e.g., on the free energy of association
or dissociation of a particular pairing, the simplest approach is to e the pairs on an
individual pair basis, though next neighbor or r analysis can also be used). In terms
of promoting dissociation: A:U is preferred over G:C; G:U is preferred over G:C; and I:C
is preferred over G:C (I=inosine). Mismatches, e.g., non-canonical or other than
canonical pairings (as described elsewhere herein) are preferred over canonical (A:T,
A:U, G:C) gs; and pairings which e a sal base are preferred over
canonical pairings.
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In one embodiment, the dsR A agent of the ion comprises at least one of
the first 1, 2, 3, 4, or 5 base pairs within the duplex regions from the 5'- end of the
antisense strand can be chosen independently from the group of: A:U, G:U, I:C, and
mismatched pairs, e.g., non-canonical or other than cal pairings or pairings which
include a universal base, to promote the dissociation of the antisense strand at the 5'-end
of the duplex.
In one embodiment, the nucleotide at the 1 position within the duplex region from
the 5'-end in the antisense strand is selected from the group consisting ofA, dA, dU, U,
and dT. Alternatively, at least one of the first 1, 2 or 3 base pair within the duplex region
from the 5'- end of the antisense strand is an AU base pair. For example, the first base
pair within the duplex region from the 5'- end of the antisense strand is an AU base pair.
In one embodiment, the sense strand ce may be represented by formula (I):
'np-Na-(X X X )i-Nb-Y Y Y -Nb-(Z Z Z )j- a- q 3' (I)
wherein:
i and j are each independently 0 or 1;
p and q are each independently 0-6;
each Na independently represents an oligonucleotide sequence sing 0-25
modified tides, each sequence comprising at least two ently modified
nucleotides;
each b independently represents an oligonucleotide sequence comprising 0-10
modified nucleotides;
each np and nq independently represent an overhang nucleotide;
wherein N b and Y do not have the same modification; and
XXX, YYY and ZZZ each independently represent one motif of three identical
modifications on three consecutive nucleotides. Preferably YYY is all 2'-F modified
nucleotides.
In one embodiment, the Na and/or b comprise cations of ating
pattern.
In one embodiment, the YYY motif occurs at or near the ge site of the
sense strand. For example, when the dsRNA agent has a duplex region of 17-23
nucleotide pairs in length, the YYY motif can occur at or the vicinity of the cleavage site
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(e.g.: can occur at positions 6, 7, 8, 7, 8, 9, 8, 9, 10, 9, 10, 11, 10, 11,12 or 11, 12, 13) of
- the sense strand, the count starting from the 1st nucleotide, from the 5'-end; or
optionally, the count starting at the 1st paired nucleotide within the duplex region, from
the 5'- end.
In one embodiment, i is 1 and j is 0, or i is 0 and j is 1, or both i and j are 1. The
sense strand can therefore be represented by the following as:
np-Na -YYY-Nb-ZZZ-Na-nq 3 (la);
np-Na -XXX-Nb-YYY-Na-nq 3 (lb); or
np-Na -XXX-Nb-YYY-Nb-ZZZ-Na-nq 3 (Ic).
When the sense strand is represented by formula (la), b represents an
oligonucleotide sequence comprising 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides.
Each Na independently can represent an oligonucleotide sequence comprising 2-20, 2-15,
or 2-10 modified nucleotides.
When the sense strand is represented as formula (lb), b represents an
oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified
nucleotides. Each Na can independently represent an oligonucleotide sequence
comprising 2-20, 2-15, or 2-10 ed nucleotides.
When the sense strand is represented as formula (Ic), each N b ndently
represents an oligonucleotide sequence comprising 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified
nucleotides. Preferably, N b is 0, 1, 2, 3, 4, 5 or 6 Each Na can independently represent an
oligonucleotide sequence comprising 2-20, 2-15, or 2-10 modified tides.
Each of X, Y and Z may be the same or different from each other.
In one embodiment, the antisense strand sequence of the dsRNA may be
ented by formula (II):
n '-Na '-(Z'Z'ZVNb '-Y'Y'Y'-Nb'-(X'X'X')i-N'a-np' 3 (II)
wherein:
k and 1are each ndently 0 or 1;
p and q are each independently 0-6;
each Na' independently represents an oligonucleotide sequence comprising 0-25
modified tides, each sequence comprising at least two differently modified
nucleotides;
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each b' independently represents an oligonucleotide sequence comprising 0-10
modified nucleotides;
each np'and nq' independently represent an ng nucleotide comprising 0-6
nucleotides;
wherein Nb' and Y ' do not have the same modification;
C 'C 'C ', Y'Y'Y' and Z'Z'Z' each ndently represent one motif of three
identical modifications on three consecutive nucleotides.
In one embodiment, the Na' and/or Nb' comprise modifications of alternating
The UΎ Ύ ' motif occurs at or near the ge site of the antisense strand. For
example, when the dsRNA agent has a duplex region of 17-23 nt in length, the U Ύ Ύ '
motif can occur at positions 9, 10, 11;10, 11, 12; 11, 12, 13; 12, 13, 14 ; or 13, 14, 15 of
the antisense strand, with the count starting from the 1st nucleotide, from the 5'-end; or
optionally, the count starting at the 1st paired nucleotide within the duplex region, from
the 5'- end. Preferably, the U Ύ Ύ ' motif occurs at ons 11, 12, 13.
In one embodiment, UΎ Ύ ' motif is all 2'-OMe modified nucleotides.
In one embodiment, k is 1 and 1is 0, or k is 0 and 1is 1, or both k and 1are 1.
The antisense strand can therefore be represented by the following formulas:
nq'-Na'-Z'Z'Z'-Nb'-Y'Y'Y'-Na'-np' 3 (Ila);
nq'-Na'-YYY'-N 'X'-np' 3 (lib); or
*nq'-Na'- Z'Z'Z'-Nb'-Y'Y'Y'-Nb'- X'X'X'-Na'-np' 3* (lie).
When the antisense strand is represented by formula (Ila), N b represents an
oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified
nucleotides. Each Na' ndently represents an oligonucleotide sequence comprising
2-20, 2-15, or 2-10 modified nucleotides.
When the antisense strand is represented as formula (lib), Nb' represents an
oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified
nucleotides. Each Na' independently represents an ucleotide sequence comprising
2-20, 2-15, or 2-10 modified nucleotides.
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When the antisense strand is represented as formula (He), each Nb' independently
represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or 0
modified nucleotides. Each Na' independently represents an oligonucleotide sequence
comprising 2-20, 2-15, or 2-10 modified nucleotides. Preferably, N b is 0, 1, 2, 3, 4, 5 or 6 .
Each of X', Y'and Z' may be the same or different from each other.
Each nucleotide of the sense strand and antisense strand may be independently
modified with LNA, HNA, CeNA, 2'-methoxyethyl, ethyl, 2'allyl, 2'-C-allyl,
or 2'-fluoro. For example, each nucleotide of the sense strand and nse strand is
independently modified with 2'methyl or 2'-fluoro. EachX, Y, Z, X', Y'and Z', in
particular, may represent a 2'methyl modification or a 2'-fluoro cation.
In one embodiment, the sense strand of the dsRNA agent comprisesYYY motif
occurring at 9, 10 and 11 positions of the strand when the duplex region is 2 1 nt, the
count starting from the 1st nucleotide from the 5'-end, or optionally, the count starting at
the 1st paired nucleotide within the duplex region, from the 5'- end; and Y represents 2'-F
modification. The sense strand may additionally contain XXX motif or ZZZ motifs as
wing modifications at the opposite end of the duplex region; and XXX and ZZZ each
independently represents a 2'-OMe modification or 2'-F modification.
In one ment the antisense strand may contain U Ύ Ύ ' motif occurring at
positions 11, 12, 13 of the strand, the count ng from the 1st nucleotide from the
'-end, or ally, the count starting at the 1st paired nucleotide within the duplex
, from the 5'- end; and Y' represents 2'methyl modification. The antisense
strand may additionally contain X'X'X' motif or Z'Z'Z' motifsas wing cations at
the opposite end of the duplex region; and X'X'X'and Z'Z'Z'each independently
ents a 2'-OMe modification or 2'-F modification.
The sense strand represented by any one of the above formulas (la), (lb) and (Ic)
forms a duplex with a antisense strand being represented by any one of formulas (Ha),
(lib) and (He), respectively.
Accordingly, the dsRNA agent may comprise a sense strand and an nse
strand, each strand having 14 to 30 tides, the dsRNA duplex represented by
formula (III):
sense: 5 ' np -Na- (X X X ) -N - Y Y Y -N -(Z Z Z) -Na-n 3 '
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antisense: 3 ' n p ' - N a ' - ( C ' X ' X ' ) k - N ' - Y Ύ Ύ ' - N ' - ( Z ' Z ' Z ' ) i-N a ' - n ' 5 '
(III)
wherein:
i, j , k, and 1are each independently 0 or 1;
p and q are each independently 0-6;
each Na and Na' ndently represents an oligonucleotide sequence comprising
0-25 modified nucleotides, each sequence comprising at least two differently modified
nucleotides;
each b and b' independently represents an oligonucleotide ce
comprising 0-10 modified nucleotides;
wherein
each np' , np, nq' , and nq independently ents an overhang nucleotide
sequence; and
XXX, YYY, ZZZ ,C 'C 'C ',U Ύ Ύ ', and Z'Z'Z' each independently represent one
motif of three cal modifications on three consecutive tides.
In one embodiment, i is 1 and j is 0; or i is 0 and j is 1; or both i and j are l.In
another embodiment, k is 1 and 1is 0; k is 0 and 1is 1; or both k and 1are 1.
In one embodiment, the dsRNA agent of the invention comprises a sense strand
and an antisense strand, each strand having 14 to 30 nucleotides, the dsRNA duplex
ented by formula (V):
sense: 5 ' Na - ( X x X ) - N - Y Y Y - N - ( Z z Z ) - N a - n 3 '
antisense: 3 ' n p ' - N ' - ( X ' X ' X ' ) k - N ' - Y Ύ Ύ ' - N ' - ( Z ' Z ' Z ' ) i-N ' 5 '
wherein:
i, j , k, and lare each independently 0 or 1;
p and q are each independently 2;
each Na and Na' independently represents an oligonucleotide sequence comprising
0-25 modified nucleotides, each sequence comprising at least two differently modified
nucleotides;
each N b and N b' independently represents an oligonucleotide sequence
comprising 0-10 modified nucleotides;
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wherein
each np' , and nq independently represents an overhang tide sequence; and
XXX, YYY, ZZZ, C 'C 'C',UΎ 'U ', and Z'Z'Z'each independently represent one
motif of three identical modifications on three consecutive nucleotides.
In one ment, i is 1 and j is 0; or i is 0 and j is 1; or both i and j are 1. In
another embodiment, k is 1 and 1is 0; k is 0 and 1is 1; or both k and 1are 1.
In one embodiment, the dsRNA agent of the invention comprises a sense strand
and an antisense strand, each strand having 14 to 30 nucleotides, the dsRNA duplex
represented by formula (Va):
sense: 5 ' N - ( X x x ) - N - Y Y Y - N - ( Z z Z ) j - N 3 '
a a
antisense: 3 ' n ' - N ' - ( X ' X ' X ' ) - N ' - Y ' Y ' Y ' - N ' - ( ' Z ' Z ' ) i-N ' 5 '
p a k a
(Va)
wherein:
i, j , k, and lare each independently 0 or 1;
p and q are each ndently 2;
each Na and Na' independently represents an oligonucleotide sequence sing
0-25 modified nucleotides, each sequence comprising at least two ently modified
nucleotides;
each b and N b' independently represents an oligonucleotide sequence
comprising 0-10 modified nucleotides;
wherein
np' represents an overhang nucleotide sequence; and
XXX, YYY, ZZZ, C 'C 'C',UΎ 'U ', and Z'Z'Z'each independently represent one
motif of three identical modifications on three consecutive nucleotides.
Exemplary combinations of the sense strand and antisense strand forming a
dsRNA duplex include the formulas below:
' r p - N - Y Y Y - N - Z Z Z - N - n 3 '
3 ' n ' - N ' - Y ' Y ' Y ' - N ' - Z ' Z ' Z ' - N ' n ' 5 '
(Ilia)
' n - N - X X X - N - Y Y Y - N - n 3 '
3 ' n ' - N ' - X ' X ' X ' - N ' - Y ' Y ' Y ' - N ' - n ' 5 '
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(nib)
' r p - N - X X X - N - Y Y Y - N - Z Z Z - N a - n 3 '
3 ' n p ' - Na ' - X ' X ' X ' - N ' - Y Ύ Ύ ' - N ' - Z ' Z ' Z ' - N a - n ' 5 '
(IIIc)
When the dsR A agent is represented by formula (Ilia), each N b and b'
independently represents an oligonucleotide sequence sing 1-10, 1-7, 1-5 or 1-4
modified tides. Each Na and Na'independently represents an oligonucleotide
sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.
When the dsRNA agent is represented as formula (Illb), each N b and Nb'
independently represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-
, 0-4, 0-2 or Omodified nucleotides. Each Na and Na' independently represents an
ucleotide sequence comprising 2-20, 2-15, or 2-10 modified nucleotides.
When the dsRNA agent is represented as formula (IIIc), each N b and Nb'
independently represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-
, 0-4, 0-2 or 0 ed tides. Each Na and Na' independently represents an
oligonucleotide ce comprising 2-20, 2-15, or 2-10 modified nucleotides. Each of
Na, Na' ,N b and N b independently comprises modifications of alternating pattern.
Each of X, Y and Z in formulas (III), (Ilia), (Illb) and (IIIc) may be the same or
different from each other.
When the dsRNA agent is represented by formula (III), (Ilia), (Illb) or (IIIc), at
least one of the Y tides may form a base pair with one of the Y' nucleotides.
Alternatively, at least two of the Y nucleotides form base pairs with the corresponding Y '
nucleotides; or all three of the Y nucleotides all form base pairs with the corresponding
Y' nucleotides.
It is understood that Na nucleotides from base pair with Na' ,N b nucleotides from
base pair with Nb', X nucleotides from base pair with X', Y nucleotides from base pair
with Y', and Z nucleotides from base pair with Z'.
When the dsRNA agent is represented by a (Ilia) or (IIIc), at least one of
the Z nucleotides may form a base pair with one of the Z' nucleotides. Alternatively, at
least two of the Z nucleotides form base pairs with the ponding Z' nucleotides; or
all three of the Z nucleotides all form base pairs with the corresponding Z' nucleotides.
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When the dsRNA agent is represented as formula (Illb) or (IIIc), at least one of
the X nucleotides may form a base pair with one of the X' nucleotides. Alternatively, at
least two of the X nucleotides form base pairs with the corresponding X' nucleotides; or
all three of the X nucleotides all form base pairs with the corresponding X' nucleotides.
In one embodiment, the modification on the Y tide is different than the
modification on the Y ' nucleotide, the modification on the Z nucleotide is different than
the cation on the Z' nucleotide, and/or the modification on the X nucleotide is
different than the modification on the X ' tide.
In one embodiment, the dsRNA agent is a multimer containing at least two
duplexes represented by formula (III), , (Illb) or (IIIc), wherein said duplexes are
connected by a linker. The linker can be cleavable or non-cleavable. Optionally, said
multimer further comprise a ligand. Each of the dsRNA can target the same gene or two
different genes; or each of the dsRNA can target same gene at two different target sites.
In one embodiment, the dsRNA agent is a multimer containing three, four, five,
six or more duplexes represented by a (III), (Ilia), (Illb) or (IIIc), wherein said
es are connected by a linker. The linker can be cleavable or non-cleavable.
Optionally, said multimer further comprises a . Each of the dsRNA can target the
same gene or two different genes; or each of the dsRNA can target same gene at two
different target sites.
In one embodiment, two dsRNA agent represented by formula (III), , (Illb)
or (IIIc) are linked to each other at the 5' end, and one or both of the 3' ends of the are
optionally conjugated to to a ligand. Each of the dsRNA can target the same gene or two
different genes; or each of the dsRNA can target same gene at two different target sites.
Various publications described multimeric siRNA and can all be used with the
dsRNA of the invention. Such publications include WO2007/091269, US Patent No.
7858769, WO2010/14151 1, WO2007/1 17686, WO2009/014887 and WO201 1/031520
which are hereby orated by their entirely.
The dsRNA agent that contains ations of one or more carbohydrate
moieties to a dsRNA agent can optimize one or more properties of the dsRNA agent. In
many cases, the carbohydrate moiety will be attached to a modified subunit of the dsRNA
agent. E.g., the ribose sugar of one or more ribonucleotide subunits of a dsRNA agent
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can be replaced with another moiety, e.g., a non-carbohydrate (preferably cyclic) carrier
to which is attached a carbohydrate ligand. A ribonucleotide subunit in which the ribose
sugar of the subunit has been so replaced is referred to herein as a ribose replacement
modification subunit . A cyclic carrier may be a carbocyclic ring system, i.e., all
ring atoms are carbon atoms, or a heterocyclic ring system, i.e., one or more ring atoms
may be a heteroatom, e.g., en, oxygen, sulfur. The cyclic carrier may be a
monocyclic ring system, or may contain two or more rings, e.g. fused rings. The cyclic
carrier may be a fully saturated ring system, or it may contain one or more double bonds.
The ligand may be attached to the polynucleotide via a carrier. The carriers
include (i) at least one "backbone ment " preferably two "backbone
attachment points" and (ii) at least one "tethering attachment point." A "backbone
attachment point" as used herein refers to a functional group, e.g. a hydroxy1group, or
generally, a bond available for, and that is suitable for oration of the carrier into the
backbone, e.g., the phosphate, or modified phosphate, e.g., sulfur containing, backbone,
of a ribonucleic acid. A "tethering attachment point" (TAP) in some embodiments refers
to a constituent ring atom of the cyclic r, e.g., a carbon atom or a heteroatom
(distinct from an atom which provides a backbone attachment , that connects a
selected moiety. The moiety can be, e.g., a carbohydrate, e.g. monosaccharide,
haride, trisaccharide, tetrasaccharide, oligosaccharide and polysaccharide.
Optionally, the selected moiety is connected by an intervening tether to the cyclic carrier.
Thus, the cyclic carrier will often include a functional group, e.g., an amino group, or
generally, provide a bond, that is suitable for incorporation or tethering of r
chemical entity, e.g., a ligand to the constituent ring.
In embodimentn the dsR A of the invention is conjugated to a ligand via a
carrier, wherein the carrier can be cyclic group or acyclic group; ably, the cyclic
group is selected from pyrrolidinyl, pyrazolinyl, pyrazolidinyl, imidazolinyl,
imidazolidinyl, piperidinyl, piperazinyl, [l,3]dioxolane, oxazolidinyl, isoxazolidinyl,
morpholinyl, thiazolidinyl, azolidinyl, quinoxalinyl, pyridazinonyl, ydrofuryl
and and decalin; preferably, the acyclic group is selected from serinol ne or
diethanolamine backbone.
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The double-stranded R A (dsRNA) agent of the invention may optionally be
conjugated to one or more ligands. The ligand can be attached to the sense strand,
antisense strand or both strands, at the 3'-end, 5'-end or bothends. For instance, the
ligand may be conjugated to the sense , in particular, the 3'-end of the sense strand.
Ligands
A wide variety of entities can be coupled to the ucleotides of the present
invention. Preferred moieties are ligands, which are coupled, preferably covalently,
either directly or ctly via an intervening tether.
In preferred embodiments, a ligand alters the bution, targeting or lifetime of
the molecule into which it is incorporated. In red embodiments a ligand provides
an enhanced affinity for a selected target, e.g., molecule, cell or cell type, compartment,
receptor e.g., a cellular or organ tment, tissue, organ or region of the body, as,
e.g., compared to a species absent such a ligand. Ligands providing enhanced affinity for
a ed target are also termed targeting ligands.
Some ligands can have endosomolytic properties. The endosomolytic ligands
promote the lysis of the me and/or transport of the composition of the invention,
or its components, from the endosome to the asm of the cell. The endosomolytic
ligand may be a polyanionic peptide or peptidomimetic which shows pH-dependent
membrane activity and fusogenicity. In one embodiment, the endosomolytic ligand
assumes its active conformation at endosomal pH. The "active" conformation is that
conformation in which the molytic ligand promotes lysis of the endosome and/or
transport of the composition of the invention, or its components, from the endosome to
the cytoplasm of the cell. Exemplary endosomolytic ligands include the GALA peptide
(Subbarao et al, Biochemistry, 1987, 26: 2964-2972), the EALA peptide (Vogel et al, J .
Am. Chem. Soc, 1996, 118: 1581-1586), and their derivatives (Turk et al, Biochem.
Biophys. Acta, 2002, 1559: 56-68). In one embodiment, the endosomolytic component
may contain a chemical group (e.g., an amino acid) which will undergo a change in
charge or protonation in response to a change in pH. The molytic component may
be linear or branched.
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Ligands can improve transport, hybridization, and specificity ties and may
also improve nuclease resistance of the resultant natural or modified oligoribonucleotide,
or a polymeric molecule sing any combination of monomers described herein
and/or natural or modified ribonucleotides.
Ligands in general can include therapeutic modifiers, e.g., for enhancing uptake;
diagnostic compounds or reporter groups e.g., for monitoring distribution; cross-linking
agents; and se-resistance conferring moieties. General examples include lipids,
steroids, vitamins, sugars, ns, es, polyamines, and peptide mimics.
Ligands can include a naturally occurring substance, such as a protein (e.g.,
human serum n (HSA), low-density lipoprotein (LDL), high-density lipoprotein
(HDL), or globulin); a carbohydrate (e.g., a dextran, pullulan, chitin, chitosan, inulin,
cyclodextrin or hyaluronic acid); or a lipid. The ligand may also be a recombinant or
synthetic molecule, such as a synthetic polymer, e.g., a synthetic polyamino acid, an
oligonucleotide (e.g. an aptamer). Examples of polyamino acids include polyamino acid
is a polylysine (PLL), poly L-aspartic acid, poly L-glutamic acid, styrene-maleic acid
anhydride copolymer, -lactide-co-glycolied) copolymer, divinyl ether-maleic
anhydride mer, N-(2-hydroxypropyl)methacrylamide copolymer ,
polyethylene glycol (PEG), polyvinyl alcohol (PVA), ethane, poly(2-ethylacryllic
acid), N-isopropylacrylamide polymers, or polyphosphazine. Example of polyamines
include: polyethylenimine, polylysine (PLL), spermine, spermidine, polyamine,
pseudopeptide-polyamine, peptidomimetic polyamine, dendrimer polyamine, arginine,
amidine, protamine, cationic lipid, cationic porphyrin, quaternary salt of a polyamine, or
an alpha helical peptide.
s can also include targeting , e.g., a cell or tissue targeting agent,
e.g., a lectin, glycoprotein, lipid or protein, e.g., an antibody, that binds to a specified cell
type such as a kidney cell. A targeting group can be a thyrotropin, melanotropin, lectin,
rotein, surfactant protein A, Mucin carbohydrate, multivalent lactose, multivalent
galactose, N-acetyl-galactosamine, N-acetyl-gulucosamine multivalent mannose,
alent fucose, glycosylated polyaminoacids, multivalent ose, transferrin,
bisphosphonate, polyglutamate, polyaspartate, a lipid, cholesterol, a steroid, bile acid,
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folate, vitamin B12, biotin, an RGD peptide, an RGD peptide mimetic or an aptamer.
Table 2 shows some examples of targeting ligands and their associated receptors.
Other examples of ligands include dyes, intercalating agents (e.g. acridines),
cross-linkers (e.g. psoralene, mitomycin C), porphyrins (TPPC4, texaphyrin, Sapphyrin),
polycyclic aromatic hydrocarbons (e.g., phenazine, dihydrophenazine), artificial
endonucleases or a chelator (e.g. EDTA), lipophilic molecules, e.g, cholesterol, cholic
acid, adamantane acetic acid, 1-pyrene butyric acid, dihydrotestosterone, 1,3-Bis-
0(hexadecyl)glycerol, geranyloxyhexyl group, hexadecylglycerol, borneol, menthol, 1,3-
propanediol, heptadecyl group, palmitic acid, myristic acid,03-(oleoyl)lithocholic acid,
03-(oleoyl)cholenic acid, dimethoxytrityl, or phenoxazine)and peptide conjugates (e.g.,
antennapedia peptide, Tat peptide), ting , ate, amino, mercapto, PEG
(e.g., PEG-40K), MPEG, [MPEG]2, polyamino, alkyl, substituted alkyl, radiolabeled
markers, enzymes, haptens (e.g. ), ort/absorption facilitators (e.g., aspirin,
vitamin E, folic acid), synthetic ribonucleases (e.g., imidazole, bisimidazole, histamine,
ole clusters, acridine-imidazole conjugates, Eu3+ xes of
tetraazamacrocycles), dinitrophenyl, HRP, or AP.
Ligands can be proteins, e.g., glycoproteins, or peptides, e.g., molecules having a
specific affinity for a co-ligand, or antibodies e.g., an antibody, that binds to a specified
cell type such as a cancer cell, endothelial cell, or bone cell. Ligands may also include
hormones and hormone receptors. They can also include non-peptidic species, such as
lipids, s, carbohydrates, vitamins, cofactors, multivalent lactose, multivalent
galactose, N-acetyl-galactosamine, N-acetyl-gulucosamine multivalent e,
multivalent fucose, or aptamers. The ligand can be, for example, a lipopolysaccharide, an
activator of p38 MAP kinase, or an tor of NF-KB.
The ligand can be a substance, e.g, a drug, which can increase the uptake of the
iRNA agent into the cell, for example, by disrupting the cell's cytoskeleton, e.g., by
disrupting the cell's microtubules, microfilaments, and/or intermediate nts. The
drug can be, for example, taxon, stine, vinblastine, cytochalasin, nocodazole,
japlakinolide, latrunculin A, phalloidin, swinholide A, indanocine, or vin.
The ligand can increase the uptake of the oligonucleotide into the cell by
activating an inflammatory se, for example. Exemplary ligands that would have
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such an effect include tumor necrosis factor alpha pha), eukin-1 beta, or
gamma interferon.
In one aspect, the ligand is a lipid or based molecule. Such a lipid or lipid-
based molecule preferably binds a serum protein, e.g., human serum albumin (HSA). An
HSA binding ligand allows for distribution of the conjugate to a target tissue, e.g., a nonkidney
target tissue of the body. For example, the target tissue can be the liver, including
parenchymal cells of the liver. Other molecules that can bind HSA can also be used as
ligands. For example, naproxen or aspirin can be used. A lipid or lipid-based ligand can
(a) increase resistance to degradation of the conjugate, (b) increase targeting or transport
into a target cell or cell membrane, and/or (c) can be used to adjust binding to a serum
protein, e.g., HSA.
A lipid based ligand can be used to modulate, e.g., control the g of the
conjugate to a target tissue. For example, a lipid or lipid-based ligand that binds to HSA
more strongly will be less likely to be targeted to the kidney and therefore less likely to
be cleared from the body. A lipid or lipid-based ligand that binds to HSA less strongly
can be used to target the ate to the kidney.
In a preferred embodiment, the lipid based ligand binds HSA. Preferably, it binds
HSA with a sufficient affinity such that the ate will be preferably distributed to a
non-kidney tissue. However, it is preferred that the ty not be so strong that the
gand binding cannot be reversed.
In another preferred embodiment, the lipid based ligand binds HSA weakly or not
at all, such that the conjugate will be preferably distributed to the kidney. Other moieties
that target to kidney cells can also be used in place of or in addition to the lipid based
ligand.
In another aspect, the ligand is a moiety, e.g., a vitamin, which is taken up by a
target cell, e.g., a proliferating cell. These are particularly useful for treating disorders
characterized by unwanted cell proliferation, e.g., of the malignant or non-malignant
type, e.g., cancer cells. Exemplary vitamins include vitamin A, E, and K . Other
exemplary vitamins include B vitamins, e.g., folic acid, B12, avin, biotin, pyridoxal
or other vitamins or nutrients taken up by cancer cells. Also ed are HAS, low
density lipoprotein (LDL) and high-density lipoprotein (HDL).
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In r aspect, the ligand is a ermeation agent, preferably a helical cell-
permeation agent. Preferably, the agent is amphipathic. An exemplary agent is a peptide
such as tat or antennopedia. If the agent is a peptide, it can be modified, including a
peptidylmimetic, invertomers, non-peptide or pseudo-peptide linkages, and use of D-
amino acids. The helical agent is preferably an alpha-helical agent, which preferably has
a lipophilic and a lipophobic phase.
The ligand can be a peptide or peptidomimetic. A peptidomimetic (also referred
to herein as an oligopeptidomimetic) is a molecule capable of folding into a defined
three-dimensional structure similar to a natural peptide. The e or peptidomimetic
moiety can be about 5-50 amino acids long, e.g., about 5, 10, 15, 20, 25, 30, 35, 40, 45, or
50 amino acids long. A peptide or peptidomimetic can be, for example, a cell permeation
e, cationic peptide, amphipathic e, or hydrophobic peptide (e.g., consisting
primarily of Tyr, Trp or Phe). The peptide moiety can be a dendrimer peptide,
constrained peptide or crosslinked peptide. In another ative, the peptide moiety can
include a hydrophobic membrane translocation sequence (MTS). An ary
hobic MTS-containing peptide is RFGF having the amino acid ce
AAVALLPAVLLALLAP. An RFGF analogue (e.g., amino acid sequence
AALLPVLLAAP) containing a hydrophobic MTS can also be a targeting moiety. The
peptide moiety can be a "delivery" peptide, which can carry large polar molecules
including peptides, ucleotides, and protein across cell membranes. For example,
sequences from the HIV Tat protein (GRKKRRQRRRPPQ) and the Drosophila
Antennapedia protein (RQIKIWFQNRRMKWKK) have been found to be e of
functioning as delivery peptides. A peptide or peptidomimetic can be encoded by a
random sequence of DNA, such as a peptide identified from a phage-display library, or
one-bead-one-compound (OBOC) combinatorial library (Lam et al., Nature, 354:82-84,
1991). Preferably the peptide or peptidomimetic tethered to an iRNA agent via an
incorporated monomer unit is a cell targeting peptide such as an arginine-glycine-aspartic
acid (RGD)-peptide, or RGD mimic. A e moiety can range in length from about 5
amino acids to about 40 amino acids. The peptide moieties can have a structural
modification, such as to increase stability or direct conformational properties. Any of the
structural modifications described below can be utilized.An RGD peptide moiety can be
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used to target a tumor cell, such as an endothelial tumor cell or a breast cancer tumor cell
(Zitzmann et al., Cancer Res., 62:5139-43, 2002). An RGD peptide can facilitate
targeting of an iRNA agent to tumors of a variety of other tissues, including the lung,
, spleen, or liver (Aoki et al, Cancer Gene Therapy 8:783-787, 2001). Preferably,
the RGD peptide will facilitate targeting of an iRNA agent to the kidney. The RGD
peptide can be linear or cyclic, and can be modified, e.g., glycosylated or methylated to
facilitate targeting to specific tissues. For example, a ylated RGD peptide can
deliver an iRNA agent to a tumor cell expressing 3 (Haubner et al, Jour. Nucl. Med.,
42:326-336, 2001). Peptides that target markers enriched in proliferating cells can be
used. E.g., RGD containing es and peptidomimetics can target cancer cells, in
particular cells that exhibit an integrin. Thus, one could use RGD peptides, cyclic
peptides containing RGD, RGD peptides that include D-amino acids, as well as synthetic
RGD mimics. In addition to RGD, one can use other es that target the integrin
ligand. Generally, such ligands can be used to control proliferating cells and
angiogeneis. Preferred conjugates of this type lignads that targets PECAM-1, VEGF, or
other cancer gene, e.g., a cancer gene described herein.
A "cell tion peptide" is capable of permeating a cell, e.g., a microbial cell,
such as a bacterial or fungal cell, or a mammalian cell, such as a human cell. A microbial
cell-permeating e can be, for example, an a-helical linear e (e.g., LL-37 or
Ceropin PI), a disulfide bond-containing peptide (e.g., a -defensin, b-defensin or
bactenecin), or a peptide containing only one or two dominating amino acids (e.g., PR-39
or indolicidin). A cell permeation peptide can also e a r zation signal
(NLS). For example, a cell permeation peptide can be a bipartite amphipathic peptide,
such as MPG, which is derived from the fusion peptide domain of HIV- 1 gp41 and the
NLS of SV40 large T antigen (Simeoni et al, Nucl. Acids Res. 31:2717-2724, 2003).
In one embodiment, a targeting peptide can be an amphipathic a-helical e.
Exemplary amphipathic a-helical peptides e, but are not limited to, cecropins,
lycotoxins, paradaxins, buforin, CPF, bombinin-like peptide (BLP), cathelicidins,
ceratotoxins, S . clava peptides, hagfish intestinal antimicrobial peptides (HFIAPs),
magainines, ins-2, dermaseptins, melittins, pleurocidin, H2A peptides, Xenopus
peptides, esculentinis-1, and caerins. A number of factors will preferably be considered
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to maintain the integrity of helix stability. For example, a m number of helix
stabilization es will be utilized (e.g., leu, ala, or lys), and a m number helix
destabilization residues will be utilized (e.g., proline, or cyclic monomeric units. The
capping residue will be considered (for example Gly is an exemplary N-capping residue
and/or C-terminal amidation can be used to provide an extra H-bond to stabilize the helix.
Formation of salt bridges between residues with opposite charges, separated by i ± 3, or i
± 4 positions can provide stability. For e, cationic residues such as lysine,
arginine, homo-arginine, ornithine or histidine can form salt s with the anionic
residues glutamate or aspartate.
Peptide and peptidomimetic ligands include those having naturally occurring or
modified peptides, e.g., D or L peptides; a, b, or g peptides; N-methyl peptides;
azapeptides; peptides having one or more amide, i.e., peptide, linkages replaced with one
or more urea, thiourea, carbamate, or sulfonyl urea linkages; or cyclic peptides.
The targeting ligand can be any ligand that is capable of targeting a specific
receptor. Examples are: folate, GalNAc, galactose, mannose, mannose-6P, clusters of
sugars such as GalNAc cluster, mannose cluster, galactose cluster, or an er. A
r is a combination of two or more sugar units. The targeting ligands also include
integrin receptor ligands, Chemokine receptor ligands, transferrin, biotin, nin
receptor ligands, PSMA, elin, GCPII, somatostatin, LDL and HDL s. The
ligands can also be based on nucleic acid, e.g., an aptamer. The aptamer can be
unmodified or have any combination of modifications disclosed herein.
Endosomal release agents include imidazoles, poly or oligoimidazoles, PEIs,
peptides, fusogenic peptides, polycaboxylates, polyacations, masked oligo or poly cations
or , acetals, polyacetals, ketals/polyketyals, orthoesters, polymers with masked or
unmasked ic or anionic charges, dendrimers with masked or unmasked cationic or
anionic charges.
PK tor stands for pharmacokinetic modulator. PK modulator include
iles, bile acids, steroids, phospholipid analogues, peptides, protein binding agents,
PEG, vitamins etc. Examplary PK tor include, but are not limited to, terol,
fatty acids, cholic acid, lithocholic acid, dialkylglycerides, diacylglyceride,
phospholipids, sphingolipids, naproxen, ibuprofen, vitamin E, biotin etc.
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Oligonucleotides that se a number of phosphorothioate linkages are also known to
bind to serum protein, thus short oligonucleotides, e.g. oligonucleotides of about 5 bases,
bases, 15 bases or 20 bases, comprising multiple of phosphorothioate linkages in the
backbaone are also amenable to the present invention as ligands (e.g. as PK modulating
ligands).
In addition, aptamers that bind serum components (e.g. serum proteins) are also
amenable to the present invention as PK modulating ligands.
Other ligand ates amenable to the invention are described in U.S. Patent
Applications USSN: ,185, filed August 10, 2004; USSN: 10/946,873, filed
ber 21, 2004; USSN: 10/833,934, filed August 3, 2007; USSN: 11/1 15,989 filed
April 27, 2005 and USSN: 11/944,227 filed November 21, 2007, which are incorporated
by reference in their entireties for all purposes.
When two or more s are present, the ligands can all have same properties,
all have different ties or some ligands have the same ties while others have
different properties. For example, a ligand can have targeting properties, have
molytic activity or have PK modulating properties. In a preferred ment, all
the ligands have different properties.
Ligands can be coupled to the oligonucleotides at s places, for example, 3'-
end, 5'-end, and/or at an internal position. In preferred embodiments, the ligand is
attached to the ucleotides via an intervening tether, e.g. a carrier described herein.
The ligand or tethered ligand may be present on a monomer when said monomer is
incorporated into the growing strand. In some embodiments, the ligand may be
incorporated via coupling to a "precursor" monomer after said "precursor" monomer has
been incorporated into the growing strand. For example, a monomer having, e.g., an
amino-terminated tether (i.e., having no associated ligand), e.g., TAP-(CH2) N H 2 may be
incorporated into a g oligonucelotide strand. In a subsequent operation, i.e., after
incorporation of the precursor monomer into the strand, a ligand having an electrophilic
group, e.g., a pentafluorophenyl ester or aldehyde group, can subsequently be attached to
the precursor monomer by coupling the ophilic group of the ligand with the
al nucleophilic group of the precursor monomer's tether.
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In another example, a r having a chemical group suitable for taking part
in Click Chemistry reaction may be incorporated e.g., an azide or alkyne terminated
tether/linker. In a subsequent operation, i.e., after incorporation of the precursor
monomer into the , a ligand having mentary chemical group, e.g. an alkyne
or azide can be attached to the precursor monomer by coupling the alkyne and the azide
together.
For double- ed oligonucleotides, ligands can be attached to one or both
strands. In some embodiments, a double-stranded iRNA agent contains a ligand
conjugated to the sense . In other embodiments, a double-stranded iRNA agent
contains a ligand conjugated to the antisense strand.
In some embodiments, ligand can be conjugated to nucleobases, sugar moieties,
or internucleosidic es of nucleic acid molecules. Conjugation to purine nucleobases
or derivatives thereof can occur at any position including, endocyclic and exocyclic
atoms. In some embodiments, the 2-, 6-, 7-, or 8-positions of a purine nucleobase are
attached to a ate moiety. Conjugation to pyrimidine nucleobases or derivatives
thereof can also occur at any position. In some embodiments, the 2-, 5-, and 6-positions
of a dine nucleobase can be substituted with a conjugate moiety. Conjugation to
sugar moieties of nucleosides can occur at any carbon atom. Example carbon atoms of a
sugar moiety that can be attached to a conjugate moiety include the 2', 3', and 5' carbon
atoms. The G position can also be attached to a ate moiety, such as in an abasic
e. Internucleosidic linkages can also bear conjugate moieties. For phosphoruscontaining
linkages (e.g., phosphodiester, phosphorothioate, orodithiotate,
phosphoroamidate, and the like), the conjugate moiety can be attached directly to the
phosphorus atom or to an O, N, or S atom bound to the phosphorus atom. For amine- or
amide-containing internucleosidic linkages (e.g., PNA), the conjugate moiety can be
attached to the nitrogen atom of the amine or amide or to an adjacent carbon atom.
Any suitable ligand in the field of RNA interference may be used, although the
ligand is typically a carbohydrate e.g. monosaccharide (such as GalNAc), disaccharide,
trisaccharide, tetrasaccharide, polysaccharide.
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Linkers that conjugate the ligand to the nucleic acid include those discussed
above. For example, the ligand can be one or more GalNAc (N -acetylglucosamine)
derivatives ed through a bivalent or trivalent ed .
In one embodiment, the dsRNA of the invention is ated to a bivalent and
trivalent branched linkers include the structures shown in an of formula IV - VII :
Formula (IV) Formula (V)
Formula (VI)
or Formula (VII)
q A, q , q A, q , q4A, q4 , q5A, q5 and q5C represent ndently for each
occurrence 0-20 and wherein the repeating unit can be the same or different;
2A 2B A B 4A ,4B A B C 2A 3A 4A 4B 4A 5B
T5C are each independently for each occurrence absent, CO, NH, O, S, OC(O), NHC(O),
CH2, CH2NH or CH20 ;
Q A, Q2 , Q A, Q , Q4A, Q4 , Q5A, Q5 , Q5C are independently for each
occurrence absent, alkylene, substituted alkylene wherin one or more methylenes can be
interrupted or terminated by one or more of O, S, S(O), S0 2, N(RN), C(R')=C(R"), CºC
or C(O);
R A, R , R A, R , R4A, R4 , R5A, R5 , R5C are each independently for each
occurrence absent, NH, O, S, CH2, C(0)0, C(0)NH, NHCH(Ra)C(0), -C(0)-CH(R a)-
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cyclyl;
L2A, L2 , L A, L , L4A, L4 , L5A, L5 and L5C represent the ligand; i.e. each
independently for each occurrence a monosaccharide (such as ), disaccharide,
trisaccharide, tetrasaccharide, oligosaccharide, or polysaccharide; and
Ra is H or amino acid side chain.
Trivalent conjugating GalNAc derivatives are particularly useful for use with
RNAi agents for inhibiting the expression of a target gene, such as those of formula
(VII):
Formula (VII)
wherein L5A, L5 and L5C represent a monosaccharide, such as GalNAc tive.
Examples of suitable bivalent and trivalent branched linker groups conjugating
GalNAc derivatives include, but are not limited to, the following compounds:
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HO HO
HO HoO H<
Hfik'
O\/\O/\/O\/\N/(\/O0%“
HO HO H O 0
HowHO i
O\/\O/\/O\/\N o
HO HO
O\/\O/\/O\/\ N
HO HoO H/K
Hfim‘-
O\/\O/\/O\/\Nip03W
HO HO H O
HO ‘0
O\/\O/\/O\/\ N 0
HO O\//\O/\\/0
NHAc \
HO NM'
HO O\/\O/\/0 HO
NHAc
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O H
HO O\/\/\n/N
NHAC O
HO OH
NHACHO OH
NHAC O NHAC
O H
AcHN OMNWNWH
AcHN H
O ON‘LHWNX
AcHN H
HO OH
HO&&’OM0 i
AcHN
HO OH
AcHN
H O=(
Ho&g/O\/\)LHO 0 )=0
AcHN IZ
4343
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Definitions
As used herein, the terms "dsRNA", "siRNA", and "iRNA agent" are used
interchangeably to agents that can mediate silencing of a target RNA, e.g., mRNA, e.g., a
transcript of a gene that encodes a protein. For convenience, such mRNA is also referred
to herein as mRNA to be silenced. Such a gene is also referred to as a target gene. In
general, the RNA to be silenced is an endogenous gene or a pathogen gene. In addition,
RNAs other than mRNA, e.g., tRNAs, and viral RNAs, can also be targeted.
As used , the phrase "mediates RNAi" refers to the ability to silence, in a
sequence specific manner, a target RNA. While not g to be bound by theory, it is
believed that silencing uses the RNAi machinery or s and a guide RNA, e.g., an
siRNA agent of 2 1 to 23 nucleotides.
As used herein, "specifically hybridizable" and ementary" are terms which
are used to indicate a sufficient degree of complementarity such that stable and specific
binding occurs between a nd of the invention and a target RNA molecule.
Specific binding requires a sufficient degree of complementarity to avoid non-specific
binding of the oligomeric nd to non-target sequences under conditions in which
specific binding is desired, i.e., under physiological conditions in the case of assays or
therapeutic treatment, or in the case of in vitro assays, under conditions in which the
assays are performed. The non-target sequences typically differ by at least 5 tides.
In one embodiment, a dsRNA agent of the invention is "sufficiently
complementary" to a target RNA, e.g., a target mRNA, such that the dsRNA agent
silences production of protein encoded by the target mRNA. In r ment, the
dsRNA agent of the ion is "exactly complementary" to a target RNA, e.g., the
target RNA and the dsRNA duplex agent anneal, for example to form a hybrid made
exclusively of Watson-Crick base pairs in the region of exact complementarity. A
"sufficiently complementary" target RNA can include an internal region {e.g., of at least
nucleotides) that is exactly complementary to a target RNA. Moreover, in some
embodiments, the dsRNA agent of the invention specifically discriminates a singlenucleotide
difference. In this case, the dsRNA agent only mediates RNAi if exact
complementary is found in the region {e.g., within 7 nucleotides of) the single-nucleotide
difference.
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As used , the term "oligonucleotide" refers to a nucleic acid le
(RNA or DNA) for example of length less than 100, 200, 300, or 400 nucleotides.
The term "halo" refers to any radical of fluorine, chlorine, bromine or iodine. The
term "alkyl" refers to saturated and rated non-aromatic hydrocarbon chains that
may be a straight chain or branched chain, containing the indicated number of carbon
atoms (these include t limitation propyl, allyl, or propargyl), which may be
optionally ed with N , O, or S . For example, Ci-Cio indicates that the group may
have from 1 to 10 (inclusive) carbon atoms in it. The term "alkoxy" refers to an -O-alkyl
radical. The term "alkylene" refers to a divalent alkyl (i.e., -R-). The term
enedioxo" refers to a divalent species of the structure -, in which R
represents an alkylene. The term "aminoalkyl" refers to an alkyl substituted with an
aminoThe term "mercapto" refers to an -SH radical. The term "thioalkoxy" refers to an -
S-alkyl radical.
The term "aryl" refers to a 6-carbon monocyclic or 10-carbon bicyclic aromatic
ring system wherein 0, 1, 2, 3, or 4 atoms of each ring may be substituted by a
substituent. es of aryl groups include phenyl, naphthyl and the like. The term
"arylalkyl" or the term "aralkyl" refers to alkyl substituted with an aryl. The term
"arylalkoxy" refers to an alkoxy substituted with aryl.
The term "cycloalkyl" as employed herein includes saturated and partially
unsaturated cyclic hydrocarbon groups having 3 to 12 carbons, for example, 3 to 8
carbons, and, for example, 3 to 6 carbons, wherein the cycloalkyl group additionally may
be optionally substituted. Cycloalkyl groups include, without limitation, cyclopropyl,
cyclobutyl, cyclopentyl, cyclopentenyl, cyclohexyl, cyclohexenyl, cycloheptyl, and
cyclooctyl.
The term "heteroaryl" refers to an aromatic 5-8 membered monocyclic, 8-12
membered bicyclic, or 11-14 membered tricyclic ring system having 1-3 heteroatoms if
monocyclic, 1-6 heteroatoms if bicyclic, or 1-9 atoms if tricyclic, said heteroatoms
selected from O, N , or S (e.g., carbon atoms and 1-3, 1-6, or 1-9 heteroatoms of N , O, or
S if monocyclic, bicyclic, or tricyclic, respectively), wherein 0, 1, 2, 3, or 4 atoms of each
ring may be substituted by a substituent. Examples of heteroaryl groups include pyridyl,
furyl or l, imidazolyl, benzimidazolyl, dinyl, thiophenyl or thienyl,
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quinolinyl, indolyl, thiazolyl, and the like. The term "heteroarylalkyl" or the term
"heteroaralkyl" refers to an alkyl substituted with a heteroaryl. The term
"heteroarylalkoxy" refers to an alkoxy substituted with heteroaryl.
The term "heterocyclyl" refers to a nonaromatic 5-8 membered monocyclic, 8-12
membered bicyclic, or 11-14 ed tricyclic ring system having 1-3 heteroatoms if
monocyclic, 1-6 heteroatoms if ic, or 1-9 heteroatoms if tricyclic, said atoms
ed from O, N , or S (e.g., carbon atoms and 1-3, 1-6, or 1-9 heteroatoms of N , O, or
S if monocyclic, bicyclic, or tricyclic, respectively), wherein 0, 1, 2 or 3 atoms of each
ring may be substituted by a substituent. Examples of heterocyclyl groups include
trizolyl, tetrazolyl, piperazinyl, pyrrolidinyl, dioxanyl, morpholinyl, tetrahydrofuranyl,
and the like.
The term "oxo" refers to an oxygen atom, which forms a carbonyl when attached
to carbon, an N-oxide when attached to nitrogen, and a sulfoxide or sulfone when
attached to sulfur.
The term "acyl" refers to an alkylcarbonyl, cycloalkylcarbonyl, arylcarbonyl,
heterocyclylcarbonyl, or heteroarylcarbonyl substituent, any of which may be further
tuted by substituents.
The term "substituted" refers to the replacement of one or more hydrogen radicals
in a given structure with the radical of a specified substituent including, but not limited
to: halo, alkyl, alkenyl, alkynyl, aryl, heterocyclyl, thiol, alkylthio, arylthio,
alkyIt hioalkyl, arylthioalkyl, ulfonyl, alkylsulfonylalkyl, arylsulfonylalkyl, alkoxy,
aryloxy, aralkoxy, aminocarbonyl, alkylamino carbonyl, arylaminocarbonyl,
alkoxycarbonyl, aryloxycarbonyl, haloalkyl, amino, trifluoromethyl, cyano, nitro,
alkylamino, ino, alkylaminoalkyl, arylaminoalkyl, lkylamino, hydroxy,
alkoxyalkyl, carboxyalkyl, alkoxycarbonylalkyl, aminocarbonylalkyl, acyl,
aralkoxycarbonyl, carboxylic acid, sulfonic acid, yl, phosphonic acid, aryl,
heteroaryl, heterocyclic, and aliphatic. It is understood that the substituent can be further
tuted.
Cleavable Linking Groups
A ble linking group is one which is sufficiently stable outside the cell, but
which upon entry into a target cell is cleaved to release the two parts the linker is holding
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together. In a preferred embodiment, the cleavable g group is cleaved at least 10
times or more, preferably at least 100 times faster in the target cell or under a first
reference condition (which can, e.g., be selected to mimic or represent intracellular
conditions) than in the blood of a subject, or under a second nce condition (which
can, e.g., be selected to mimic or represent conditions found in the blood or serum).
Cleavable linking groups are susceptible to cleavage agents, e.g., pH, redox
potential or the presence of degradative molecules. Generally, cleavage agents are more
prevalent or found at higher levels or activities inside cells than in serum or blood.
Examples of such degradative agents include: redox agents which are selected for
particular ates or which have no substrate specificity, including, e.g., ive or
reductive enzymes or reductive agents such as mercaptans, present in cells, that can
degrade a redox cleavable linking group by reduction; esterases; endosomes or agents
that can create an acidic environment, e.g., those that result in a pH of five or lower;
enzymes that can hydrolyze or degrade an acid cleavable linking group by acting as a
general acid, peptidases (which can be substrate specific), and phosphatases.
A cleavable linkage group, such as a disulfide bond can be susceptible to pH. The
pH of human serum is 7.4, while the average intracellular pH is slightly lower, ranging
from about 7.1-7.3. Endosomes have a more acidic pH, in the range of 5.5-6.0, and
lysosomes have an even more acidic pH at around 5.0. Some linkers will have a
cleavable linking group that is cleaved at a preferred pH, thereby releasing the cationic
lipid from the ligand inside the cell, or into the desired tment of the cell.
A linker can include a cleavable linking group that is cleavable by a particular
enzyme. The type of cleavable g group orated into a linker can depend on
the cell to be ed. For e, liver targeting ligands can be linked to the cationic
lipids through a linker that includes an ester group. Liver cells are rich in esterases, and
therefore the linker will be cleaved more efficiently in liver cells than in cell types that
are not esterase-rich. Other cell-types rich in esterases include cells of the lung, renal
cortex, and testis.
Linkers that n peptide bonds can be used when targeting cell types rich in
peptidases, such as liver cells and synoviocytes.
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In general, the suitability of a candidate cleavable linking group can be evaluated
by testing the ability of a degradative agent (or condition) to cleave the candidate linking
group. It will also be desirable to also test the candidate cleavable linking group for the
ability to resist cleavage in the blood or when in contact with other non-target tissue.
Thus one can determine the relative tibility to cleavage between a first and a
second condition, where the first is ed to be indicative of cleavage in a target cell
and the second is selected to be indicative of cleavage in other s or biological fluids,
e.g., blood or serum. The evaluations can be carried out in cell free systems, in cells, in
cell culture, in organ or tissue culture, or in whole s. It may be useful to make
initial evaluations in cell-free or e conditions and to confirm by further evaluations
in whole animals. In preferred embodiments, useful candidate compounds are cleaved at
least 2, 4, 10 or 100 times faster in the cell (or under in vitro conditions selected to mimic
intracellular conditions) as compared to blood or serum (or under in vitro conditions
selected to mimic extracellular conditions).
Redox cleavable linking groups
One class of cleavable linking groups are redox cleavable linking groups that are
cleaved upon reduction or oxidation. An e of reductively cleavable linking group
is a disulphide linking group (-S-S-). To determine if a ate cleavable linking group
is a le "reductively cleavable linking " or for example is suitable for use with
a particular iR A moiety and particular targeting agent one can look to methods
bed herein. For example, a candidate can be evaluated by incubation with
dithiothreitol (DTT), or other reducing agent using reagents know in the art, which mimic
the rate of cleavage which would be observed in a cell, e.g., a target cell. The candidates
can also be ted under conditions which are ed to mimic blood or serum
conditions. In a preferred embodiment, candidate compounds are cleaved by at most
% in the blood. In preferred embodiments, useful candidate compounds are degraded
at least 2, 4, 10 or 100 times faster in the cell (or under in vitro conditions selected to
mimic intracellular conditions) as compared to blood (or under in vitro conditions
selected to mimic extracellular conditions). The rate of cleavage of candidate compounds
can be ined using standard enzyme kinetics assays under conditions chosen to
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mimic intracellular media and compared to conditions chosen to mimic extracellular
media.
Phosphate-based cleavable linking groups
Phosphate-based cleavable linking groups are cleaved by agents that degrade or
hydrolyze the phosphate group. An example of an agent that cleaves ate groups in
cells are enzymes such as phosphatases in cells. Examples of phosphate-based linking
groups are P(0)(ORk), )(ORk), P(S)(SRk), -S-P(0)(ORk), -
0-P(0)(ORk)-S-, -S-P(0)(ORk)-S-, P(S)(ORk)-S-, -S-P(S)(ORk), P(0)(Rk)-
0-, P(S)(Rk), -S-P(0)(Rk), -S-P(S)(Rk), -S-P(0)(Rk)-S-, P(S)( Rk)-S-.
Preferred embodiments are P(0)(OH), P(S)(OH), P(S)(SH), -S-
P(0)(OH), P(0)(OH)-S-, -S-P(0)(OH)-S-, )(OH)-S-, -S-P(S)(OH), -O-
R(0)( H), P(S)(H), -S-P(0)(H), -S-P(S)(H), -S-P(0)(H)-S-, P(S)(H)-
S-. A preferred embodiment is P(0)(OH). These candidates can be evaluated
using s analogous to those described above.
Acid cleavable linking groups
Acid cleavable linking groups are linking groups that are cleaved under acidic
conditions. In preferred embodiments acid cleavable linking groups are cleaved in an
acidic nment with a pH of about 6.5 or lower (e.g., about 6.0, 5.5, 5.0, or lower), or
by agents such as enzymes that can act as a general acid. In a cell, specific low pH
organelles, such as endosomes and lysosomes can provide a cleaving environment for
acid cleavable linking groups. Examples of acid cleavable linking groups e but are
not limited to hydrazones, esters, and esters of amino acids. Acid cleavable groups can
have the general formula -C=NN- C(0)0, or -OC(O). A red embodiment is when
the carbon attached to the oxygen of the ester (the alkoxy group) is an aryl group,
tuted alkyl group, or tertiary alkyl group such as dimethyl pentyl or t-butyl. These
candidates can be evaluated using methods analogous to those described above.
Ester-based linking groups
Ester-based cleavable linking groups are cleaved by s such as esterases
and amidases in cells. Examples of ester-based cleavable linking groups include but are
not limited to esters of alkylene, alkenylene and alkynylene groups. Ester cleavable
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linking groups have the general formula -C(0)0-, or -OC(O)-. These candidates can be
evaluated using methods analogous to those described above.
Peptide-based cleaving groups
Peptide-based cleavable linking groups are cleaved by enzymes such as
peptidases and proteases in cells. Peptide-based cleavable linking groups are peptide
bonds formed between amino acids to yield oligopeptides (e.g., ides, tripeptides
etc.) and polypeptides. Peptide-based cleavable groups do not include the amide group (-
C(O)NH-). The amide group can be formed between any alkylene, alkenylene or
alkynelene. A peptide bond is a special type of amide bond formed between amino acids
to yield peptides and proteins. The peptide based cleavage group is generally limited to
the peptide bond (i.e., the amide bond) formed between amino acids yielding es
and proteins and does not include the entire amide functional group. Peptide-based
ble linking groups have the general formula - NHCHRAC(0)NHCHR C(0)-,
where RA and R are the R groups of the two adjacent amino acids. These candidates can
be evaluated using s analogous to those described above.As used ,
"carbohydrate" refers to a compound which is either a carbohydrate per se made up of
one or more monosaccharide units having at least 6 carbon atoms (which may be ,
branched or cyclic) with an oxygen, nitrogen or sulfur atom bonded to each carbon atom;
or a compound having as a part thereof a carbohydrate moiety made up of one or more
monosaccharide units each having at least six carbon atoms (which may be linear,
branched or cyclic), with an , nitrogen or sulfur atom bonded to each carbon atom.
Representative carbohydrates include the sugars (mono-, di-, tri- and oligosaccharides
ning from about 4-9 monosaccharide units), and polysaccharides such as starches,
glycogen, cellulose and ccharide gums. Specific monosaccharides include C and
above (preferably C -C8) sugars; di- and trisaccharides e sugars having two or
three monosaccharide units (preferably C -C8) .
Alternative embodiments
In another embodiment, the invention s to a dsRNA agent capable of
inhibiting the expression of a target gene. The dsRNA agent comprises a sense strand
and an antisense strand, each strand having 14 to 30 nucleotides. The sense strand
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contains at least one motif of three identical modifications on three consecutive
nucleotides, where at least one of the motifs occurs at or near the cleavage site in the
antisense strand. Every nucleotide in the sense strand and nse strand has been
ed. The modifications on sense strand and antisense strand each independently
comprises at least two different cations.
In another embodiment, the invention relates to a dsR A agent capable of
inhibiting the expression of a target gene. The dsRNA agent comprises a sense strand
and an antisense strand, each strand having 14 to 30 nucleotides. The sense strand
contains at least one motif of three identical modifications on three utive
nucleotides, where at least one of the motifs occurs at or near the cleavage site in the
antisense strand. The antisense strand contains at least one motif of three identical
modifications on three consecutive nucleotides. The cation pattern of the antisense
strand is shifted by one or more nucleotides relative to the modification pattern of the
sense strand.
In another embodiment, the ion relates to a dsRNA agent capable of
inhibiting the expression of a target gene. The dsRNA agent comprises a sense strand
and an nse strand, each strand having 14 to 30 nucleotides. The sense strand
ns at least two motifs of three identical modifications on three consecutive
nucleotides, when at least one of the motifs occurs at the cleavage site in the strand and at
least one of the motifs occurs at another portion of the strand that is separated from the
motif at the cleavage site by at least one tide. The antisense strand contains at least
one motif of three identical modifications on three consecutive nucleotides, where at least
one of the motifs occurs at or near the cleavage site in the strand and at least one of the
motifs occurs at another n of the strand that is separated from the motif at or near
cleavage site by at least one nucleotide.
In another embodiment, the invention relates to a dsRNA agent capable of
inhibiting the expression of a target gene. The dsRNA agent comprises a sense strand
and an antisense strand, each strand having 14 to 30 nucleotides. The sense strand
contains at least two motifs of three identical modifications on three consecutive
nucleotides, where at least one of the motifs occurs at the cleavage site in the strand and
at least one of the motifs occurs at r portion of the strand that is separated from the
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motif at the ge site by at least one tide. The antisense strand contains at least
one motif of three identical modifications on three consecutive nucleotides, where at least
one of the motifs occurs at or near the ge site in the strand and at least one of the
motifs occurs at another portion of the strand that is separated from the motif at or near
cleavage site by at least one nucleotide. The modification in the motif occurring at the
cleavage site in the sense strand is different than the modification in the motif occurring
at or near the cleavage site in the antisense strand. In another embodiment, the invention
relates to a dsR A agent e of ting the expression of a target gene. The
dsR A agent comprises a sense strand and an antisense strand, each strand having 1 to
nucleotides. The sense strand contains at least one motif of three 2'-F modifications
on three consecutive nucleotides, where at least one of the motifs occurs at the cleavage
site in the strand. The antisense strand contains at least one motif of three 2'methyl
modifications on three consecutive tides.
The sense strand may further comprises one or more motifs of three identical
modifications on three consecutive nucleotides, where the one or more additional motifs
occur at r portion of the strand that is separated from the three 2'-F modifications
at the cleavage site by at least one nucleotide. The antisense strand may further
comprises one or more motifs of three identical modifications on three consecutive
nucleotides, where the one or more additional motifs occur at another portion of the
strand that is separated from the three ethyl modifications by at least one
nucleotide. At least one of the nucleotides having a 2'-F cation may form a base
pair with one of the nucleotides having a 2'methyl modification.
In one embodiment, the dsRNA of the ion is administered in buffer.
In one embodiment, siR A compounds described herein can be formulated for
administration to a subject. A formulated siRNA ition can assume a variety of
states. In some examples, the composition is at least lly crystalline, mly
crystalline, and/or anhydrous (e.g., less than 80, 50, 30, 20, or 10% water). In another
example, the siRNA is in an aqueous phase, e.g., in a solution that includes water.
The aqueous phase or the crystalline compositions can, e.g., be incorporated into a
delivery vehicle, e.g., a liposome (particularly for the aqueous phase) or a particle (e.g., a
microparticle as can be appropriate for a crystalline composition). Generally, the siRNA
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composition is formulated in a manner that is compatible with the intended method of
administration, as described herein. For example, in particular embodiments the
composition is prepared by at least one of the following methods: spray drying,
lyophilization, vacuum drying, evaporation, fluid bed drying, or a combination of these
techniques; or sonication with a lipid, freeze-drying, condensation and other self-
assembly.
A siRNA preparation can be formulated in combination with another agent, e.g.,
another therapeutic agent or an agent that stabilizes a siRNA, e.g., a protein that
complexes with siRNA to form an iRNP. Still other agents include chelators, e.g., EDTA
(e.g., to remove divalent cations such as Mg +), salts, RNAse tors (e.g., a broad
icity RNAse inhibitor such as RNAsin) and so forth.
In one embodiment, the siRNA ation includes another siNA compound,
e.g., a second siRNA that can mediate RNAi with respect to a second gene, or with
respect to the same gene. Still other preparation can include at least 3, 5, ten, twenty,
fifty, or a hundred or more different siRNA species. Such siRNAs can e RNAi
with respect to a similar number of different genes.
In one embodiment, the siRNA preparation es at least a second therapeutic
agent (e.g., an agent other than a RNA or a DNA). For example, a siRNA composition
for the treatment of a viral disease, e.g., HIV, might include a known antiviral agent (e.g.,
a se inhibitor or reverse transcriptase inhibitor). In another e, a siRNA
ition for the treatment of a cancer might further comprise a chemotherapeutic
agent.
Exemplary formulations are discussed below.
Liposomes. For ease of exposition the formulations, compositions and methods in
this section are discussed largely with regard to unmodified siRNA compounds. It may
be understood, however, that these formulations, compositions and methods can be
practiced with other siRNA compounds, e.g., modified siRNAs, and such practice is
within the invention. An siRNA compound, e.g., a double-stranded siRNA compound, or
ssiRNA compound, (e.g., a sor, e.g., a larger siRNA compound which can be
processed into a ssiRNA compound, or a DNA which encodes an siRNA compound, e.g.,
a -stranded siRNA compound, or ssiRNA nd, or precursor thereof)
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preparation can be ated for delivery in a membranous molecular assembly, e.g., a
liposome or a micelle. As used herein, the term "liposome" refers to a vesicle composed
of amphiphilic lipids arranged in at least one bilayer, e.g., one bilayer or a plurality of
bilayers. Liposomes include unilamellar and multilamellar vesicles that have a
membrane formed from a lipophilic material and an s or. The aqueous
portion contains the siR A composition. The lipophilic material isolates the aqueous
interior from an s exterior, which typically does not include the siRNA
composition, although in some examples, it may. Liposomes are useful for the transfer
and delivery of active ingredients to the site of action. Because the liposomal membrane
is structurally similar to biological nes, when liposomes are applied to a tissue,
the liposomal bilayer fuses with bilayer of the cellular nes. As the merging of the
liposome and cell progresses, the internal aqueous contents that include the siRNA are
red into the cell where the siRNA can specifically bind to a target RNA and can
mediate RNAi. In some cases the mes are also specifically targeted, e.g., to direct
the siRNA to ular cell types.
A liposome containing a siRNA can be prepared by a variety of methods. In one
example, the lipid component of a liposome is dissolved in a detergent so that micelles
are formed with the lipid component. For example, the lipid component can be an
athic ic lipid or lipid conjugate. The detergent can have a high critical
micelle concentration and may be ic. Exemplary detergents include cholate,
CHAPS, octylglucoside, deoxycholate, and lauroyl sarcosine. The siRNA preparation is
then added to the micelles that include the lipid component. The cationic groups on the
lipid interact with the siRNA and condense around the siRNA to form a liposome. After
condensation, the detergent is removed, e.g., by dialysis, to yield a liposomal preparation
of siRNA.
If necessary a carrier compound that assists in condensation can be added during
the condensation reaction, e.g., by controlled addition. For example, the carrier
compound can be a polymer other than a nucleic acid {e.g., ne or spermidine). pH
can also adjusted to favor sation.
Further description of methods for producing stable polynucleotide delivery
vehicles, which incorporate a cleotide/cationic lipid x as structural
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components of the delivery vehicle, are described in, e.g., WO 96/37194. Liposome
formation can also include one or more aspects of exemplary methods described in
r, P. L . et al., Proc. Natl. Acad. Sci., USA 8:7413-7417, 1987; U.S. Pat. No.
4,897,355; U.S. Pat. No. 5,171,678; Bangham, et al. M . Mol. Biol. 23:238, 1965; Olson,
et al. Biochim. Biophys. Acta 557:9, 1979; Szoka, et al. Proc. Natl. Acad. Sci. 75: 4194,
1978; Mayhew, et al. Biochim. Biophys. Acta 775:169, 1984; Kim, et al. Biochim.
Biophys. Acta 728:339, 1983; and Fukunaga, et al. inol. 115:757, 1984.
Commonly used techniques for preparing lipid aggregates of appropriate size for use as
delivery vehicles include sonication and freeze-thaw plus extrusion (see, e.g., Mayer, et
al. Biochim. Biophys. Acta 858:161, 1986). Microfluidization can be used when
consistently small (50 to 200 nm) and relatively uniform aggregates are desired
(Mayhew, et al. Biochim. Biophys. Acta 775:169, 1984). These methods are readily
adapted to packaging siRNA preparations into liposomes.
Liposomes that are pH-sensitive or negatively-charged entrap nucleic acid
molecules rather than complex with them. Since both the nucleic acid molecules and the
lipid are similarly charged, repulsion rather than complex formation occurs.
heless, some nucleic acid molecules are entrapped within the aqueous interior of
these liposomes. pH-sensitive liposomes have been used to r DNA encoding the
thymidine kinase gene to cell monolayers in e. Expression of the exogenous gene
was detected in the target cells (Zhou et al., Journal of Controlled Release, 19, (1992)
269-274).
One major type of liposomal composition es phospholipids other than
naturally-derived atidylcholine. Neutral liposome compositions, for example, can
be formed from dimyristoyl phosphatidylcholine (DMPC) or dipalmitoyl
atidylcholine (DPPC). Anionic liposome itions generally are formed from
dimyristoyl phosphatidylglycerol, while c fusogenic liposomes are formed
primarily from dioleoyl phosphatidylethanolamine (DOPE). Another type of liposomal
composition is formed from phosphatidylcholine (PC) such as, for example, soybean PC,
and egg PC. Another type is formed from mixtures of phospholipid and/or
atidylcholine and/or cholesterol.
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Examples of other methods to uce liposomes into cells in vitro and include
U.S. Pat. No. 5,283,185; U.S. Pat. No. 5,171,678; WO 94/00569; WO 93/24640; WO
91/16024; Feigner, J. Biol. Chem. 50, 1994; Nabel, Proc. Natl. Acad. Sci.
90:11307, 1993; Nabel, Human Gene Ther. 3:649, 1992; n, m. 32:7143,
1993; and Strauss EMBO J. 11:417, 1992.
In one embodiment, cationic liposomes are used. Cationic liposomes possess the
advantage of being able to fuse to the cell membrane. Non-cationic liposomes, although
not able to fuse as efficiently with the plasma membrane, are taken up by macrophages in
vivo and can be used to r siRNAs to macrophages.
Further advantages of liposomes include: liposomes obtained from natural
phospholipids are biocompatible and biodegradable; liposomes can incorporate a wide
range of water and lipid soluble drugs; liposomes can protect encapsulated siRNAs in
their internal compartments from metabolism and degradation f, in
"Pharmaceutical Dosage Forms," Lieberman, Rieger and Banker , 1988, volume 1,
p . 245). Important considerations in the preparation of liposome formulations are the lipid
surface charge, vesicle size and the s volume of the liposomes.
A positively charged synthetic cationic lipid, N-[l-(2,3-dioleyloxy)propyl]-
N ,N ,N -trimethylammonium chloride (DOTMA) can be used to form small liposomes that
interact spontaneously with nucleic acid to form lipid-nucleic acid complexes which are
capable of fusing with the negatively charged lipids of the cell nes of tissue
culture cells, resulting in ry of siRNA (see, e.g., Feigner, P. L . et al., Proc. Natl.
Acad. Sci., USA 8:7413-7417, 1987 and U.S. Pat. No. 4,897,355 for a description of
DOTMA and its use with DNA).
A DOTMA analogue, l,2-bis(oleoyloxy)(trimethylammonia)propane
(DOTAP) can be used in combination with a phospholipid to form DNA-complexing
vesicles. Lipofectin™ Bethesda Research Laboratories, Gaithersburg, Md.) is an
effective agent for the delivery of highly anionic nucleic acids into living tissue culture
cells that comprise vely d DOTMA liposomes which interact spontaneously
with negatively charged polynucleotides to form complexes. When enough positively
charged mes are used, the net charge on the resulting complexes is also positive.
Positively charged complexes prepared in this way spontaneously attach to negatively
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charged cell surfaces, fuse with the plasma membrane, and efficiently deliver functional
nucleic acids into, for example, tissue culture cells. r commercially ble
cationic lipid, l,2-bis(oleoyloxy)-3,3-(trimethylammonia)propane ("DOTAP")
(Boehringer Mannheim, Indianapolis, a) differs from DOTMA in that the oleoyl
moieties are linked by ester, rather than ether linkages.
Other reported cationic lipid compounds include those that have been conjugated
to a variety o f moieties including, for example, carboxyspermine which has been
conjugated to one o f two types of lipids and includes compounds such as 5-
carboxyspermylglycine dioctaoleoylamide ("DOGS") (Transfectam™, Promega,
Madison, Wisconsin) and itoylphosphatidylethanolamine 5-carboxyspermyl-amide
("DPPES") (see, e.g., U.S. Pat. No. 5,171,678).
Another cationic lipid conjugate includes derivatization of the lipid with
cholesterol ("DC-Choi") which has been formulated into liposomes in combination with
DOPE (See, Gao, X . and Huang, L., Biochim. Biophys. Res. Commun. 179:280, 1991).
Lipopolylysine, made by conjugating polylysine to DOPE, has been reported to b e
effective for transfection in the presence o f serum (Zhou, X . et al., Biochim. Biophys.
Acta 1065:8, 1991). For certain cell lines, these liposomes containing conjugated ic
lipids, are said to exhibit lower toxicity and provide more ent transfection than the
DOTMA-containing compositions. Other cially available cationic lipid products
include DMRIE and DMRIE-HP (Vical, L a Jo 11a, California) and Lipofectamine
(DOSPA) (Life Technology, Inc., rsburg, nd). Other cationic lipids suitable
for the delivery of oligonucleotides are described in W O 98/39359 and W O 96/37194.
mal formulations are particularly suited for topical administration,
liposomes present several advantages over other formulations. Such advantages include
reduced side effects related to high systemic absorption of the administered drug,
increased accumulation of the administered drug at the desired target, and the ability to
administer siRNA, into the skin. In some implementations, liposomes are used for
delivering siRNA to epidermal cells and also to enhance the penetration of siRNA into
dermal s, e.g., into skin. For example, the mes can b e applied topically.
Topical delivery o f drugs formulated as liposomes to the skin has been nted (see,
e.g., Weiner et al., Journal of Drug Targeting, 1992, vol. 2,405-410 and du Plessis et al.,
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Antiviral Research, 18, 1992, 259-265; Mannino, R . J . and Fould-Fogerite, S.,
Biotechniques 6:682-690, 1988; Itani, T. et al. Gene 56:267-276. 1987; Nicolau, C . et al.
Meth. Enz. 149:157-176, 1987; Straubinger, R . M . and Papahadjopoulos, D . Meth. Enz.
101:512-527, 1983; Wang, C . Y . and Huang, L., Proc. Natl. Acad. Sci. USA 84:7851-
7855, 1987).
Non-ionic liposomal systems have also been examined to determine their utility in
the delivery of drugs to the skin, in particular systems sing non-ionic tant
and cholesterol. Non-ionic liposomal ations comprising me I (glyceryl
dilaurate/cholesterol/polyoxyethylenestearyl ether) and Novasome II (glyceryl
distearate/ cholesterol/polyoxyethylenestearyl ether) were used to deliver a drug into
the dermis of mouse skin. Such formulations with siRNA are useful for ng a
dermatological disorder.
Liposomes that include siRNA can be made highly deformable. Such
deformability can enable the liposomes to penetrate through pore that are smaller than the
average radius of the liposome. For example, transfersomes are a type of deformable
liposomes. Transferosomes can be made by adding e edge activators, y
surfactants, to a standard liposomal composition. Transfersomes that include siRNA can
be delivered, for e, subcutaneously by infection in order to deliver siRNA to
keratinocytes in the skin. In order to cross intact mammalian skin, lipid vesicles must
pass through a series of fine pores, each with a diameter less than 50 nm, under the
influence of a suitable transdermal gradient. In addition, due to the lipid properties, these
transferosomes can be self-optimizing (adaptive to the shape of pores, e.g., in the skin),
self-repairing, and can frequently reach their targets without fragmenting, and often self-
loading.
Other ations amenable to the present ion are described in United
States provisional application serial nos. 61/018,616, filed January 2, 2008; 61/018,61 1,
filed January 2, 2008; 61/039,748, filed March 26, 2008; 61/047,087, filed April 22, 2008
and 61/051,528, filed May 8, 2008. PCT application no ,
filed October 3, 2007 also describes formulations that are amenable to the t
invention.
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tants. For ease of exposition the formulations, itions and methods
in this section are discussed largely with regard to fied siRNA compounds. It
may be understood, however, that these formulations, compositions and methods can be
practiced with other siRNA compounds, e.g., modified siRNA nds, and such
ce is within the scope of the invention. Surfactants find wide application in
formulations such as emulsions (including microemulsions) and liposomes (see above).
siRNA (or a precursor, e.g., a larger dsiRNA which can be processed into a siRNA, or a
DNA which encodes a siRNA or precursor) compositions can include a surfactant. In
one embodiment, the siRNA is formulated as an emulsion that includes a surfactant. The
most common way of classifying and g the properties of the many different types
of surfactants, both natural and synthetic, is by the use of the hydrophile/lipophile
balance (HLB). The nature of the hydrophilic group provides the most useful means for
categorizing the different surfactants used in formulations (Rieger, in "Pharmaceutical
Dosage Forms," Marcel Dekker, Inc., New York, NY, 1988, p . 285).
If the surfactant le is not ionized, it is classified as a ic surfactant.
Nonionic tants find wide application in pharmaceutical products and are usable
over a wide range of pH values. In general their HLB values range from 2 to about 18
depending on their structure. Nonionic surfactants e nonionic esters such as
ethylene glycol esters, propylene glycol esters, glyceryl esters, polyglyceryl esters,
sorbitan esters, sucrose esters, and ethoxylated esters. Nonionic alkanolamides and ethers
such as fatty alcohol ethoxylates, propoxylated alcohols, and ethoxylated/propoxylated
block polymers are also included in this class. The polyoxy ethylene surfactants are the
most popular members of the nonionic surfactant class.
If the surfactant molecule carries a negative charge when it is dissolved or
dispersed in water, the surfactant is classified as anionic. Anionic surfactants include
carboxylates such as soaps, acyl lactylates, acyl amides of amino acids, esters of sulfuric
acid such as alkyl sulfates and lated alkyl sulfates, sulfonates such as alkyl
benzene sulfonates, acyl isethionates, acyl es and sulfosuccinates, and phosphates.
The most important members of the anionic tant class are the alkyl sulfates and the
soaps.
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If the surfactant molecule carries a positive charge when it is dissolved or
dispersed in water, the surfactant is classified as cationic. Cationic surfactants include
quaternary ammonium salts and ethoxylated amines. The quaternary ammonium salts are
the most used members of this class.
If the surfactant molecule has the ability to carry either a positive or negative
charge, the surfactant is classified as eric. Amphoteric surfactants include acrylic
acid derivatives, substituted alkylamides, N-alkylbetaines and phosphatides.
The use of surfactants in drug products, formulations and in emulsions has been
reviewed (Rieger, in "Pharmaceutical Dosage " Marcel Dekker, Inc., New York,
NY, 1988, p . 285).
Micelles and other Membranous Formulations. For ease of exposition the
micelles and other formulations, compositions and methods in this section are discussed
largely with regard to unmodified siRNA compounds. It may be understood, however,
that these micelles and other ations, compositions and methods can be practiced
with other siRNA compounds, e.g., modified siRNA compounds, and such practice is
within the invention. The siRNA compound, e.g., a double-stranded siRNA compound,
or ssiRNA compound, {e.g., a precursor, e.g., a larger siRNA nd which can be
processed into a ssiRNA compound, or a DNA which encodes an siRNA compound, e.g.,
a double-stranded siRNA compound, or ssiRNA compound, or precursor thereof))
composition can be provided as a micellar formulation. "Micelles" are defined herein as
a particular type of molecular assembly in which amphipathic molecules are arranged in a
spherical structure such that all the hydrophobic portions of the molecules are directed
, leaving the hydrophilic portions in contact with the surrounding aqueous phase.
The se arrangement exists if the nment is hobic.
A mixed micellar formulation suitable for delivery h transdermal
membranes may be ed by mixing an aqueous solution of the siRNA composition,
an alkali metal C to C alkyl sulphate, and a micelle forming compounds. ary
e forming compounds include lecithin, hyaluronic acid, pharmaceutically
acceptable salts of hyaluronic acid, glycolic acid, lactic acid, chamomile t,
cucumber extract, oleic acid, linoleic acid, linolenic acid, monoolein, monooleates,
urates, borage oil, evening of primrose oil, l, trihydroxy oxo cholanyl
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glycine and pharmaceutically acceptable salts thereof, in, polyglycerin, lysine,
polylysine, triolein, polyoxy ethylene ethers and ues thereof, polidocanol alkyl
ethers and analogues thereof, chenodeoxycholate, deoxycholate, and mixtures thereof.
The e forming compounds may be added at the same time or after addition of the
alkali metal alkyl sulphate. Mixed micelles will form with substantially any kind of
mixing of the ingredients but vigorous mixing in order to provide smaller size micelles.
In one method a first micellar composition is prepared which contains the siR A
ition and at least the alkali metal alkyl te. The first micellar composition is
then mixed with at least three micelle forming compounds to form a mixed micellar
composition. In another method, the micellar composition is prepared by mixing the
siRNA composition, the alkali metal alkyl sulphate and at least one of the micelle
forming compounds, followed by on of the remaining micelle forming compounds,
with vigorous mixing.
Phenol and/or ol may be added to the mixed micellar composition to
stabilize the formulation and protect against bacterial . Alternatively, phenol
and/or m-cresol may be added with the micelle forming ingredients. An isotonic agent
such as in may also be added after formation of the mixed micellar composition.
For delivery of the micellar formulation as a spray, the formulation can be put
into an aerosol dispenser and the dispenser is charged with a propellant. The lant,
which is under pressure, is in liquid form in the dispenser. The ratios of the ingredients
are adjusted so that the aqueous and lant phases become one, i.e., there is one
phase. If there are two phases, it is necessary to shake the dispenser prior to dispensing a
portion of the contents, e.g., through a metered valve. The dispensed dose of
pharmaceutical agent is propelled from the metered valve in a fine spray.
Propellants may include hydrogen-containing chlorofluorocarbons, hydrogencontaining
fluorocarbons, dimethyl ether and diethyl ether. In certain embodiments, HFA
134a (1,1,1,2 tetrafluoroethane) may be used.
The specific concentrations of the essential ingredients can be determined by
relatively straightforward experimentation. For absorption h the oral cavities, it is
often desirable to se, e.g., at least double or triple, the dosage for through injection
or administration through the gastrointestinal tract.
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Particles. For ease of exposition the particles, formulations, compositions and
methods in this section are discussed largely with regard to modified siRNA compounds.
It may be understood, however, that these particles, formulations, compositions and
methods can be practiced with other siRNA compounds, e.g., unmodified siRNA
compounds, and such practice is within the invention. In another embodiment, an siRNA
compound, e.g., a double-stranded siRNA compound, or ssiRNA compound, {e.g., a
precursor, e.g., a larger siRNA compound which can be processed into a ssiRNA
compound, or a DNA which encodes an siRNA compound, e.g., a double-stranded
siRNA compound, or ssiRNA compound, or precursor thereof) preparations may be
incorporated into a particle, e.g., a microparticle. Microparticles can be ed by
spray-drying, but may also be produced by other methods including lyophilization,
ation, fluid bed drying, vacuum drying, or a combination of these techniques.
Pharmaceutical itions
The iRNA agents of the ion may be formulated for pharmaceutical use.
Pharmaceutically acceptable compositions comprise a therapeutically-effective amount of
one or more of the the dsRNA agents in any of the preceding ments, taken alone
or formulated together with one or more pharmaceutically acceptable carriers (additives),
excipient and/or diluents.
The pharmaceutical compositions may be specially formulated for administration
in solid or liquid form, including those adapted for the following: (1) oral administration,
for example, drenches us or non-aqueous ons or suspensions), tablets, e.g.,
those targeted for , sublingual, and systemic absorption, boluses, powders,
granules, pastes for application to the tongue; (2) parenteral administration, for example,
by subcutaneous, intramuscular, intravenous or epidural injection as, for example, a
sterile solution or suspension, or ned-release formulation; (3) l application,
for example, as a cream, ointment, or a controlled-release patch or spray applied to the
skin; (4) intravaginally or ectally, for example, as a pessary, cream or foam; (5)
sublingually; (6) ly; (7) transdermally; or (8) nasally. Delivery using subcutaneous
or intravenous methods can be particularly ageous.
The phrase "therapeutically-effective amount" as used herein means that amount
of a compound, material, or ition comprising a compound of the invention which
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is effective for producing some d therapeutic effect in at least a pulation of
cells in an animal at a reasonable benefit/risk ratio applicable to any medical treatment.
The phrase "pharmaceutically acceptable" is employed herein to refer to those
compounds, materials, compositions, and/or dosage forms which are, within the scope of
sound medical judgment, suitable for use in contact with the tissues of human beings and
animals without ive toxicity, irritation, allergic response, or other problem or
complication, commensurate with a reasonable benefit/risk ratio.
The phrase "pharmaceutically-acceptable carrier" as used herein means a
pharmaceutically-acceptable material, composition or vehicle, such as a liquid or solid
filler, diluent, excipient, manufacturing aid (e.g., lubricant, talc magnesium, calcium or
zinc stearate, or steric acid), or solvent encapsulating material, ed in ng or
transporting the subject compound from one organ, or portion of the body, to another
organ, or portion of the body. Each carrier must be "acceptable" in the sense of being
ible with the other ingredients of the ation and not injurious to the t.
Some examples of materials which can serve as pharmaceutically-acceptable carriers
include: (1) sugars, such as lactose, glucose and sucrose; (2) starches, such as corn starch
and potato starch; (3) cellulose, and its derivatives, such as sodium carboxymethyl
cellulose, ethyl cellulose and cellulose acetate; (4) powdered tragacanth; (5) malt; (6)
gelatin; (7) lubricating agents, such as magnesium state, sodium lauryl sulfate and talc;
(8) excipients, such as cocoa butter and suppository waxes; (9) oils, such as peanut oil,
seed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; (10) glycols,
such as propylene glycol; ( 1 1) polyols, such as glycerin, sorbitol, mannitol and
polyethylene glycol; (12) esters, such as ethyl oleate and ethyl e; (13) agar; (14)
buffering agents, such as magnesium hydroxide and um hydroxide; (15) alginic
acid; (16) pyrogen-free water; (17) ic saline; (18) Ringer's solution; (19) ethyl
alcohol; (20) pH buffered solutions; (21) polyesters, polycarbonates and/or
polyanhydrides; (22) bulking agents, such as polypeptides and amino acids (23) serum
ent, such as serum albumin, HDL and LDL; and (22) other non-toxic compatible
substances employed in ceutical formulations.
The formulations may conveniently be presented in unit dosage form and may be
prepared by any methods well known in the art of pharmacy. The amount of active
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ingredient which can be combined with a carrier material to produce a single dosage form
will vary depending upon the host being treated, the particular mode of stration.
The amount of active ingredient which can be combined with a r material to
produce a single dosage form will lly be that amount of the compound which
produces a therapeutic effect. Generally, out of one hundred per cent, this amount will
range from about 0 .1 per cent to about ninety-nine percent of active ingredient, preferably
from about 5 per cent to about 70 per cent, most preferably from about 10 per cent to
about 30 per cent.
In certain embodiments, a formulation of the present invention comprises an
excipient selected from the group consisting of cyclodextrins, celluloses, liposomes,
e forming agents, e.g., bile acids, and polymeric carriers, e.g., polyesters and
polyanhydrides; and a compound of the present invention. In certain embodiments, an
aforementioned formulation renders orally ilable a compound of the present
invention.
iR A agent preparation can be formulated in combination with another agent,
e.g., another therapeutic agent or an agent that stabilizes a iRNA, e.g., a protein that
complexes with iRNA to form an iRNP. Still other agents include chelators, e.g., EDTA
(e.g., to remove divalent cations such as Mg +), salts, RNAse inhibitors (e.g., a broad
specificity RNAse inhibitor such as RNAsin) and so forth.
Methods of preparing these formulations or compositions include the step of
bringing into ation a compound of the present invention with the carrier and,
optionally, one or more accessory ingredients. In general, the formulations are prepared
by uniformly and tely bringing into association a compound of the t
invention with liquid carriers, or finely divided solid carriers, or both, and then, if
ary, shaping the product.
In some cases, in order to prolong the effect of a drug, it is desirable to slow the
absorption of the drug from subcutaneous or uscular injection. This may be
accomplished by the use of a liquid suspension of crystalline or amorphous material
having poor water solubility. The rate of absorption of the drug then depends upon its
rate of ution which, in turn, may depend upon crystal size and crystalline form.
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Alternatively, delayed absorption of a parenterally-administered drug form is
lished by dissolving or suspending the drug in an oil vehicle.
The compounds according to the invention may be formulated for administration
in any convenient way for use in human or veterinary medicine, by analogy with other
pharmaceuticals .
The term "treatment" is ed to encompass also prophylaxis, therapy and
cure. The patient receiving this treatment is any animal in need, including primates, in
particular humans, and other mammals such as equines, cattle, swine and sheep; and
poultry and pets in general.
Double-stranded RNAi agents are produced in a cell in vivo, e.g., from exogenous
DNA templates that are delivered into the cell. For example, the DNA templates can be
inserted into vectors and used as gene therapy vectors. Gene therapy vectors can be
delivered to a subject by, for example, intravenous ion, local administration (U.S.
Pat. No. 470), or by stereotactic injection (see, e.g., Chen et al. (1994) Proc. Natl.
Acad. Sci. USA 9 1:3054-3057). The pharmaceutical preparation of the gene therapy
vector can include the gene therapy vector in an acceptable diluent, or can comprise a
slow release matrix in which the gene ry vehicle is imbedded. The DNA templates,
for example, can include two transcription units, one that produces a transcript that
es the top strand of a dsRNA agent and one that produces a transcript that includes
the bottom strand of a dsRNA agent. When the templates are transcribed, the dsRNA
agent is produced, and processed into siRNA agent fragments that mediate gene
silencing.
Routes of Delivery
A composition that es an iRNA can be red to a subject by a variety of
routes. ary routes include: enous, subcutaneous, topical, rectal, anal,
vaginal, nasal, pulmonary, ocular.
The iRNA molecules of the invention can be incorporated into pharmaceutical
compositions suitable for administration. Such compositions typically include one or
more s of iRNA and a pharmaceutically acceptable carrier. As used herein the
language "pharmaceutically acceptable carrier" is intended to include any and all
solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and
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absorption delaying , and the like, compatible with pharmaceutical administration.
The use of such media and agents for pharmaceutically active substances is well known
in the art. Except insofar as any tional media or agent is incompatible with the
active compound, use thereof in the compositions is contemplated. mentary active
compounds can also be incorporated into the compositions.
The compositions of the present invention may be administered in a number of
ways depending upon whether local or systemic treatment is desired and upon the area to
be treated. Administration may be topical (including ophthalmic, vaginal, rectal,
intranasal, transdermal), oral or parenteral. Parenteral administration includes
intravenous drip, subcutaneous, intraperitoneal or intramuscular injection, or intrathecal
or intraventricular administration.
The route and site of administration may be chosen to enhance targeting. For
example, to target muscle cells, intramuscular injection into the muscles of interest would
be a logical choice. Lung cells might be targeted by administering the iR A in aerosol
form. The vascular endothelial cells could be targeted by coating a balloon er with
the iRNA and ically introducing the DNA.
Dosage
In one aspect, the invention features a method of administering a dsRNA agent,
e.g., a siRNA agent, to a subject {e.g., a human subject). The method includes
administering a unit dose of the dsRNA agent, e.g., a siRNA agent, e.g., double stranded
siRNA agent that (a) the double-stranded part is 14-30 nucleotides (nt) long, for example,
21-23 nt, (b) is complementary to a target RNA {e.g., an endogenous or pathogen target
RNA), and, ally, (c) includes at least one 3'overhang 1-5 nucleotide long. In one
ment, the unit dose is less than 10 mg per kg of bodyweight, or less than 10, 5, 2,
1, 0.5, 0.1, 0.05, 0.01, 0.005, 0.001, 0.0005, 0.0001, 0.00005 or 0.00001 mg per kg of
bodyweight, and less than 200 nmole of RNA agent {e.g., about 4.4 x 10 16 copies) per kg
of bodyweight, or less than 1500, 750, 300, 150, 75, 15, 7.5, 1.5, 0.75, 0.15, 0.075, 0.015,
0.0075, , 0.00075, 0.00015 nmole of RNA agent per kg of bodyweight.
The defined amount can be an amount effective to treat or prevent a disease or
disorder, e.g., a disease or disorder associated with the target RNA. The unit dose, for
example, can be administered by injection {e.g., intravenous, subcutaneous or
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uscular), an inhaled dose, or a topical application. In some ebmodiments dosages
may be less than 10, 5, 2, 1, or 0.1 mg/kg of body weight.
In some embodiments, the unit dose is administered less frequently than once a
day, e.g., less than every 2, 4, 8 or 30 days. In another embodiment, the unit dose is not
administered with a frequency {e.g., not a regular frequency). For example, the unit dose
may be stered a single time.
In one embodiment, the effective dose is administered with other traditional
therapeutic modalities. In one embodiment, the subject has a viral infection and the
modality is an antiviral agent other than a dsRNA agent, e.g., other than a siR A agent.
In another embodiment, the t has atherosclerosis and the effective dose of a dsRNA
agent, e.g., a siRNA agent, is stered in combination with, e.g., after surgical
intervention, e.g., angioplasty.
In one embodiment, a subject is administered an initial dose and one or more
maintenance doses of a dsRNA agent, e.g., a siRNA agent, {e.g., a precursor, e.g., a
larger dsRNA agent which can be processed into a siRNA agent, or a DNA which
encodes a dsRNA agent, e.g., a siRNA agent, or precursor thereof). The maintenance
dose or doses can be the same or lower than the initial dose, e.g., one-half less of the
initial dose. A maintenance regimen can include treating the subject with a dose or doses
ranging from 0.01 mg to 15 mg/kg of body weight per day, e.g., 10, 1, 0.1, 0.01, 0.001, or
1 mg per kg of bodyweight per day. The nance doses are, for example,
administered no more than once every 2, 5, 10, or 30 days. Further, the treatment
n may last for a period of time which will vary depending upon the nature of the
particular e, its severity and the overall condition of the t. In certain
embodiments the dosage may be delivered no more than once per day, e.g., no more than
once per 24, 36, 48, or more hours, e.g., no more than once for every 5 or 8 days.
Following treatment, the patient can be monitored for changes in his condition and for
alleviation of the symptoms of the disease state. The dosage of the compound may either
be increased in the event the patient does not respond significantly to current dosage
levels, or the dose may be decreased if an alleviation of the symptoms of the e state
is observed, if the disease state has been ablated, or if undesired ffects are observed.
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The effective dose can be administered in a single dose or in two or more doses,
as desired or ered appropriate under the specific circumstances. If desired to
facilitate repeated or frequent infusions, implantation of a delivery device, e.g., a pump,
semi-permanent stent (e.g., intravenous, intraperitoneal, intracisternal or intracapsular), or
reservoir may be advisable.
In one embodiment, the composition includes a plurality of dsRNA agent s.
In r embodiment, the dsRNA agent species has sequences that are non-overlapping
and non-adjacent to another species with respect to a naturally occurring target sequence.
In another embodiment, the plurality of dsRNA agent species is specific for different
naturally occurring target genes. In another embodiment, the dsRNA agent is allele
specific.
The dsRNA agents of the invention described herein can be administered to
mammals, particularly large mammals such as nonhuman primates or humans in a
number of ways.
In one ment, the stration of the dsRNA agent, e.g., a siRNA agent,
composition is parenteral, e.g., intravenous (e.g., as a bolus or as a diffusible infusion),
intradermal, intraperitoneal, intramuscular, intrathecal, intraventricular, intracranial,
aneous, transmucosal, buccal, sublingual, endoscopic, rectal, oral, vaginal, topical,
pulmonary, intranasal, urethral or ocular. Administration can be provided by the subject
or by another person, e.g., a health care provider. The medication can be provided in
measured doses or in a ser which delivers a metered dose. Selected modes of
delivery are discussed in more detail below.
The invention provides methods, compositions, and kits, for rectal administration
or delivery of dsRNA agents described herein
s of inhibiting expression of the target gene
ments of the invention also relate to methods for inhibiting the expression
of a target gene. The method comprises the step of administering the dsRNA agents in
any of the preceding embodiments, in an amount sufficient to inhibit expression of the
target gene.
Another aspect the invention relates to a method of ting the expression of
a target gene in a cell, comprising ing to said cell a dsRNA agent of this invention.
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In one embodiment, the target gene is selected from the group consisting of Factor VII,
Eg5, PCSK9, TPX2, apoB, SAA, TTR, RSV, PDGF beta gene, Erb-B gene, Src gene,
CPvK gene, GRB2 gene, RAS gene, MEK gene, JNK gene, RAF gene, Erkl/2 gene,
PCNA (p21 ) gene, MYB gene, JUN gene, FOS gene, BCL-2 gene, en, Activated
Protein C, Cyclin D gene, VEGF gene, EGFR gene, Cyclin A gene, Cyclin E gene,
WNT-1 gene, beta-catenin gene, c-MET gene, PKC gene, NFKB gene, STAT3 gene,
survivin gene, Her2/Neu gene, topoisomerase I gene, topoisomerase II alpha gene,
mutations in the p73 gene, mutations in the p21(WAFl/CIPl) gene, mutations in the
p27(KIPl) gene, mutations in the PPM ID gene, mutations in the RAS gene, mutations in
the caveolin I gene, mutations in the MIB I gene, mutations in the MTAI gene, mutations
in the M68 gene, mutations in tumor ssor genes, and mutations in the p53 tumor
suppressor gene.
The invention is further illustrated by the following examples, which should not
be construed as further limiting. The contents of all references, pending patent
applications and published patents, cited throughout this application are hereby expressly
orated by reference.
EXAMPLES
Example 1. In vitro screening of siRNA duplexes
Cell culture and trans fections:
Human Hep3B cells or rat H.II.4.E cells (ATCC, Manassas, VA) were grown to
near confluence at 37 °C in an atmosphere of 5% C0 2 in RPMI (ATCC) supplemented
with 10% FBS, streptomycin, and glutamine (ATCC) before being released from the
plate by trypsinization. Transfection was carried out by adding 14.8 mΐ of Opti-MEM
plus 0.2 mΐ of Lipofectamine RNAiMax per well (Invitrogen, Carlsbad CA. cat # 13778-
150) to 5 mΐ of siRNA duplexes per well into a 96-well plate and incubated at room
temperature for 15 minutes. 80 mΐ of complete growth media t antibiotic
containing ~2 xlO4 Hep3B cells were then added to the siRNA mixture. Cells were
incubated for either 24 or 120 hours prior to RNA cation. Single dose experiments
were med at IOhM and O.lnM final duplex concentration and dose response
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experiments were done using 8, 4 fold serial dilutions with a maximum dose of lOnM
final duplex concentration.
Total RNA isolation using DYNABEADS mRNA Isolation Kit flnvitrogen. part # : 610-
Cells were harvested and lysed in 150 mΐ of Lysis/Binding Buffer then mixed for
minute at 850rpm using an Eppendorf Thermomixer (the mixing speed was the same
throughout the process). Ten microliters of magnetic beads and 80 mΐ Lysis/Binding
Buffer mixture were added to a round bottom plate and mixed for 1 minute. Magnetic
beads were ed using magnetic stand and the supernatant was removed without
disturbing the beads. After removing supernatant, the lysed cells were added to the
remaining beads and mixed for 5 minutes. After removing supernatant, ic beads
were washed 2 times with 150 mΐ Wash Buffer A and mixed for 1 minute. Beads were
capture again and supernatant removed. Beads were then washed with 150 mΐ Wash
Buffer B, captured and supernatant was removed. Beads were next washed with 150 mΐ
n Buffer, captured and supernatant removed. Beads were allowed to dry for 2
minutes. After drying, 50 mΐ of Elution Buffer was added and mixed for 5 s at
70°C. Beads were captured on magnet for 5 minutes. 40 mΐ of atant was d
and added to another 96 well plate.
cDNA sis using ABI High capacity cDNA reverse transcription kit (Applied
Biosvstems, Foster City, CA, Cat #4368813):
A master mix of 1 mΐ 10X Buffer, 0.4m125X dNTPs, I mΐ Random primers, 0.5 mΐ
Reverse Transcriptase, 0.5 mΐ RNase inhibitor and 1.6m1of H20 per reaction were added
into 5 mΐ total RNA. cDNA was generated using a Bio-Rad C-1000 or S-1000 thermal
cycler (Hercules, CA) through the ing steps: 25 °C 10 min, 37 °C 120 min, 85 °C 5
sec, 4 °C hold.
Real time PCR:
2m1of cDNA were added to a master mix containing 0.5m1GAPDH TaqMan
Probe (Applied Biosystems Cat #4326317E (human) Cat # 3 (rodent)), 0.5 m1TTR
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TaqMan probe (Applied Biosystems cat # HS00174914 m l (human) cat #
Rn00562124_ml (rat)) and 5m1Lightcycler 480 probe master mix (Roche Cat
#04887301001) per well in a 384 well plate (Roche cat # 04887301001). Real time PCR
was done in a Roche LC 480 Real Time PCR machine (Roche). Each duplex was tested
in at least two ndent transfections and each transfection was assayed in duplicate,
unless otherwise noted.
To calculate relative fold change, real time data were analyzed using the DD
method and normalized to assays performed with cells transfected with lOnM AD- 1955,
or mock transfected cells. IC50S were calculated using a 4 parameter fit model using
XLFit and normalized to cells transfected with AD- 1955 or na ve cells over the same
dose range, or to its own lowest dose. IC50S were ated for each individual
transfection as well as in combination, where a single IC50 was fit to the data from both
transfections.
The results of gene silencing of the exemplary siRNA duplex with various motif
cations of the invention are shown in the table below.
[Annotation] kjm
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[Annotation] kjm
MigrationNone set by kjm
ation] kjm
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Example 2. RNA Synthesis and Duplex Annealing
1. Oligonucleotide Synthesis:
All oligonucleotides were synthesized on an AKTAoligopilot synthesizer or an
ABI 394 izer. Commercially available lled pore glass solid support (dT-
CPG, 500A, Prime Synthesis) and RNA phosphoramidites with standard protecting
groups, 5'dimethoxytrityl N6-benzoyl-2'-t-butyldimethylsilyl-adenosine-3 '- - N ,N '-
diisopropylcyanoethylphosphoramidite, 5'dimethoxytrityl-N4-acetyl-2 '-t-
butyldimethylsilyl-cytidine-3 'N,N'-diisopropylcyanoethylphosphoramidite, 5'
dimethoxytrityl-N2~isobutryl-2 '-t-butyldimethylsilyl-guanosine-3 '-O-N,N '-diisopropyl-
2-cyanoethylphosphoramidite, and 5'dimethoxytrityl-2 '-t-butyldimethylsilyl-uridine-
3'N,N'-diisopropylcyanoethylphosphoramidite (Pierce Nucleic Acids
Technologies) were used for the oligonucleotide synthesis unless otherwise specified.
The 2'-F phosphoramidites, 5'-O-dimethoxytrityl-N4-acetyl-2'-fluro-cytidine-3 '-O-
N,N'-diisopropylcyanoethyl-phosphoramidite and 5'-O-dimethoxytrityl-2 '-flurouridine-3'N
,N'-diisopropylcyanoethyl-phosphoramidite were purchased from
(Promega). All phosphoramidites were used at a concentration of 0.2M in acetonitrile
(CH3CN) except for guanosine which was used at 0.2M concentration in 10% THF/ANC
(v/v). Coupling/recycling time of 16 minutes was used. The activator was 5-ethyl
thiotetrazole (0.75M, American International Chemicals), for the PO-oxidation
Iodine/Water/Pyridine was used and the PS-oxidation PADS (2 %>) in 2,6-lutidine/ACN
(1:1 v/v) was used. .
Ligand conjugated s were synthesized using solid support ning the
corresponding ligand. For example, the introduction of carbohydrate moiety/ligand (for
e.g., ) at the 3'-end of a sequence was achieved by starting the synthesis with the
corresponding carbohydrate solid support. Similarly a cholesterol moiety at the 3'-end
was uced by ng the synthesis on the cholesterol support. In general, the ligand
moiety was tethered to hydroxyprolinol via a tether of choice as described in the
previous examples to obtain a ypro lino 1- ligand moiety. The hydroxyprolinolligand
moiety was then coupled to a solid support via a succinate linker or was converted
to phosphoramidite via standard itylation conditions to obtain the desired
ydrate conjugate building blocks. Fluorophore labeled siRNAs were synthesized
[Annotation] kjm
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ed set by kjm
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from the corresponding phosphoramidite or solid support, purchased from Biosearch
Technologies. The oleyl lithocholic (GalNAc)3 polymer support made in house at a
loading of 38.6 ram. The Mannose (Man)3 polymer support was also made in
house at a loading of 42.0 umol/gram.
Conjugation of the ligand of choice at desired on, for example at the 5'-end
of the sequence, was achieved by coupling of the corresponding phosphoramidite to the
growing chain under standard phosphoramidite ng conditions unless otherwise
specified. An extended 15 min coupling of 0.1 M solution of phosphoramidite in
anhydrous CH3CN in the ce of 5-(ethylthio)-l H-tetrazole activator to a solid bound
oligonucleotide. Oxidation of the internucleotide phosphite to the phosphate was carried
out using standard iodine-water as reported (1) or by treatment with tert-butyl
hydroperoxide/acetonitrile/water (10: 87: 3) with 10 min oxidation wait time conjugated
oligonucleotide. Phosphorothioate was introduced by the oxidation of ite to
phosphorothioate by using a sulfur transfer reagent such as DDTT (purchased from AM
Chemicals), PADS and or Beaucage reagent The cholesterol phosphoramidite was
synthesized in house, and used at a concentration of 0.1 M in dichloromethane. Coupling
time for the cholesterol phosphoramidite was 16 s.
2. Deprotection- 1 (Nucleobase Deprotection)
After completion of synthesis, the support was transferred to a 100 ml glass bottle
(VWR). The ucleotide was cleaved from the support with simultaneous
ection of base and phosphate groups with 80 mL of a mixture of ethanolic
a [ammonia: ethanol (3:1)] for 6.5h at 55°C. The bottle was cooled briefly on ice
and then the ethanolic ammonia mixture was filtered into a new 250 ml bottle. The CPG
was washed with 2 x 40 mL portions of l/water (1:1 v/v). The volume of the
mixture was then reduced to ~ 30 ml by roto-vap. The mixture was then frozen on dry ice
and dried under vacuum on a speed vac.
3. Deprotection-II (Removal of 2' TBDMS group)
The dried residue was ended in 26 ml of triethylamine, triethylamine
trihydro fluoride (TEA.3HF) or pyridine-HF and DMSO (3:4:6) and heated at 60°C for 90
s to remove the t rt-butyldimethylsilyl (TBDMS) groups at the 2' position. The
[Annotation] kjm
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MigrationNone set by kjm
[Annotation] kjm
Unmarked set by kjm
[Annotation] kjm
None set by kjm
[Annotation] kjm
MigrationNone set by kjm
[Annotation] kjm
Unmarked set by kjm
reaction was then quenched with 50 ml of 20mM sodium acetate and pH adjusted to 6.5,
and stored in freezer until purification.
4. Analysis
The oligoncuelotides were analyzed by high-performance liquid chromatography
(HPLC) prior to purification and selection of buffer and column depends on nature of the
sequence and or conjugated .
. HPLC Purification
The ligand conjugated oligonucleotides were purified reverse phase preparative
HPLC. The unconjugated oligonucleotides were ed by anion-exchange HPLC on a
TSK gel column packed in house. The buffers were 20 mM sodium phosphate (pH 8.5) in
% CH3CN (buffer A) and 20 mM sodium ate (pH 8.5) in 10% CH3CN, 1M
NaBr (buffer B). Fractions containing full-length ucleotides were pooled, desalted,
and lyophilized. imately 0.15 OD of desalted oligonucleotidess were d in
water to 150 mΐ and then pipetted in special vials for CGE and LC/MS analysis.
Compounds were finally analyzed by LC-ESMS and CGE.
6. siRNA preparation
For the preparation of siRNA, equimolar amounts of sense and antisense strand
were heated in lxPBS at 95°C for 5 min and slowly cooled to room temperature.
Integrity of the duplex was confirmed by HPLC analysis.
[Annotation] kjm
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[Annotation] kjm
MigrationNone set by kjm
[Annotation] kjm
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[Annotation] kjm
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[Annotation] kjm
MigrationNone set by kjm
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duplex 3 modified Table 2.
Hofiod mofiod vofiod oofiod wmfiod wfiod wfiod wfiod R366 306 HNod NHNod OHNod NNNod vaod mmNod mmNod mNod mNod NmNod mmNod mNod HmNod wNod omod 38.0 omod
5N6 Ea Elfld EEEa
mod mod mod mad Hd mod mod mod No.0 mod 8.0
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Hovfim Novfim movfim wovfim movfim wovfim movfim wovfim movfim oHva HHva NHva mavfim vfivfim mHva ofivfim mfivfim
H035 E wovfio movfio wovfio movfio wovfio movfio Davao HHvHQ NHvHQ mavfio vfivfio mHvHQ ofivfio mfivfio vaHQ mHvHQ
Example 3 : In vitro silencing activity with various chemical modifications on TTR
siRNA
The IC for each modified siRNA is determined in Hep3B cells by standard
e transfection using Lipofectamine RNAiMAX. In brief, reverse transfection is
carried out by adding 5 m of Opti-MEM to 5 of siRNA duplex per well into a 96-
well plate along with 10 of EM plus 0.5 mΐ of Lipofectamine RNAiMax per
well (Invitrogen, Carlsbad CA. cat # 13778-150) and incubating at room temperature for
-20 minutes. Following tion, 100 mΐ of complete growth media without
antibiotic containing 12,000-15,000 Hep3B cells is then added to each well. Cells are
incubated for 24 hours at 37°C in an atmosphere of 5% C02 prior to lysis and analysis of
ApoB and GAPDH niRNA by bDNA (Quantigene). Seven different siRNA
concentrations ranging from IOhM to 0.6pM are assessed for IC determination and
ApoB/GAPDH for ApoB transfected cells is ized to cells transfected with IOhM
Luc siRNA.
3 modified duplex Table 3.
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Example 4 : In vitro silencing activity with various chemical modifications on ANGPTL3
siRNA
Cell culture and transfections
Hep3B cells (ATCC, Manassas, VA) were grown to near confluence at 37°C in an
atmosphere of 5% C0 2 in RPMI (ATCC) supplemented with 10% FBS, streptomycin,
and glutamine (ATCC) before being released from the plate by trypsinization.
Transfection was carried out by adding 14.8 mΐ of Opti-MEM plus 0.2m1of
Lipofectamine RNAiMax per well (Invitrogen, Carlsbad CA. cat # 13778-150) to 5 mΐ of
siRNA duplexes per well into a 96-well plate and incubated at room temperature for 15
s. 80 mΐ of complete growth media without antibiotic containing 2 xlO4 Hep3B
cells were then added to the siRNA mixture. Cells were incubated for either 24 or 120
hours prior to RNA cation. Single dose ments were performed at IOhM and
O.lnM final duplex concentration and dose response experiments were done at 10, 1, 0.5,
0.1,0.05, 0.01, 0.005, 0.001, 0.0005, 0.0001, 0.00005 and 0.00001 nM final duplex
concentration unless otherwise stated.
cDNA sis using ABI High capacity cDNA e transcription kit (Applied
Biosystems, Foster City, CA, Cat #4368813)
A master mix of 2m1 10X Buffer, 0.8 mΐ 25X dNTPs, 2m1Random primers, I mΐ
Reverse Transcriptase, 1 mΐ RNase inhibitor and 3.2m1of H20 per reaction were added
into IOmI total RNA. cDNA was generated using a Bio-Rad C-1000 or S-1000 l
cycler (Hercules, CA) through the following steps: 25°C 10 min, 37°C 120 min, 85°C 5
sec, 4°C hold.
Real time PCR
2 mΐ of cDNA was added to a master mix ning 0.5 m1GAPDH TaqMan
Probe (Applied Biosystems Cat #43263 17E), 0.5m1ANGPTL TaqMan probe (Applied
Biosystems cat # Hs00205581_ml) and 5m1Lightcycler 480 probe master mix (Roche
Cat #04887301001) per well in a 384 well 50 plates (Roche cat # 04887301001). Real
time PCR was done in an ABI 7900HT Real Time PCR system (Applied Biosystems)
using the Q) assay. Each duplex was tested in two independent transfections, and
each transfection was assayed in duplicate, unless otherwise noted in the summary tables.
To calculate relative fold change, real time data was analyzed using the AACt
method and normalized to assays performed with cells transfected with lOnM AD- 1955,
or mock ected cells. IC50S were calculated using a 4 parameter fit model using
XLFit and normalized to cells transfected with AD- 1955 or na ve cells over the same
dose range, or to its own lowest dose. AD- 1955 sequence, used as a ve control,
targets luciferase and has the following sequence:
sense: cuuAcGcuGAGuAcuucGAdTsdT;
antisense : uACUcAGCGuAAGdTsdT .
The various embodiments described above can be combined to provide further
embodiments. All of the U.S. patents, U.S. patent application publications, foreign
patents, foreign patent applications and non-patent publications referred to in this
specification are incorporated herein by reference, in their ty. Aspects of the
embodiments can be modified, if necessary to employ concepts of the various patents,
ations and publications to e yet r embodiments.
These and other changes can be made to the embodiments in light of the abovedetailed
description. In general, in the following claims, the terms used should not be
construed to limit the claims to the specific embodiments disclosed in the specification
and the claims, but should be construed to include all possible embodiments along with
the full scope of equivalents to which such claims are entitled. Accordingly, the claims
are not limited by the disclosure.
[Annotation] kjm
None set by kjm
[Annotation] kjm
MigrationNone set by kjm
ation] kjm
Unmarked set by kjm
[Annotation] kjm
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[Annotation] kjm
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Claims (45)
1. A double-stranded RNAi agent capable of inhibiting the expression of a target gene, comprising a sense strand and an antisense strand, each strand having 14 to 30 nucleotides, wherein the duplex is represented by formula (III): sense: 5' np -Na -(X X X)i-Nb -Y Y Y -Nb -(Z Z Z)j -Na - nq 3' antisense: 3' np’-Na’-(X’X′X′)k-Nb’-Y′Y′Y′-Nb’-(Z′Z′Z′)l-Na’- nq’ 5' (III) wherein: i, j, k, and l are each independently 0 or 1; p and q are each independently 0-6; each Na and Na’independently represents an oligonucleotide sequence comprising 0-25 nucleotides which are either modified or unmodified or combinations thereof, each sequence comprising at least two differently modified nucleotides, each Nb and Nb’independently represents an oligonucleotide sequence comprising 1-10 modified nucleotides; each np, np’, nq and nq’ independently ents an overhang nucleotide sequence comprising 0-6 nucleotides; and XXX, YYY, ZZZ, X′X′X′, Y′Y′Y′, and Z′Z′Z′ each independently represent one motif of three identical modifications on three consecutive nucleotides; wherein the modification on Nb is ent than the cation on Y and the modification on Nb’is different than the modification on Y’; and n the Y’Y’Y’ motif occurs at the 11, 12 and 13 positions of the antisense strand from the .
2. The double-stranded RNAi agent of claim 1, wherein i is 1; j is 1; or both i and j are 1.
3. The double-stranded RNAi agent of claim 1 or claim 2, wherein k is 1; l is 1; or both k and l are 1.
4. The double-stranded RNAi agent of any preceding claim, wherein the YYY motif occurs at or near the cleavage site of the sense strand.
5. The -stranded RNAi agent of any preceding claim, n the Y’ is 2’-OMe.
6. The double- stranded RNAi agent of claim 1, wherein formula (III) is represented as formula (IIIa): [Annotation] kjm None set by kjm [Annotation] kjm MigrationNone set by kjm [Annotation] kjm Unmarked set by kjm [Annotation] kjm None set by kjm [Annotation] kjm MigrationNone set by kjm [Annotation] kjm Unmarked set by kjm 5' np -Na -Y Y Y -Nb -Z Z Z -Na-nq 3' 3' np’-Na’-Y′Y′Y′-Nb’-Z′Z′Z′-Na’nq’ 5' (IIIa) wherein each Nb and Nb’ independently represents an oligonucleotide sequence comprising 1-5 ed nucleotides.
7. The double-stranded RNAi agent of claim 1, n formula (III) is ented as formula (IIIb): 5' np-Na-X X X -Nb-Y Y Y -Na-nq 3' 3' np-Na-X′X′X′-Nb-Y′Y′Y′-Na-nq 5' (IIIb) wherein each Nb and Nb’ ndently ents an oligonucleotide sequence comprising 1-5 modified nucleotides.
8. The double-stranded RNAi agent of claim 1, wherein formula (III) is represented as formula (IIIc): 5' np-Na-X X X -Nb-Y Y Y -Nb-Z Z Z -Na-nq 3' 3' np-Na-X′X′X′-Nb-Y′Y′Y′-Nb-Z′Z′Z′-Na-nq 5' (IIIc) wherein each Nb and Nb’ independently represents an oligonucleotide sequence sing 1-5 modified nucleotides and each Na and Na’ independently represents an ucleotide sequence comprising 2-10 modified nucleotides.
9. The double-stranded RNAi agent of any one of claims 1 to 8, wherein the duplex region is 17-30 nucleotide pairs in length.
10. The double-stranded RNAi agent of any one of claims 1 to 8, wherein the duplex region is 17-19 nucleotide pairs in length.
11. The double-stranded RNAi agent of any one of claims 1 to 8, wherein the duplex region is 27-30 nucleotide pairs in length.
12. The double-stranded RNAi agent of any preceding claim, wherein each strand has 17-30 nucleotides. [Annotation] kjm None set by kjm [Annotation] kjm MigrationNone set by kjm [Annotation] kjm ed set by kjm [Annotation] kjm None set by kjm [Annotation] kjm MigrationNone set by kjm [Annotation] kjm Unmarked set by kjm
13. The double-stranded RNAi agent of any preceding claim, wherein the modifications on the nucleotides are ed from the group consisting of LNA, HNA, CeNA, 2′-methoxyethyl, 2′-O- alkyl, 2′-O-allyl, 2′-C- allyl, 2′-fluoro, 2’-deoxy, and combinations thereof.
14. The double-stranded RNAi agent of claim 13, wherein the nucleotides are ed with either 2’-OCH3 or 2’-F.
15. The double-stranded RNAi agent of any preceding claim, further comprising at least one ligand.
16. The double-stranded RNAi agent of claim 15, wherein the ligand is one or more GalNAc derivatives attached through a bivalent or trivalent branched linker.
17. The double-stranded RNAi agent of any one of claims 1 to 12, wherein the modifications on the nucleotides are selected from the group ting of 2'-O-methyl nucleotide, xyfluoro nucleotide, 2'-O-N-methylacetamido (2'-O-NMA) nucleotide, a 2'-O-dimethylaminoethoxyethyl (2'- O-DMAEOE) nucleotide, 2'-O-aminopropyl (2'-O-AP) nucleotide, 2'-ara-F, and combinations thereof.
18. The double-stranded RNAi agent of claim 15 or claim 16, wherein the ligand is attached to the 3’ end of the sense strand.
19. The -stranded RNAi agent of any preceding claim, further comprising at least one phosphorothioate or methylphosphonate internucleotide linkage.
20. The -stranded RNAi agent of any preceding claim, wherein the nucleotide at the 1 position of the 5’-end of the duplex in the antisense strand is ed from the group consisting of A, dA, dU, U, and dT.
21. The double-stranded RNAi agent of any ing claim, wherein the base pair at the 1 position of the 5’-end of the duplex is an AU base pair.
22. The double-stranded RNAi agent of any preceding claim, wherein the Y tides contain a 2’-fluoro modification.
23. The double-stranded RNAi agent of any preceding claim, wherein the Y’ nucleotides contain a 2’-O-methyl modification. [Annotation] kjm None set by kjm [Annotation] kjm MigrationNone set by kjm [Annotation] kjm Unmarked set by kjm [Annotation] kjm None set by kjm [Annotation] kjm MigrationNone set by kjm [Annotation] kjm Unmarked set by kjm
24. A double-stranded RNAi agent capable of inhibiting the expression of a target gene, comprising a sense strand and an antisense strand, each strand having 14 to 30 nucleotides, wherein the sense strand contains at least two motifs of three identical modifications on three consecutive nucleotides, one of said motifs ing at the cleavage site in the strand and at least one of said motifs occurring at r portion of the strand that is separated from the motif at the cleavage site by at least one modified nucleotide, wherein the cation on the at least one modified nucleotide is different than the modification on the three consecutive modified nucleotides; and n the antisense strand contains at least a first motif of three identical modifications on three consecutive nucleotides, one of said motifs occurring at or near the ge site in the strand and a second motif occurring at another portion of the strand that is separated from the first motif by at least one modified tide, wherein the modification on the at least one ed nucleotide is different than the modification on the three consecutive modified nucleotides; wherein the modification in the motif occurring at the cleavage site in the sense strand is different than the modification in the motif occurring at or near the cleavage site in the antisense strand; and n the first or the second motif in the antisense strand occurs at the 11, 12 and 13 positions of the antisense strand from the .
25. The double-stranded RNAi agent of claim 24, wherein at least one of the nucleotides occurring at the cleavage site in the sense strand forms a base pair with one of the nucleotides in the motif occurring at or near the cleavage site in the antisense strand.
26. The double-stranded RNAi agent of claim 24 or claim 25, wherein the duplex has 17-30 nucleotides.
27. The double-stranded RNAi agent of claim 24 or claim 25, wherein the duplex has 17-19 nucleotides.
28. The double-stranded RNAi agent of claim 24 or claim 25, wherein each strand has 17-23 nucleotides.
29. The double-stranded RNAi agent of any one of claims 24 to 28, n the modifications on the nucleotides are selected from the group consisting of LNA, HNA, CeNA, 2′-methoxyethyl, lkyl, 2′-O-allyl, 2′-C- allyl, 2′-fluoro, 2’-deoxy, and combinations thereof.
30. The double-stranded RNAi agent of claim 29, wherein the modifications on the nucleotide are 2’-OCH3 or 2’-F. [Annotation] kjm None set by kjm ation] kjm MigrationNone set by kjm [Annotation] kjm Unmarked set by kjm [Annotation] kjm None set by kjm [Annotation] kjm MigrationNone set by kjm [Annotation] kjm Unmarked set by kjm
31. The double-stranded RNAi agent of any one of claims 24 to 30, further comprising a ligand ed to the 3’ end of the sense strand.
32. A double-stranded RNAi agent capable of inhibiting the expression of a target gene, comprising a sense strand and an antisense strand, each strand having 14 to 30 nucleotides, wherein the sense strand contains at least one motif of three 2’-F modifications on three consecutive nucleotides, one of said motifs occurring at or near the cleavage site in the strand, and wherein a polynucleotide adjacent to the three consecutive nucleotides is a modified nucleotide having a cation other than a 2’-F modification; and wherein the antisense strand contains at least one motif of three 2’-O-methyl modifications on three consecutive nucleotides, one of said motifs occurring at or near the ge site, and wherein a polynucleotide adjacent to the three consecutive tides is a modified tide having a modification other than a 2’-O-methyl modification; and wherein one of the at least one motif in the antisense strand occurs at the 11, 12 and 13 ons of the antisense strand from the 5’-end.
33. The double-stranded RNAi agent of claim 32, wherein the sense strand comprises one or more motifs of three identical modifications on three utive nucleotides, said motifs occurring at another portion of the strand that is separated from the three 2’-F modifications at the cleavage site by at least one nucleotide.
34. The double-stranded RNAi agent of claim 32 or claim 33, wherein the antisense strand comprises one or more motifs of three cal modifications on three consecutive nucleotides, said motifs occurring at another portion of the strand that is separated from the three 2’-O-methyl modifications by at least one nucleotide.
35. The double-stranded RNAi agent of any one of claims 32 to 34, wherein at least one of the nucleotides having a 2’-F cation forms a base pair with one of the nucleotides having a 2’-O- methyl modification.
36. The double-stranded RNAi agent of any one of claims 32 to 34, wherein the duplex is 17-30 nucleotide pairs in length.
37. The double-stranded RNAi agent of any one of claims 32 to 36, wherein the duplex is 17-19 nucleotide pairs in length. ation] kjm None set by kjm [Annotation] kjm MigrationNone set by kjm [Annotation] kjm Unmarked set by kjm [Annotation] kjm None set by kjm [Annotation] kjm MigrationNone set by kjm [Annotation] kjm Unmarked set by kjm
38. The double-stranded RNAi agent of any one of claims 32 to 37, wherein each strand has 17-23 tides.
39. The double-stranded RNAi agent of any one of claims 32 to 38, further comprising a ligand attached to the 3’ end of the sense strand.
40. A pharmaceutical composition comprising the double-stranded RNAi agent according to any one of the preceding claims alone or in combination with a pharmaceutically acceptable carrier or excipient.
41. Use of the double-stranded RNAi agent according to any one of claims 1 to 39 in the manufacture of a medicament for inhibiting the expression of a target gene.
42. The use of claim 41, wherein the medicament is provided for subcutaneous or intravenous administration.
43. Use of a dsRNA agent ented by formula (III): sense: 5' np -Na -(X X X) i-Nb -Y Y Y -Nb -(Z Z Z)j -Na - nq 3' antisense: 3' np’-Na’-(X’X′X′)k-Nb’-Y′Y′Y′-Nb’-(Z′Z′Z′)l-Na’- nq’ (III) wherein: i, j, k, and l are each independently 0 or 1; p and q are each independently 0-6; each Na and Na′ independently represents an oligonucleotide sequence comprising 0-25 nucleotides which are either modified or unmodified or combinations thereof, each sequence comprising at least two differently modified tides; each Nb and Nb′ independently represents an oligonucleotide sequence comprising 1-10 ed nucleotides; each np, np’, nq and nq’ ndently represents an overhang nucleotide ce comprising 0-6 nucleotide ce; and XXX, YYY, ZZZ, X′X′X′, Y′Y′Y′, and Z′Z′Z′ each independently represent one motif of three identical modifications on three utive nucleotides; and wherein the modifications on Nb is different than the modification on Y and the modification on Nb’ is different than the modification on Y’; and wherein the Y’Y’Y’ motif occurs at the 11, 12 and 13 positions of the antisense strand from the 5’-end [Annotation] kjm None set by kjm [Annotation] kjm MigrationNone set by kjm [Annotation] kjm Unmarked set by kjm [Annotation] kjm None set by kjm [Annotation] kjm MigrationNone set by kjm [Annotation] kjm ed set by kjm in the manufacture of a medicament for delivering a polynucleotide to a specific target in a subject.
44. The use of claim 43 , wherein the medicament is provided for uscular, intrabronchial, intrapleural, intraperitoneal, intraarterial, lymphatic, intravenous, subcutaneous or ospinal administration, or combinations thereof.
45. Use of the dsRNAi agent of any one of claims 1 to 39 in the manufacture of a medicament for delivering a polynucleotide to a specific target of a subject, wherein the medicament is provided for aneous administration.
Applications Claiming Priority (3)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US201161561710P | 2011-11-18 | 2011-11-18 | |
US61/561,710 | 2011-11-18 | ||
PCT/US2012/065601 WO2013074974A2 (en) | 2011-11-18 | 2012-11-16 | Modified rnai agents |
Publications (2)
Publication Number | Publication Date |
---|---|
NZ624471A NZ624471A (en) | 2016-08-26 |
NZ624471B2 true NZ624471B2 (en) | 2016-11-29 |
Family
ID=
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