WO2025259747A2 - Dystrophy myotonic protein kinase (dmpk) irna compositions and methods of use thereof - Google Patents
Dystrophy myotonic protein kinase (dmpk) irna compositions and methods of use thereofInfo
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- WO2025259747A2 WO2025259747A2 PCT/US2025/033136 US2025033136W WO2025259747A2 WO 2025259747 A2 WO2025259747 A2 WO 2025259747A2 US 2025033136 W US2025033136 W US 2025033136W WO 2025259747 A2 WO2025259747 A2 WO 2025259747A2
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- C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
- C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
- C12N15/1137—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing against enzymes
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- C12N2320/32—Special delivery means, e.g. tissue-specific
Definitions
- DMPK dystrophy myotonic protein kinase
- MT-PK myotonin-protein kinase
- MT-PK myotonin-protein kinase
- DM1 Myotonic dystrophy
- CTG cytosine thymine guanine
- DM1 is a multisystem disorder characterized by myotonia, muscular dystrophy, cataracts, hypogonadism, frontal balding, cardiac conduction defects, endocrine abnormalities, and iridescent cataracts, 25 although the clinical features of DM1 and the severity of disease vary with the number of repeats: normal individuals have 5 to 37 repeats, mildly affected persons have 50 to 150 repeats, patients with classic DM1 have 100 to 1,000 repeats, and those with onset at birth can have more than 2,000 repeats. Effective therapies and treatments for DM1 are currently not available and, instead, 30 treatments and therapies focus on managing symptoms and improving quality of life.
- RNA-induced silencing complex RISC
- the DMPK gene may be within a cell, e.g., a cell within a subject, such as a human subject.
- the present disclosure also provides methods of using the iRNA compositions of the disclosure for inhibiting the expression of a DMPK gene, and/or for treating a subject who would benefit from inhibiting or reducing the expression of an DMPK gene, e.g., a subject suffering or prone 5 to suffering from an DMPK-associated disorder, e.g., Myotonic dystrophy (DM) type 1 (DM1).
- DM Myotonic dystrophy
- the disclosure provides a double stranded ribonucleic acid (dsRNA) agent for inhibiting expression of a dystrophy myotonic protein kinase (DMPK) gene in a cell, or a pharmaceutically acceptable salt thereof, comprising a sense strand and an antisense strand forming a double stranded region, wherein the antisense strand comprises at least 15, e.g., 15, 16, 18, 10 18, 19, 20, 21, 22, or 23, contiguous nucleotides differing by no more than three nucleotides from any one of the antisense strand nucleotide sequences in any one of Tables 2-3.
- dsRNA double stranded ribonucleic acid
- DMPK dystrophy myotonic protein kinase
- the disclosure provides a double stranded ribonucleic acid (dsRNA) agent for inhibiting expression of a dystrophy myotonic protein kinase (DMPK) gene in a cell, or a pharmaceutically acceptable salt thereof, comprising a sense strand and an antisense strand forming a 15 double stranded region; wherein the sense strand comprises at least 15, e.g., 15, 16, 18, 18, 19, 20, or 21, contiguous nucleotides differing by no more than three, e.g., 3, 2, 1, or 0, nucleotides from the nucleotide sequence of SEQ ID NO:1 and the antisense strand comprises at least 15, e.g., 15, 16, 18, 18, 19, 20, 21, 22, or 23, contiguous nucleotides differing by no more than three, e.g., 3, 2, 1, or 0, nucleotides from the corresponding portion of the nucleotide sequence of SEQ ID NO:2; at least one 20 alpha-v-beta
- the present disclosure provides a double stranded ribonucleic acid (dsRNA) agent for inhibiting expression of a dystrophy myotonic protein kinase (DMPK) gene in a cell, or a 25 pharmaceutically acceptable salt thereof, comprising a sense strand and an antisense strand forming a double stranded region; wherein the antisense strand comprises at least 15, e.g., 15, 16, 18, 18, 19, 20, 21, 22, or 23, contiguous nucleotides differing by no more than three, e.g., 3, 2, 1, or 0, nucleotides from any one of the antisense strand nucleotide sequences in any one of Tables 2-3; at least one alpha- v-beta-6 ( ⁇ v ⁇ 6) integrin targeting ligand that mediates delivery to muscle tissue conjugated to at least 30 one strand; and at least one in vivo delivery enhancing moiety conjugated to one or more internal positions on at least one strand.
- dsRNA double strande
- the sense strand comprises at least 15, e.g., 15, 16, 18, 18, 19, 20, or 21, contiguous nucleotides differing by no more than three, e.g., 3, 2, 1, or 0, nucleotides from any one of the sense strand nucleotide sequences in any one of Tables 2-3.
- the sense strand comprises at least 15, e.g., 15, 16, 18, 18, 19, 20, or 21, contiguous nucleotides differing by no more than two nucleotides from any one of the sense strand nucleotide sequences in any one of Tables 2-3 and the antisense strand comprises at least 15, e.g., 15, 2 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 16, 18, 18, 19, 20, 21, 22, or 23, contiguous nucleotides differing by no more than two nucleotides from any one of the antisense strand nucleotide sequences in any one of Tables 2-3.
- the sense strand comprises at least 15, e.g., 15, 16, 18, 18, 19, 20, or 21, contiguous nucleotides differing by no more than one nucleotide from any one of the sense strand 5 nucleotide sequences in any one of Tables 2-3 and the antisense strand comprises at least 15, e.g., 15, 16, 18, 18, 19, 20, 21, 22, or 23, contiguous nucleotides differing by no more than one nucleotide from any one of the antisense strand nucleotide sequences in any one of Tables 2-3.
- the sense strand comprises a nucleotide sequence selected from the group consisting of any one of the sense strand nucleotide sequences in any one of Tables 2-3 and the 10 antisense strand comprises a nucleotide sequence selected from the group consisting of any one of the antisense strand nucleotide sequences in any one of Tables 2-3.
- the dsRNA agent, or a pharmaceutically acceptable salt thereof comprises at least one nucleotide comprising a nucleotide modification.
- all of the nucleotides of the sense strand comprise a nucleotide 15 modification; all of the nucleotides of the antisense strand comprise a nucleotide modification; or all of the nucleotides of the sense strand and all of the nucleotides of the antisense strand comprise a nucleotide modification.
- At least one of the nucleotide modifications is selected from the group consisting of a deoxy-nucleotide modification, a 3’-terminal deoxythimidine (dT) nucleotide 20 modification, a 2'-O-methyl nucleotide modification, a 2'-fluoro nucleotide modification, a 2'-deoxy nucleotide modification, a locked nucleotide modification, an unlocked nucleotide modification, a conformationally restricted nucleotide modification, a constrained ethyl nucleotide modification, an abasic nucleotide modification, a 2’-amino nucleotide modification, a 2’-O-allyl nucleotide modification, 2’-C-alkyl nucleotide modification, 2’-hydroxly nucleotide modification, a 2’- 25 methoxyethyl nucleotide modification, a 2’-O-alkyl
- At least one of the modified nucleotides is selected from the group 35 consisting of LNA, HNA, CeNA, 2’-methoxyethyl, 2’-O-alkyl, 2’-O-allyl, 2’-C- allyl, 2’-fluoro, 2’- deoxy, 2’-hydroxyl, and glycol; and combinations thereof.
- at least one of the modified nucleotides is selected from the group consisting of a deoxy-nucleotide, a 2'-O-methyl modified nucleotide, a 2'-fluoro modified nucleotide, 3 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- ALN-529-WO a 2'-deoxy-modified nucleotide, a glycol modified nucleotide (GNA), a nucleotide comprising a 2’ phosphate, a nucleotide comprising a phosphorothioate group, and a vinyl-phosphonate nucleotide; and combinations thereof.
- GAA glycol modified nucleotide
- At least one of the modified nucleotides is a nucleotide modified with a 5 thermally destabilizing nucleotide modification, e.g., selected from the group consisting of an abasic modification; a mismatch with the opposing nucleotide in the duplex; a destabilizing sugar modification, a 2’-deoxy modification, an acyclic nucleotide, an unlocked nucleic acid (UNA), and a glycerol nucleic acid (GNA).
- a 5 thermally destabilizing nucleotide modification e.g., selected from the group consisting of an abasic modification; a mismatch with the opposing nucleotide in the duplex; a destabilizing sugar modification, a 2’-deoxy modification, an acyclic nucleotide, an unlocked nucleic acid (UNA), and a glycerol nucleic acid (GNA).
- a 5 thermally destabilizing nucleotide modification
- the dsRNA agent, or a pharmaceutically acceptable salt thereof, further 10 comprises a phosphate or phosphate mimic at the 5’-end of the antisense strand, e.g., a 5’-vinyl phosphonate (VP).
- a phosphate or phosphate mimic at the 5’-end of the antisense strand e.g., a 5’-vinyl phosphonate (VP).
- the 3’ end of the sense strand is protected via an end cap which is a cyclic group having an amine, said cyclic group being selected from the group consisting of pyrrolidinyl, pyrazolinyl, pyrazolidinyl, imidazolinyl, imidazolidinyl, piperidinyl, piperazinyl, 15 [1,3]dioxolanyl, oxazolidinyl, isoxazolidinyl, morpholinyl, thiazolidinyl, isothiazolidinyl, quinoxalinyl, pyridazinonyl, tetrahydrofuranyl, and decalinyl.
- an end cap which is a cyclic group having an amine, said cyclic group being selected from the group consisting of pyrrolidinyl, pyrazolinyl, pyrazolidinyl, imidazolinyl, imidazolidinyl, pipe
- the double stranded region may be 19-30 nucleotide pairs in length; 19-25 nucleotide pairs in length; 19-23 nucleotide pairs in length; 23-27 nucleotide pairs in length; or 21-23 nucleotide pairs in length.
- each strand is independently no more than 30 nucleotides in length.
- the sense strand is 21 nucleotides in length and the antisense strand is 23 nucleotides in length.
- the dsRNA agent, or a pharmaceutically acceptable salt thereof comprises at least one single-stranded overhang, e.g., a single-stranded overhang that is 1, 2 or 3 25 nucleotides in length.
- the dsRNA agent, or a pharmaceutically acceptable salt thereof is blunt-ended.
- the dsRNA agent, or a pharmaceutically acceptable salt thereof further comprises at least one phosphorothioate or methylphosphonate internucleotide linkage.
- the phosphorothioate or methylphosphonate internucleotide linkage is at the 3’-terminus of one strand. In another embodiment, the phosphorothioate or methylphosphonate internucleotide linkage is at the 5’-terminus of one strand.
- the phosphorothioate or methylphosphonate internucleotide linkage is at 35 both the 5’- and 3’-terminus of one strand.
- the dsRNA agent, or a pharmaceutically acceptable salt thereof comprises 6-10, e.g., 6, 7, 8, 9, or 10, phosphorothioate or methylphosphonate internucleotide linkages. 4 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
- the dsRNA agent, or a pharmaceutically acceptable salt thereof comprises 7 phosphorothioate or methylphosphonate internucleotide linkages.
- the ⁇ v ⁇ 6 integrin targeting ligand the ⁇ v ⁇ 6 integrin targeting ligand comprises a structure represented by Formula (X): 5 or a salt thereof, wherein: or CH2; , wherein m is 0, 1, 2, 3, or 4; and each R 2 is independently R, or two R 2 groups on adjacent carbon atoms taken together with the atoms 10 to which they are bound form a fused 4 – 8 membered ring that is optionally substituted by 1, 2, 3 or 4 groups independently selected from group consisting of R and a nitrogen protecting group;
- A is an 5-membered heteroaryl optionally substituted with 1 or 2 substituents independently selected from methyl, ethyl, fluoro, hydroxymethyl, 2-hydroxypropan-2-yl, trifluoromethyl, difluoromethyl, and fluoromethyl;
- 15 Q is -COOR1 or tetrazolyl (e.g., 1,2,3,4-tetrazol-5-yl), wherein R 1 is hydrogen or
- the ⁇ v ⁇ 6 integrin targeting ligand of Formula (X) is 6 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO , wherein Y’ is O or S, and R P and R 1 are as defined for Formula (X) or any embodiment thereof.
- Y’ is O.
- Y’ is S. 5
- R 1 is hydrogen.
- R 1 is C1-6alkyl (e.g., methyl or t-butyl).
- R P is hydrogen.
- Y’ is O, R 1 is hydrogen and R P is a nitrogen protecting group. In one embodiment, Y’ is S, R 1 is hydrogen and R P is a nitrogen protecting group. In one embodiment, Y’ is O, R 1 is C1-6alkyl and R P is hydrogen. 25 In one embodiment, Y’ is S, R 1 is C1-6alkyl and R P is hydrogen. In one embodiment, Y’ is O, R 1 is C1-6alkyl and R P is a nitrogen protecting group. In one embodiment, Y’ is S, R 1 is C1-6alkyl and R P is a nitrogen protecting group. 7 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 56.
- the ⁇ v ⁇ 6 integrin targeting ligand is wherein a broken bond represents a bond to the remainder of the dsRNA, or a pharmaceutically acceptable salt thereof.
- the in vivo delivery enhancing moiety comprises at least one C10-C26 hydrocarbon chain. In one embodiment, the in vivo delivery enhancing moiety comprises at least one C 22 hydrocarbon chain. In one embodiment, the at least one C 22 hydrocarbon chains is an aliphatic, alicyclic, or 10 polyalicyclic compound.
- the at least one C 22 hydrocarbon chains contains a functional group selected from the group consisting of hydroxyl, amine, carboxylic acid, sulfonate, phosphate, thiol, azide, and alkyne. In one embodiment, the at least one C 22 hydrocarbon chains is a C 22 acid.
- the C 22 acid is selected from the group consisting of docosanoic acid, 6- octyltetradecanoic acid, 10-hexylhexadecanoic acid, all-cis-7,10,13,16,19-docosapentaenoic acid, all- cis-4,7,10,13,16,19-docosahexaenoic acid, all-cis-13,16-docosadienoic acid, all-cis-7,10,13,16- docosatetraenoic acid, all-cis-4,7,10,13,16-docosapentaenoic acid, and cis-13-docosenoic acid.
- the at least one C 22 hydrocarbon chains is a C 22 alcohol.
- the C 22 alcohol is selected from the group consisting of 1-docosanol, 6- octyltetradecan-1-ol, 10-hexylhexadecan-1-ol, cis-13-docosen-1-ol, docosan-9-ol, docosan-2-ol, docosan-10-ol, docosan-11-ol, andcis-4,7,10,13,16,19-docosahexanol.
- the at least one C 22 hydrocarbon chains is a C 22 amide.
- the C 22 amide is selected from the group consisting of (E)-Docos-4- 25 enamide, (E)-Docos-5-enamide, (Z)-Docos-9-enamide, (E)-Docos-11-enamide,12-Docosenamide, 8 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- the at least one C10-C26 hydrocarbon chain is unsubstituted or 5 substituted with at least one functional group selected from the group consisting of hydroxyl, amine, carboxylic acid, sulfonate, phosphate, thiol, azide, and alkyne.
- the at least one C10-C26 hydrocarbon chains is substituted with a carboxylic acid group.
- the in vivo delivery enhancing moiety is attached to the dsRNA agent, or 10 a pharmaceutically acceptable salt thereof, via a linker or via a carrier or via an internucleotide phosphate linkage. In one embodiment, the in vivo delivery enhancing moiety is attached to the dsRNA agent via a linker.
- the linker comprises –(CH2)n-NH-C(O)- or –(CH2)n-NH-C(O)-(CH2)2- C(COOH)-NH-C(O)-, wherein n is a number from 1 to 20.
- the linker comprises –(CH)2-O-(CH2CH2)-(O)-(CH2CH2)-NH-C(O)-.
- the in vivo delivery enhancing moiety is represented by the following structure: 25 , 30 , 9 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- the at least one ⁇ v ⁇ 6 integrin targeting ligand is conjugated to the 3’ end antisense strand. In another embodiment, the at least one ⁇ v ⁇ 6 integrin targeting ligand is conjugated to the 5’ end of the antisense strand. In one embodiment, the at least one ⁇ v ⁇ 6 integrin targeting ligand is conjugated to both the 5’-end and the 3’-end of the antisense strand. 10 In one embodiment, the at least one ⁇ v ⁇ 6 integrin targeting ligand is conjugated to an internal position of the antisense strand. In one embodiment, the at least one in vivo delivery enhancing moiety is conjugated to an internal position of the sense strand.
- the at least one ⁇ v ⁇ 6 integrin targeting ligand and the at least one in vivo delivery enhancing moiety are both conjugated to the antisense strand. In one embodiment, the at least one ⁇ v ⁇ 6 integrin targeting ligand is conjugated to the sense 35 strand and the at least one in vivo delivery enhancing moiety is conjugated to the antisense strand. In one embodiment, the at least one ⁇ v ⁇ 6 integrin targeting ligand is conjugated to the antisense strand and the at least one in vivo delivery enhancing moiety is conjugated to the sense strand. 11 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- the cell is a muscle cell, e.g., a skeletal muscle cell, a cardiac muscle cell, and/or a smooth muscle cell.
- the cell is within a subject, e.g., a human, such as a subject having an DMPK-associated disorder, e.g., myotonic dystrophy type 1 (DM1).
- contacting the cell with the dsRNA agent inhibits the expression of the 20 DMPK gene by at least 50%, 60%, 70%, 80%, 90%, or 95%.
- inhibiting expression of the DMPK gene decreases DMPK protein level in serum of the subject by at least 50%, 60%, 70%, 80%, 90%, or 95%.
- the dsRNA agent is administered to the subject subcutaneously. 5 In another embodiment, the dsRNA agent, or a pharmaceutically acceptable salt thereof, is administered to the subject intramuscularly. In one embodiment, the method further comprises administering to the subject an additional therapeutic agent for treatment of a DMPK-associated disorder.
- the present disclosure further provides a kit, a vial, or a syringe comprising the dsRNA agent, 10 or a pharmaceutically acceptable salt thereof, of the disclosure or the pharmaceutical composition of the disclosure.
- the present disclosure provides an RNA-induced silencing complex (RISC) comprising an antisense strand of any of the dsRNA agents, or a pharmaceutically acceptable salt thereof, of the disclosure.
- RISC RNA-induced silencing complex
- the iRNAs of the disclosure have been designed to target the human DMPK gene, including portions of the gene that are conserved in orthologs of other mammalian species. Without intending to be limited by theory, it is believed that a combination or sub-combination of the foregoing properties and the specific target sites or the specific modifications in these iRNAs confer to the 35 iRNAs of the disclosure improved efficacy, stability, potency, durability, and safety. Accordingly, the present disclosure provides methods for treating and preventing a DMPK- associated disorder, e.g., myotonic dystrophy type 1 (DM1), using dsRNA compositions which effect 13 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- DM1 myotonic dystrophy type 1
- the iRNAs of the disclosure include an RNA strand (the antisense strand) having a region which is up to about 30 nucleotides or less in length, e.g., 19-30, 19-29, 19-28, 19-27, 19-26, 19-25, 19-24, 5 19-23, 19-22, 19-21, 19-20, 20-30, 20-29, 20-28, 20-27, 20-26, 20-25, 20-24,20-23, 20-22, 20-21, 21- 30, 21-29, 21-28, 21-27, 21-26, 21-25, 21-24, 21-23, or 21-22 nucleotides in length, which region is substantially complementary to at least part of an mRNA transcript of a DMPK gene.
- one or both of the strands of the double stranded RNA agents of the disclosure is up to 66 nucleotides in length, e.g., 36-66, 26-36, 25-36, 31-60, 22-43, 27-53 nucleotides 10 in length, with a region of at least 19 contiguous nucleotides that is substantially complementary to at least a part of an mRNA transcript of a metabolic disorder-associated target gene, i.e., DMPK.
- DMPK metabolic disorder-associated target gene
- such dsRNA agents having longer length antisense strands may, for example, include a second RNA strand (the sense strand) of 20-60 nucleotides in length wherein the sense and antisense strands form a duplex of 18-30 contiguous nucleotides.
- iRNAs of the disclosure enables the targeted degradation of the DMPK mRNAs in mammals. Using in vitro and in vivo assays, the present inventors have demonstrated that iRNAs targeting the gene can potently mediate RNAi, resulting in significant inhibition of expression of the DMPK gene.
- compositions including these iRNAs are useful for treating a subject having a DMPK-associated disorder, e.g., myotonic dystrophy type 1 (DM1), or for treating a 20 subject at risk of developing a DMPK-associated disorder.
- a DMPK-associated disorder e.g., myotonic dystrophy type 1 (DM1)
- the present disclosure provides methods and combination therapies for treating a subject having a disorder that would benefit from inhibiting or reducing the expression of a DMPK gene, e.g., a DMPK-associated disorder, e.g., myotonic dystrophy type 1 (DM1), using iRNA compositions which effect the RNA-induced silencing complex (RISC)-mediated cleavage of RNA 25 transcripts of a DMPK gene.
- RISC RNA-induced silencing complex
- the present disclosure also provides methods for preventing at least one symptom in a subject having a disorder that would benefit from inhibiting or reducing the expression of a DMPK gene, e.g., a DMPK-associated disorder, e.g., myotonic dystrophy type 1 (DM1).
- a DMPK-associated disorder e.g., myotonic dystrophy type 1 (DM1).
- the following detailed description discloses how to make and use compositions containing 30 iRNAs to inhibit the expression of DMPK, as well as compositions, uses, and methods for treating subjects that would benefit from inhibition and/or reduction of the expression of DMPK, e.g., subjects susceptible to or diagnosed with a DMPK-associated disorder, e.g., myotonic dystrophy type 1 (DM1). 35 I.
- sense strand or antisense strand is 10 understood as “sense strand or antisense strand or sense strand and antisense strand.”
- the term “about” is used herein to mean within the typical ranges of tolerances in the art. For example, “about” can be understood as about 2 standard deviations from the mean. In certain embodiments, about means +10%. In certain embodiments, about means +5%.
- nucleotides in a nucleic acid molecule must be an integer.
- at least 19 nucleotides of a 20 21 nucleotide nucleic acid molecule means that 19, 20, or 21 nucleotides have the indicated property.
- methods of detection can include determination that the amount of analyte present is below the level of detection of the method. 30
- the indicated sequence takes precedence.
- the nucleotide sequence recited in the specification takes precedence.
- “dystrophy myotonic protein kinase,” used interchangeably with the terms 35 “DMPK,” refers to the serine-threonine kinase that is closely related to other kinases that interact with members of the Rho family of small GTPases.
- Substrates for this enzyme include myogenin, the beta- subunit of the L-type calcium channels, and phospholemman.
- the 3' untranslated region of this gene contains 5-38 copies of a CTG trinucleotide repeat. Expansion of this unstable motif to 50-5,000 15 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO copies causes myotonic dystrophy type I, which increases in severity with increasing repeat element copy number. Repeat expansion is associated with condensation of local chromatin structure that disrupts the expression of genes in this region.
- An exemplary sequence of a human DMPK mRNA transcript can be found at, for example, 5 GenBank Accession No.
- NM_004409.5 (GI: 1677499213, SEQ ID NO:1; reverse complement, SEQ ID NO:2).
- An exmplary sequence of mouse DMPK mRNA can be found at, for example, GenBank Accession No. NM_032418.3 (SEQ ID NO:3; reverse complement, SEQ ID NO:4).
- An exemplary sequence of rat DMPK mRNA can be found at, for example, GenBank Accession No. NM_001415847 (SEQ ID NO:5; reverse complement, SEQ ID NO:6).
- An exemplary sequence of 10 Macaca mulatta DMPK mRNA can be found at, for example, GenBank Accession No.
- NM_001260568 (SEQ ID NO:7; reverse complement, SEQ ID NO:8).
- target sequence refers to a contiguous portion of the nucleotide sequence of an mRNA molecule formed during the transcription of a DMPK gene, including mRNA that is a product of RNA processing of a primary transcription product.
- the target portion of the sequence will be at least long enough to serve as a substrate for 30 RNAi-directed cleavage at or near that portion of the nucleotide sequence of an mRNA molecule formed during the transcription of a DMPK gene.
- the target sequence is within the protein coding region of the DMPK gene. In another embodiment, the target sequence is within the 3’ UTR of the DMPK gene.
- the target nucleic acid can be a cellular gene (or mRNA transcribed from the gene) whose expression is associated with a particular disorder or disease state. 35
- the target sequence may be from about 19-36 nucleotides in length, e.g., about 19-30 nucleotides in length.
- the target sequence can be about 19-30 nucleotides, 19-30, 19-29, 19-28, 19-27, 19-26, 19-25, 19-24, 19-23, 19-22, 19-21, 19-20, 20-30, 20-29, 20-28, 20-27, 20-26, 20- 25, 20-24, 20-23, 20-22, 20-21, 21-30, 21-29, 21-28, 21-27, 21-26, 21-25, 21-24, 21-23, or 21-22 16 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO nucleotides in length.
- the target sequence is 19-23 nucleotides in length, optionally 21-23 nucleotides in length. Ranges and lengths intermediate to the above recited ranges and lengths are also contemplated to be part of the disclosure.
- the term “strand comprising a sequence” refers to an oligonucleotide 5 comprising a chain of nucleotides that is described by the sequence referred to using the standard nucleotide nomenclature. “G,” “C,” “A,” “T,” and “U” each generally stand for a nucleotide that contains guanine, cytosine, adenine, thymidine, and uracil as a base, respectively.
- ribonucleotide or “nucleotide” can also refer to a modified nucleotide, as further detailed 10 below, or a surrogate replacement moiety (see, e.g., Table 1).
- guanine, cytosine, adenine, and uracil can be replaced by other moieties without substantially altering the base pairing properties of an oligonucleotide comprising a nucleotide bearing such replacement moiety.
- a nucleotide comprising inosine as its base can base pair with nucleotides containing adenine, cytosine, or uracil.
- nucleotides containing uracil, 15 guanine, or adenine can be replaced in the nucleotide sequences of dsRNA featured in the disclosure by a nucleotide containing, for example, inosine.
- adenine and cytosine anywhere in the oligonucleotide can be replaced with guanine and uracil, respectively to form G-U Wobble base pairing with the target mRNA. Sequences containing such replacement moieties are suitable for the compositions and methods featured in the disclosure.
- RNAi agent refers to an agent that contains RNA as that term is defined herein, and which mediates the targeted cleavage of an RNA transcript via an RNA-induced silencing complex (RISC) pathway.
- RISC RNA-induced silencing complex
- iRNA directs the sequence-specific degradation of mRNA through a process known as RNA interference (RNAi).
- RNAi RNA interference
- the iRNA modulates, e.g., inhibits, the expression of a DMPK gene in a 25 cell, e.g., a muscle cell , within a subject, such as a mammalian subject.
- RNAi agent and “dsRNA agent” may be used interchangeably herein.
- an RNAi agent of the disclosure includes a single stranded RNA that interacts with a target RNA sequence, e.g., a DMPK mRNA sequence, to direct the cleavage of the 30 target RNA.
- a target RNA sequence e.g., a DMPK mRNA sequence
- Dicer Type III endonuclease
- Dicer a ribonuclease-III-like enzyme, processes the dsRNA into 19- 23 base pair short interfering RNAs with characteristic two base 3' overhangs (Bernstein, et al., (2001) Nature 409:363).
- the siRNAs are then incorporated into an RNA-induced silencing complex 35 (RISC) where one or more helicases unwind the siRNA duplex, enabling the complementary antisense strand to guide target recognition (Nykanen, et al., (2001) Cell 107:309).
- RISC RNA-induced silencing complex 35
- the disclosure relates to a 17 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO single stranded RNA (siRNA) generated within a cell and which promotes the formation of a RISC complex to effect silencing of the DMPK gene.
- siRNA is also used herein to refer to an iRNA as described above.
- the RNAi agent may be a single-stranded siRNA (ssRNAi) that is 5 introduced into a cell or organism to inhibit a target mRNA.
- Single-stranded RNAi agents bind to the RISC endonuclease, Argonaute 2, which then cleaves the target mRNA.
- the single-stranded siRNAs are generally 15-30 nucleotides and are chemically modified. The design and testing of single- stranded siRNAs are described in U.S. Patent No.8,101,348 and in Lima et al., (2012) Cell 150:883- 894, the entire contents of each of which are hereby incorporated herein by reference.
- an “iRNA” for use in the compositions, uses, and methods of the disclosure is a double stranded RNA and is referred to herein as a “double stranded RNA agent,” “double stranded RNA (dsRNA) molecule,” “dsRNA agent,” or “dsRNA”.
- dsRNA refers to a 15 complex of ribonucleic acid molecules, having a duplex structure comprising two anti-parallel and substantially complementary nucleic acid strands, referred to as having “sense” and “antisense” orientations with respect to a target RNA, i.e., a DMPK mRNA sequence.
- a double stranded RNA dsRNA triggers the degradation of a target RNA, e.g., an mRNA, through a post-transcriptional gene-silencing mechanism referred to herein as RNA 20 interference or RNAi.
- each or both strands can also include one or more non-ribonucleotides, e.g., a deoxyribonucleotide or a modified nucleotide.
- an “iRNA” may include ribonucleotides with chemical modifications; an iRNA may 25 include substantial modifications at multiple nucleotides.
- modified nucleotide refers to a nucleotide having, independently, a modified sugar moiety, a modified internucleotide linkage, or modified nucleobase, or any combination thereof.
- modified nucleotide encompasses substitutions, additions or removal of, e.g., a functional group or atom, to internucleoside linkages, sugar moieties, or nucleobases.
- the modifications suitable for use in the 30 agents of the disclosure include all types of modifications disclosed herein or known in the art. Any such modifications, as used in a siRNA type molecule, are encompassed by “iRNA” or “RNAi agent” for the purposes of this specification and claims.
- the duplex region may be of any length that permits specific degradation of a desired target RNA through a RISC pathway, and may range from about 19 to 36 base pairs in length, e.g., about 19-30 base pairs in length, for example, about 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, or 36 base pairs in length, such as about 19-30, 19-29, 18 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- the duplex region is 19-21 base pairs in length, e.g., 21 base pairs in length. Ranges and lengths intermediate to the above recited ranges and lengths are also 5 contemplated to be part of the disclosure.
- the two strands forming the duplex structure may be different portions of one larger RNA molecule, or they may be separate RNA molecules. Where the two strands are part of one larger molecule, and therefore are connected by an uninterrupted chain of nucleotides between the 3’-end of one strand and the 5’-end of the respective other strand forming the duplex structure, the connecting 10 RNA chain is referred to as a “hairpin loop.”
- a hairpin loop can comprise at least one unpaired nucleotide. In some embodiments, the hairpin loop can comprise at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 23 or more unpaired nucleotides. In some embodiments, the hairpin loop can be 10 or fewer nucleotides.
- the hairpin loop can be 8 or fewer unpaired nucleotides. In some embodiments, the hairpin loop can be 4-10 unpaired nucleotides. In some embodiments, the hairpin 15 loop can be 4-8 nucleotides.
- the two strands of double-stranded oligomeric compound can be linked together. The two strands can be linked to each other at both ends, or at one end only. By linking at one end is meant that 5'-end of first strand is linked to the 3'-end of the second strand or 3'- end of first strand is linked to 5'-end of the second strand.
- first strand is linked to 3'-end of second strand and 3'-end of first strand is linked to 5'-end of second strand.
- the two strands can be linked together by an oligonucleotide linker including, but not limited to, (N)n; wherein N is independently a modified or unmodified nucleotide and n is 3-23. In some embodiemtns, n is 3-10, e.g., 3, 4, 5, 6, 7, 8, 9, or 10.
- the oligonucleotide linker is selected from the group consisting of GNRA, (G)4, (U)4, and (dT)4, 25 wherein N is a modified or unmodified nucleotide and R is a modified or unmodified purine nucleotide.
- N is a modified or unmodified nucleotide
- R is a modified or unmodified purine nucleotide.
- Hairpin and dumbbell type oligomeric compounds will have a duplex region equal to or at least 14, 15, 15, 16, 17, 18, 19, 29, 21, 22, 23, 24, or 25 nucleotide pairs.
- the duplex region can be equal to or less than 200, 100, or 50, in length. In some embodiments, ranges for the duplex region are 15-30, 17 to 23, 19 to 23, and 19 to 21 nucleotides pairs in length.
- the hairpin oligomeric compounds can have a single strand overhang or terminal unpaired 35 region, in some embodiments at the 3', and in some embodiments on the antisense side of the hairpin. In some embodiments, the overhangs are 1-4, more generally 2-3 nucleotides in length.
- the hairpin oligomeric compounds that can induce RNA interference are also referred to as "shRNA" herein.
- shRNA The hairpin oligomeric compounds that can induce RNA interference
- 19 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
- the two substantially complementary strands of a dsRNA are comprised by separate RNA molecules, those molecules need not be, but can be covalently connected.
- the connecting 5 structure is referred to as a “linker.”
- the RNA strands may have the same or a different number of nucleotides.
- an RNAi may comprise one or more nucleotide overhangs.
- at least one strand comprises a 3’ overhang of at least 1 nucleotide.
- at least one 10 strand comprises a 3’ overhang of at least 2 nucleotides, e.g., 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, or 15 nucleotides.
- at least one strand of the RNAi agent comprises a 5’ overhang of at least 1 nucleotide.
- At least one strand comprises a 5’ overhang of at least 2 nucleotides, e.g., 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, or 15 nucleotides.
- both the 3’ and the 5’ end of one strand of the RNAi agent comprise an overhang of at least 1 15 nucleotide.
- an iRNA agent of the disclosure is a dsRNA, each strand of which comprises 19-23 nucleotides, that interacts with a target RNA sequence, e.g., a DMPK mRNA sequence, to direct cleavage of the target RNA.
- an iRNA of the disclosure is a dsRNA of 24-30 nucleotides that 20 interacts with a target RNA sequence, e.g., a DMPK mRNA sequence, to direct the cleavage of the target RNA.
- a target RNA sequence e.g., a DMPK mRNA sequence
- nucleotide overhang refers to at least one unpaired nucleotide that protrudes from the duplex structure of a double stranded iRNA. For example, when a 3'-end of one strand of a dsRNA extends beyond the 5'-end of the other strand, or vice versa, there is a nucleotide 25 overhang.
- a dsRNA can comprise an overhang of at least one nucleotide; alternatively the overhang can comprise at least two nucleotides, at least three nucleotides, at least four nucleotides, at least five nucleotides or more.
- a nucleotide overhang can comprise or consist of a nucleotide/nucleoside analog, including a deoxynucleotide/nucleoside.
- the overhang(s) can be on the sense strand, the antisense strand, or any combination thereof.
- the nucleotide(s) of an overhang can be 30 present on the 5'-end, 3'-end, or both ends of either an antisense or sense strand of a dsRNA.
- the antisense strand of a dsRNA has a 1-10 nucleotide, e.g., a 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotide, overhang at the 3’-end or the 5’-end.
- the sense strand of a dsRNA has a 1-10 nucleotide, e.g., a 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotide, overhang at the 3’-end or the 5’-end.
- one or more of the nucleotides in the overhang is 35 replaced with a nucleoside thiophosphate.
- the antisense strand of a dsRNA has a 1-10 nucleotide, e.g., 0-3, 1-3, 2-4, 2-5, 4-10, 5-10, e.g., a 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotide, overhang at the 3’-end or the 5’- end.
- the sense strand of a dsRNA has a 1-10 nucleotide, e.g., a 1, 2, 3, 4, 5, 6, 7, 20 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- the antisense strand of a dsRNA has a 1-10 nucleotides, e.g., a 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotide, overhang at the 3’-end or the 5’-end.
- the 5 overhang on the sense strand or the antisense strand, or both can include extended lengths longer than 10 nucleotides, e.g., 1-30 nucleotides, 2-30 nucleotides, 10-30 nucleotides, 10-25 nucleotides, 10-20 nucleotides, or 10-15 nucleotides in length.
- an extended overhang is on the sense strand of the duplex.
- an extended overhang is present on the 3’ end of the sense strand of the duplex.
- an extended overhang is present on the 5’ end 10 of the sense strand of the duplex.
- an extended overhang is on the antisense strand of the duplex.
- an extended overhang is present on the 3’end of the antisense strand of the duplex. In certain embodiments, an extended overhang is present on the 5’end of the antisense strand of the duplex. In certain embodiments, one or more of the nucleotides in the extended overhang is replaced with a nucleoside thiophosphate. In certain embodiments, the overhang 15 includes a self-complementary portion such that the overhang is capable of forming a hairpin structure that is stable under physiological conditions. “Blunt” or “blunt end” means that there are no unpaired nucleotides at that end of the double stranded RNA agent, i.e., no nucleotide overhang.
- a “blunt ended” double stranded RNA agent is double stranded over its entire length, i.e., no nucleotide overhang at either end of the molecule.
- the 20 RNAi agents of the disclosure include RNAi agents with no nucleotide overhang at one end (i.e., agents with one overhang and one blunt end) or with no nucleotide overhangs at either end. Most often such a molecule will be double-stranded over its entire length.
- antisense strand or "guide strand” refers to the strand of an iRNA, e.g., a dsRNA, which includes a region that is substantially complementary to a target sequence, e.g., a DMPK 25 mRNA.
- region of complementarity refers to the region on the antisense strand that is substantially complementary to a sequence, for example a target sequence, e.g., a DMPK nucleotide sequence, as defined herein. Where the region of complementarity is not fully complementary to the target sequence, the mismatches can be in the internal or terminal regions of the 30 molecule.
- a double stranded RNA agent of the disclosure includes a nucleotide mismatch in the antisense strand.
- the antisense strand of the double stranded RNA agent of the disclosure includes no more than 4 mismatches with the target mRNA, e.g., the antisense strand includes 4, 3, 2, 1, or 0 mismatches with 35 the target mRNA.
- the antisense strand double stranded RNA agent of the disclosure includes no more than 4 mismatches with the sense strand, e.g., the antisense strand includes 4, 3, 2, 1, or 0 mismatches with the sense strand.
- a double stranded RNA agent of the disclosure includes a nucleotide mismatch in the sense strand.
- the sense strand of the double stranded RNA agent of the disclosure includes no more than 4 mismatches with the antisense strand, e.g., the sense strand includes 4, 3, 2, 1, or 0 mismatches with the antisense strand.
- the nucleotide mismatch is, for example, within 5, 4, 3 nucleotides from the 3’-end of the iRNA.
- the nucleotide mismatch is, for 5 example, in the 3’-terminal nucleotide of the iRNA agent.
- the mismatch(s) is not in the seed region.
- an RNAi agent as described herein can contain one or more mismatches to the target sequence.
- an RNAi agent as described herein contains no more than 3 mismatches (i.e., 3, 2, 1, or 0 mismatches). In one embodiment, an RNAi agent as described herein 10 contains no more than 2 mismatches. In one embodiment, an RNAi agent as described herein contains no more than 1 mismatch. In one embodiment, an RNAi agent as described herein contains 0 mismatches. In certain embodiments, if the antisense strand of the RNAi agent contains mismatches to the target sequence, the mismatch can optionally be restricted to be within the last 5 nucleotides from either the 5’- or 3’-end of the region of complementarity.
- RNAi agent for 15 a 23 nucleotide RNAi agent, the strand which is complementary to a region of DMPK, generally does not contain any mismatch within the central 13 nucleotides.
- the methods described herein or methods known in the art can be used to determine whether an RNAi agent containing a mismatch to a target sequence is effective in inhibiting the expression of a target gene. Consideration of the efficacy of RNAi agents with mismatches in inhibiting expression of a DMPK gene is important, especially if the 20 particular region of complementarity in the target gene is known to have polymorphic sequence variation within the population.
- sense strand or “passenger strand” as used herein, refers to the strand of an iRNA that includes a region that is substantially complementary to a region of the antisense strand as that term is defined herein. 25 As used herein, “substantially all of the nucleotides are modified” are largely but not wholly modified and can include not more than 5, 4, 3, 2, or 1 unmodified nucleotides.
- cleavage region refers to a region that is located immediately adjacent to the cleavage site. The cleavage site is the site on the target at which cleavage occurs.
- the cleavage region comprises three bases on either end of, and immediately 30 adjacent to, the cleavage site. In some embodiments, the cleavage region comprises two bases on either end of, and immediately adjacent to, the cleavage site. In some embodiments, the cleavage site specifically occurs at the site bound by nucleotides 10 and 11 of the antisense strand, and the cleavage region comprises nucleotides 11, 12 and 13.
- the term “complementary,” when used to 35 describe a first nucleotide sequence in relation to a second nucleotide sequence refers to the ability of an oligonucleotide or polynucleotide comprising the first nucleotide sequence to hybridize and form a duplex structure under certain conditions with an oligonucleotide or polynucleotide comprising the second nucleotide sequence, as will be understood by the skilled person. Such conditions can, for 22 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- ALN-529-WO example be stringent conditions, where stringent conditions can include: 400 mM NaCl, 40 mM PIPES pH 6.4, 1 mM EDTA, 50 o C or 70 o C for 12-16 hours followed by washing (see, e.g., “Molecular Cloning: A Laboratory Manual, Sambrook, et al. (1989) Cold Spring Harbor Laboratory Press). Other conditions, such as physiologically relevant conditions as can be encountered inside an 5 organism, can apply. The skilled person will be able to determine the set of conditions most appropriate for a test of complementarity of two sequences in accordance with the ultimate application of the hybridized nucleotides.
- Complementary sequences within an iRNA include base-pairing of the oligonucleotide or polynucleotide comprising a first nucleotide sequence to an 10 oligonucleotide or polynucleotide comprising a second nucleotide sequence over the entire length of one or both nucleotide sequences.
- Such sequences can be referred to as “fully complementary” with respect to each other herein.
- first sequence is referred to as “substantially complementary” with respect to a second sequence herein
- the two sequences can be fully complementary, or they can form one or more, but generally not more than 5, 4, 3, or 2 mismatched 15 base pairs upon hybridization for a duplex up to 30 base pairs, while retaining the ability to hybridize under the conditions most relevant to their ultimate application, e.g., inhibition of gene expression, in vitro or in vivo.
- two oligonucleotides are designed to form, upon hybridization, one or more single stranded overhangs, such overhangs shall not be regarded as mismatches with regard to the determination of complementarity.
- a dsRNA comprising one oligonucleotide 20 21 nucleotides in length and another oligonucleotide 23 nucleotides in length, wherein the longer oligonucleotide comprises a sequence of 21 nucleotides that is fully complementary to the shorter oligonucleotide, can yet be referred to as “fully complementary” for the purposes described herein.
- “Complementary” sequences, as used herein, can also include, or be formed entirely from, non- Watson-Crick base pairs or base pairs formed from non-natural and modified nucleotides, in so far as 25 the above requirements with respect to their ability to hybridize are fulfilled.
- non-Watson-Crick base pairs include, but are not limited to, G:U Wobble or Hoogsteen base pairing.
- the terms “complementary,” “fully complementary” and “substantially complementary” herein can be used with respect to the base matching between the sense strand and the antisense strand of a dsRNA, or between two oligonucletoides or polynucleotides, such as the antisense strand of a 30 double stranded RNA agent and a target sequence, as will be understood from the context of their use.
- a polynucleotide that is “substantially complementary to at least part of” a messenger RNA (mRNA) refers to a polynucleotide that is substantially complementary to a contiguous portion of the mRNA of interest (e.g., an mRNA encoding DMPK).
- mRNA messenger RNA
- a polynucleotide is complementary to at least a part of a DMPK mRNA if the sequence is substantially 35 complementary to a non-interrupted portion of an mRNA encoding DMPK.
- the antisense strand polynucleotides disclosed herein are fully complementary to the target gene, i.e., DMPK sequence.
- the antisense strand polynucleotides disclosed herein are substantially complementary to the target gene sequence and comprise a contiguous nucleotide sequence which is at least about 80% complementary over its entire length to the equivalent region of the nucleotide sequence of SEQ ID NOs: 1, 3, 5, and 7, for DMPK, or a fragment of SEQ ID NOs: 1, 3, 5, and 7, 5 such as about 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or about 99% complementary.
- the antisense polynucleotides disclosed herein are substantially complementary to the target DMPK sequence and comprise a contiguous nucleotide sequence which is at least about 80% complementary over its entire length to any one of the sense strand nucleotide 10 sequences in any one of Tables 2-3, or a fragment of any one of the sense strand nucleotide sequences in any one of Tables 2-3, such as about 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or about 99% complementary.
- an RNAi agent of the disclosure includes a sense strand that is substantially complementary to an antisense polynucleotide which, in turn, is the same as a target 15 DMPK sequence, and wherein the sense strand polynucleotide comprises a contiguous nucleotide sequence which is at least about 80% complementary over its entire length to the equivalent region of the nucleotide sequence of SEQ ID NOs: 2, 4, 6, and 8, or a fragment of any one of SEQ ID NOs: 2, 4, 6, and 8, 10, such as about 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or about 99% complementary.
- an iRNA of the disclosure includes a sense strand that is substantially complementary to an antisense polynucleotide which, in turn, is complementary to a target DMPK sequence, and wherein the sense strand polynucleotide comprises a contiguous nucleotide sequence which is at least about 80% complementary over its entire length to any one of the antisense strand nucleotide sequences in any one of any one of Tables 2-3, or a fragment of any one of the antisense 25 strand nucleotide sequences in any one of Tables 2-3, such as about 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or about 99% complementary.
- the double-stranded region of a double-stranded iRNA agent is equal to or at least, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 23, 24, 25, 26, 27, 28, 29, 30 or more nucleotide pairs in length.
- the antisense strand of a double-stranded iRNA agent is equal to or at least 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length.
- the sense strand of a double-stranded iRNA agent is equal to or at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length.
- the sense and antisense strands of the double-stranded iRNA agent are each independently 15 to 30 nucleotides in length. In one embodiment, the sense and antisense strands of the double-stranded iRNA agent are each independently 19 to 25 nucleotides in length. 24 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In one embodiment, the sense and antisense strands of the double-stranded iRNA agent are each independently 21 to 23 nucleotides in length.
- the sense strand of the iRNA agent is 21-nucleotides in length
- the antisense strand is 23-nucleotides in length, wherein the strands form a double-stranded region of 21 5 consecutive base pairs having a 2-nucleotide long single stranded overhang at the 3'-end.
- an “iRNA” includes ribonucleotides with chemical modifications. Such modifications may include all types of modifications disclosed herein or known in the art. Any such modifications, as used in a dsRNA molecule, are encompassed by “iRNA” for the purposes of this specification and claims.
- an agent for use in the methods and compositions of the disclosure is a single-stranded antisense oligonucleotide molecule that inhibits a target mRNA via an antisense inhibition mechanism.
- the single-stranded antisense oligonucleotide molecule is 15 complementary to a sequence within the target mRNA.
- the single-stranded antisense oligonucleotides can inhibit translation in a stoichiometric manner by base pairing to the mRNA and physically obstructing the translation machinery, see Dias, N. et al., (2002) Mol Cancer Ther 1:347- 355.
- the single-stranded antisense oligonucleotide molecule may be about 14 to about 30 nucleotides in length and have a sequence that is complementary to a target sequence.
- the single- 20 stranded antisense oligonucleotide molecule may comprise a sequence that is at least about 14, 15, 16, 17, 18, 19, 20, or more contiguous nucleotides from any one of the antisense sequences described herein.
- a dsRNA agent of the disclosure comprises: (a) a sense strand having: (i) a length of 21 nucleotides; (ii) an in vivo delivery enhancing moiety, (iii) an ⁇ v ⁇ 6 integrin targeting 25 ligand, and (iv) 2’-fluoro modifications at positions 1, 3, 5, 7, 9 to 11, 13, 17, 19, and 21, and 2’-O- methyl modifications at positions 2, 4, 6, 8, 12, 14 to 16, 18, and 20 (counting from the 5’ end); and (b) an antisense strand having: (i) a length of 23 nucleotides; (ii) 2’-O-methyl modifications at positions 1, 3, 5, 9, 11 to 13, 15, 17, 19, 21, and 23, and 2’-fluoro modifications at positions 2, 4, 6 to 8, 10, 14, 16, 18, 20, and 22 (counting from the 5’ end); and (iii) phosphorothioate linkages between 30 nucleotide positions 21 and 22, and between nucleotide positions 22 and 23 (count
- a dsRNA agent of the disclosure comprises: (a) a sense strand having: (i) a length of 21 nucleotides; (ii) an in vivo delivery enhancing moiety, (iii) an ⁇ v ⁇ 6 integrin targeting 35 ligand; (iv) 2’-fluoro modifications at positions 1, 3, 5, 7, 9 to 11, 13, 15, 17, 19, and 21, and 2’-O- methyl modifications at positions 2, 4, 6, 8, 12, 14, 16, 18, and 20 (counting from the 5’ end); and (v) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, and between nucleotide positions 2 and 3 (counting from the 5’ end); and (b) an antisense strand having: (i) a 25 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- a dsRNA agent of the disclosure comprises: (a) a sense strand having: (i) a length of 21 nucleotides; (ii) an in vivo delivery enhancing moiety, (iii) an ⁇ v ⁇ 6 integrin targeting 10 ligand; (iv) 2’-O-methyl modifications at positions 1 to 6, 8, 10, and 12 to 21, 2’-fluoro modifications at positions 7 and 9, and a deoxy-nucleotide (e.g.
- dT phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, and between nucleotide positions 2 and 3 (counting from the 5’ end); and (b) an antisense strand having: (i) a length of 23 nucleotides; (ii) 2’-O-methyl modifications at positions 1, 3, 7, 9, 11, 13, 15, 17, and 19 15 to 23, and 2’-fluoro modifications at positions 2, 4 to 6, 8, 10, 12, 14, 16, and 18 (counting from the 5’ end); and (iii) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, between nucleotide positions 2 and 3, between nucleotide positions 21 and 22, and between nucleotide positions 22 and 23 (counting from the 5’ end); wherein the dsRNA agent has a two- nucleotide overhang at the 3’-end of the antisense strand, and a
- a dsRNA agent of the disclosure comprises: (a) a sense strand having: (i) a length of 21 nucleotides; (ii) an in vivo delivery enhancing moiety, (iii) an ⁇ v ⁇ 6 integrin targeting ligand; (iv) 2’-O-methyl modifications at positions 1 to 6, 8, 10, 12, 14, and 16 to 21, and 2’-fluoro modifications at positions 7, 9, 11, 13, and 15 (counting from the 5’ end); and (v) phosphorothioate 25 internucleotide linkages between nucleotide positions 1 and 2, and between nucleotide positions 2 and 3 (counting from the 5’ end); and (b) an antisense strand having: (i) a length of 23 nucleotides; (ii) 2’- O-methyl modifications at positions 1, 5, 7, 9, 11, 13, 15, 17, 19, and 21 to 23, and 2’-fluoro modifications at positions 2 to 4, 6, 8, 10, 12, 14, 16, 18, and 20 (counting from the 5’
- a dsRNA agent of the disclosure comprises: (a) a sense strand having: (i) a length of 21 nucleotides; (ii) an in vivo delivery enhancing moiety, (iii) an ⁇ v ⁇ 6 integrin targeting 35 ligand; (iv) 2’-O-methyl modifications at positions 1 to 9, and 12 to 21, and 2’-fluoro modifications at positions 10, and 11 (counting from the 5’ end); and (v) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, and between nucleotide positions 2 and 3 (counting from the 5’ end); and (b) an antisense strand having: (i) a length of 23 nucleotides; (ii) 2’-O-methyl modifications 26 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- a dsRNA agent of the disclosure comprises: (a) a sense strand having: (i) a length of 21 nucleotides; (ii) an in vivo delivery enhancing moiety, (iii) an ⁇ v ⁇ 6 integrin targeting ligand; (iv) 2’-fluoro modifications at positions 1, 3, 5, 7, 9 to 11, and 13, and 2’-O-methyl 10 modifications at positions 2, 4, 6, 8, 12, and 14 to 21 (counting from the 5’ end); and (v) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, and between nucleotide positions 2 and 3 (counting from the 5’ end); and (b) an antisense strand having: (i) a length of 23 nucleotides; (ii) 2’-O-methyl modifications at positions 1, 3, 5 to 7, 9, 11 to 13, 15, 17 to 19, and 21 to 23, and 2’-fluoro modifications at positions 2, 4, 8, 10, 14, 16, and 20 (counting from 15 the
- a dsRNA agent of the disclosure comprises: (a) a sense strand having: (i) a length of 21 nucleotides; (ii) an in vivo delivery enhancing moiety, (iii) an ⁇ v ⁇ 6 integrin targeting ligand; (iv) 2’-O-methyl modifications at positions 1 to 6, 8, and 12 to 21, and 2’-fluoro modifications at positions 7, and 9 to 11 (counting from the 5’ end); and (v) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, and between nucleotide positions 2 and 3 (counting 25 from the 5’ end); and (b) an antisense strand having: (i) a length of 23 nucleotides; (ii) 2’-O-methyl modifications at positions 1, 3 to 5, 7, 8, 10 to 13, 15, and 17 to 23, and 2’-fluoro modifications at positions 2, 6, 9, 14, and 16 (counting from the 5’ end); and (iii)
- a dsRNA agent of the disclosure comprises: (a) a sense strand having: (i) a length of 21 nucleotides; (ii) an in vivo delivery enhancing moiety, (iii) an ⁇ v ⁇ 6 integrin targeting ligand; (iv) 2’-O-methyl modifications at positions 1 to 6, 8, and 12 to 21, and 2’-fluoro modifications 35 at positions 7, and 9 to 11; and (v) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, and between nucleotide positions 2 and 3 (counting from the 5’ end); and (b) an antisense strand having: (i) a length of 23 nucleotides; (ii) 2’-O-methyl modifications at positions 1, 3 to 5, 7, 10 to 13, 15, and 17 to 23, and 2’-fluoro modifications at positions 2, 6, 8, 9, 14, and 16 27 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Aln
- a dsRNA agent of the disclosure comprises: (a) a sense strand having: (i) a length of 19 nucleotides; (ii) an in vivo delivery enhancing moiety, (iii) an ⁇ v ⁇ 6 integrin targeting ligand; (iv) 2’-O-methyl modifications at positions 1 to 4, 6, and 10 to 19, and 2’-fluoro modifications at positions 5, and 7 to 9; and (v) phosphorothioate internucleotide linkages between nucleotide 10 positions 1 and 2, and between nucleotide positions 2 and 3 (counting from the 5’ end); and (b) an antisense strand having: (i) a length of 21 nucleotides; (ii) 2’-O-methyl modifications at positions 1, 3 to 5, 7, 10 to 13, 15, and 17 to 21, and 2’-fluoro modifications at positions 2, 6, 8, 9, 14, and 16 (counting from the 5’ end); and (iii) phosphorothioate internu
- a dsRNA agent of the disclosure comprises: (a) a sense strand having: (i) a length of 21 nucleotides; (ii) an in vivo delivery enhancing moiety, (iii) an ⁇ v ⁇ 6 integrin targeting 20 ligand; (iv) 2’-O-methyl modifications at positions 1 to 8, and 12 to 21, and 2’-fluoro modifications at positions 9 to 11; and (v) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, and between nucleotide positions 2 and 3 (counting from the 5’ end); and (b) an antisense strand having: (i) a length of 23 nucleotides; (ii) 2’-O-methyl modifications at positions 1, 3, 4, 6, 8 to 11, 13, 15 to 23, and a 2’-fluoro modification at position 14 (counting from the 5’ end), and 2’- 25 deoxy-modified nucleotides at positions 2, 5, 7, and 12; and
- a dsRNA agent of the disclosure comprises: (a) a sense strand having: (i) a length of 21 nucleotides; (ii) an in vivo delivery enhancing moiety, (iii) an ⁇ v ⁇ 6 integrin targeting ligand; (iv) 2’-O-methyl modifications at positions 1 to 6, 8, and 12 to 21, and 2’-fluoro modifications at positions 7, and 9 to 11; and (v) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, and between nucleotide positions 2 and 3 (counting from the 5’ end); and (b) an 35 antisense strand having: (i) a length of 23 nucleotides; (ii) 2’-O-methyl modifications at positions 1, 3 to 4, 6, 8 to 13, 15, and 17 to 23, 2’-fluoro modifications at positions 2, 14, and 16, a 2’-deoxy- modified nucleotide at position 5, and a GNA at position 7 (count
- the dsRNA agent has a two-nucleotide overhang at the 3’-end of the antisense strand, and a blunt end at the 5’-end of the antisense strand.
- a dsRNA agent of the disclosure comprises: (a) a sense strand having: 5 (i) a length of 21 nucleotides; (ii) an in vivo delivery enhancing moiety at position 5, 6, 16 or 17 (counting from the 5’ end), (iii) an ⁇ v ⁇ 6 integrin targeting ligand on the 3’ end; (iv) 2’-O-methyl modifications at positions 1 to 6, 8, and 12 to 21, and 2’-fluoro modifications at positions 7 and 9 to 11 (counting from the 5’ end); and (v) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, between nucleotide positions 2 and 3, between positions 20 and 21, and between 10 position 21 and the ⁇ v ⁇ 6 integrin targeting ligand (counting from the 5’ end); and (b) an antisense strand having: (i) a length of 23 nucleotides; (ii) 2’-O-methyl modifications at positions 1, 3 to
- a dsRNA agent of the disclosure comprises: (a) a sense strand having: (i) a length of 21 nucleotides; (ii) an in vivo delivery enhancing moiety at position 5, 6, 16 or 17 20 (counting from the 5’ end), (iii) an ⁇ v ⁇ 6 integrin targeting ligand on the 3’ end; (iv) 2’-O-methyl modifications at positions 1 to 6, 8, and 12 to 21, and 2’-fluoro modifications at positions 7, and 9 to 11 (counting from the 5’ end); and (v) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, between nucleotide positions 2 and 3, between positions 20 and 21, and between position 21 and the ⁇ v ⁇ 6 integrin targeting ligand (counting from the 5’ end); and (b) an antisense 25 strand having: (i) a length of 23 nucleotides; (ii) 2’-O-methyl modifications at positions 1, 3 to
- the sense strand of the dsRNA agent has 2’-F modifications at positions 7, 9, 10 and 11 (counting from the 5’ end). In some embodiments, the sense strand of the dsRNA agent has 2’-F modifications at positions 9 to 11 (counting from the 5’ end). In some 35 embodiments, the sense strand of the dsRNA agent has 2’-F modifications at positions 7 to 9 (counting from the 5’ end). In some embodiments, the sense strand of the dsRNA agent has 2’-F modifications at positions 5, 7, 8, and 9 (counting from the 5’ end).
- the sense strand of the dsRNA agent has 2’-F modifications at positions 9, 11, and 13 (counting from the 5’ 29 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO end). In some embodiments, the sense strand of the dsRNA agent has 2’-F modifications at positions 9, 11, and 12 (counting from the 5’ end). In some embodiments, the sense strand of the dsRNA agent has 2’-F modifications at positions 2, 4, 6, 8, 10, 12, 14, 16, 18, and 20 (counting from the 5’ end).
- the antisense strand of the dsRNA agent has 2’-F modifications at 5 positions 1, 2, 6, 14, and 16 (counting from the 5’ end). In some embodiments, the antisense strand of the dsRNA agent has 2’-F modifications at positions 2, 4, 6, 8, 10, 12, 14, 16, 18, and 20 (counting from the 5’ end). In some embodiments, the antisense strand of the dsRNA agent has 2’-F modifications at positions 2, 4, 6, 12, 14, 16, 18, and 19 (counting from the 5’ end). In some embodiments, the antisense strand of the dsRNA agent has 2’-F modifications at positions 2, 3, 5, 10, 10 12, 14, and 16 (counting from the 5’ end).
- the antisense strand of the dsRNA agent has 2’-F modifications at positions 2, 4, 12, 14 and 16 (counting from the 5’ end). In some embodiments, the antisense strand of the dsRNA agent has 2’-F modifications at positions 2, 12, 14, and 16 (counting from the 5’ end). In some embodiments, the antisense strand of the dsRNA agent has 2’-F modifications at positions 2, 6, 14, and 16 (counting from the 5’ end). In some embodiments, the 15 antisense strand of the dsRNA agent has 2’-F modifications at positions 2, 14, and 16 (counting from the 5’ end).
- the antisense strand of the dsRNA agent has 2’-F modifications at positions 2 and 14 (counting from the 5’ end). In some embodiments, the antisense strand of the dsRNA agent has a 2’-F modification at only position 14 (counting from the 5’ end). In some embodiments, the antisense strand of the dsRNA agent has 2’-deoxy-modified 20 nucleotides at positions 2, 5, 7, and 12 (counting from the 5’ end). In some embodiments, the antisense strand of the dsRNA agent comprises a 2’-deoxy-modified nucleotide at position 5 (counting from the 5’ end).
- the antisense strand of the dsRNA agent comprises a GNA modified nucleotide at position 7 (counting from the 5’ end).
- a “pharmaceutically acceptable salt” of the dsRNA agents of the disclosure includes any salt which is pharmaceutically acceptable, e.g., a sodium salt of the dsRNA agent.
- an “alpha-v-beta-6 ( ⁇ v ⁇ 6) integrin targeting ligand”, as used herein, includes any moiety (e.g., peptides and small molecules) which bind an ⁇ v ⁇ 6 integrin and are able to mediate delivery of a dsRNA agent to which they are attached to skeletal muscle (e.g., a skeletal muscle cell or skeletal 30 muscle tissue) and/or cardiac muscle (e.g., a cardiac muscle cell or cardiac muscle tissue).
- the ⁇ v ⁇ 6 integrin targeting ligands bind ⁇ v ⁇ 6 integrin or the ⁇ v ⁇ 6 integrin receptor on skeletal muscle/cardiac myocytes (cells).
- Exemplary ⁇ v ⁇ 6 integrin targeting ligands are described below. Exemplary ⁇ v ⁇ 6 integrin targeting ligands are also described in WO2024/086633, the entire contents of which are incorporated by reference herein. 35
- the phrase “contacting a cell with an iRNA,” such as a dsRNA, as used herein, includes contacting a cell by any possible means. Contacting a cell with an iRNA includes contacting a cell in vitro with the iRNA or contacting a cell in vivo with the iRNA. The contacting may be done directly or indirectly.
- the iRNA may be put into physical contact with the cell by the 30 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO individual performing the method, or alternatively, the iRNA may be put into a situation that will permit or cause it to subsequently come into contact with the cell.
- Contacting a cell in vitro may be done, for example, by incubating the cell with the iRNA.
- Contacting a cell in vivo may be done, for example, by injecting the iRNA into or near the tissue 5 where the cell is located, or by injecting the iRNA into another area, e.g., the bloodstream or the subcutaneous space, such that the agent will subsequently reach the tissue where the cell to be contacted is located.
- the iRNA may contain or be coupled to alpha-v-beta-6 ( ⁇ v ⁇ 6) integrin targeting ligand that mediates delivery to muscle tissue and at least one in vivo delivery enhancing moiety. 10
- Combinations of in vitro and in vivo methods of contacting are also possible.
- a cell may also be contacted in vitro with an RNAi agent and subsequently transplanted into a subject.
- contacting a cell with an iRNA includes “introducing” or “delivering the iRNA into the cell” by facilitating or effecting uptake or absorption into the cell.
- Absorption or uptake of an iRNA can occur through unaided diffusion or active cellular processes, or by auxiliary 15 agents or devices.
- Introducing an iRNA into a cell may be in vitro or in vivo.
- iRNA can be injected into a tissue site or administered systemically.
- In vitro introduction into a cell includes methods known in the art such as electroporation and lipofection.
- lipid nanoparticle is a vesicle comprising a lipid layer encapsulating a 20 pharmaceutically active molecule, such as a nucleic acid molecule, e.g., an iRNA or a plasmid from which an iRNA is transcribed.
- LNPs are described in, for example, U.S. Patent Nos.6,858,225, 6,815,432, 8,158,601, and 8,058,069, the entire contents of which are hereby incorporated herein by reference.
- a “subject” is an animal, such as a mammal, including a primate (such as a 25 human, a non-human primate, e.g., a monkey, and a chimpanzee), a non-primate (such as a cow, a pig, a horse, a goat, a rabbit, a sheep, a hamster, a guinea pig, a cat, a dog, a rat, or a mouse), or a bird that expresses the target gene, either endogenously or heterologously.
- a primate such as a 25 human, a non-human primate, e.g., a monkey, and a chimpanzee
- a non-primate such as a cow, a pig, a horse, a goat, a rabbit, a sheep, a hamster, a guinea pig, a cat, a dog, a rat, or a mouse
- the subject is a human, such as a human being treated or assessed for a disease or disorder that would benefit from reduction in DMPK expression; a human at risk for a disease or disorder that would benefit from 30 reduction in DMPK expression; a human having a disease or disorder that would benefit from reduction in DMPK expression; or human being treated for a disease or disorder that would benefit from reduction in DMPK expression as described herein.
- the subject is a female human.
- the subject is a male human.
- the subject is an adult subject.
- the subject is a pediatric subject.
- treating refers to a beneficial or desired result, such as reducing at least one sign or symptom associated with DMPK expression or DMPK protein production, e.g., a DMPK-associated disease, e.g., myotonic dystrophy type 1 (DM1), in a subject.
- Treatment also includes a reduction of one or more sign or symptoms associated with unwanted 31 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO DMPK expression; diminishing the extent of unwanted DMPK activation or stabilization; amelioration or palliation of unwanted DMPK activation or stabilization.
- “Treatment” can also mean prolonging survival as compared to expected survival in the absence of treatment.
- the term “lower” in the context of the level of DMPK in a subject or a disease marker or 5 symptom refers to a statistically significant decrease in such level.
- the decrease can be, for example, at least 10%, 15%, 20%, 25%, 30%, %, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or more.
- a decrease is at least 20%.
- the decrease is at least 50% in a disease marker, e.g., protein or gene expression level.
- “Lower” in the context of the level of DMPK in a subject is a decrease to a level accepted as within the range of 10 normal for an individual without such disorder.
- “lower” is the decrease in the difference between the level of a marker or symptom for a subject suffering from a disease and a level accepted within the range of normal for an individual.
- the term “lower” can also be used in association with normalizing a symptom of a disease or condition, i.e. decreasing the difference between a level in a subject suffering from a DMPK- 15 associated disorder towards or to a level in a normal subject not suffering from a DMPK-associated disorder.
- prevention when used in reference to a disease, disorder or 20 condition thereof, may be treated or ameliorated by a reduction in expression of a DMPK gene or production of a DMPK protein, refers to a reduction in the likelihood that a subject will develop a symptom associated with such a disease, disorder, or condition, e.g., a symptom of a DMPK- associated disorder, e.g., DM1.
- DMPK-associated disorder or “DMPK-associated disease” is a disease or disorder that would benefit from reduction in the mRNA expression or activity of DMPK.
- DMPK-associated disease is a disease or disorder that is caused by, or associated with, 30 DMPK mRNA expression or DMPK protein production.
- DMPK-associated disease includes a disease, disorder or condition that would benefit from a decrease in DMPK mRNA expression or DMPK protein activity.
- the DMPK-associated disease is a myotonic dystrophy.
- Myotonic dystrophy refers to a part of a group of inherited disorders called 35 muscular dystrophies. It is the most common form of muscular dystrophy that begins in adulthood. Myotonic dystrophy is characterized by progressive muscle wasting and weakness. People with this disorder often have prolonged muscle contractions (myotonia) and are not able to relax certain muscles after use.
- myotonic dystrophy Other signs and symptoms of myotonic dystrophy include clouding of the lens of 32 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO the eye (cataracts) and abnormalities of the electrical signals that control the heartbeat (cardiac conduction defects).
- Some affected individuals develop a condition called diabetes mellitus, in which blood sugar levels can become dangerously high.
- the features of myotonic dystrophy often develop during a person's twenties or thirties, although they can occur at any age.
- the severity of the condition 5 varies widely among affected people, even among members of the same family. There are two major types of myotonic dystrophy: type 1 and type 2.
- type 2 tends to be milder than type 1.
- the muscle weakness associated with type 1 particularly affects muscles farthest from the center of the body (distal muscles), such as those of the lower legs, hands, neck, and face.
- Muscle weakness in type 2 primarily involves muscles close to the center of the body 10 (proximal muscles), such as the those of the neck, shoulders, elbows, and hips.
- the two types of myotonic dystrophy are caused by mutations in different genes.
- Myotonic dystrophy type 1 is caused by mutations in the DMPK gene, while type 2 results from mutations in the CNBP gene.
- the protein produced from the DMPK gene likely plays a role in communication within cells.
- the protein produced from the CNBP gene is found primarily in the heart and in skeletal muscles, where it helps regulate the function of other genes. Similar changes in the structure of the DMPK and CNBP genes cause myotonic dystrophy type 1 and type 2. In each case, a segment of DNA is abnormally repeated many times, forming an unstable region in the gene. The gene with the abnormal segment produces an unusually 20 long messenger RNA, which is a molecular blueprint of the gene that guides the production of proteins. The unusually long messenger RNA forms clumps inside the cell that interfere with the production of many other proteins.
- the DMPK-associated disease is myotonic dystrophy type 1 (DM1).
- “Therapeutically effective amount,” as used herein, is intended to include the amount of an RNAi agent that, when administered to a subject having a DMPK-associated disorder, is sufficient to effect treatment of the disease (e.g., by diminishing, ameliorating, or maintaining the existing disease 30 or one or more symptoms of disease).
- the "therapeutically effective amount” may vary depending on the RNAi agent, how the agent is administered, the disease and its severity and the history, age, weight, family history, genetic makeup, the types of preceding or concomitant treatments, if any, and other individual characteristics of the subject to be treated. “Prophylactically effective amount,” as used herein, is intended to include the amount of an 35 RNAi agent that, when administered to a subject having a DMPK-associated disorder, is sufficient to prevent or ameliorate the disease or one or more symptoms of the disease. Ameliorating the disease includes slowing the course of the disease or reducing the severity of later-developing disease.
- the “prophylactically effective amount” may vary depending on the RNAi agent, how the agent is 33 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO administered, the degree of risk of disease, and the history, age, weight, family history, genetic makeup, the types of preceding or concomitant treatments, if any, and other individual characteristics of the patient to be treated.
- a “therapeutically-effective amount” or “prophylactically effective amount” also includes an 5 amount of an RNAi agent that produces some desired effect at a reasonable benefit/risk ratio applicable to any treatment.
- the iRNA employed in the methods of the present disclosure may be administered in a sufficient amount to produce a reasonable benefit/risk ratio applicable to such treatment.
- phrases "pharmaceutically acceptable” is employed herein to refer to those compounds, 10 materials, compositions, or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human subjects and animal subjects without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.
- pharmaceutically-acceptable carrier means a pharmaceutically- 15 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, involved in carrying or transporting the subject compound from one organ, or portion of the body, to another organ, or portion of the body.
- manufacturing aid e.g., lubricant, talc magnesium, calcium or zinc stearate, or steric acid
- solvent encapsulating material involved in carrying 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 compatible with the other ingredients of the formulation and not injurious to the 20 subject being treated.
- Pharmaceutically acceptable carriers include carriers for administration by injection.
- sample includes a collection of similar fluids, cells, or tissues isolated from a subject, as well as fluids, cells, or tissues present within a subject.
- biological fluids include blood, serum and serosal fluids, plasma, cerebrospinal fluid, ocular fluids, 25 lymph, urine, saliva, and the like.
- Tissue samples may include samples from tissues, organs, or localized regions. For example, samples may be derived from particular organs, parts of organs, or fluids or cells within those organs. In certain embodiments, samples may be derived from the liver (e.g., whole liver or certain segments of liver or certain types of cells in the liver, such as, e.g., hepatocytes).
- a “sample derived from a subject” refers to urine obtained from 30 the subject.
- a “sample derived from a subject” can refer to blood or blood derived serum or plasma from the subject.
- alkyl group can be both a monovalent radical or divalent radical; in the latter case, it would be apparent to one skilled in the art that an additional hydrogen atom is removed from a monovalent alkyl radical to provide a suitable divalent moiety.
- oligonucleotides may be an RNA, a DNA, a single-stranded RNA, such as an 10 antisense oligonucleotide (ASO), a sense or an antisense strand of an siRNA, and oligonucleotide derivatives such as phosphorodiamidate morpholino oligomers (PMOs).
- ASO antisense oligonucleotide
- siRNA oligonucleotide derivatives
- PMOs phosphorodiamidate morpholino oligomers
- conjugated means that the moiety is covalently attached to a dsRNA agent directly or via a linker or via a carrier or via an internucleotide phosphate linkage.
- alkenyl as used herein, means a straight or branched chain hydrocarbon containing from 2 to 10 carbons, unless otherwise specified, and containing at least one carbon-carbon double 20 bond.
- Representative examples of alkenyl include, but are not limited to, ethenyl, 2-propenyl, 2- methyl-2-propenyl, 3-butenyl, 4-pentenyl, 5-hexenyl, 2-heptenyl, 2-methyl-1-heptenyl, 3-decenyl, and 3,7-dimethylocta-2,6-dienyl.
- alkynyl as used herein means a straight or branched hydrocarbon chain containing from 2 to 10 carbons, unless otherwise specified, and containing at least one carbon-carbon triple 25 bond. Representative examples of alkynyl include, but are not limited to, 1-butynyl, 2-butynyl, 1- propynyl and the like.
- alkoxy as used herein, means an alkyl group, as defined herein, appended to the parent molecular moiety through an oxygen atom.
- alkoxy examples include, but are not limited to, methoxy, ethoxy, n-propoxy, 2-propoxy, n-butoxy, tert-butoxy, n-pentyloxy, and n- 30 hexyloxy.
- alkyl as used herein, means a straight or branched chain hydrocarbon containing from 1 to 10 carbon atoms, unless otherwise specified.
- alkyl include, but are not limited to, methyl, ethyl, n-propyl, iso-propyl, n-butyl, sec -butyl, iso-butyl, tert-butyl, n- pentyl, isopentyl, neopentyl, n-hexyl, 3-methylhexyl, 2,2-dimethylpentyl, 2,3-dimethylpentyl, n- 35 heptyl, n-octyl, n-nonyl, and n-decyl.
- aryl means a phenyl (i.e., monocyclic aryl); naphthyl or azulenyl; a bicyclic ring system containing a phenyl fused to a cycloalkyl, cycloalkenyl, or heterocyclyl ring.
- bicyclic aryls include, but are not limited to, azulenyl, naphthyl, 2,3- dihydroinden-1-yl, 2,3-dihydroinden-2-yl, 2,3-dihydroinden-3-yl, 2,3-dihydroinden-4-yl, 2,3- 5 dihydroinden-5-yl, 2,3-dihydroindol-1-yl, indolin-2-yl, indolin-3-yl, indolin-4-yl, indolin-5-yl, indolin-6-yl, indolin-7-yl, inden-1-yl, inden-2-yl, inden-3-yl, inden-4-yl, dihydronaphthalen-2-yl, dihydronaphthalen-3-yl, dihydronaphthalen-4-yl, dihydronaphthalen-1-yl, 5,6,7,8- tetrahydronaphthalen-1-
- the bicyclic aryl is (i) naphthyl or (ii) a phenyl ring fused to either a 5 25 or 6 membered monocyclic cycloalkyl, a 5 or 6 membered monocyclic cycloalkenyl, or a 5 or 6 membered monocyclic heterocyclyl, wherein the fused cycloalkyl, cycloalkenyl, and heterocyclyl groups are optionally substituted with one or two groups which are independently oxo or thia.
- arylalkyl means an aryl group, as defined herein, appended to the parent molecular moiety through an alkyl group, as defined 30 herein.
- Representative examples of arylalkyl include, but are not limited to, benzyl, 2-phenylethyl, 3- phenylpropyl, and 2-naphth-2-ylethyl.
- azido means a -N3 group.
- carboxy means a -COOH group.
- cyano and "nitrile” as used herein, mean a -CN group.
- cycloalkyl as used herein, means a monocyclic or a bicyclic cycloalkyl ring system.
- Monocyclic ring systems are cyclic hydrocarbon groups containing from 3 to 10 carbon atoms, where such groups are saturated. Examples of monocyclic cycloalkyls include cyclopropyl, 36 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, and cyclooctyl.
- Bicyclic cycloalkyl ring systems are bridged monocyclic rings or fused bicyclic rings.
- Bridged monocyclic rings contain a monocyclic cycloalkyl ring where two non-adjacent carbon atoms of the monocyclic ring are linked by an alkylene bridge of between one and three additional carbon atoms (i.e., a bridging group of the form - 5 (CH2)w-, where w is 1, 2, or 3).
- Representative examples of bridged bicyclic ring systems include, but are not limited to, bicyclo[3.1.1]heptane, bicyclo[2.2.1]heptane, bicyclo[2.2.2]octane, bicyclo[3.2.2]nonane, bicyclo[3.3.1]nonane, and bicyclo[4.2.1]nonane.
- Fused bicyclic cycloalkyl ring systems contain a monocyclic cycloalkyl ring fused to a monocyclic cycloalkyl.
- Representative examples of fused bicyclic ring systems include, but are not limited to, decaliyl.
- Cycloalkyl groups 10 are optionally substituted with one or two groups which are independently oxo or thia.
- the fused bicyclic cycloalkyl is a 5 or 6 membered monocyclic cycloalkyl ring fused to a 5 or 6 membered monocyclic cycloalkyl, wherein the fused bicyclic cycloalkyl is optionally substituted by one or two groups which are independently oxo or thia.
- Cycloalkenyl refers to a monocyclic or a bicyclic cycloalkenyl ring system. 15 Monocyclic ring systems are cyclic hydrocarbon groups containing from 3 to 8 carbon atoms, where such groups are unsaturated (i.e., containing at least one annular carbon-carbon double bond), but not aromatic. Examples of monocyclic ring systems include cyclopentenyl and cyclohexenyl. Bicyclic cycloalkenyl rings are bridged monocyclic rings or a fused bicyclic rings.
- Bridged monocyclic rings contain a monocyclic cycloalkenyl ring where two non-adjacent carbon atoms of the monocyclic ring 20 are linked by an alkylene bridge of between one and three additional carbon atoms (i.e., a bridging group of the form -(CH2)w-, where w is 1, 2, or 3).
- alkylene bridge of between one and three additional carbon atoms
- bicyclic cycloalkenyls include, but are not limited to, norbornenyl and bicyclo[2.2.2]oct-2-enyl.
- Fused bicyclic cycloalkenyl ring systems contain a monocyclic cycloalkenyl ring fused to either a monocyclic cycloalkyl or a monocyclic cycloalkenyl. Cycloalkenyl groups are optionally substituted with one or two groups 25 which are independently oxo or thia.
- the term “monocyclic ring”, as used herein, comprises monocyclic aryl, monocyclic cycloalkyl, monocyclic cycloalkenyl and monocyclic heterocyclyl.
- halo or "halogen” as used herein, means -CI, -Br, -I or -F.
- H means hydrogen.
- haloalkyl means at least one halogen, as defined herein, appended to the parent molecular moiety through an alkyl group, as defined herein.
- Representative examples of haloalkyl include, but are not limited to, chloromethyl, 2-fluoroethyl, trifluoromethyl, pentafluoroethyl, and 2-chloro-3-fluoropentyl.
- heteroaryl as used herein, means a monocyclic heteroaryl or a bicyclic ring 35 system containing at least one heteroaromatic ring (i.e., a monocyclic or bicyclic aromatic ring system containing at least one heteroatom within the aromatic system).
- the monocyclic heteroaryl can be a 5 or 6 membered ring.
- the 5 membered ring consists of two double bonds and one, two, three or four nitrogen atoms and optionally one oxygen or sulfur atom.
- the 6 membered ring consists of three 37 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO double bonds and one, two, three or four nitrogen atoms.
- the 5 or 6 membered heteroaryl is connected to the parent molecular moiety through any carbon atom or any nitrogen atom contained within the heteroaryl.
- monocyclic heteroaryl include, but are not limited to, furyl, imidazolyl, isoxazolyl, isothiazolyl, oxadiazolyl, oxazolyl, pyridinyl, pyridazinyl, 5 pyrimidinyl, pyrazinyl, pyrazolyl, pyrrolyl, tetrazolyl, thiadiazolyl, thiazolyl, thienyl, triazolyl, and triazinyl.
- the bicyclic heteroaryl consists of a monocyclic heteroaryl fused to a phenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, a monocyclic heterocyclyl, or a monocyclic heteroaryl.
- the fused cycloalkyl or heterocyclyl portion of the bicyclic heteroaryl group is optionally substituted with one or two groups which are independently oxo or thia.
- bicyclic 10 heteroaryl include, but are not limited to, benzimidazolyl, benzofuranyl, benzothienyl, benzoxadiazolyl, benzoxathiadiazolyl, benzothiazolyl, cinnolinyl, 5 ,6-dihydroquinolin-2-yl, 5,6- dihydroquinolin-8-yl, 5,6-dihydroisoquinolin-1-yl, furopyridinyl, indazolyl, indolyl, isoquinolinyl, naphthyridinyl, quinolinyl, purinyl, 5,6,7,8-tetrahydroquinolin-2-yl, 5,6,7,8-tetrahydroquinolin-3-yl, 5,6,7,8-tetrahydroquinolin-4-yl, 5,6,7,8-tetrahydroquinolin-5-yl, 5,6,7,8-tetrahydro
- the fused bicyclic heteroaryl is a 5 or 6 membered monocyclic heteroaryl ring fused to either a phenyl ring, a 5 or 6 membered monocyclic cycloalkyl, a 5 or 6 membered monocyclic cycloalkenyl, a 5 or 6 membered monocyclic 20 heterocyclyl, or a 5 or 6 membered monocyclic heteroaryl, wherein the fused cycloalkyl, cycloalkenyl, and heterocyclyl groups are optionally substituted with one or two groups which are independently oxo or thia.
- heteroarylalkyl and "-alkylheteroaryl” as used herein, means a heteroaryl, as defined herein, appended to the parent molecular moiety through an alkyl group, as defined herein.
- Representative examples of heteroarylalkyl include, but are not limited to, fur-3-ylmethyl, 1H- imidazol-2-ylmethylm 1H-imidazol-4-ylmethyl, 1-(pyridin-4-yl)ethyl, pyridin-3-ylmethyl, pyridin-4- ylmethyl, pyrimidin-5-ylmethyl, 2-(pyrimidin-2-yl)propyl, thien-2-ylmethyl, and thien-3-ylmethyl.
- heterocyclyl as used herein, means a monocyclic heterocycle or a bicyclic heterocycle.
- the monocyclic heterocycle is a 3, 4, 5, 6, or 7 membered ring containing at least one 30 heteroatom independently selected from the group consisting of O, N, and S where the ring is saturated or unsaturated, but not aromatic.
- the 3 or 4 membered ring contains 1 heteroatom selected from the group consisting of O, N and S.
- the 5 membered ring can contain zero or one double bond and one, two or three heteroatoms selected from the group consisting of O, N and S.
- the 6 or 7 membered ring contains zero, one, or two double bonds and one, two or three heteroatoms selected 35 from the group consisting of O, N and S.
- monocyclic heterocycles include, but are not limited to, azetidinyl, azepanyl, aziridinyl, diazepanyl, 1,3-dioxan-2-yl, 1,3- dioxolan-2-yl, 1,3-dithiolan-2-yl, 1,2-dithiolan-3-yl, 1,2-dithiolan-4-yl, 1,3-dithian-2-yl, 1,2-dithian-3- yl, 1,2-dithian-4-yl, imidazolinyl, imidazolidinyl, isothiazolinyl, isothiazolidinyl, isoxazolinyl, 38 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- ALN-529-WO isoxazolidinyl, morpholinyl, oxadiazolinyl, oxadiazolidinyl, oxazolinyl, oxazolidinyl, piperazinyl, piperidinyl, pyranyl, pyrazolinyl, pyrazolidinyl, pyrrolinyl, pyrrolidinyl, tetrahydrofuranyl, tetrahydrothienyl, thiadiazolinyl, thiadiazolidinyl, thiazolinyl, thiazolidinyl, thiomorpholinyl, 1,1- dioxidothiomorpholinyl (thiomorpholine sulfone), thiopyranyl, and trithianyl.
- the bicyclic 5 heterocycle is a monocyclic heterocycle fused to either a monocyclic cycloalkyl, a monocyclic cycloalkenyl, or a monocyclic heterocycle.
- Representative examples of bicyclic heterocyclyls include, but are not limited to, decahydroquinolinyl, decahydroisoquinolinyl, octahydro-1H-indolyl, and octahydrobenzofuranyl.
- Heterocyclyl groups are optionally substituted with one or two groups which are independently oxo or thia.
- the bicyclic heterocyclyl is a 5 or 6 10 membered monocyclic heterocyclyl ring fused to a 5 or 6 membered monocyclic cycloalkyl, a 5 or 6 membered monocyclic cycloalkenyl, or a 5 or 6 membered monocyclic heterocyclyl, wherein the bicyclic heterocyclyl is optionally substituted by one or two groups which are independently oxo or thia.
- hydroxy or “hydroxyl” as used herein means an -OH group.
- thiol as 15 used herein means an –SH group.
- hydroxyl protecting group refers to a labile chemical moiety which protects a hydroxyl group against undesired reactions during synthetic procedure(s). After the synthetic procedure(s), the hydroxy protecting group may be selectively removed. Hydroxy protecting groups as known in the art are described generally in T. H. Greene and P. G. M. Wuts, Protective 20 Groups in Organic Synthesis, 3rd edition, John Wiley & Sons, New York (1999).
- hydroxyl protecting groups include, but are not limited to, benzyloxycarbonyl, 4- nitrobenzyloxycarbonyl, 4-bromobenzyloxycarbonyl, 4-methoxybenzyloxycarbonyl, methoxycarbonyl, tert-butoxycarbonyl, isopropoxycarbonyl, diphenylmethoxycarbonyl, 2,2,2- trichloroethoxycarbonyl, 2-(trimethylsilyl) ethoxycarbonyl, 2-furfuryloxycarbonyl, allyloxycarbonyl, 25 acetyl, formyl, chloroacetyl, trifluoroacetyl, methoxyacetyl, phenoxyacetyl, benzoyl, methyl, t-butyl, 2,2,2-trichloroethyl, 2-trimethylsilyl ethyl, l,l-dimethyl-2-propenyl, 3-methyl-3-butenyl, allyl, ally
- hydroxyl protecting groups can be selected from acetyl (Ac or — C(O)CH3), benzoyl (Bz or —C(O)C6H5), and trimethylsilyl (TMS or -Si(CH3)3).
- nitro as used herein means a -NO2 group.
- saturated as used herein means the referenced chemical structure does not contain 35 any multiple carbon-carbon bonds. For example, a saturated cycloalkyl group as defined herein includes cyclohexyl, cyclopropyl, and the like.
- amine or “amino” encompasses compounds where a nitrogen atom is covalently bonded to at least one carbon or heteroatom.
- alkyl amino includes groups and compounds wherein the nitrogen is bound to at least one additional alkyl group.
- dialkyl amino includes groups wherein the nitrogen atom is bound to at least two additional alkyl groups. 5
- unsaturated as used herein means the referenced chemical structure contains at least one multiple carbon-carbon bond (i.e., double or triple bond, or both), but is not aromatic.
- an unsaturated cycloalkyl group as defined herein includes cyclohexenyl, cyclopentenyl, cyclohexadienyl, and the like.
- the term “leaving group” as used herein means an atom or group (charged or uncharged) that 10 becomes detached from an atom in what is considered to be the residual or main part of the substrate in a specified reaction.
- the specified reaction herein unless otherwise noted, is an SN1 or an SN2 reaction as is understood by one skilled in the art. In certain embodimentns, the specified reaction herein, is an SN2 reaction.
- a“substituted” as used herein, whether preceded by the term“optionally” or not, 15 means that at least one hydrogen present on a group (e.g., a carbon or nitrogen atom) is replaced with a permissible substituent, e.g., a substituent which upon substitution results in a stable compound, e.g., a compound which does not spontaneously undergo transformation such as by rearrangement, cyclization, elimination, or other reaction.
- a“substituted” group has a substituent at one or more substitutable positions of the group, and when more than one position in 20 any given structure is substituted, the substituent is either the same or different at each position.
- Suitable substituents include, but are not limited to, halogen, hydroxy, thiol, nitro, alkoxy, azido, carboxy, cyano, amino, C1-6alkyl, C2-6alkenyl, C1-6alkoxy, C1-6alkylamino.
- support linking group means a divalent chemical moiety that covalent connects a surface-bound functional group of a solid support (e.g., an amino group of an amino-modified solid support) to 25 another chemical moiety.
- reactive pair means two functional groups known by one skilled in the art to be capable of reacting, alone or in the presence of other reagents, to form a covalent linkage between the two chemical entities which each contain one of member of the reactive pair, respectively; the latter, herein, is referred to as “linking group formed by a reactive pair”.
- a reactive pair is a click pair, i.e., two functional groups capable of reacting in a click reaction to form a covalent linkage.
- the term “Michael acceptor” as used herein means an alpha, beta-unsaturated compound capable of reacting with a nucleophile at the beta-carbon of the electrophilic alkene of the alpha, beta -unsaturated compound.
- alpha, beta-unsaturated compound include, but are not limited 35 to, such as an alpha, beta-unsaturated aldehyde, ester, amide, sulfonyl, ketone, nitrile, or nitro.
- Alpha, beta-unsaturated refers to the carbon-carbon multiple bond that connects the carbon atom that is immediately adjacent to the referenced aldehyde, ester, amide, sulfonyl, ketone, nitrile, or nitro group, to its adjacent carbon atom.
- Michael acceptor group include, but are not limited 40 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- ALN-529-WO to, N-maleimide, acrylaldehyde, acrylonitrile, acrylic acid, acrylamide (e.g., N-isoproprylacrylamide), acrylate esters (e.g., methyl acrylate), vinyl sulfones, vinylsulfonates, and vinylsulfonamides.
- nitrogen protecting group means those functional groups that are well known in the art and include those described in detail, for example, in Protecting Groups in 5 Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3rd edition, John Wiley & Sons, 1999, the entirety of which is incorporated herein by reference.
- Suitable nitrogen protecting groups include but are not limited to, allyl (Alloc), acetyl (Ac), Adpoc (1-(1-Adamantyl)-1-methylethoxycarbonyl), Boc ( tert-butyloxy carbonyl), Dde Dnp (2,4-dinitrophenyl), Mmt (4-methoxytrityl), Mtt (4-methyltrityl), Teoc (2-trimethylsilylethoxycarbonyl, Tfa (trifluoroacetyl),10 optionally substituted trityl (e.g., trityl (Trt), 2-chlorotrityl (Clt), 4-methoxytrityl (Mmt), 4- methyltrityl (Mtt), 4,4’-dimethoxytrityl (DMT)), and 4,4’,4’’-trimethoxytrityl), optionally substituted benzyloxycarbonyl (e.g., benz
- the term “remainder of the dsRNA agent”, refers to an oligonucleotide strand (i.e. the sense strand or the antisense strand) that forms a dsRNA agent and any intervening linking group that connects the parent moiety (e.g., one or more ⁇ v ⁇ 6 integrin targeting ligand or one or more 25 in vivo delivery enhancing moieties) to the oligonucleotide strand.
- linker refers to a chemical moiety connecting at least one ⁇ v ⁇ 6 integrin targeting ligand or at least one in vivo delivery enhancing moiety to at least one strand of the dsRNA agent of the disclosure.
- iRNAs of the Disclosure Described herein are iRNAs for use in the methods of the present disclosure.
- the iRNAs are double stranded ribonucleic acid (dsRNA) molecules.
- the dsRNA agent targets an DMPK gene and inhibits the expression of the DMPK gene.
- the iRNA agent 41 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO includes dsRNA molecules for inhibiting the expression of an DMPK gene in a cell, such as a liver cell, such as a muscle cell within a subject, e.g., a mammal, such as a human having DM1.
- the iRNA agents provided herein comprise a sense strand and an antisense strand and at least one of the strands is modified for targeting delivery to extrahepatic tissue, e.g., muscle tissue, e.g., 5 skeletal muscle tissue and/or cardiac muscle tissue.
- the iRNA agents are modified by conjugation to at least one alpha-v-beta-6 ( ⁇ v ⁇ 6) integrin ligand and conjugation to at least one in vivo delivery enhancing moiety.
- integrin ligand is meant any ligand that binds to an integrin or an integrin receptor. Integrin ligands comprise binding sequences that are recognized and bound by integrins or ntegrin 10 receptors.
- Various ligands, including peptides and small molecules, which bind ⁇ v ⁇ 6 integrins or ⁇ v ⁇ 6 integrin receptors ( ⁇ v ⁇ 6 integrin targeting ligands) have been designed and synthesized herein and in, e.g., U.S.
- An exemplary linker to conjugate a ⁇ v ⁇ 6 integrin targeting ligand to the dsRNA agent is: 15 42 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 5 43 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO .
- at least one of the strands of the iRNA agent is conjugated to at least one ⁇ v ⁇ 6 integrin targeting ligand and at least one in vivo delivery enhancing moiety.
- the 5 iRNA agent may be conjugated to one, two, three, four, or more ⁇ v ⁇ 6 integrin targeting ligands and one, two, three, four or more in vivo delivery enhancing moieties.
- the ⁇ v ⁇ 6 integrin targeting ligand is conjugated to the sense strand.
- the ⁇ v ⁇ 6 integrin targeting ligand may be conjugated to an extrernal position of sense strand, e.g., the 3’-end of the sense strand, to the 5’-end of the sense strand, or to both the 5-end and the 3’-end of the 10 sense strand.
- the ⁇ v ⁇ 6 integrin targeting ligand may be conjugated to an internal position of the sense strand. In other embodiments, the ⁇ v ⁇ 6 integrin targeting ligand is conjugated to the antisense strand.
- the ⁇ v ⁇ 6 integrin targeting ligand may be conjugated to an external position of the antisense strand, e.g., the 3’-end of the antisense strand, to the 5’-end of the antisense strand, or to both the 5-end and 15 the 3’-end of the antisense strand. In some embodiments, the ⁇ v ⁇ 6 integrin targeting ligand may be conjugated to an internal position of the antisense strand.
- the in vivo delivery enhancing moiety is conjugated to the sense strand.
- the in vivo delivery enhancing moiety may be conjugated to an extrernal position of sense strand, e.g., the 3’-end of the sense strand, to the 5’-end of the sense strand, or to both the 5-end and 20 the 3’-end of the sense strand.
- the in vivo delivery enhancing moiety may be conjugated to an internal position of the sense strand.
- the in vivo delivery enhancing moiety is not conjugated to an external position of the sense strand.
- the ⁇ v ⁇ 6 integrin targeting ligand is conjugated to the antisense strand.
- the in vivo delivery enhancing moiety may be conjugated to an external position of the antisense25 strand, e.g., the 3’-end of the antisense strand, to the 5’-end of the antisense strand, or to both the 5- end and the 3’-end of the antisense strand.
- the in vivo delivery enhancing 44 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO moiety may be conjugated to an internal position of the antisense strand.
- the in vivo delivery enhancing moiety is not conjugated to an external position of the antisense strand.
- the ⁇ v ⁇ 6 integrin targeting ligand and the in vivo delivery enhancing moiety are both conjugated to the sense strand of the dsRNA agent.
- the ⁇ v ⁇ 6 integrin 5 targeting ligand is conjugated to an external position of the sense strand, e.g., the 3’-end of the sense strand or the 5’-end of the sense strand
- the in vivo delivery enhancing moiety is conjugated to an internal position of the sense strand.
- the ⁇ v ⁇ 6 integrin targeting ligand and the in vivo delivery enhancing moiety are both conjugated to the antisense strand of the dsRNA agent.
- the ⁇ v ⁇ 6 10 integrin targeting ligand is conjugated to an external position of the antisense strand, e.g., the 3’-end of the sense strand or the 5’-end of the antisense strand, and the in vivo delivery enhancing moiety is conjugated to an internal position of the antisense strand.
- the ⁇ v ⁇ 6 integrin targeting ligand is conjugated to a sense strand, and the in vivo delivery enhancing moiety is conjugated to an antisense strand.
- the 15 ⁇ v ⁇ 6 integrin targeting ligand is conjugated to an antisense strand, and the in vivo delivery enhancing moiety is conjugated to a sense strand.
- the dsRNA agent includes an antisense strand having a region of complementarity which is complementary to at least a part of an mRNA formed in the expression of a DMPK gene.
- the region of complementarity is about 19-30 nucleotides in length (e.g., about 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, or 19 nucleotides in length).
- the iRNA Upon contact with a cell expressing the DMPK gene, the iRNA inhibits the expression of the DMPK gene (e.g., a human, a primate, a non-primate, or a rat gene) by at least about 50% as assayed by, for example, a PCR or branched DNA (bDNA)-based method, or by a protein-based method, such as by immunofluorescence analysis, using, for example, western blotting or flow cytometric techniques.
- inhibition of expression is determined by the qPCR method 25 provided in the examples herein with the siRNA at, e.g., a 10 nM concentration, in an appropriate organism cell line provided therein.
- inhibition of expression in vivo is determined by knockdown of the human gene in a rodent expressing the human gene, e.g., a mouse or an AAV-infected mouse expressing the human target gene, e.g., when administered as single dose, e.g., at 3 mg/kg at the nadir of RNA expression.
- a dsRNA includes two RNA strands that are complementary and hybridize to form a duplex structure under conditions in which the dsRNA will be used.
- One strand of a dsRNA (the antisense s trand) includes a region of complementarity that is substantially complementary, and generally fully complementary, to a target sequence.
- the target sequence can be derived from the sequence of an mRNA formed during the expression of a DMPK gene.
- the other strand includes a 35 region that is complementary to the antisense strand, such that the two strands hybridize and form a duplex structure when combined under suitable conditions.
- the complementary sequences of a dsRNA can also be contained as self- 45 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO complementary regions of a single nucleic acid molecule, as opposed to being on separate oligonucleotides.
- the duplex structure is 15 to 30 base pairs in length, e.g., 15-29, 15-28, 15-27, 15- 26, 15-25, 15-24, 15-23, 15-22, 15-21, 15-20, 15-19, 15-18, 15-17, 18-30, 18-29, 18-28, 18-27, 18-26, 5 18-25, 18-24, 18-23, 18-22, 18-21, 18-20, 19-30, 19-29, 19-28, 19-27, 19-26, 19-25, 19-24, 19-23, 19- 22, 19-21, 19-20, 20-30, 20-29, 20-28, 20-27, 20-26, 20-25, 20-24,20-23, 20-22, 20-21, 21-30, 21-29, 21-28, 21-27, 21-26, 21-25, 21-24, 21-23, or 21-22 base pairs in length.
- the duplex structure is 18 to 25 base pairs in length, e.g., 18-25, 18-24, 18-23, 18-22, 18-21, 18-20, 19-25, 19-24, 19-23, 19-22, 19-21, 19-20, 20-25, 20-24,20-23, 20-22, 20-21, 21-25, 21-24, 21-23, 21-22, 22- 10 25, 22-24, 22-23, 23-25, 23-24 or 24-25 base pairs in length, for example, 19-21 basepairs in length. Ranges and lengths intermediate to the above recited ranges and lengths are also contemplated to be part of the disclosure.
- the region of complementarity to the target sequence is 15 to 30 nucleotides in length, e.g., 15-29, 15-28, 15-27, 15-26, 15-25, 15-24, 15-23, 15-22, 15-21, 15-20, 15-19, 15-18, 15- 15 17, 18-30, 18-29, 18-28, 18-27, 18-26, 18-25, 18-24, 18-23, 18-22, 18-21, 18-20, 19-30, 19-29, 19-28, 19-27, 19-26, 19-25, 19-24, 19-23, 19-22, 19-21, 19-20, 20-30, 20-29, 20-28, 20-27, 20-26, 20-25, 20- 24,20-23, 20-22, 20-21, 21-30, 21-29, 21-28, 21-27, 21-26, 21-25, 21-24, 21-23, or 21-22 nucleotides in length, for example 19-23 nucleotides in length or 21-23 nucleotides in length.
- the duplex structure is 19 to 30 base pairs in length.
- the region of complementarity to the target sequence is 19 to 30 nucleotides in length.
- the dsRNA is about 19 to about 23 nucleotides in length, or about 25 to about 30 nucleotides in length.
- the dsRNA is long enough to serve as a substrate for the Dicer enzyme. For example, it is well-known in the art that dsRNAs longer than about 21-23 25 nucleotides in length may serve as substrates for Dicer.
- RNAi-directed cleavage i.e., cleavage through a RISC pathway
- the duplex region is a primary functional portion of a dsRNA, e.g., a duplex region of about 19 to about 30 base pairs, e.g., about 19-30, 19-29, 19-28, 19-27, 19-26, 19-25, 19-24, 19-23, 19-22, 19-21, 19-20, 20-30, 20-29, 20-28, 20-27, 20-26, 20- 25, 20-24,20-23, 20-22, 20-21, 21-30, 21-29, 21-28, 21-27, 21-26, 21-25, 21-24, 21-23, or 21-22 base pairs.
- an RNA molecule or complex of RNA molecules having a duplex region greater than 30 base pairs is a dsRNA.
- a miRNA is a dsRNA.
- a 46 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO dsRNA is not a naturally occurring miRNA.
- an iRNA agent useful to target DMPK gene expression is not generated in the target cell by cleavage of a larger dsRNA.
- a dsRNA as described herein can further include one or more single-stranded nucleotide overhangs, e.g., 1-4, 2-4, 1-3, 2-3, 1, 2, 3, or 4 nucleotides. dsRNAs having at least one nucleotide 5 overhang can have superior inhibitory properties relative to their blunt-ended counterparts.
- a nucleotide overhang can comprise or consist of a nucleotide/nucleoside analog, including a deoxynucleotide/nucleoside.
- the overhang(s) can be on the sense strand, the antisense strand, or any combination thereof. Furthermore, the nucleotide(s) of an overhang can be present on the 5'-end, 3'- end, or both ends of an antisense or sense strand of a dsRNA. 10
- a dsRNA can be synthesized by standard methods known in the art. Double stranded RNAi compounds of the disclosure may be prepared using a two-step procedure. First, the individual strands of the double stranded RNA molecule are prepared separately. Then, the component strands are annealed. The individual strands of the siRNA compound can be prepared using solution-phase or solid-phase organic synthesis or both.
- a dsRNA of the disclosure includes at least two nucleotide sequences, a sense sequence and an anti-sense sequence.
- the sense strand is selected from the group of sequences 20 provided in any one of Tables 2-3, and the corresponding antisense strand of the sense strand is selected from the group of sequences of any one of Tables 2-3.
- one of the two sequences is complementary to the other of the two sequences, with one of the sequences being substantially complementary to a sequence of an mRNA generated in the expression of a-associated target gene.
- a dsRNA will include two oligonucleotides, where one 25 oligonucleotide is described as the sense strand in any one of Tables 2-3, and the second oligonucleotide is described as the corresponding antisense strand of the sense strand in any one of Tables 2-3.
- the substantially complementary sequences of the dsRNA are contained on separate oligonucleotides.
- the substantially complementary 30 sequences of the dsRNA are contained on a single oligonucleotide.
- the RNA of the iRNA of the disclosure e.g., a dsRNA of the disclosure, may comprise any one of the sequences set forth in any one of Tables 2-3 that is un- modified, un-conjugated, or modified or conjugated differently than described therein.
- the disclosure encompasses dsRNA of Tables 2-3 which are un-modified, un-conjugated, modified, or conjugated, as described herein.
- dsRNAs having a duplex structure of about 20 to 23 base pairs, e.g., 21, base pairs have been hailed as particularly effective in inducing RNA interference 47 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO (Elbashir et al., EMBO 2001, 20:6877-6888).
- ALN-529-WO Elbashir et al., EMBO 2001, 20:6877-6888.
- others have found that shorter or longer RNA duplex structures can also be effective (Chu and Rana (2007) RNA 14:1714-1719; Kim et al. (2005) Nat Biotech 23:222-226).
- dsRNAs described herein can include at 5 least one strand of a length of minimally 21 nucleotides. It can be reasonably expected that shorter duplexes having any one of the sequences in any one of Tables 2-3 minus only a few nucleotides on one or both ends can be similarly effective as compared to the dsRNAs described above.
- dsRNAs having a sequence of at least 19, 20, or more contiguous nucleotides derived from any one of the sequences of any one of Tables 2-3, and differing in their ability to inhibit the expression of a 10 DMPK gene by not more than about 5, 10, 15, 20, 25, or 30 % inhibition from a dsRNA comprising the full sequence, are contemplated to be within the scope of the present disclosure.
- the RNAs provided in Tables 2-3 identify a site(s) in a DMPK transcript that is susceptible to RISC-mediated cleavage. As such, the present disclosure further features iRNAs that target within one of these sites.
- an iRNA is said to target within a particular site of an 15 RNA transcript if the iRNA promotes cleavage of the transcript anywhere within that particular site.
- Such an iRNA will generally include at least about 19 contiguous nucleotides from any one of the sequences provided in any one of Tables 2-3 coupled to additional nucleotide sequences taken from the region contiguous to the selected sequence in a DMPK gene. 20 III. Modifications for the RNAi Agents of the Disclosure
- the iRNA for use in the methods of the disclosure e.g., a dsRNA, is un- m odified, and does not comprise, e.g., chemical modifications and/or conjugations known in the art and described herein.
- the iRNA for use in the methods of the disclosure is chemically modified to enhance stability or other beneficial characteristics.
- substantially all of the nucleotides of an iRNA of the disclosure are modified.
- all of the nucleotides of an iRNA of the disclosure are modified.
- iRNAs of the disclosure in which “substantially all of the nucleotides are modified” are largely but not wholly modified and can include not more than 5, 4, 3, 2, or 1 unmodified nucleotides.
- substantially all of the nucleotides of an iRNA of the disclosure 30 are modified and the iRNA agents comprise no more than 10 nucleotides comprising 2’-fluoro modifications (e.g., no more than 92 ⁇ -fluoro modifications, no more than 82 ⁇ -fluoro modifications, no more than 72 ⁇ -fluoro modifications, no more than 62 ⁇ -fluoro modifications, no more than 52 ⁇ -fluoro modifications, no more than 42 ⁇ -fluoro modifications, no more than 52 ⁇ -fluoro modifications, no more than 42 ⁇ -fluoro modifications, no more than 32 ⁇ -fluoro modifications, or no more than 22 ⁇ -fluoro 35 modifications).
- 2’-fluoro modifications e.g., no more than 92 ⁇ -fluoro modifications, no more than 82 ⁇ -fluoro modifications, no more than 72 ⁇ -fluoro modifications, no more than 62 ⁇ -fluoro modifications, no more than 52 ⁇ -fluoro modifications, no more than 42 ⁇ -fluoro modifications, no more than 52
- the sense strand comprises no more than 4 nucleotides comprising 2 ⁇ -fluoro modifications (e.g., no more than 32 ⁇ -fluoro modifications, or no more than 22 ⁇ -fluoro modifications).
- the antisense strand comprises no more than 6 nucleotides comprising 2 ⁇ -fluoro modifications (e.g., no more than 52 ⁇ -fluoro modifications, no more than 48 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 42 ⁇ -fluoro modifications, no more than 42 ⁇ -fluoro modifications, or no more than 22 ⁇ -fluoro modifications).
- all of the nucleotides of an iRNA of the disclosure are modified and the iRNA agents comprise no more than 10 nucleotides comprising 2’-fluoro modifications (e.g., no 5 more than 92 ⁇ -fluoro modifications, no more than 82 ⁇ -fluoro modifications, no more than 72 ⁇ -fluoro modifications, no more than 62 ⁇ -fluoro modifications, no more than 52 ⁇ -fluoro modifications, no more than 42 ⁇ -fluoro modifications, no more than 52 ⁇ -fluoro modifications, no more than 42 ⁇ -fluoro modifications, no more than 32 ⁇ -fluoro modifications, or no more than 22 ⁇ -fluoro modifications).
- 2’-fluoro modifications e.g., no 5 more than 92 ⁇ -fluoro modifications, no more than 82 ⁇ -fluoro modifications, no more than 72 ⁇ -fluoro modifications, no more than 62 ⁇ -fluoro modifications, no more than 52 ⁇ -fluoro modifications, no more than 42 ⁇ -fluoro modifications, no more than 52 ⁇
- nucleic acids featured in the disclosure can be synthesized and/or modified by methods well 10 established in the art, such as those described in “Current protocols in nucleic acid chemistry,” Beaucage, S.L. et al. (Edrs.), John Wiley & Sons, Inc., New York, NY, USA, which is hereby incorporated herein by reference.
- Modifications include, for example, end modifications, e.g., 5’-end modifications (phosphorylation, conjugation, inverted linkages) or 3’-end modifications (conjugation, DNA nucleotides, inverted linkages, etc.); base modifications, e.g., replacement with stabilizing bases, destabilizing bases, or 15 bases that base pair with an expanded repertoire of partners, removal of bases (abasic nucleotides), or conjugated bases; sugar modifications (e.g., at the 2’-position or 4’-position) or replacement of the sugar; and/or backbone modifications, including modification or replacement of the phosphodiester linkages.
- end modifications e.g., 5’-end modifications (phosphorylation, conjugation, inverted linkages) or 3’-end modifications (conjugation, DNA nucleotides, inverted linkages, etc.
- base modifications e.g., replacement with stabilizing bases, destabilizing bases, or 15 bases that base pair with an expanded repertoire of partners, removal of bases (abasic
- RNAs having 20 modified backbones include, among others, those that do not have a phosphorus atom in the backbone.
- modified RNAs that do not have a phosphorus atom in their internucleoside backbone can also be considered to be oligonucleosides.
- a modified iRNA will have a phosphorus atom in its internucleoside backbone.
- Modified RNA backbones include, for example, phosphorothioates, chiral phosphorothioates, 25 phosphorodithioates, phosphotriesters, aminoalkylphosphotriesters, methyl and other alkyl phosphonates including 3'-alkylene phosphonates and chiral phosphonates, phosphinates, phosphoramidates including 3'- amino phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, and boranophosphates having normal 3'-5' linkages, 2'-5'-linked analogs of these, and those having inverted polarity wherein the adjacent pairs of nucleoside units are linked 3'-5' to 5'-3' or 2'-5' 30 to 5'-2'.
- the dsRNA agents of the disclosure are in a free acid form. In other embodiments of the disclosure, the dsRNA agents of the disclosure are in a salt form. In one embodiment, the dsRNA agents of the disclosure are in a sodium salt form. In certain embodiments, when the dsRNA agents of the disclosure are in the sodium salt form, sodium ions are present in the agent as counterions for substantially all of the phosphodiester and/or 35 phosphorothiotate groups present in the agent.
- Agents in which substantially all of the phosphodiester and/or phosphorothioate linkages have a sodium counterion include not more than 5, 4, 3, 2, or 1 phosphodiester and/or phosphorothioate linkages without a sodium counterion.
- sodium ions are present in the agent as counterions for all of the phosphodiester and/or phosphorothiotate groups present in the agent.
- Representative U.S. patents that teach the preparation of the above phosphorus-containing linkages include, but are not limited to, U.S.
- Modified RNA backbones that do not include a phosphorus atom therein have backbones that are formed by short chain alkyl or cycloalkyl internucleoside linkages, mixed heteroatoms and alkyl or cycloalkyl internucleoside linkages, or one or more short chain heteroatomic or heterocyclic internucleoside linkages.
- patents that teach the preparation of the above oligonucleosides include, but 20 are not limited to, U.S. Patent Nos.5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141; 5,235,033; 5,64,562; 5,264,564; 5,405,938; 5,434,257; 5,466,677; 5,470,967; 5,489,677; 5,541,307; 5,561,225; 5,596,086; 5,602,240; 5,608,046; 5,610,289; 5,618,704; 5,623,070; 5,663,312; 5,633,360; 5,677,437; and, 5,677,439, the entire contents of each of which are hereby incorporated herein by reference.
- RNA mimetics are contemplated for use in iRNAs, in which both 25 the sugar and the internucleoside linkage, i.e., the backbone, of the nucleotide units are replaced with novel groups.
- the base units are maintained for hybridization with an appropriate nucleic acid target compound.
- a peptide nucleic acid PNA
- PNA peptide nucleic acid
- the sugar backbone of an RNA is replaced with an amide containing backbone, in particular an aminoethylglycine 30 backbone.
- nucleobases are retained and are bound directly or indirectly to aza nitrogen atoms of the amide portion of the backbone.
- Representative U.S. patents that teach the preparation of PNA compounds include, but are not limited to, U.S. Patent Nos.5,539,082; 5,714,331; and 5,719,262, the entire contents of each of which are hereby incorporated herein by reference. Additional PNA compounds suitable for use in the iRNAs of the disclosure are described in, for example, in Nielsen et al., Science, 1991, 254, 35 1497-1500.
- RNAs with phosphorothioate backbones and oligonucleosides with heteroatom backbones and in particular --CH2--NH--CH2-, --CH2--N(CH3)--O-- CH2--[known as a methylene (methylimino) or MMI backbone], --CH2--O--N(CH3)--CH2--, --CH2-- 50 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- RNAs featured herein have morpholino backbone structures of the above-referenced U.S. Patent No.5,034,506. 5 Modified RNAs can also contain one or more substituted sugar moieties.
- the iRNAs e.g., dsRNAs, featured herein can include one of the following at the 2'-position: OH; F; O-, S-, or N-alkyl; O-, S-, or N-alkenyl; O-, S- or N-alkynyl; or O-alkyl-O-alkyl, wherein the alkyl, alkenyl and alkynyl can be substituted or unsubstituted C1 to C10 alkyl or C2 to C10 alkenyl and alkynyl.
- Exemplary suitable modifications include O[(CH2)nO] mCH3, O(CH2).nOCH3, O(CH2)nNH2, O(CH2) nCH3, O(CH2)nONH2, and 10 O(CH2)nON[(CH2)nCH3)]2, where n and m are from 1 to about 10.
- dsRNAs include one of the following at the 2' position: C1 to C10 lower alkyl, substituted lower alkyl, alkaryl, aralkyl, O- alkaryl or O-aralkyl, SH, SCH3, OCN, Cl, Br, CN, CF3, OCF3, SOCH3, SO2CH3, ONO2, NO2, N3, NH2, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl, an RNA cleaving group, a reporter group, an intercalator, a group for improving the pharmacokinetic properties of 15 an iRNA, or a group for improving the pharmacodynamic properties of an iRNA, and other substituents having similar properties.
- the modification includes a 2'-methoxyethoxy (2'-O-- CH2CH2OCH3, also known as 2'-O-(2-methoxyethyl) or 2'-MOE) (Martin et al., Helv. Chim. Acta, 1995, 78:486-504) i.e., an alkoxy-alkoxy group.
- 2'-dimethylaminooxyethoxy i.e., a O(CH2)2ON(CH3)2 group, also known as 2'-DMAOE, as described in examples herein below
- 2'- 20 dimethylaminoethoxyethoxy also known in the art as 2'-O-dimethylaminoethoxyethyl or 2'-DMAEOE
- 2'-O--CH2--O--CH2--N(CH2)2 2'-dimethylaminooxyethoxy
- modifications include : 5’-Me-2’-F nucleotides, 5’- Me-2’-OMe nucleotides, 5’-Me-2’-deoxynucleotides, (both R and S isomers in these three families); 2’- alkoxyalkyl; and 2’-NMA (N-methylacetamide).
- Other modifications include 2'-methoxy (2'-OCH3), 2'-aminopropoxy (2'-OCH2CH2CH2NH2) and 25 2'-fluoro (2'-F).
- RNA of an iRNA can also have sugar mimetics such as cyclobutyl moieties in place of the pentofuranosyl sugar.
- Representative U.S. patents that teach the preparation of such modified sugar structures include, but are not limited to, U.S. Pat.
- nucleobase of the disclosure can also include nucleobase (often referred to in the art simply as 35 “base”) modifications or substitutions.
- nucleobases include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) and uracil (U).
- Modified nucleobases include other synthetic and natural nucleobases such as 5-methylcytosine (5- me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl 51 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- nucleobases include those disclosed in U.S. Pat. No.3,687,808, those disclosed in Modified Nucleosides in Biochemistry, Biotechnology and Medicine, Herdewijn, P. ed. Wiley-VCH, 2008; those disclosed in The Concise Encyclopedia Of Polymer Science And Engineering, pages 858-859, 10 Kroschwitz, J. L, ed. John Wiley & Sons, 1990, these disclosed by Englisch et al., (1991) Angewandte Chemie, International Edition, 30:613, and those disclosed by Sanghvi, Y S., Chapter 15, dsRNA Research and Applications, pages 289-302, Crooke, S. T. and Lebleu, B., Ed., CRC Press, 1993.
- nucleobases are particularly useful for increasing the binding affinity of the oligomeric compounds featured in the disclosure.
- These include 5-substituted pyrimidines, 6-azapyrimidines and N- 15 2, N-6 and 0-6 substituted purines, including 2-aminopropyladenine, 5-propynyluracil and 5- propynylcytosine.5-methylcytosine substitutions have been shown to increase nucleic acid duplex stability by 0.6-1.2 °C (Sanghvi, Y. S., Crooke, S. T.
- An iRNA of the disclosure can also be modified to include one or more locked nucleic acids (LNA).
- LNA locked nucleic acids
- a locked nucleic acid is a nucleotide having a modified ribose moiety in which the ribose moiety comprises an extra bridge connecting the 2' and 4' carbons. This structure effectively "locks" the ribose in 30 the 3'-endo structural conformation.
- the addition of locked nucleic acids to siRNAs has been shown to increase siRNA stability in serum, and to reduce off-target effects (Elmen, J. et al., (2005) Nucleic Acids Research 33(1):439-447; Mook, OR. et al., (2007) Mol Canc Ther 6(3):833-843; Grunweller, A.
- An iRNA of the disclosure can also be modified to include one or more bicyclic sugar moities.
- a 35 “bicyclic sugar” is a furanosyl ring modified by the bridging of two atoms.
- A“bicyclic nucleoside” (“BNA”) is a nucleoside having a sugar moiety comprising a bridge connecting two carbon atoms of the sugar ring, thereby forming a bicyclic ring system. In certain embodiments, the bridge connects the 4′- carbon and the 2′-carbon of the sugar ring.
- an agent of the disclosure may 52 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO include one or more locked nucleic acids (LNA).
- LNA locked nucleic acids
- a locked nucleic acid is a nucleotide having a modified ribose moiety in which the ribose moiety comprises an extra bridge connecting the 2' and 4' carbons.
- an LNA is a nucleotide comprising a bicyclic sugar moiety comprising a 4'-CH2-O-2' bridge. This structure effectively "locks" the ribose in the 3'-endo structural conformation.
- bicyclic nucleosides for use in the polynucleotides of the disclosure include without limitation nucleosides comprising a bridge between the 4′ and the 2′ ribosyl ring atoms.
- the antisense polynucleotide agents of the disclosure include one or more bicyclic nucleosides comprising a 4′ to 2′ bridge.
- 4′ to 2′ bridged bicyclic nucleosides include but are not limited to 4′-(CH2)—O-2′ (LNA); 4′-(CH2)—S-2′; 4′-(CH2)2—O-2′ (ENA); 4′-CH(CH3)—O- 2′ (also referred to as “constrained ethyl” or “cEt”) and 4′-CH(CH2OCH3)—O-2′ (and analogs thereof; see, e.g., U.S. Pat.
- any of the foregoing bicyclic nucleosides can be prepared having one or more stereochemical sugar configurations including for example ⁇ -L-ribofuranose and ⁇ -D-ribofuranose (see WO 99/14226).
- An iRNA of the disclosure can also be modified to include one or more constrained ethyl 30 nucleotides.
- a "constrained ethyl nucleotide” or “cEt” is a locked nucleic acid comprising a bicyclic sugar moiety comprising a 4'-CH(CH3)-0-2' bridge.
- an iRNA of the disclosure comprises one or more monomers that are UNA 5 (unlocked nucleic acid) nucleotides.
- UNA is unlocked acyclic nucleic acid, wherein any of the bonds of the sugar has been removed, forming an unlocked "sugar" residue.
- UNA also encompasses monomer with bonds between C1'-C4' have been removed (i.e. the covalent carbon-oxygen- carbon bond between the C1' and C4' carbons).
- the C2'-C3' bond i.e. the covalent carbon-carbon bond between the C2' and C3' carbons
- the antisense strand comprises at least one (e.g., one, two, three, four, five or more) 54 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO thermally destabilizing modification of the duplex within the first 9 nucleotide positions of the 5’ region of the antisense strand.
- one or more thermally destabilizing modification(s) of the duplex is/are located in positions 2-9, or preferably positions 4-8, from the 5’- end of the antisense strand.
- the thermally destabilizing modification(s) 5 of the duplex is/are located at position 6, 7 or 8 from the 5’-end of the antisense strand.
- the thermally destabilizing modification of the duplex is located at position 7 from the 5’-end of the antisense strand.
- the thermally destabilizing modification of the duplex is located at position 2, 3, 4, 5 or 9 from the 5’-end of the antisense strand.
- acyclic nucleotide refers to any nucleotide having an acyclic ribose sugar, for example, where any of bonds between the ribose carbons (e.g., C1’-C2’, C2’-C3’, C3’-C4’, C4’-O4’, or C1’-O4’) is absent or at least one of ribose carbons or oxygen (e.g., C1’, C2’, C3’, C4’ or O4’) are independently or in combination absent from the nucleotide.
- bonds between the ribose carbons e.g., C1’-C2’, C2’-C3’, C3’-C4’, C4’-O4’, or C1’-O4’
- acyclic nucleotide 56 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO is a modified or unmodified nucleobase, R 1 and R 2 independently are H, halogen, OR 3 , or alkyl; and R 3 is H, alkyl, cycloalkyl, aryl, aralkyl, heteroaryl or sugar).
- the term “UNA” refers to unlocked acyclic nucleic acid, wherein any of the bonds of the sugar has been removed, forming an unlocked 5 "sugar" residue.
- UNA also encompasses monomers with bonds between C1'-C4' being removed (i.e. the covalent carbon-oxygen-carbon bond between the C1' and C4' carbons).
- bonds between C1'-C4' being removed i.e. the covalent carbon-oxygen-carbon bond between the C1' and C4' carbons.
- the C2'-C3' bond i.e. the covalent carbon-carbon bond between the C2' and C3' carbons
- the acyclic derivative provides greater backbone flexibility without affecting the Watson- Crick pairings.
- the acyclic nucleotide can be linked via 2’-5’ or 3’-5’ linkage.
- the term ‘GNA’ refers to glycol nucleic acid which is a polymer similar to DNA or RNA but differing in the composition of its “backbone” in that is composed of repeating glycerol units linked by phosphodiester bonds: 15 .
- the thermally destabilizing modification of the duplex can be mismatches (i.e., noncomplementary base pairs) between the thermally destabilizing nucleotide and the opposing nucleotide in the opposite strand within the dsRNA duplex.
- mismatch base pairs include G:G, G:A, G:U, G:T, A:A, A:C, C:C, C:U, C:T, U:U, T:T, U:T, or a combination thereof.
- Other 20 mismatch base pairings known in the art are also amenable to the present disclosure.
- a mismatch can occur between nucleotides that are either naturally occurring nucleotides or modified nucleotides, i.e., the mismatch base pairing can occur between the nucleobases from respective nucleotides independent of the modifications on the ribose sugars of the nucleotides.
- the dsRNA molecule contains at least one nucleobase in the mismatch pairing that is a 2’-deoxy 25 nucleobase; e.g., the 2’-deoxy nucleobase is in the sense strand.
- 57 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
- the thermally destabilizing modification of the duplex in the seed region of the antisense strand includes nucleotides with impaired W-C H-bonding to complementary base on the target mRNA, such as: .
- thermally destabilizing modifications may also include universal base with reduced or abolished capability to form hydrogen bonds with the opposing bases, and phosphate modifications.
- the thermally destabilizing modification of the duplex includes nucleotides with non-canonical bases such as, but not limited to, nucleobase modifications with impaired or completely abolished capability to form hydrogen bonds with bases in the opposite strand.
- the thermally destabilizing modification of the duplex in the seed region of the antisense strand includes one or more ⁇ -nucleotide complementary to the base on the target mRNA, such as: 5 wherein R is H, OH, OCH3, F, NH2, NHMe, NMe2 or O-alkyl.
- the alkyl for the R group can be a C1-C6alkyl.
- Specific alkyls for the R group include, but are 10 not limited to methyl, ethyl, propyl, isopropyl, butyl, pentyl and hexyl.
- nucleobase modifications can be performed in the various manners as described herein, e.g., to introduce destabilizing modifications into an RNAi agent of the disclosure, e.g., for purpose of enhancing on-target effect relative to off-target effect, the 15 range of modifications available and, in general, present upon RNAi agents of the disclosure tends to be much greater for non-nucleobase modifications, e.g., modifications to sugar groups or phosphate backbones of polyribonucleotides.
- the dsRNA agent further comprises a phosphate or phosphate mimic at the 5’-end of the sense or antisense strand. In one embodiment, there is a phosphate or phosphate mimic at the 5’-end of the sense strand. In one embodiment, there is a phosphate or phosphate mimic at the 5’-end of the antisense strand.
- the phosphate mimic is 5’-end phosphorothioate (5’-PS), 5’- 25 end phosphorodithioate (5’-PS2), 5’ end vinylphosphonate (5’-VP), 5’-end m ethylphosphonate (MePhos), or 5’-deoxy-5’-C-malonyl one embodiment, the phosphate mimic is a 5’-vinyl phosphonate (VP).
- the phosphate mimic is a 5’-(E)-vinyl phosphonate (VP) isomer (i.e., trans-vinylphosphate), 5’-(Z)-VP isomer (i.e., cis-vinylphosphate), or mixtures thereof.
- VP 5’-(E)-vinyl phosphonate
- 5’-(Z)-VP isomer i.e., cis-vinylphosphate
- 59 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- the -CH2OH group at the 4’-position of the 5’-terminal nucleotide is 15 replaced with a phosphate mimic of the formula -O-CH2-P(O)(OR)2, wherein each R is independently hydrogen or C1-4 alkyl (e.g., one R group is hydrogen and one R group is methyl; or both R groups are hydrogen).
- the phosphate mimic is a 5’-cyclopropyl phosphonate (VP) (i.e., the CH 2 OH group at the 4’-position of the 5’-terminal nucleotide is replaced with a group of the formula -Cy- 20 P(O)(OR) 2 , wherein Cy is a cyclopropyl ring and each R is independently hydrogen or C 1-4 alkyl (e.g., one R group is hydrogen or both R groups are hydrogen).
- the 5’-end phosphate mimic i , salt (e.g., sodium salt) thereof, wherein B is an optionally modified nucleobase (e.g., U).
- the 5’-end phosphate mimic is part of a modified 5’-terminal nucleotide.
- the phosphate mimic may be part of a modified 5’-terminal nucleotide 60 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO having the structure , wherein B is an optionally modified nucleobase.
- the 5’-end phosphate mimic can also include a 5’-phosphate prodrug or 5’-phosphonate prodrug.
- the 5’-phosphate prodrug or 5’-phosphonate 5 prodrug has a structure of formulas disclosed in WO2022/147214, which is incorporated herein by reference.
- the 5’-phosphate prodrug or 5’-phosphonate prodrug is: 10 -methoxyphenyl)-3,3-dimethyl-1,2-dithiolan-4-ol) 61 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
- the 5’-phosphate prodrug or 5’-phosphonate prodrug is: .
- the siRNA containing one of the above list of 5’ modified phosphate prodrugs generally has an activity comparable to that of the siRNA containing 5’-VP.
- the 5’- 5 phosphate prodrug or 5’-phosphonate prodrug is: .
- the siRNA containing one of the above list of 5’ modified phosphate prodrugs can have an improved stability than that of the siRNA containing 5’-VP and better or comparable activity than that of the siRNA containing 5’-VP.
- the 5’-end of the antisense strand of the dsRNA agent does not contain a 5’-vinyl phosphonate (VP). IV.
- a dsRNA agent comprises an antisense strand and a sense strand; at least one ⁇ v ⁇ 6 integrin targeting ligand that mediates delivery to muscle tissue conjugated to at least one strand; and at least one in vivo delivery enhancing moiety conjugated to at least one strand.
- Suitable in vivo delivery enhancing moieties for use in the present disclosure are described in 20 International Application No. PCT/US2022/046668, filed on October 14, 2022, in U.S.
- the at least one in vivo delivery enhancing moiety may be conjugated to any internal position of the antisense strand or the sense strand. In some embodiments, the at least one in vivo delivery enhancing moiety may be conjugated to a position that is not an external position of the antisense strand or the sense strand.
- the at least one in vivo delivery enhancing moiety may be conjugated to an external positon of the antisense strand or the sense strand.
- the term “in vivo delivery enhancing moiety” refers to a moiety which, when conjugated to a dsRNA agent, enhances delivery of the dsRNA agent to a target tissue, e.g., muscle, 62 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO or a cell type, such as a muscle cell (e.g., a skeletal muscle cell or a cardiac muscle cell).
- the in vivo delivery enhancing moiety has pharmacokinetic (PK) enhancing properties, such as increasing the residence time in the blood of the dsRNA agent, and/or increasing tissue PK, including increasing tissue exposure of the dsRNA agent.
- PK pharmacokinetic
- the in vivo delivery 5 enhancing moiety can have a cooperative or synergistic effect with an ⁇ v ⁇ 6 compound in increasing tissue exposure when both elements are conjugated to the dsRNA agent.
- the in vivo delivery enhancing moiety is lipophilic.
- the in vivo delivery enhancing moiety increases lipophilicity of the dsRNA agent and provides optimal 10 hydrophobicity for the enhanced in vivo delivery of dsRNA to muscle tissue, e.g., skeletal muscle tissue or cardiac muscle tissue.
- muscle tissue e.g., skeletal muscle tissue or cardiac muscle tissue.
- One way to characterize lipophilicity is by the octanol-water partition coefficient, logKow, where Kow is the ratio of a chemical’s concentration in the octanol-phase to its concentration in the aqueous phase of a two-phase system at equilibrium.
- the octanol-water partition coefficient is a 15 laboratory-measured property of a substance.
- a chemical substance is lipophilic in character when its logKow exceeds 0.
- the lipophilic moiety possesses a logKow exceeding 1, exceeding 1.5, exceeding 2, exceeding 3, exceeding 4, exceeding 5, or exceeding 10.
- the logKow of 6- amino hexanol for instance, is predicted to be approximately 0.7.
- the logKow of cholesteryl N-(hexan-6-ol) carbamate is predicted to be 10.7. 25
- the lipophilicity of a molecule can change with respect to the functional group it carries. For instance, adding a hydroxyl group or amine group to the end of a hydrocarbon chain, e.g., a C22 hydrocarbon chain, can increase or decrease the partition coefficient (e.g., logKow) value of the hydrocarbon chain.
- the hydrophobicity of the dsRNA agent conjugated to at least one in vivo 30 delivery enhancing moiety can be measured by its protein binding characteristics.
- the unbound fraction in the plasma protein binding assay of the dsRNA agent can be determined to positively correlate to the relative hydrophobicity of the dsRNA agent, which can positively correlate to the silencing activity of the dsRNA agent.
- the plasma protein binding assay determined is an electrophoretic 35 mobility shift assay (EMSA) using human serum albumin protein.
- ESA electrophoretic 35 mobility shift assay
- the hydrophobicity of the dsRNA agent measured by fraction of unbound dsRNA agent in the binding assay, exceeds 0.15, exceeds 0.2, exceeds 0.25, exceeds 0.3, exceeds 0.35, exceeds 0.4, exceeds 0.45, or exceeds 0.5 for an enhanced in vivo delivery of dsRNA agent.
- the at least one in vivo delivery enhancing moiety may be attached to the dsRNA agent of the disclosure by any method known in the art, including via a functional grouping already present in the in vivo delivery enhancing moiety or introduced into the dsRNA agent, such as a hydroxy group (e.g., —CO—CH2—OH).
- the functional groups already present in the in vivo delivery enhancing moiety 5 or introduced into the dsRNA agent include, but are not limited to, hydroxyl, amine, carboxylic acid, sulfonate, phosphate, thiol, azide, and alkyne. Conjugation of the dsRNA agent and the in vivo delivery enhancing moiety may occur, for example, through formation of an ether or a carboxylic or carbamoyl ester linkage between the hydroxy and an alkyl group R—, an alkanoyl group RCO— or a substituted carbamoyl group 10 RNHCO—.
- the alkyl group R may be cyclic (e.g., cyclohexyl) or acyclic (e.g., straight-chained or branched; and saturated or unsaturated).
- Alkyl group R may be a butyl, pentyl, hexyl, heptyl, octyl, nonyl, decyl, undecyl, dodecyl, tridecyl, tetradecyl, pentadecyl, hexadecyl, heptadecyl or octadecyl group, or the like.
- more than one in vivo delivery enhancing moiety can be conjugated 15 to the dsRNA agent of the disclosure.
- two or more in vivo delivery enhancing moieties are conjugated to the same strand of the dsRNA agent.
- each strand of the dsRNA agent is conjugated to one or more in vivo delivery enhancing moieties.
- two or more in vivo delivery enhancing moieties are conjugated to the same position (i.e., the same nucleobase, same sugar moiety, or same internucleosidic linkage) of the dsRNA agent.
- the in vivo delivery enhancing moiety may comprise at least one C10- 25 C26 hydrocarbon chain, e.g., a C10 hydrocarbon chain, a C11 hydrocarbon chain, a C12 hydrocarbon chain, a C13 hydrocarbon chain, a C14 hydrocarbon chain, a C15 hydrocarbon chain, a C16 hydrocarbon chain, a C17 hydrocarbon chain, a C18 hydrocarbon chain, a C19 hydrocarbon chain, a C20 hydrocarbon chain, a C21 hydrocarbon chain, a C22 hydrocarbon chain, a C23 hydrocarbon chain, a C24 hydrocarbon chain, a C25 hydrocarbon chain or a C26 hydrocarbon chain.
- a C10 hydrocarbon chain e.g., a C10 hydrocarbon chain, a C11 hydrocarbon chain, a C12 hydrocarbon chain, a C13 hydrocarbon chain, a C14 hydrocarbon chain, a C15 hydrocarbon chain, a C16 hydrocarbon chain, a C17 hydrocarbon chain, a C18 hydrocarbon chain,
- the C10-C26 30 hydrocarbon chain may be a straight hydrocarbon chain. In other embodiments, the C10-C26 hydrocarbon chain may be a branched hydrocarbon chain. In some embodiments, the C10-C26 hydrocarbon chain may be a saturated hydrocarbon chain. In other embodiments, the C10-C26 hydrocarbon chain may be an unsaturated hydrocarbon chain, e.g., comprising one or more double bonds and/or one or more triple bonds. 35
- the in vivo delivery enhancing moiety may comprise at least one C11 hydrocarbon chain. In one embodiment, the at least one in vivo delivery enhancing moiety may comprise at least one C17 hydrocarbon chain.
- the in vivo delivery enhancing moiety may comprise at least one C22 hydrocarbon chain. 64 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
- the C10-C26 hydrocarbon chain may be unsubstituted.
- the C10-C26 hydrocarbon chain may be substituted with at least one functional group selected from the group consisting of hydroxyl, amine, carboxylic acid, sulfonate, phosphate, thiol, azide, and alkyne.
- the C10-C26 hydrocarbon chain is substituted with a carboxylic 5 acid group.
- the C10-C26 hydrocarbon chain is represented by –(CH2)n-, wherein n is a number from 10 to 26, e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26; and — is a bond connecting the C10-C26 hydrocarbon chain to other portions of the in vivo delivery enhancing moiety.
- the C10-C26 hydrocarbon chain is connected at both ends to the 10 remainder of the in vivo delivery enhancing moiety.
- the C10-C26 hydrocarbon chain is represented by the following structure: –linker-(CH2)n(CH3), wherein n is a number from 10 to 25, e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or 25; the linker is as described hereinbelow; and – is a bond connecting the C10-C26 hydrocarbon chain to other portions of the in vivo delivery enhancing moiety.
- the C10-C26 hydrocarbon chain is connected at one end to other portions of the in vivo delivery enhancing moiety.
- the C10-C26 hydrocarbon chain is represented by the following structure: –linker-(CH2)n-A, wherein n is a number from 10 to 26, e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26; the linker as described hereinbelow and A is a functional group 20 selected from the group consisting of hydroxyl, amine, carboxylic acid, sulfonate, phosphate, thiol, azide, and alkyne; or A1 or A2 with a structure shown below: In one embodiment, A is carboxylic acid. 25 In one embodiment, A is A1. In one embodiment, A is A2.
- in vivo delivery enhancing moieties useful in the context of the present disclosure are described, e.g., in WO 2023/064530, the entire contents of which are incorporated herein by reference.
- the in vivo delivery enhancing moiety an comprise at least one C10-C26 h ydrocarbon chain.
- the in vivo delivery enhancing moiety comprises a C22 hydrocarbon chain, e.g., one or more C22 hydrocarbon chains.
- the C22 hydrocarbon chain is a C22 acid, e.g., a C22 acid selected from the group consisting of docosanoic acid, 5 6-octyltetradecanoic acid, 10-hexylhexadecanoic acid, all-cis-7,10,13,16,19-docosapentaenoic acid, all-cis-4,7,10,13,16,19-docosahexaenoic acid, all-cis-13,16-docosadienoic acid, all-cis-7,10,13,16- docosatetraenoic acid, all-cis-4,7,10,13,16-docosapentaenoic acid, and cis-13-docosenoic acid.
- a C22 acid selected from the group consisting of docosanoic acid, 5 6-octyltetradecanoic acid, 10-hexylhexadecanoic acid, all-
- the C 22 hydrocarbon chain is a C 22 alcohol, e.g. the C 22 alcohol selected10 from the group consisting of 1-docosanol, 6-octyltetradecan-1-ol, 10-hexylhexadecan-1-ol, cis-13- docosen-1-ol, docosan-9-ol, docosan-2-ol, docosan-10-ol, docosan-11-ol, and cis-4,7,10,13,16,19- docosahexanol.
- the C 22 alcohol selected10 from the group consisting of 1-docosanol, 6-octyltetradecan-1-ol, 10-hexylhexadecan-1-ol, cis-13- docosen-1-ol, docosan-9-ol, docosan-2-ol, docosan-10-ol, docosan-11-ol, and cis-4,7,
- the C22 hydrocarbon chain is a C22 amide, e.g., the C22 amide selected 15 from the group consisting of (E)-Docos-4-enamide, (E)-Docos-5-enamide, (Z)-Docos-9-enamide, (E)-Docos-11-enamide,12-Docosenamide, (Z)-Docos-13-enamide, (Z)-N-Hydroxy-13- docoseneamide, (E)-Docos-14-enamide, 6-cis-Docosenamide, 14-Docosenamide Docos-11-enamide, (4E,13E)-Docosa-4,13-dienamide, and (5E,13E)-Docosa-5,13-dienamide.
- the C22 amide selected 15 from the group consisting of (E)-Docos-4-enamide, (E)-Docos-5-enamide, (Z)-Docos-9-enamide, (E)-Doco
- the C22 hydrocarbon chain includes, but are not limited to, docosan-2-yl, 20 docosan-3-yl, docosan-4-yl, docosan-5-yl, docosan-6-yl, docosan-7-yl, docosan-8-yl, docosan-9-yl, docosan-10-yl, docosan-11-yl, 2-(decyl)dodecan-1-yl, 2-(nonyl)tridecan-1-yl, 2-(octyl)tetradecan-1- yl, 2-(heptyl)pentadecan-1-yl, 2-(hexyl)hexadecan-1-yl, 2-(pentyl)heptadecan-1-yl, 2- 66 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- the at least one C10-C26 hydrocarbon chain comprised in the in vivo delivery enhancing moiety may be conjugated to the remainder of the dsRNA agent via a linker or via a carrier or via an internucleotide phosphate linkage.
- the at least one C10-C26 hydrocarbon chain is conjugated to the remainder of the dsRNA agent via a linker.
- the linker may be a cleavable linker, i.e., the linker comprises a portion that can be 20 cleavable chemically or enzymatically.
- amide linkages can be enzymatically cleavable.
- the linker comprises —(CH2)n-NH-C(O)- or –(CH2)n-NH-C(O)-(CH2)2- C(COOH)-NH-C(O)-, wherein n is a number from 1 to 20, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20.
- the linker comprises –(CH)2-O-(CH2CH2)-(O)- (CH2CH2)-NH-C(O)-.
- the linker may comprise a group selected from the group consisting of an ether, a thioether, a urea, a carbonate, an amine, an amide, a maleimide-thioether, a disulfide, a phosphodiester, a sulfonamide linkage, a product of a click reaction, and a carbamate.
- the linker may be selected from the group consisting of -(CH2)nNH-; -C(O)(CH2)nNH-; -NR’’’’(CH2)nNH-, -C(O)-(CH2)n-C(O)-; -C(O)-(CH2)n-C(O)O-; -C(O)-O-; -C(O)-(CH2)n-NH-C(O)-; 30 -C(O)-(CH2)n-; -C(O)-NH-; -C(O)-; -(CH2)n-C(O)-; -(CH2)n-C(O)O-; -(CH2)n-; and -(CH2)n-NH- C(O)-; wherein n is a number from 1 to 20; and R’’’’ is C1-C6 alkyl, e.g., C1 alkyl, C2 alkyl, C3 alkyl
- n may be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19 or 20.
- the ⁇ v ⁇ 6 integrin targeting ligand is linked to the remainder of the 35 dsRNA agent as shown in the exemplary schematics below, wherein “2’-N6” refers to attachment of a lipophilic moiety (e.g., C22) at the 2’ position on the nucleotide at position 6 on the sense strand (counting from the 5’ end): 67 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- the in vivo delivery enhancing moiety that may be conjugated to the 15 dsRNA agent of the disclosure is represented by the following structure: , 20 , 69 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 5 wherein the broken bond represents the bond to the remainder of the dsRNA agent (e.g., to a 2’- 10 oxygen of a nucleoside).
- the in vivo delivery enhancing moiety may be attached to the remainder of the dsRNA agent at a 2’ position on an internal nucleotide.
- the at least one in vivo delivery enhancing moiety may be conjugated to the dsRNA agent via a direct attachment to the ribosugar of the dsRNA agent, e.g., an antisense strand or a sense strand.
- the at least one in vivo delivery enhancing moiety may be conjugated to the dsRNA agent via a linker or a carrier.
- at least one in vivo delivery enhancing moiety may be conjugated to the iRNA agent via one or more linkers (tethers).
- the at least one in vivo delivery enhancing moiety is conjugated to the20 dsRNA agent via a linker containing an ether, thioether, urea, carbonate, amine, amide, maleimide- thioether, disulfide, phosphodiester, sulfonamide linkage, a product of a click reaction (e.g., a triazole from the azide-alkyne cycloaddition), or carbamate.
- a linker containing an ether, thioether, urea, carbonate, amine, amide, maleimide- thioether, disulfide, phosphodiester, sulfonamide linkage, a product of a click reaction (e.g., a triazole from the azide-alkyne cycloaddition), or carbamate.
- the in vivo delivery enhancing moiety and the targeting moiety are independently present within: (a) an internally-modified nucleosides such as, 5 (b) a modified internucleotide linkage such as, -OP(Y)(X)O-, wherein Y is O or S (e.g., O), (c) a 5’-terminal modification such as 10 C(O), S(O) 2 , or -P(Y’)(OH)-O-; or (ii) -P(Y)(OH)O-R L or -C(O)N(H)R L , wherein Y is O or S; (d) a 3’-terminal modification such as -P(Y)(OH)-R 3 , wherein Y is O or S; and R 3 is 15 wherein: B is an optionally modified nucleobase; 71 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Aln
- ALN-529-WO B 1 is a nucleobase modified with a lipophilic moiety or a targeting moiety (e.g., a pyrimidine nucleobase modified at the 5-position);
- R L , R L1 , and R L2 are each a group containing a lipophilic moiety or a targeting moiety;
- R 2 ’ or R 3 ’ may be any functional group that is an acceptable 2’-modification for a ribose 5 sugar.
- R 2 ’ or R 3 ’groups include, but are not limited to, hydrogen, halogen (e.g., 2’-fluoro), hydroxy, 2’-O-alkyl (e.g., 2’-OMethyl), 2’-O-methoxyalkyl (e.g., 2’-O-methoxymethyl, 2’-O-methoxyethyl, or 2’-O-2-methoxypropanyl) modification, 2’-O-allyl modification, 2’-C-allyl modification, 2'-O-N-methylacetamido (2'-O-NMA, i.e.
- halogen e.g., 2’-fluoro
- hydroxy hydroxy
- 2’-O-alkyl e.g., 2’-OMethyl
- 2’-O-methoxyalkyl e.g., 2’-O-methoxymethyl, 2’-O-methoxyethyl, or 2
- R 2 ’ or R 3 ’ may be H, OH, F, OMe, O-methoxyalkyl, O-allyl, O-N-methylacetamido, O-dimethylaminoethoxyethyl, or O-aminopropyl.
- R L , R L1 , and R L2 are each a group containing a lipophilic moiety, such as a saturated or unsaturated C22-hydrocarbon chain.
- R L when R L comprises a lipophilic moiety, then R L can be selected from the group consisting of: 15 wherein integer m is 0-8 (e.g., 0; or 1-8; or 0-6; or 1; or 2; or 3; or 4; or 5; or 6; or 7; or 8); integer n is 1-21 (e.g., 1-12, 1-10, 1-8, 1-6, 1-4, or 1-2; or 2 or 3 or 4 or 5 or 6); W is C 1 -C 4 alkyl (e.g., methyl, ethyl, propyl, isopropyl, butyl, isobutyl, or t-butyl); R and R’ are each independently H or C 1 -C 4 alkyl (e.g., methyl, e
- ALN-529-WO the group consisting of halogen, -OR G , -SR G , -N(R G ) 2 , -C(O)OR G , -OC(O)R G , -C(O)N(R G ) 2 , - N(R G )C(O)R G , -N(R G )C(O)OR G , -N(R G )SO 2 (R G ), or -SO 2 N(R G ) 2 , wherein each R G is independently hydrogen or C 1- C 6 alkyl (for instance, G is optionally substituted with a -OR G , -C(O)OR G , or - N(R G )C(O)R G ); and 5 G 1 is a saturated or unsaturated C 22 hydrocarbon chain (for instance, G 1 may be a linear or branched C 22 alkyl group), wherein G 1 is optionally substituted with one or two groups selected from the group consist
- E xamples of RL include, but are not limited to the following structures: F urther examples of RL include, but are not limited to the following structures: , 73 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO ,
- R L1 can be selected from the group consisting of
- R L2 can be selected from the group consisting of the following 5 structures: 74 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- integer m is 0-8 (for instance, m is 0; or m is 1-8; or m is 0-6; or m is 1; or 2; or 3; or 4; or 5; or 6; or 7; or 8); integer n is 1-21 (for instance, 1-12, 1-10, 1-8, 1-6, 1-4, or 1-2; or 2 or 3 or 4 or 5 or 6); 5 R and R’ are each independently H or an alkyl group such as a C1-C4 alkyl (e.g., methyl, ethyl, propyl, isopropyl, t-butyl); G is G1 or a saturated or unsaturated C21 hydrocarbon chain (i.e., G together with the carbonyl to which it is attached may form a group with 22 carbons) (for instance, G may be a linear or branched C 21 alkyl group), wherein G is optionally substituted with one or two groups selected from10 the group consisting of hal
- B 1 is a nucleobase modified with a G or G 1 group, wherein G and G 1 are as defined above (e.g., a pyrimidine nucleobase modified at the 5’-position with a group c omprising G or G1).
- B1 include, but are not limited to, .
- in vivo delivery enhancing moiety is present within a modified nucleoside of the formula: wherein: B is an optionally modified nucleobase; 10 G 3 is a saturated or unsaturated C 1-20 hydrocarbon group (e.g., C 1-6 alkylene; C 2-6 alkylene; or hexylene); L K is a linking group such as -O-, -N(H)-, -S-, -S-S-, -C(O)O-, OC(O)-, -C(O)N(H)-, - N(H)C(O), -OC(O)N(H)-, -N(H)C(O)O-, -S(O) 2 -, -S(O) 2 O-, -S(O) 2 N(H)-, -P(O)(OH)O-, - OP(O)(OH)-, -P(S)(OH)O-, - OP(O)
- R G is hydrogen.
- R G is OH, 76 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
- R G is COOH.
- R G is CONH 2 .
- R G is amino.
- the monomers may also contain one or more asymmetric centers and thus occur as racemates and racemic mixtures, single enantiomers, 5 individual diastereomers and diastereomeric mixtures. All such isomeric forms of the monomers are expressly included.
- a modified internucleotide linkage is shown with substituent atoms fully described at the phosphorous atom, e.g., , where C’ is the 2’-carbon or 3’-carbon atom of a ribose ring, it is understood that the oxygen having the broken bond is the 5'-oxygen of the subsequent nucleotide.
- the in vivo delivery enhancing moiety is present within a modified n ucleoside of the formula: . In one embodiment, the in vivo delivery enhancing moiety is present within a modified n ucleoside of the formula: . In one embodiment, the in vivo delivery enhancing moiety is present within a modified 15 nucleoside of the formula: . In one embodiment, the in vivo delivery enhancing moiety is present within a modified n ucleoside of the formula: .
- the in vivo delivery enhancing moiety is present within a modified nucleoside of the formula: 20 1-10, 1-8, 1-6, 1-4, or 1-2, or 2 or 3 or 4 or 5 or 6);
- G is a C22 hydrocarbon chain, optionally substituted with one or two groups selected from the group consisting of halogen, -OR G , -SR G , - N(R G )2, -C(O)OR G , -OC(O)R G , -C(O)N(R G )2, -N(R G )C(O)R G , -N(R G )C(O)OR G , -N(R G )SO2(R G ), or - 77 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- each R G is independently hydrogen or C 1- C 6 alkyl; and nucleobase B is a modified or unmodified nucleobase.
- n is 1. In one embodiment, n is 2-6. In one embodiment, n is 6. In one embodiment, G is C 22 alkyl chain.
- the in vivo delivery enhancing moiety is present within a modified 5 nucleoside of the formula: , wherein n is an integer of 1-21, for instance, 1-12, 1- 10, 1-8, 1-6, 1-4, or 1-2, or 2 or 3 or 4 or 5 or 6); G is a C22 hydrocarbon chain, optionally substituted with one or two groups selected from the group consisting of halogen, -OR G , -SR G , -N(R G )2, - C(O)OR G , -OC(O)R G , -C(O)N(R G ) 2, -N(R G )C(O)R G , -N(R G )C(O)OR G , -N(R G )SO2(R G ), or - SO2N(R G )2, wherein each R G is independently hydrogen or C1-C6 alkyl; and nucleobase B is a 10 modified or unmodified nucleobase
- n is 1. In one embodiment, n is 2-6. In one embodiment, n is 6. In one embodiment, G is C22 alkyl chain.
- the in vivo delivery enhancing moiety is present within a modified n ucleoside of the formula: . In one embodiment, the in vivo delivery enhancing moiety is present within a modified 15 nucleoside of the formula: . In one embodiment, the in vivo delivery enhancing moiety is present within a modified n ucleoside of the formula: . In one embodiment, the in vivo delivery enhancing moiety is present within a modified .
- the in vivo delivery enhancing moiety is present within a modified internucleotide linkage of the form, -OP(Y)(X)O-, wherein Y is O or S (e.g., O), and X is -N(H)(R L1 ), wherein R L1 is -G 1 or S(O) 2 -G 1 , each as defined above, wherein the phosphorous atom in the internucleotide linkage is optionally enriched in the Sp or Rp isomer, or is racemic.
- 78 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- the in vivo delivery enhancing moiety is present within a modified internucleotide linkage of the form, -OP(O)(X)O-, wherein X is -N(H)(R L1 ), wherein R L1 is , wherein the phosphorous atom in the internucleotide linkage is optionally enriched in the Sp or Rp isomer, or is racemic.
- the in vivo delivery enhancing moiety is present within a a modified internucleotide linkage of the form, wherein the 3’-O is from the preceding nucleoside and the 5’-O is from the subsequent nucleoside, and wherein the phosphorous atom in the internucleotide linkage is optionally enriched in the Sp or Rp isomer, or is racemic.
- the preceding nucleotide contains a 2’-fluoro modification.
- the preceding nucleotide contains a 2’-O-methyl modification.
- the preceding nucleotide contains a 2’-H modification.
- the in vivo delivery enhancing moiety is present within a a modified internucleotide linkage of the form, wherein the 3’-O is from the preceding nucleoside and the 5’-O is from the subsequent nucleoside, and wherein the phosphorous 15 atom in the internucleotide linkage is optionally enriched in the Sp or Rp isomer, or is racemic.
- the preceding nucleotide contains a 2’-fluoro modification.
- the preceding nucleotide contains a 2’-O-methyl modification.
- the preceding nucleotide contains a 2’-H modification.
- the in vivo delivery enhancing moiety is present within a 20 a modified internucleotide linkage of the form, -OP(Y)(X)O-, whereinY is O or S and X is , wherein G 1 is defined above, such .
- in vivo delivery enhancing moiety is conjugated to the 3’-end or 5’- end of one of the sense and antisense strands via a direct bond or through a carrier or linker.
- in vivo delivery enhancing moiety is conjugated to the 3’-end of the sense or antisense 25 strand via a direct bond or through a carrier or linker.
- in vivo delivery enhancing moiety is conjugated to the 5’-end of the sense or antisense strand via a direct bond or through a carrier or linker.
- in vivo delivery enhancing moiety is conjugated to the 5’-end of one of t he sense and antisense strands and is of the formula: , or a salt thereof, wherein X is O or S (e.g., S); L is a divalent linking group (e.g., C1-20 alkyl or C1-10 alkyl-S-S-C1-10 alkyl).
- in vivo delivery enhancing moiety is conjugated to the 5’-end of one of the 5 sense and antisense strands and is of the formula , or a salt thereof, wherein X is O or S (e.g., S).
- R ligand is selected from the groups listed in Table R-1. Table R-1. An exemplary list of groups for R ligand 80 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- in vivo delivery enhancing moiety is bonded to the 5’-oxygen of the 5’- terminal nucleotide, and is of the formula 5 . In one embodiment, in vivo delivery enhancing moiety is bonded to the 5’-oxygen of the 5’- terminal nucleotide, and is of the formula -P(Y)(OH)-R 5 , wherein Y is O or S and R 5 is: .
- in vivo delivery enhancing moiety is bonded to the 3’-oxygen of the 3’- terminal nucleotide, and is of the formula -P(Y)(OH)-R 3 , wherein Y is O or S and R 3 is: 81 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- in vivo delivery enhancing moiety is conjugated to the 3’-end or 5’- end of one of the sense and antisense strands via a carrier or linker, and the carrier or linker is an inverted abasic nucleotide, such as an inverted abasic deoxyribonucleotide or an inverted abasic ribonucleotide, each connected to the remainder of the oligonucleotide via a phosphodiester (PO) or 5 phosphorothioate (PS) linkage.
- PO phosphodiester
- PS 5 phosphorothioate
- in vivo delivery enhancing moiety is bonded to the 5’-oxygen of the 5’-terminal nucleotide and is of the formula salt thereof, wherein each10 X is independently O or S (e.g., each is S); R ligand is selected from the groups listed in Table R-1; and L is a divalent linking group (e.g., C 1-20 alkyl or C 1-10 alkyl-S-S-C 1-10 alkyl).
- in vivo delivery enhancing moiety is bonded to the 5’-oxygen of the 5’-terminal nucleotide, and is of the formula salt thereof, wherein each X is independently O or S 15 (e.g., each is S) and R ligand is selected from the groups listed in Table R-1. In some embodiments, R ligand is selected from the groups listed in Table R-2.
- in vivo delivery enhancing moiety is bonded to the 5’-oxygen of the 5’-terminal nucleotide, and is of the formula 82 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- ALN-529-WO salt thereof wherein each X is independently O or S (e.g., e ach is S) and Rligand is selected from the groups listed in Table R-1, and L is a divalent linking group (e.g., C 1-20 alkyl or C 1-10 alkyl-S-S-C 1-10 alkyl.
- in vivo delivery enhancing moiety is bonded to the 5’-oxygen of the 5’- 5 terminal nucleotide, and is of the formula salt thereof, wherein each X is O or S (e.g., each is S) and R ligand is selected from the groups listed in Table R-1.
- R ligand is selected from the groups listed in Table R-2.
- R L , R L1 , and R L2 are each a group containing at least one targeting 10 moiety, such as an ⁇ v ⁇ 6 integrin targeting ligand described herein.
- the targeting moiety can be selected from:
- the broken bond is connected to a group of the formula, **-L-ZZ-L’- , wherein ** represents the bond to the targeting ligand.
- click adduct include those adducts formed by a copper(I)- catalyzed azide-alkyne cycloaddition reaction, a strain-promoted azide-alkyne cycloaddition, a strain- 15 promoted azide-trans-cycloalkene cycloaddition, and a thiol-maleimide Michael-addition reaction 84 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO including, for example, (i) an azide with a terminal alkyne or cycloalkyne (e.g.
- cyclooctyne BCN, or DBCO
- a tetrazine with a terminal alkyne or cycloalkyne e.g. cyclooctyne
- a thiol and maleimide with or without hydrolysis of the product.
- L and L’ are independently one of: 5 (a) -L1-[G-L2]q-G-L3-* wherein q is 0 or an integer selected from 1-10; (b) -L1-G-L2-G-L3-*; (c) -L1-G-L3-*; (d) -G-L3-*; (e) -L1-G-*; or 10 (f) -G-*.
- L 1 is selected from one of the following groups: (a) a bond, C(O), C(S), C(NR N ), S(O)2, P(O)(OH), or P(S)(OH), wherein and R N is hydrogen or C1-6alkyl; 15 (b) a bond, C(O), P(O)(OH), or P(S)(OH); (c) a bond; (d) C(O); (e) P(O)(OH); or (f) P(S)(OH); 20 each L 2 and L 3 is independently selected from one of the following groups: ( a) -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(RN)C(O)-, -OC(O)O-, -OC(O)N(RN)-, - N(R N )C(O)O-, -N(R N )
- each R group is independently selected from the group consisting of R’, C 1-6 alkyl, C 1- 6 haloalkyl, C 2-6 alkenyl, C 2-6 alkynyl, C 3-8 cycloalkyl, heterocyclyl, aryl, heteroaryl, C 3- 5 8 cycloalkylC 1-6 alkyl, heterocyclylC 1-6 alkyl, aryl C 1-6 alkyl, and heteroarylC 1-6 alkyl, each of which, other than R’, is optionally substituted with 1, 2, or 3 R’ groups, wherein each R’ is independently halogen, cyano, azido, nitro, -N(R b ) 2 , -O(R a ), -S(R 0 ), -C(O)OR 0 ,
- q is 0, 1, 2, 3, 4, or 5. In another embodiment of L or L’, q is 0, 1, 2, 3, or 4. In another embodiment of L or L’, q is 0, 1, 2, or 3. In another embodiment of L or L’, q is 0, 1, or 2. In another embodiment of L or L’, q is 1, 2, 3, 4, or 5, In another embodiment of L or L’, q is 1, 2, 3, or 4. In another embodiment of L or L’, q is 1, 2, or 3. In another embodiment of L or L’, q is 1 or 2. In another embodiment of L or L’, q is 4. In another embodiment of L or L’, q is 3. In 20 another embodiment of L or L’, q is 2.
- L is one of: ( a) , wherein k is an integer from 1 to 10; L1 is bond, C(O), C(S), C(NRN), S(O)2, P(O)(OH), or P(S)(OH) (e.g., L 1 is a bond, C(O), P(O)(OH), or P(S)(OH)); and R N is hydrogen or C 1-6 alkyl; 25 (b) , wherein k is an integer from 1 to 10; or an integer from 2 to 10; or an integer from 3 to 10; or an integer from 4 to 10; or an integer from 5 to 10; or an integer from 5 to 9; or an integer from 5 to 8; or an integer from 5 to 7; ( c) , wherein t is an integer from 0 to 10 (e.g., an integer from 1 to 5; or 1; or 2; or 3); 30 (d) , wherein t is an integer from 0 to 10 (e.g., an integer from 1 to 10 (e.
- ALN-529-WO 24 (e.g., an integer from 1 to 16; an integer from 1 to 10; an integer from 3 to 10; an integer from 3 to 7; or an integer from 4 to 6); ( e) wherein and s, s’, and s’’ are independently is an integer from 1 to 24 (e.g., an integer from 1 to 16, an integer from 1 to 10, 5 an integer from 3 to 10, an integer from 3 to 7, or an integer from 4 to 6); independently is an integer from 1 to 20 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6); and w is an integer from 1 to 20 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an 10 integer from 3 to 7 or an integer from 4 to 6); or and wherein in each of the preceding embodiments of L, * represents the bond to ZZ.
- * represents the bond to ZZ.
- L’ is one of: (a)*-G-L 1 -, wherein L 1 is a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); and G is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, each of which is optionally substituted with 1, 2, 3, or 4 R groups; 15 or L 1 is a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); and G is C1-10alkyl; (b)*-G-[L 2 -G]q-L 1 -, wherein L 1 is a bond, CH2, C(O), S(O)2, P(O)(OH), or P(S)(OH); each L 2 is independently -A-B-A-; each A is independently a bond, -O-, -S-, or -N(R N )-, wherein R
- each G is independently C 1-10 alkyl or C 2-10 alkenyl, each of which is optionally substituted with 1 or 2 R groups; (f) -[G-L 2 ] q -G-*, wherein each L 2 is independently C(O)(NR N ) , N(R N )C(O), OP(O)(OH)O, or OP(S)(OH)O wherein each R N is independently hydrogen or C 1-6 alkyl; and each G is 5 independently C 1-10 alkyl, each of which is optionally substituted with 1 or 2 R groups; (g) -C 2-30 alkyl-*, such as -C 5-20 alkyl-* or -C 10-20 alkyl-*; (h) -C 1-10 alkyl-*, optionally substituted with 1 or 2 R groups; (i) -C(O)-C 2-30 alkyl-*, such as -C(O)-C
- R L and R L1 that comprise a targeting ligand include, but are not limited to the following structures: 15 Additional examples of R L and R L1 that comprise a targeting ligand include, but are not l imited to the following structures: 88 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO Examples of R L2 that comprise a targeting ligand include, but are not limited to the following structures: A dditional examples of RL2 that comprise a targeting ligand include, but are not limited to the 5 following structures: 89 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- targeting moiety is bonded to the 3’-oxygen of the 3’-terminal nucleotide, and is of the formula -P(Y)(OH)-R 3 , wherein Y is O or S and R 3 is: .
- targeting moiety is bonded to the 5’-oxygen of the 5’-terminal nucleotide, and is of the formula -P(Y)(OH)-R 5 , wherein Y is O or S and R 5 is: 90 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO .
- R L , R L1 , and R L2 can comprise a branched linking group ( ⁇ ) capable 5 of supporting multiple targeting ligands (e.g., at least 2; or 2-8; or 2-6; or 2-4; or 2; or 3).
- the mutiple targeting moieties can be connected through an R L , R L1 , and R L2 of the form, (R X -L-ZZ-)z- ⁇ -T- , wherein each R X is a targeting moiety; z is at least 2; or 2-8; or 2-6; or 2-4; or 2; or 3, 10 T is -L’-T’-**, wherein ** is the bond to ⁇ , and T’ is O, S, N(H), C(O), S(O)2, C(O)N(H), N(H)C(O), OC(O), OC(O), -P(O)(OH)-, -P(S)(OH)-, -OP(O)(OH)-, -OP(S)(OH)-, -P(O)(OH)O-, - P(S)(OH)O-, -OP(O)(OH)O-, or -OP(S)(OH)
- T is selected from the following, wherein ** is the bond to ⁇ : ( a) -C(O)-X1-L5-X2-C(O)-**, wherein X1 and X2 are each independently C1-10alkyl; or C 2-10 alkyl; or C 4-10 alkyl; or C 6-10 alkyl; or C 2-8 alkyl; or C 2-6 alkyl; or C 2-4 alkyl; ( b) -C(O)-C2-20alkyl-C(O)-**, such as -C(O)-C2-12alkyl-C(O)-**, (c) -C(O)-C6-20alkyl-C(O)-**, such as -C(O)-C6-12alkyl-C(O)-**, 20 (d) -C(O)-C10alkyl-C(O)-** and (e) -C(O)-CH2CH2-C(O)-**
- T is selected from the following, ** is the bond to ⁇ : ( f) -N(H)C(O)-C2-20alkyl-C(O)-**, (g) - N(H)C(O)-C6-20alkyl-C(O)-**, such as - N(H)C(O)-C6-12alkyl-C(O)-**, 30 (h) - N(H)C(O)-C10alkyl-C(O)-**, (i) -C(O)-C2-20alkyl-C(O)N(H)-**, 91 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- T is selected from the following, ** is the bond to ⁇ : ( a) -N(H)C(O)-X3-ZZ-X4-C(O)-**, 10 (b) -C(O)-X3-ZZ-X4-C(O)N(H)-**, (c) N(H)C(O)-X3-ZZ- X4-C(O)N(H)-**, wherein X 3 and X4 are independently C2-12alkyl; or C4-10alkyl; or C6-10alkyl; or C4-8alkyl; and ZZ is as described above (such as -C(O)N(H)-, N(H)C(O)-, -OP(O)(OH)O-, -OP(S)(OH)O-, or a click adduct).
- T is selected from the following 15 (w) -L 6 -[G 5 -O]q5-G 5 -L 4 -**, wherein L 4 and L 6 are independently -A 1 -B 1 -A 1 -, wherein each A 1 is independently a bond, -O-, -S-, or -N(R N1 )-, wherein R N1 is hydrogen or C1-6alkyl; each B 1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); each G 5 is independently C1-10alkyl; (x) -C(O)-[CH2CH2-O]q5-G 5 -L 4 -**, L 4 is -A 1 -B 1 -A 1 -, wherein each A 1 is independently a 20 bond, -O-, -S-, or -N(R N1 )-, wherein R N1 is hydrogen or C1-6
- L 4 is -A 1 -B 1 or -B 1 -A 1 -, wherein each A 1 is independently -O- or -N(H)-, and each B 1 is independently C(O), G 5 is C1-10alkyl (e.g., C2- 10alkyl or C2-6alkyl); and 25 (z) -C(O)-[CH2CH2-O]q5- C2-10alkyl-C(O)N(H)-**; wherein in each of the preceding ** is the bond to ⁇ , and q5, when present, is an integer selected from 1 to 20 (e.g., 1 to 10, or 2 to 10; or 2 – 8; or 1; or 2; or 3; or 4.)
- Examples of branched linking group ( ⁇ ) include, but are not limited to, 92 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-240
- ALN-529-WO wherein the broken bond is the bond to L’.
- Examples of -T 1 - ⁇ - include, but are not limited to, , 5
- Examples of R L and R L1 that comprise a branched linker to a targeting ligand include, but are not limited to the following structures: 93 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
- E xamples of branched RL and RL1 include, but are not limited to, the following structures: 5 94 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- branched R L2 examples include, but are not limited to, the following structures: 5 .
- targeting moiety is bonded to the 3’-oxygen of the 3’-terminal nucleotide, and is of the formula -P(Y)(OH)-R 3 , wherein Y is O or S and R 3 is: , wherein , r is an integer 10 selected from 1 - 10 (e.g., r is 7); and each R is: .
- targeting moiety is bonded to the 3’-oxygen of the 3’-terminal nucleotide, and is of the formula -P(Y)(OH)-R 3 , wherein Y is O or S and R 3 is: 95 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO .
- targeting moiety is bonded to the 3’-oxygen of the 3’-terminal nucleotide, and is of the formula -P(Y)(OH)-R 3 , wherein Y is O or S and R 3 is: .
- targeting moiety is bonded to the 5’-oxygen of the 5’-terminal nucleotide, and is of the formula -P(Y)(OH)-R 5 , wherein Y is O or S and R 5 is: selected from 1 - 10 (e.g., r is 7); and each R is: , wherein R X is a targeting ligand. 10
- targeting moiety is bonded to the 5’-oxygen of the 5’-terminal nucleotide, and is of the formula -P(Y)(OH)-R 5 , wherein Y is O or S and R 5 is: ligand.
- each R X is an integrin-receptor targeting ligand such as, .
- the dsRNA agent comprises a double-stranded region formed between the sense and antisense strands and optionally one or two single-stranded non-loop overhang, and 5 wherein the one or more lipophilic moieties are conjugated to either the double-stranded region or the non-loop overhang.
- the dsRNA agent does not contain a loop (e.g., stem loop) region.
- the dsRNA agent contains a loop (e.g., stem loop) region, and the one or more lipophilic moieties are not conjugated to the loop (e.g., stem loop) region.
- the dsRNA agent comprises a sense strand of 10 to 53 nucleotides in 10 length, in which the sense strand forms a duplex region with the antisense strand.
- the sense strand may be 10 to 49, 12 to 49, 12 to 45, 12 to 42, 12 to 40, 15 to 49, 15 to 45, 15 to 42, 15 to 40, 15 to 38, or 15 to 36 nucleotides in length.
- the duplex region is at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 nucleotides in length. In some embodiments, the region of complementarity to the target sequence is at least 19 contiguous 15 nucleotides in length.
- the sense strand comprises at its 3′-end a stem-loop set forth as: S1-L- S2, in which S1 is complementary to S2, and in which L forms a loop between S1 and S2.
- the first 17 to 25 nucleotides counting from 5’ end of the sense strand forms a duplex region with the antisense strand, and the last 11 to 28 counting from 5’ end of the 20 sense strand forms a 3′-end a stem-loop set forth as: S1-L-S2.
- the length of the stem loop S1-L-S2 is 11 to 28, 13 to 26, or 15 to 24 nucleotides in length.
- the stem loop S1-L-S2 is 16 nucleotides in length.
- the stem loop S1-L-S2 comprises a sequence of 5’-GCAGCCGAAAGGCUGC-3’ (SEQ ID NO: 47).
- L is at least 3, 4, or 5 nucleotides in length. In some embodiments, L comprises a sequence of GAAA. In some embodiments, the sense strand is 36 nucleotides in length, the first 20 nucleotide counting from 5’ end of the sense strand forms a duplex region with the antisense strand, and the last 16 nucleotides forms a stem loop S1-L-S2. In one embodiment, the 16-nucleotide stem loop S1-L-S2 30 has the sequence of 5’-GCAGCCGAAAGGCUGC-3’ (SEQ ID NO: 161), wherein L is GAAA.
- the one or more lipophilic moieties are conjugated to a non-terminal position of the sense strand. In some embodiments, the one or more lipophilic moieties are conjugated to one or more nucleotides of the stem loop S 1 -L-S 2 . In some embodiments, the one or more lipophilic moieties are 5 conjugated to one or more nucleotides of the loop L. In some embodiments, S 1 and S 2 are complementary and contain 4-10 nucleotides, e.g., S 1 and S 2 each contain 6 complementary nucleotides.
- S 1 and S 2 are complementary and contain 4-10 nucleotides and L is GAAA, e.g., S 1 and S 2 each contain 6 complementary nucleotides and L is GAAA.
- the one or more lipophilic moieties containing one or more saturated or unsaturated C 22 hydrocarbon chains are conjugated to one or more internal positions on at least one strand of the dsRNA agent. Dual Conjugation 15
- in vivo delivery enhancing moiety is connected in series with a t argeting moiety, e.g., ⁇ v ⁇ 6 integrin targeting ligand, as described herein.
- a sense or antisense strand can contain a series modification at the 3’-end or 5’-end of the oligonucleotide, 20 . such that one of L1 and L2 comprises the in vivo delivery enhancing moiety and the other comprises t he targeting moiety, e.g., ⁇ v ⁇ 6 integrin targeting ligand as described herein.
- the series modification is of the form, wherein Q is s elected from wherein RL2 is according to any preceding 25 embodiment, wherein one of the broken bonds connects to a 5’-oxygen of a nucleoside or a 3’-oxygen of a nucleoside and the other connects to a 5’-terminal or 3’-terminal modification as described herein.
- 98 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- a sense or antisense strand can contain a series modification of the form, wherein RL2 is according to any preceding embodiment, each Y is independently O or S; one of the broken bonds connects to a 5’-oxygen of a nucleoside or a 3’-oxygen of a nucleoside and the other connects any of 5 the 5’-terminal modifications described above or 3’-terminal modifications described above.
- a sense or antisense strand can contain a series modification of the form, the broken bond connects to the 5’-oxygen of a 5’-terminal nucleoside; each Y is independently O or S; 10 one of R 51 and R 52 comprises a lipophilic group (e.g., an in vivo delivery enhancing moiety) and the other comprises a second ligand moiety (e.g., a targeting moiety, such as a ⁇ v ⁇ 6 integrin targeting ligand as described herein).
- a lipophilic group e.g., an in vivo delivery enhancing moiety
- a second ligand moiety e.g., a targeting moiety, such as a ⁇ v ⁇ 6 integrin targeting ligand as described herein.
- a sense or antisense strand can contain a series modification of the 15 the broken bond connects to the 5’-oxygen of a 5’-terminal nucleoside; each Y is independently O or S; one of R 51 and R 52 comprises a lipophilic group (e.g., an in vivo delivery enhancing moiety, such as any of R L or R L2 above) and the other comprises a second ligand moiety (e.g., a targeting moiety).
- an oligonucleotide may have a series modification at the 5’-end of the formula: 99 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- a sense or antisense strand can contain a series modification of the 5 form, wherein the broken bond connects to the 3’-oxygen of a 3’-terminal nucleoside; each Y is independently O or S; one of R 31 and R 32 comprises a lipophilic group (e.g., an in vivo delivery enhancing moiety, such as any of R L2 above) and the other comprises a second ligand moiety (e.g., a targeting ligand).
- a lipophilic group e.g., an in vivo delivery enhancing moiety, such as any of R L2 above
- a second ligand moiety e.g., a targeting ligand
- an oligonucleotide may have a series modification at the 3’-end of the formula: 100 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO , wherein each Y is independently O or S. 5
- a sense or antisense strand can contain two different ligand modifications, one at the 3'-end of the strand and the other at the 5'-end of the strand: such that one of L1 and L2 comprises the in vivo delivery enhancing moiety and the other comprises t he targeting moiety, such as a ⁇ v ⁇ 6 integrin targeting ligand as described herein.
- a sense or antisense strand can contain two different ligand modifications, one is an internal modified nuceloside or modified internucleotide linkage of the strand and the other at the 3’-end or 5'-end of the strand: 15 such that one of L1 and L2 comprises the in vivo delivery enhancing moiety and the other comprises t he targeting moiety, such as a ⁇ v ⁇ 6 integrin targeting ligand as described herein.
- the modified 101 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- ALN-529-WO nucleoside represented by L1 can be located at a position in the strand selected from positions 2 to n- 1 , where the strand contains n nucleotides (e.g., n-1 is 20 when n is 21). For example, when L1 is at position 6, then segment (1) of the strand contains 5 nucleotides and segment (2) contains the remainder of the nucleotides within the strand.
- L1 comprises the in vivo delivery enhancing moiety and a sense or antisense strand can be represented by one of: 10 wherein B is an optionally modified nucleobase (e.g., A, C, G, U, or T); R L or R L1 comprises the in vivo delivery enhancing moiety, L2 comprises the targeting moiety.
- B is an optionally modified nucleobase (e.g., A, C, G, U, or T)
- R L or R L1 comprises the in vivo delivery enhancing moiety
- L2 comprises the targeting moiety.
- R L is selected from the group consisting of: In one embodiment, R L1 is selected from the group consisting of: and 15 . 1 .
- Linkers/Tethers are connected to the at least one in vivo delivery enhancing moiety at a “tethering attachment point (TAP).”
- TAP tethering attachment point
- Linkers/Tethers may include any C1-C100 carbon-containing 20 moiety, (e.g. C1-C75, C1-C50, C1-C20, C1-C10; C1, C2, C3, C4, C5, C6, C7, C8, C9, or C10), and may have at 102 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- the nitrogen atom forms part of a terminal amino or amido (NHC(O)-) group on the linker/tether, which may serve as a connection point for the lipophilic moiety.
- Non-limited examples of linkers/tethers include TAP-(CH2)nNH-; TAP- C(O)(CH2)nNH-; TAP-NR’’’’(CH2)nNH-, TAP-C(O)-(CH2)n-C(O)-; TAP-C(O)-(CH2)n-C(O)O-; TAP- 5 C(O)-O-; TAP-C(O)-(CH2)n-NH-C(O)-; T TAP-C(O)-NH-; TAP-C(O)-; TAP- (CH2)n-C(O)-; TAP-(CH2)n-C(O)O-; TAP- CH2)n-NH-C(O)-; in which n is 1-20 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20) and R’’’’ is C1-C6 alkyl.
- n is 1-20 (e.g., 1, 2,
- n is 5, 6, or 11.
- the nitrogen may form part of a terminal oxyamino group, e.g., -ONH2, or hydrazino group, -NHNH2.
- the linker/tether may optionally be substituted, 10 e.g., with hydroxy, alkoxy, perhaloalkyl, and/or optionally inserted with one or more additional heteroatoms, e.g., N, O, or S.
- Preferred tethered ligands may include, e.g., TAP- (CH2)nNH(LIGAND); TAP-C(O)(CH2)nNH(LIGAND); TAP-NR’’’’(CH2)nNH(LIGAND); TAP- (CH2)nONH(LIGAND); TAP-C(O)(CH2)nONH(LIGAND); TAP-NR’’’’(CH2)nONH(LIGAND); TAP-(CH2)nNHNH2(LIGAND), TAP-C(O)(CH2)nNHNH2(LIGAND); TAP- 15 NR’’’(CH2)nNHNH2(LIGAND); TAP-C(O)-(CH2)n-C(O)(LIGAND); TAP-C(O)-(CH2)n- C(O)O(LIGAND); TAP-C(O)-O(LIGAND); TAP-C(O)-(CH2)n-NH-C(O)(L
- amino terminated linkers/tethers e.g., NH2, ONH2, NH2NH2
- the 25 tether may optionally be substituted, e.g., with hydroxy, alkoxy, perhaloalkyl, and/or optionally inserted with one or more additional heteroatoms, e.g., N, O, or S.
- the double bond can be cis or trans or E or Z.
- the linker/tether may include an electrophilic moiety, preferably at the terminal position of the linker/tether.
- Exemplary electrophilic moieties include, e.g., an aldehyde, 30 alkyl halide, mesylate, tosylate, nosylate, or brosylate, or an activated carboxylic acid ester, e.g. an NHS ester, or a pentafluorophenyl ester.
- Preferred linkers/tethers include TAP- (CH2)nCHO; TAP-C(O)(CH2)nCHO; or TAP-NR’’’’(CH2)nCHO, in which n is 1-6 and R’’’’ is C1-C6 alkyl; or TAP-(CH2)nC(O)ONHS; TAP-C(O)(CH2) nC(O)ONHS; or TAP-NR’’’(CH2) nC(O)ONHS, in which n is 1-6 and R’’’’’ is C1-C6 alkyl; TAP-(CH2)nC(O)OC6F5; TAP-C(O)(CH2) nC(O) OC6F5; or 35 TAP-NR’’’’(CH2) nC(O) OC6F5, in which n is 1-11 and R’’’’ is C1-C6 alkyl; or -(CH2)nCH2LG; TAP- C(O)
- Alnylam Reference No. ALN-529-WO Tethering can be carried out by coupling a nucleophilic group of a ligand, e.g., a thiol or amino group with an electrophilic group on the tether.
- a nucleophilic group of a ligand e.g., a thiol or amino group
- an electrophilic group on the tether it can be desirable for the monomer to include a phthalimido group (K) a t the terminal position of the l .
- linker/tether e.g., alloc, monomethoxy trityl (MMT), trifluoroacetyl, Fmoc, or aryl sulfonyl (e.g., the aryl portion can be ortho-nitrophenyl or ortho, para-dinitrophenyl).
- At least one of the linkers/tethers can be a redox cleavable linker, an acid cleavable linker, an esterase cleavable linker, a phosphatase cleavable linker, or a peptidase cleavable linker.
- at least one of the linkers/tethers can be a reductively cleavable linker (e.g., a disulfide group).
- At least one of the linkers/tethers can be an acid cleavable linker (e.g., a hydrazone group, an ester group, an acetal group, or a ketal group). In one embodiment, at least one of the linkers/tethers can be an esterase cleavable linker (e.g., 20 an ester group). In one embodiment, at least one of the linkers/tethers can be a phosphatase cleavable linker (e.g., a phosphate group). In one embodiment, at least one of the linkers/tethers can be a peptidase cleavable linker (e.g., a peptide bond).
- 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.
- degradative agents include: redox agents which are selected for particular substrates or which have no substrate specificity, including, e.g., oxidative or reductive enzymes or reductive agents such as mercaptans, present in 30 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 35 human serum is 7.4, while the average intracellular pH is slightly lower, ranging from about 7.1-7.3.
- 104 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 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 tethers will have a linkage group that is cleaved at a preferred pH, thereby releasing the iRNA agent from a ligand (e.g., a targeting or cell-permeable ligand, such as cholesterol) inside the cell, or into the desired compartment of the cell.
- a ligand e.g., a targeting or cell-permeable ligand, such as cholesterol
- a chemical junction that links a ligand to an iRNA agent can include a disulfide bond.
- a disulfide bond When the iRNA agent/ligand complex is taken up into the cell by endocytosis, the acidic environment of the endosome will cause the disulfide bond to be cleaved, thereby releasing the iRNA agent from the ligand (Quintana et al., Pharm Res.19:1310-1316, 2002; Patri et al., Curr. Opin. Curr. Biol.6:466-471, 2002).
- the ligand can be a targeting ligand or a second therapeutic agent that 10 may complement the therapeutic effects of the iRNA agent.
- a tether can include a linking group that is cleavable by a particular enzyme.
- the type of linking group incorporated into a tether can depend on the cell to be targeted by the iRNA agent. Tethers that contain peptide bonds can be conjugated to iRNA agents target to cell types rich in peptidases. 15
- 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, e.g., tissue the iRNA agent would be exposed to when administered to a subject.
- the evaluations can be carried out in cell free systems, in cells, in cell culture, in organ or tissue culture, or in whole animals. It may be useful to make initial evaluations in cell-free or culture conditions and to confirm by further evaluations in whole animals.
- 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 30 One class of cleavable linking groups are redox cleavable linking groups that are cleaved upon reduction or oxidation. An example of reductively cleavable linking group is a disulphide linking group (—S—S—).
- a candidate cleavable linking group is a suitable “reductively cleavable linking group,” or for example is suitable for use with a particular iRNA moiety and particular in vivo delivery enhancing moiety, one can look to methods described herein. 35
- 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.
- DTT dithiothreitol
- the candidates can also be evaluated under conditions which are selected to mimic blood or serum conditions.
- candidate compounds are cleaved by at 105 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO most 10% in the blood.
- 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 determined using standard enzyme 5 kinetics assays under conditions chosen to mimic intracellular media and compared to conditions chosen to mimic extracellular media. 4 .
- Phosphate-Based Cleavable Linking Groups are cleaved by agents that degrade or hydrolyze the 10 phosphate group.
- agents that degrade or hydrolyze the 10 phosphate group are enzymes such as phosphatases in cells.
- phosphate-based linking groups are —O—P(O)(ORk)-O—, — O—P(S)(ORk)-O—, —O—P(S)(SRk)-O—, —S—P(O)(ORk)-O—, —O—P(O)(ORk)-S—, —S— P(O)(ORk)-S—, —O—P(S)(ORk)-S—, —S—P(S)(ORk)-O—, —O—P(O)(Rk)-O—, —O— P(S)(Rk)-O—, —S—P(O)(Rk)-O—, —S—P(O)(Rk)-O—, —S—P(O)(Rk)-O—, —S—P(O)(Rk)-O—, —S—P(O)(Rk)-S—, —O—P(
- Preferred embodiments are —O—P(O)(OH)—O—, —O—P(S)(OH)—O—, —O—P(S)(SH)—O—, —S—P(O)(OH)—O—, —O—P(O)(OH)—S—, —S—P(O)(OH)—S—, —O—P(S)(OH)—S—, — S—P(S)(OH)—O—, —O—P(O)(H)—O—, —O—P(S)(H)—O—, —S—P(O)(H)—O—, —S— P(S)(H)—O—, —S—P(O)(H)—S—, —O—P(H)—S—.
- Acid cleavable linking groups are linking groups that are cleaved under acidic conditions.
- acid cleavable linking groups are cleaved in an acidic environment with a pH 25 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.
- specific low pH organelles such as endosomes and lysosomes can provide a cleaving environment for acid cleavable linking groups.
- acid cleavable linking groups include but are not limited to hydrazones, ketals, acetals, esters, and esters of amino acids.
- Acid cleavable groups can have the general formula —C ⁇ NN—, C(O)O, or —OC(O).
- a preferred 30 embodiment is when the carbon attached to the oxygen of the ester (the alkoxy group) is an aryl group, substituted 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. 6 .
- Ester-Based Linking Groups 35 Ester-based linking groups are cleaved by enzymes such as esterases and amidases in cells.
- ester-based cleavable linking groups include but are not limited to esters of alkylene, alkenylene and alkynylene groups.
- Ester cleavable linking groups have the general formula — 106 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO C(O)O—, or —OC(O)—. These candidates can be evaluated using methods analogous to those described above. 7 .
- Peptide-Based Cleaving Groups 5 Peptide-based 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., dipeptides, 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 10 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 peptides and proteins and does not include the entire amide functional group.
- Peptide cleavable linking groups have the general formula —NHCHR 1 C(O)NHCHR 2 C(O)—, where R 1 and R 2 are the R groups of the two adjacent amino acids. These candidates can be evaluated using methods analogous to those described above. 15 8.
- Biocleavable linkers/tethers The linkers can also include biocleavable linkers that are nucleotide and non-nucleotide linkers or combinations thereof that connect two parts of a molecule.
- the non-nucleotide linkers include tethers or linkers derived from monosaccharides, disaccharides, oligosaccharides, and 20 derivatives thereof, aliphatic, alicyclic, hetercyclic, and combinations thereof.
- At least one of the linkers is a bio-clevable linker selected from the group consisting of DNA, RNA, disulfide, amide, functionalized monosaccharides or oligosaccharides of galactosamine, glucosamine, glucose, galactose, and mannose, and combinations thereof.
- the bio-cleavable carbohydrate linker may have 1 to 10 saccharide units, which have at least one anomeric linkage capable of connecting two siRNA units. When two or more saccharides are present, these units can be linked via 1-3, 1-4, or 1-6 sugar linkages, or via alkyl chains.
- Exemplary bio-cleavable linkers include: 107 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 5 108 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 109 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO . 5 More discussion about the biocleavable linkers may be found in WO2018136620, entitled “Endosomal Cleavable Linkers,” the entire contents of which are incorporated herein by reference. 9.
- the at least one in vivo delivery enhancing moiety is conjugated to 10 the dsRNA agent via a carrier that replaces one or more nucleotide(s).
- the carrier can be a cyclic group or an acyclic group.
- the cyclic group is selected from the group consisting of pyrrolidinyl, pyrazolinyl, pyrazolidinyl, imidazolinyl, imidazolidinyl, piperidinyl, piperazinyl, [1,3]dioxolane, oxazolidinyl, isoxazolidinyl, morpholinyl, thiazolidinyl, isothiazolidinyl, quinoxalinyl, pyridazinonyl, tetrahydrofuryl, and decalin.
- the acyclic group is a moiety based on a serinol backbone or a diethanolamine backbone.
- the carrier replaces one or more nucleotide(s) in the internal position(s) of the dsRNA agent. In other embodiments, the carrier replaces the nucleotides at the terminal end of the sense 20 strand or antisense strand. In one embodiment, the carrier replaces the terminal nucleotide on the 3’ end of the sense strand, thereby functioning as an end cap protecting the 3’ end of the sense strand. In one embodiment, the carrier is a cyclic group having an amine, for instance, the carrier may be 110 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- a ribonucleotide subunit in which the ribose sugar of the subunit has been so replaced is 5 referred to herein as a ribose replacement modification subunit (RRMS).
- the carrier can be a cyclic or acyclic moiety and include two “backbone attachment points” (e.g., hydroxyl groups) and a ligand (e.g., the lipophilic moiety).
- the one or more C22 hydrocarbon chains can be directly attached to the carrier or indirectly attached to the carrier by an intervening linker/tether, as described above.
- the ligand-conjugated monomer subunit may be the 5’ or 3’ terminal subunit of the iRNA molecule, i.e., one of the two “W” groups may be a hydroxyl group, and the other “W” group may be a chain of two or more unmodified or modified ribonucleotides.
- the ligand-conjugated monomer subunit may occupy an internal position, and both “W” groups may be one or more unmodified or modified ribonucleotides. More than one ligand-conjugated monomer subunit may be 15 present in an iRNA agent.
- Cyclic sugar replacement-based monomers e.g., sugar replacement-based ligand-conjugated monomers
- the carriers may have the 20 general formula (LCM-2) provided below (in that structure preferred backbone attachment points can be chosen from R 1 or R 2 ; R 3 or R 4 ; or R 9 and R 10 if Y is CR 9 R 10 (two positions are chosen to give two backbone attachment points, e.g., R 1 and R 4 , or R 4 and R 9 )).
- Preferred tethering attachment points include R 7 ; R 5 or R 6 when X is CH 2 .
- the carriers are described below as an entity, which can be incorporated into a strand.
- the structures also encompass the situations 25 wherein one (in the case of a terminal position) or two (in the case of an internal position) of the attachment points, e.g., R 1 or R 2 ; R 3 or R 4 ; or R 9 or R 10 (when Y is CR 9 R 10 ), is connected to the phosphate, or modified phosphate, e.g., sulfur containing, backbone.
- one of the above-named R groups can be -CH 2 -, wherein one bond is connected to the carrier and one to a backbone atom, e.g., a linking oxygen or a central phosphorus atom.
- 111 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- X is N(CO)R 7 , NR 7 or CH 2 ; 5 Y is NR 8 , O, S, CR 9 R 10 ; Z is CR 11 R 12 or absent;
- R 1 , R 2 , R 3 , R 4 , R 9 , and R 10 is, independently, H, OR a , or (CH 2 ) n OR b , provided that at least two of R 1 , R 2 , R 3 , R 4 , R 9 , and R 10 are OR a and/or (CH 2 ) n OR b ;
- Each of R 5 , R 6 , R 11 , and R 12 is, independently, a ligand, H, C 1 -C 6 alkyl optionally substituted 10 with 1-3 R 13 , or C(O)NHR 7 ; or R 5 and R 11 together are C 3 -C 8 cycloalkyl optionally substituted with R 14 ;
- R 7 can be a
- R b is P(O)(O-)H, P(OR 15 )N(R 16 ) 2 or L-R 17 ; 25 R c is H or C 1 -C 6 alkyl; R d is H or a ligand; Each Ar is, independently, C 6 -C 10 aryl optionally substituted with C 1 -C 4 alkoxy; n is 1-4; and q is 0-4.
- the carrier may be based on the pyrroline ring system or the 4- 35 hydroxyproline ring system, e.g., X is N(CO)R 7 or NR 7 , Y is CR 9 R 10 , and Z is absent (D).
- OFG 1 is preferably attached to a primary carbon, e.g., an exocyclic alkylene group, e.g., a methylene group, connected to one of the carbons in the five-membered ring (- CH2OFG 1 in D).
- OFG 2 is preferably attached directly to one of the carbons in the five-membered ring (-OFG 2 in D).
- -CH2OFG 1 may be attached to C-2 and OFG 2 may be 5 attached to C-3; or -CH2OFG 1 may be attached to C-3 and OFG 2 may be attached to C-4.
- CH2OFG 1 and OFG 2 may be geminally substituted to one of the above-referenced carbons.
- -CH2OFG 1 may be attached to C-2 and OFG 2 may be attached to C-4.
- the pyrroline- and 4-hydroxyproline-based monomers may therefore contain linkages (e.g., carbon-carbon bonds) wherein bond rotation is restricted about that particular linkage,10 e.g. restriction resulting from the presence of a ring.
- linkages e.g., carbon-carbon bonds
- CH2OFG 1 and OFG 2 may be cis or trans with respect to one another in any of the pairings delineated above Accordingly, all cis/trans isomers are expressly included.
- the monomers may also contain one or more asymmetric centers and thus occur as racemates and racemic mixtures, single enantiomers, individual diastereomers and diastereomeric mixtures.
- the 15 centers bearing CH2OFG 1 and OFG 2 can both have the R configuration; or both have the S configuration; or one center can have the R configuration and the other center can have the S configuration and vice versa).
- the tethering attachment point is preferably nitrogen.
- Preferred examples of carrier D include the following: 20 . 113 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO I n certain embodiments, the carrier may be based on the piperidine ring system (E), e.g., X is .
- OFG 2 is preferably attached directly to one of the carbons in the six- membered ring (-OFG 2 in E).
- -(CH2)nOFG 1 and OFG 2 may be disposed in a geminal manner on the ring, i.e., both groups may be attached to the same carbon, e.g., at C-2, C-3, or C-4.
- - (CH2)nOFG 1 and OFG 2 may be disposed in a vicinal manner on the ring, i.e., both groups may be 10 attached to adjacent ring carbon atoms, e.g., -(CH2)nOFG 1 may be attached to C-2 and OFG 2 may be attached to C-3; -(CH2)nOFG 1 may be attached to C-3 and OFG 2 may be attached to C-2; - (CH2)nOFG 1 may be attached to C-3 and OFG 2 may be attached to C-4; or -(CH2)nOFG 1 may be attached to C-4 and OFG 2 may be attached to C-3.
- the piperidine-based monomers may therefore contain linkages (e.g., carbon-carbon bonds) wherein bond rotation is restricted about that particular 15 linkage, e.g. restriction resulting from the presence of a ring.
- linkages e.g., carbon-carbon bonds
- -(CH2)nOFG 1 and OFG 2 may be cis or trans with respect to one another in any of the pairings delineated above. Accordingly, all cis/trans isomers are expressly included.
- the monomers may also contain one or more asymmetric centers and thus occur as racemates and racemic mixtures, single enantiomers, individual diastereomers and diastereomeric mixtures.
- the carriers may be based on the piperazine ring system (F), e.g., X is r the morpholine ring system (G), e.g., X is N(CO)R7 25 .
- OFG 1 is preferably attached to a primary carbon, e.g., an exocyclic alkylene group, e.g., a methylene group, connected to one of the carbons in the six-membered ring (-CH 2 OFG 1 in F or G).
- OFG 2 is preferably attached directly to one of the carbons in the six-membered rings (-OFG 2 in F or 114 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO G).
- -CH2OFG 1 may be attached to C-2 and OFG 2 may be attached to C-3; or vice versa.
- CH2OFG 1 and OFG 2 may be geminally substituted to one of the above-referenced carbons.
- the piperazine- and morpholine-based monomers may therefore contain linkages (e.g., carbon-carbon bonds) wherein bond rotation is restricted about that particular linkage, 5 e.g. restriction resulting from the presence of a ring.
- linkages e.g., carbon-carbon bonds
- CH2OFG 1 and OFG 2 may be cis or trans with respect to one another in any of the pairings delineated above. Accordingly, all cis/trans isomers are expressly included.
- the monomers may also contain one or more asymmetric centers and thus occur as racemates and racemic mixtures, single enantiomers, individual diastereomers and diastereomeric mixtures.
- R can be, e.g., C1-C6 alkyl, preferably CH3.
- the tethering attachment point is preferably nitrogen in both F and G.
- OFG 2 is preferably attached directly to one of C-2, C-3, C-4, or C-5 (-OFG 2 in H).
- -(CH2)nOFG 1 and OFG 2 may be disposed in a geminal manner on the ring, i.e., both groups may be attached to the same carbon, e.g., at C-2, C-3, C-4, or C-5.
- -(CH2)nOFG 1 and OFG 2 may be disposed in a vicinal manner on the ring, i.e., both groups may be attached to adjacent ring carbon atoms, e.g., - 25 (CH2)nOFG 1 may be attached to C-2 and OFG 2 may be attached to C-3; -(CH2)nOFG 1 may be attached to C-3 and OFG 2 may be attached to C-2; -(CH2)nOFG 1 may be attached to C-3 and OFG 2 may be attached to C-4; or -(CH2)nOFG 1 may be attached to C-4 and OFG 2 may be attached to C-3; - (CH2)nOFG 1 may be attached to C-4 and OFG 2 may be attached to C-5; or -(CH2)nOFG 1 may be attached to C-5 and OFG 2 may be attached to C-4.
- the decalin or indane-based monomers may 30 therefore contain linkages (e.g., carbon-carbon bonds) wherein bond rotation is restricted about that particular linkage, e.g. restriction resulting from the presence of a ring.
- linkages e.g., carbon-carbon bonds
- -(CH2)nOFG 1 and OFG 2 may be cis or trans with respect to one another in any of the pairings delineated above. Accordingly, all cis/trans isomers are expressly included.
- the monomers may also contain one or more asymmetric centers and thus occur as racemates and racemic mixtures, single enantiomers, individual 35 diastereomers and diastereomeric mixtures.
- the monomers may also contain one or more asymmetric centers and thus occur as racemates and racemic mixtures, single enantiomers, individual 10 diastereomers and diastereomeric mixtures. All such isomeric forms of the monomers are expressly included (e.g., the centers bearing CH2OFG 1 and OFG 2 can both have the R configuration; or both have the S configuration; or one center can have the R configuration and the other center can have the S configuration and vice versa).
- the tethering attachment point is preferably nitrogen. Details about more representative cyclic, sugar replacement-based carriers can be found in 15 U.S.
- Acyclic sugar replacement-based monomers e.g., sugar replacement-based ligand-conjugated 20 monomers, are also referred to herein as ribose replacement monomer subunit (RRMS) monomer compounds.
- Preferred acyclic carriers can have formula LCM-3 or LCM-4: .
- each of x, y, and z can be, independently of one another, 0, 1, 2, or 3.
- I n formula LCM-3, when y and z are different, then the tertiary carbon can have either the R or S 25 configuration.
- x is zero and y and z are each 1 in formula LCM-3 (e.g., based on serinol), and y and z are each 1 in formula LCM-3.
- formula LCM-3 or LCM-4 below can optionally be substituted, e.g., with hydroxy, alkoxy, perhaloalkyl. Details about more representative acyclic, sugar replacement-based carriers can be found in U.S. Patent Nos.7,745,608 and 8,017,762, which are herein incorporated by reference in their 30 entireties. 116 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- the at least one in vivo delivery enhancing moiety may be conjugated to one or more internal positions on at least one strand, e.g., a sense strand or an antisense strand.
- Internal positions of a strand refers to the nucleotide on any position of the strand, except the terminal position from the 3’ end and 5’ end of the strand (e.g., excluding 2 positions: position 1 counting from the 3’ end and 5 position 1 counting from the 5’ end).
- the at least one in vivo delivery enhancing moiety may be conjugated to one or more internal positions on at least one strand, which include all positions except the terminal two positions from each end of the strand (e.g., excluding 4 positions: positions 1 and 2 counting from the 3’ end and positions 1 and 2 counting from the 5’ end).
- the at least one in 10 vivo delivery enhancing moiety is conjugated to one or more internal positions on at least one strand, which include all positions except the terminal three positions from each end of the strand (e.g., excluding 6 positions: positions 1, 2, and 3 counting from the 3’ end and positions 1, 2, and 3 counting from the 5’ end).
- the at least one in vivo delivery enhancing moiety may be conjugated to 15 one or more internal positions on at least one strand, except the cleavage site region of the sense strand, for instance, the at least one in vivo delivery enhancing moiety is not conjugated to positions 9- 12 counting from the 5’-end of the sense strand, for example, the at least one in vivo delivery enhancing moiety is not conjugated to positions 9-11 counting from the 5’-end of the sense strand.
- the internal positions exclude positions 11-13 counting from the 3’-end of the sense 20 strand.
- the at least one in vivo delivery enhancing moiety may be conjugated to one or more internal positions on at least one strand, which exclude the cleavage site region of the antisense strand. For instance, the internal positions exclude positions 12-14 counting from the 5’-end of the antisense strand. 25 In one embodiment, the at least one in vivo delivery enhancing moiety may be conjugated to one or more internal positions on at least one strand, which exclude positions 11-13 on the sense strand, counting from the 3’-end, and positions 12-14 on the antisense strand, counting from the 5’- end.
- the at least one in vivo delivery enhancing moiety may be conjugated to 30 one or more of the following internal positions: positions 4-8 and 13-18 on the sense strand, and positions 6-10 and 15-18 on the antisense strand, counting from the 5’end of each strand. In one embodiment, the at least one in vivo delivery enhancing moiety may be conjugated to one or more of the following internal positions: positions 5, 6, 7, 15, and 17 on the sense strand, and positions 15 and 17 on the antisense strand, counting from the 5’end of each strand. 35 In one embodiment, the at least one in vivo delivery enhancing moiety may be conjugated to position 6 on the sense strand, counting from the 5’end of each strand.
- the at least one in vivo delivery enhancing moiety may be conjugated to a nucleobase, sugar moiety, or internucleosidic phosphate linkage of the dsRNA agent.
- the at least one in vivo delivery enhancing moiety is conjugated to a sugar moiety of the dsRNA agent.
- the at least one in vivo delivery enhancing moiety is conjugated to the 2’ position of a ribose sugar of the dsRNA agent. 5 V.
- a dsRNA agent comprises an antisense strand and a sense strand; at least one ⁇ v ⁇ 6 integrin targeting ligand that mediates delivery to muscle tissue conjugated to at least one strand; and at least one in vivo delivery enhancing moiety conjugated to at 10 least one strand.
- S are described in U.S.
- Integrins are cell surface receptors that, upon ligand binding, activate signal transduction pathways including signaling pathways involved in cytoskeleton organization and cell cycle 20 regulation. Integrins are also involved in cell attachment to the extracellular matrix and the integrin ligands comprise common extracellular matrix components, including fibronectin, collagen, laminin, fibrinogen, thrombospondin, and glycoproteins (e.g., tenascin C, osteopontin, and nefronectin). In humans there are at least twenty-four known integrin heterodimers composed of an alpha and a beta subunit, e.g., ⁇ v ⁇ 6.
- ⁇ v ⁇ 6 cytokine transforming growth factor-b1
- LAP pro-peptide latency associated 30 peptide
- TGF- ⁇ 1 regulates multiple processes including cell proliferation, differentiation, angiogenesis, epithelial-mesenchymal- transition (EMT) and immune suppression. These processes combine to heal wounds but when uncontrolled can promote tissue pathologies.
- the present disclosure provides dual conjugated dsRNA agents for inhibiting expression of a 35 DMPK gene that comprise an antisense strand and a sense strand; at least one ⁇ v ⁇ 6 integrin targeting ligand that mediates delivery to muscle tissue conjugated to at least one strand; and at least one in vivo delivery enhancing moiety conjugated to at least one strand.
- 118 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO A .
- the dsRNA agent of the present disclosure is conjugated to at least one ⁇ v ⁇ 6 integrin targeting ligand.
- the at least one ⁇ v ⁇ 6 integrin targeting ligand may be conjugated to the dsRNA agent via a direct attachment to the dsRNA agent, e.g., a ribosugar of the dsRNA agent.
- the at least one ⁇ v ⁇ 6 integrin targeting ligand may be conjugated to the dsRNA agent via a linker or a carrier as described herein.
- Exemplary ⁇ v ⁇ 6 integrin targeting ligands that can conjugated to the dsRNA agents of the disclosure can be found, e.g., in U.S. Patent Nos 10,023,568, 10,450,312, 10,144,733, 10,487,080, 105,13,517, and 10,000,489, as well as in International Patent Application No. PCT/US2023/083947, 10 filed on December 14, 2023, the entire contents of each of which are incorporated herein by reference.
- Exemplary ⁇ v ⁇ 6 integrin targeting ligands are also described in WO2024/086633, incorporated herein by reference.
- the ⁇ v ⁇ 6 integrin targeting ligand may be conjugated to the dsRNA agent via a linker comprising a compound of the structure 15 L333 N-(aminocaproyl-DBCO)-4-hydroxyprolinol, wherein * represents the bond to the remainder of the dsRNA agent.
- the ⁇ v ⁇ 6 integrin targeting ligand comprises the structure: 20 119 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 5 bond from R Lig to the nitrogen, # is the bond to the integrin ligand, and * represents the bond to the remainder of the dsRNA agent.
- the ⁇ v ⁇ 6 integrin targeting ligand comprises the structure: 10 wherein R Lig is 120 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO bond to the remainder of the dsRNA agent. In one embodiment, the ⁇ v ⁇ 6 integrin targeting ligand comprises the structure: 1 121 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO bond from R Lig to the nitrogen, # is the bond to the integrin ligand, and * represents the bond to the 5 remainder of the dsRNA agent.
- the ⁇ v ⁇ 6 integrin targeting ligand comprises the structure: 10 122 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 5 bond from R Lig to the nitrogen, # is the bond to the integrin ligand, and * represents the bond to the remainder of the dsRNA agent.
- the ⁇ v ⁇ 6 integrin targeting ligand comprises the structure: 10 wherein R Lig is 123 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO bond to the remainder of the dsRNA agent.
- the ⁇ v ⁇ 6 integrin targeting ligand comprises the structure: , 5 wherein * represents the bond to the remainder of the dsRNA agent. In one embodiment, the ⁇ v ⁇ 6 integrin targeting ligand comprises the structure: , wherein * represents the bond to the remainder of the dsRNA agent. 10 In one embodiment, the ⁇ v ⁇ 6 integrin targeting ligand comprises the structure: , wherein * represents the bond to the remainder of the dsRNA agent. In one embodiment, the ⁇ v ⁇ 6 integrin targeting ligand comprises the structure: 124 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- the ⁇ v ⁇ 6 integrin targeting ligand comprises the structure: 5 , wherein * represents the bond to the remainder of the dsRNA agent. In one embodiment, the ⁇ v ⁇ 6 integrin targeting ligand comprises the structure: , wherein * represents the bond to the remainder of the dsRNA agent. 10 In some embodiments, the ⁇ v ⁇ 6 integrin targeting ligand or the ⁇ v ⁇ 6 integrin targeting ligand to the dsRNA agent of the present disclosure comprises a structure selected from the table below: 125 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- ALN-529-WO 126 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein Z1 is a linker linking the ⁇ v ⁇ 6 integrin targeting ligand to the remainder of the dsRNA agent and wherein * represents the bond to the remainder of the dsRNA agent.
- Z1 is a linker linking the ⁇ v ⁇ 6 integrin targeting ligand to the remainder of the dsRNA agent and wherein * represents the bond to the remainder of the dsRNA agent.
- 127 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO B .
- the alpha-v-beta-6 ( ⁇ v ⁇ 6) integrin targeting ligand may be conjugated to the dsRNA agent of the disclosure, e.g., to at least one strand of the dsRNA agent of the disclosure, 5 via a carrier group.
- the alpha-v-beta-6 ( ⁇ v ⁇ 6) integrin targeting ligand conjugated to the dsRNA agent of the disclosure is represented by a compound of the Formula (X): or a salt thereof, wherein: 10 r CH2; (e.g., O or CH2) , wherein m is 0, 1, 2, 3, or 4; and each R2 is independently R, or two R2 groups on adjacent carbon atoms taken together with the atoms to which they are bound form a fused 4 – 8 membered ring (e.g,.
- A is an 5-membered heteroaryl optionally substituted with 1 or 2 substituents independently selected from methyl, ethyl, fluoro, hydroxymethyl, 2-hydroxypropan-2-yl, trifluoromethyl, difluoromethyl, and fluoromethyl;
- 20 Q is -COOR1 or tetrazolyl (e.g., 1,2,3,4-tetrazol-5-yl), wherein R1 is hydrogen or C1-6alkyl (e.g., methyl) ; and R L is -N(R 3 )(R 4 ), -O(R 5 ), -S(R 5 ), or -R 5 , wherein R 3 and R 4 are either 25 (i) R3 is hydrogen or C1-6alkyl and R4 is R5; or (ii) R3 and R4 taken together with the nitrogen
- ALN-529-WO q is 0 or an integer selected from 1 – 25; (e.g., 1-20, or 1-15);
- L 1 is a bond or -B-A-;
- each L 2 is independently -A-B-A-;
- L 3 is a bond or -A-B-A-;
- 5 each G is independently -D-E-F-, wherein D, E, and F are independently a bond, C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups;
- each A is independently a bond, -O-, -S-, or -N(R N )-;
- each B is independently a bond, CH2, C(O), C(S), C(NR N ), S(O), S(O)2, P(O)(
- each -D-E-F- group at least one of D, E, and F is not a bond; and R L is not N-morpholinyl.
- R 3 and R 4 do not form a morpholino ring. 5
- B is only a bond when one of the A groups is not a bond.
- each R group is independently selected from the group consisting of R’, C 1-6 alkyl, C 1-6 haloalkyl, C 2-6 alkenyl, C 2-6 alkynyl, C 3-8 cycloalkyl, heterocyclyl, aryl, heteroaryl, C 3- 8 cycloalkylC 1-6 alkyl, heterocyclylC 1-6 alkyl, aryl C 1-6 alkyl and heteroaryl 1-6 alkyl, each of which, other 10 than R’, is optionally substituted with 1, 2, or 3 R’ groups, wherein each R’ is independently halogen, cyano, azido, nitro, -N(R b ) 2 , -O(R a ), -S(R 0 ), -C(O)OR 0 , -C(O)R 0 , -C(O)N(R 0 ) 2 , -N(R 0 )C(O)R 0 ,
- each R group is independently selected from the group consisting of R’, C 1-6 alkyl, C 1-6 haloalkyl, C 2-6 alkenyl, C 2-6 alkynyl, C 3-6 cycloalkyl, 5-6 membered heterocyclyl, phenyl, 5-6 membered heteroaryl, and benzyl, each of which, other than R’, is optionally substituted with 1, 2, or 3 R’ groups, wherein each R’ is independently halogen, cyano, azido, nitro, -N(R b )2, - O(R a ), -S(R 0 ), -C(O)OR 0 , -C(O)R 0 , -C(O)N(R 0 )2, -N(R 0 )C(O)R 0 , -OC(O)OR 0 , or -OC(O)R 0 ,20 wherein each R 0 is independently hydrogen
- each R group is independently selected from the group consisting of R’, C1-6alkyl, C3-6cycloalkyl, 5-6 membered heterocyclyl, phenyl, 5-6 membered heteroaryl, and benzyl, each of which, other than R’, is optionally substituted with 1, 2, or 3 R’ groups, wherein each25 R’ is independently halogen, cyano, azido, nitro, -N(R b )2, -O(R a ), -S(R 0 ), -C(O)OR 0 , - C(O)R 0 , -C(O)N(R 0 )2, -N(R 0 )C(O)R 0 , -OC(O)OR 0 , or -OC(O)R 0 , wherein each R 0 is independently hydrogen or C1-6alkyl; each R a is independently hydrogen or C1-6alkyl; and each R b is independently hydrogen, C
- the compound of formula ( 30 In certain embodiments, the compound of formula ( 130 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In certain embodiments, the compound of formula ( In certain embodiments, the compound of formula ( 5 A.
- Formula (X) is selected from an optionally substituted N- or a C- linked pyrazole, an optionally substituted N- or a C-linked triazole, and an optionally substituted N- or C-linked imidazole, wherein the optionally substituted N- or a C-linked pyrazole, the optionally substituted N- or a C-linked triazole, and the optionally substituted N- or C-linked imidazole is 10 optionally substituted by 1 or 2 substituents independently selected from methyl, ethyl, fluoro, hydroxymethyl, 2-hydroxypropan-2-yl, trifluoromethyl, difluoromethyl, and fluoromethyl.
- R1 is hydrogen, methyl, or ethyl
- R2 is hydrogen or fluoro
- R3 is hydrogen, methyl, or ethyl.
- R1 is hydrogen, methyl, or ethyl
- R2 is hydrogen or fluoro
- R3 is hydrogen, methyl, or ethyl.
- Formulae (X) In some embodiments of any one of Formula (X), in R Y , each R 2 is independently R as defined in Formula (X). 5
- R Y is (or its tautomer, ). In some embodiments, .
- R Y two R 2 groups on adjacent carbon atoms taken together with the atoms 10 to which they are bound form a fused 4 – 8 membered ring that is optionally substituted with 1, 2, 3 or 4 groups independently selected from group consisting of R and a nitrogen protecting group, wherein R is as defined in Formula (IV).
- R is as defined in Formula (IV).
- 15 4; and each R 21 is independently selected from group consisting of R and a nitrogen protecting group, wherein R is as defined in Formula (IV).
- R Y is , wherein p is 0, 1, 2, 3 or 4; and each R 21 is independently selected from the group consisting of R and a nitrogen protecting group, wherein R is as defined in Formula (IV).
- R P is , wherein r is 0, 1, 2, or 3; each R P2 is independently halogen, nitro, cyano, C 1- 4 alkoxy, C 1-4 alkyl, C 1-4 haloalkyl; and each R P3 is independently hydrogen, methyl, or ethyl.
- R P is methoxyacetyl (mac), phenoxyacetyl (pac), 2- 5 chlorophenoxyacetyl, 3-chlorophenoxyacetyl, 4-chlorophenoxyacetyl, 2,4-dichlorophenoxyacetyl, 2- methylphenoxyacetyl, 3-methylphenoxyacetyl, 4-methylphenoxyacetyl, 4-chloro-2- methylphenoxyacetyl, 2-nitrophenoxyacetyl, 3-nitrophenoxyacetyl, 4-nitrophenoxyacetyl, 2- isopropylphenoxyacetyl, 3-isopropylphenoxyacetyl, 4-isopropylphenoxyacetyl, 2-(t- butyl)phenoxyacetyl, 3-(t-butyl)phenoxyacetyl, 4-(t-butyl)phenoxyacetyl, 2-fluorophenoxyacetyl, 3-10 fluorophenoxyacetyl,
- R P is methoxyacetyl (mac), phenoxyacetyl (pac), 2- chlorophenoxyacetyl, 4-chlorophenoxyacetyl, 2-methylphenoxyacetyl, 4-methylphenoxyacetyl, or 4- 15 isopropylphenoxyacetyl.
- R P is methoxyacetyl (mac).
- R P is phenoxyacetyl (pac).
- R 1 is C1-6alkyl , wherein 20 r is 0, 1, 2, or 3; each R P2 is independently halogen, nitro, cyano, C1-4alkoxy, C1-4alkyl, C1-4haloalkyl; and each R P3 is independently hydrogen, methyl, or ethyl.
- R 1 is C1-6alkyl and R P is methoxyacetyl (mac), phenoxyacetyl (pac), 2-chlorophenoxyacetyl, 3-chlorophenoxyacetyl, 4-chlorophenoxyacetyl, 2,4-dichlorophenoxyacetyl, 2-methylphenoxyacetyl, 3-methylphenoxyacetyl, 4-methylphenoxyacetyl, 25 4-chloro-2-methylphenoxyacetyl, 2-nitrophenoxyacetyl, 3-nitrophenoxyacetyl, 4-nitrophenoxyacetyl, 2-isopropylphenoxyacetyl, 3-isopropylphenoxyacetyl, 4-isopropylphenoxyacetyl, 2-(t- butyl)phenoxyacetyl, 3-(t-butyl)phenoxyacetyl, 4-(t-butyl)phenoxyacetyl, 2-fluorophenoxyacetyl,
- R 1 is C 1-6 alkyl and R P is methoxyacetyl (mac), phenoxyacetyl (pac), 2-chlorophenoxyacetyl, 4-chlorophenoxyacetyl, 2-methylphenoxyacetyl, 4- methylphenoxyacetyl, or 4-isopropylphenoxyacetyl.
- R 1 is C 1-6 alkyl and R P is methoxyacetyl (mac).
- R 1 when present, R 1 is C 1-6 alkyl and R P is phenoxyacetyl (pac). In some embodiments, when present, R 1 is methyl , wherein r is 0, 1, 2, or 3; each R P2 is independently halogen, nitro, cyano, C 1-4 alkoxy, C 1-4 alkyl, C 1-4 haloalkyl; and each R P3 is independently hydrogen, methyl, or ethyl.
- R 1 is methyl and R P is methoxyacetyl (mac),10 phenoxyacetyl (pac), 2-chlorophenoxyacetyl, 3-chlorophenoxyacetyl, 4-chlorophenoxyacetyl, 2,4- dichlorophenoxyacetyl, 2-methylphenoxyacetyl, 3-methylphenoxyacetyl, 4-methylphenoxyacetyl, 4- chloro-2-methylphenoxyacetyl, 2-nitrophenoxyacetyl, 3-nitrophenoxyacetyl, 4-nitrophenoxyacetyl, 2- isopropylphenoxyacetyl, 3-isopropylphenoxyacetyl, 4-isopropylphenoxyacetyl, 2-(t- butyl)phenoxyacetyl, 3-(t-butyl)phenoxyacetyl, 4-(t-butyl)phenoxyacetyl, 2-fluorophenoxyacetyl, 3-15 fluorophenoxyacet
- R 1 when present, R 1 is methyl and R P is methoxyacetyl (mac), phenoxyacetyl (pac), 2-chlorophenoxyacetyl, 4-chlorophenoxyacetyl, 2-methylphenoxyacetyl, 4- 20 methylphenoxyacetyl, or 4-isopropylphenoxyacetyl.
- R 1 when present, R 1 is methyl and R P is methoxyacetyl (mac). In some embodiments, when present, R 1 is methyl and R P is phenoxyacetyl (pac).
- R 1 is hydrogen , wherein r is 0, 1, 2, or 3; each R P2 is independently halogen, nitro, cyano, C1-4alkoxy, C1-4alkyl, C1-4haloalkyl; and 25 each R P3 is independently hydrogen, methyl, or ethyl.
- R 1 is hydrogen and R P is methoxyacetyl (mac), phenoxyacetyl (pac), 2-chlorophenoxyacetyl, 3-chlorophenoxyacetyl, 4-chlorophenoxyacetyl, 2,4- dichlorophenoxyacetyl, 2-methylphenoxyacetyl, 3-methylphenoxyacetyl, 4-methylphenoxyacetyl, 4- chloro-2-methylphenoxyacetyl, 2-nitrophenoxyacetyl, 3-nitrophenoxyacetyl, 4-nitrophenoxyacetyl, 2-30 isopropylphenoxyacetyl, 3-isopropylphenoxyacetyl, 4-isopropylphenoxyacetyl, 2-(t- butyl)phenoxyacetyl, 3-(t-butyl)phenoxyacetyl, 4-(t-butyl)phenoxyacetyl, 2-fluorophenoxyacetyl, 3- 135 ME1 ⁇ 53453057
- R 1 when present, R 1 is hydrogen and R P is methoxyacetyl (mac), 5 phenoxyacetyl (pac), 2-chlorophenoxyacetyl, 4-chlorophenoxyacetyl, 2-methylphenoxyacetyl, 4- methylphenoxyacetyl, or 4-isopropylphenoxyacetyl.
- R 1 when present, R 1 is hydrogen and R P is methoxyacetyl (mac).
- R 1 when present, R 1 is hydrogen and R P is phenoxyacetyl (pac). 10 R T Embodiments, Formula (X) In some embodiments of Formula (X), R T is R T1 .
- R T is -G 0 -OR T1 , wherein R T1 is as defined for Formula (X) and G 0 is selected from: ( a) G0 is absent or -D0-E0-F0-, wherein D0, E0, and F0 are independently a bond, C1- 15 10 alkyl, C 2-10 alkenyl, C 2-10 alkynyl, C 3-10 cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups; ( b) G0 is -D0-E0-F0-, wherein D 0 and F 0 are independently a bond or C 1-10 alkyl optionally substituted with 1, 2, 3, or 4 R groups; and 20 E 0 is C 3-10 cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups; ( a) G0 is absent or
- R groups e.g., 1 or 2 R groups
- G0 is C1-10alkyl or C2-10alkenyl, each of which is optionally substituted with 1 or 2 R groups
- h G0 is C1-10alkyl optionally substituted with 1 or 2 R groups
- 10 (i) G0 is C1-10alkyl, optionally substituted with -O(Ra), wherein Ra is independently hydrogen or C1-6alkyl
- j G0 is C1-10alkyl
- G0 is absent (a bond); wherein * represents the bond to L’, the broken bond represents the bond to OR T1 , and R is - 15 C1-6alkyl-OR a or -OR a , wherein R a is independently hydrogen or C1-6alkyl.
- Formula (X) I n some embodiments of Formula (X), -L’- is *-G-L1-, wherein * is the bond to ZZ; and (a) L1 is a bond or -B-A-, wherein 20 A is a bond, -O-, -S-, or -N(R N )-; B is a bond, CH2, C(O), C(S), C(NR N ), S(O), S(O)2, P(O)(OH), P(S)(OH), or P(S)(SH); each R N is independently hydrogen or C1-6alkyl; and G is -D-E-F-, wherein D, E, and F are independently a bond, C1-10alkyl, C2-10alkenyl, C2- 10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is 25 optionally substituted with 1, 2, 3, or
- ALN-529-WO G is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups;
- ( c) L1 is a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); and G is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, each of which is optionally substituted with 1, 2, 3, 5 or 4 R groups;
- ( d) L1 is a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); and
- G is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, each of which is optionally substituted with 1, 2, 3, or 4 R groups; or 10 (e
- -L’- is *-G-[L2-G]q-L1-, wherein * is the bond to ZZ; q, is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 (e.g., an integer selected from 1 to 8, an integer selected from 1 to 5, or an integer from 1 to 3); and ( a) L1 is a bond or -B-A-; 15 each L 2 is independently -A-B-A-; each A is independently a bond, -O-, -S-, or -N(R N )-; each B is independently a bond, CH2, C(O), C(S), C(NR N ), S(O), S(O)2, P(O)(OH), P(S)(OH), or P(S)(SH); each R N is independently hydrogen or C1-6alkyl; 20 each G is independently -D-E-F-, wherein D, E, and F are independently a bond, C1-10alkyl, C2-10alkeny
- ( c) L1 is a bond, CH2, C(O), C(S), C(NRN), S(O), S(O)2, P(O)(OH), P(S)(OH), or P(S)(SH); each L 2 is independently -A-B-A-; each A is independently a bond, -O-, -S-, or -N(R N )-, wherein R N is hydrogen or C1-6alkyl 35 each B is independently a bond, CH2, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); each G is independently C1-10alkyl, optionally substituted with 1, 2, 3, or 4 R groups ( d) L1 is a bond, CH2, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH) each L 2 is independently -A-B-A-; 138 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Aln
- each A is independently a bond, -O-, -S-, or -N(R N )-, wherein R N is hydrogen or C1-6alkyl each B is independently a bond, CH2, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); each G is independently C1-10alkyl, optionally substituted with 1, 2, 3, or 4 R groups; or 5 (e) L1 is a bond, CH2, C(O), S(O)2, P(O)(OH), or P(S)(OH); each L 2 is independently -A-B-A-; each A is independently a bond, -O-, -S-, or -N(R N )-, wherein R N is hydrogen or C1-6alkyl each B is independently a bond, CH2, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); each G is independently C1-10alkyl; 10 In some embodiment
- each L 2 is independently OP(O)(OH)O, or OP(S)(OH)O (e.g., each is OP(O)(OH)O); each G is independently C1-10alkyl, each of which is optionally substituted with 1 or 2 R groups; or 5 (vii) q is 0, 1, 2, or 3 (e.g., q is 0, 1, or 2; or 0 or 1; or 0; or 1; or 2); each L 2 is a bond; each G is independently C1-10alkyl, each of which is optionally substituted with 1 or 2 R groups.
- -L’- is *-L 3 -G-L 1 -, wherein * is the bond to ZZ; and ( a) L1 and L3 are independently -A-B-A-; 10 each G is independently C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, or 3 R groups; each A is independently a bond, -O-, -S-, or -N(R N )-, wherein R N is hydrogen or C1-6alkyl; and each B is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); 15 (b) L3 is -C(O)O- or C(O)N(RN)-, wherein RN is hydrogen or C1-6alkyl; L 1 is -OP(O)
- -L’- is *-G-, wherein * is the bond to ZZ; and G is C1-10alkyl is optionally substituted with 1 or 2 R groups.
- -L’- is --L 1 -[G-L 2 ]q-G-L 3 -*, wherein * is the bond to ZZ;
- -L’- is -L 1 -G-L 3 -*, wherein * is the bond to ZZ;
- 35 In some embodiments, -L’- is -L 1 -[G-L 2 ]q-G-L 3 -*, wherein * is the bond to ZZ; q is 0, 1, 2, 3, 4, or 5; 140 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- ALN-529-WO L 1 is a bond or -B-A-; each L 2 is independently -A-B-A-; L 3 is a bond or -A-B-A-; each A is independently a bond, -O-, -S-, or -N(R N )-; 5 each B is independently a bond, CH2, C(O), C(S), C(NR N ), S(O), S(O)2, P(O)(OH), P(S)(OH), or P(S)(SH); each R N is independently hydrogen or C1-6alkyl; and each G is independently C1-10alkyl, C2-10alkenyl, C2-10alkynyl, each of which is optionally substituted with 1, 2, 3, or 4 R groups.
- -L’- is -L 1 -[G-L 2 ]q-G-*, wherein * is the bond to ZZ; q is 0, 1, 2, or 3; L 1 is a bond or -B-A-; each L 2 is independently a bond, C(O)O, OC(O), C(O)(NR N ), N(R N )C(O), SO2N(R N ), N(R N )SO2, OP(O)(OH), OP(S)(OH), P(O)(OH)O, P(S)(OH)O, OP(O)(OH)O, or OP(S)(OH)O, wherein 15 each R N is independently hydrogen or C1-6alkyl; and each G is independently C1-10alkyl, C2-10alkenyl, C2-10alkynyl, each of which is optionally substituted with 1 or 2 R groups.
- -L’- is -L 1 -[G-L 2 ]q-G-*, wherein * is the bond to ZZ; q is 0, 1, 2, or 3; 20 L 1 is a bond or -B-A-; each L 2 is independently a bond, C(O)O, OC(O), C(O)(NR N ), N(R N )C(O), OP(O)(OH)O, or OP(S)(OH)O, wherein each R N is independently hydrogen or C1-6alkyl; each G is independently C1-10alkyl or C2-10alkenyl, each of which is optionally substituted with 1 or 2 R groups.
- -L’- is -[G-L 2 ]q-G-*, wherein * is the bond to ZZ; and ( a) q is 0, 1, 2, or 3 (e.g., q is 0, 1, or 2; or 0 or 1; or 0; or 1; or 2); each L 2 is independently C(O)O or OC(O); each G is independently C1-10alkyl, each of which is optionally substituted with 1 or 2 R groups; ( b) q is 0, 1, 2, or 3 (e.g., q is 0, 1, or 2; or 0 or 1; or 0; or 1; or 2); 30 each L 2 is independently C(O)(NR N ) or N(R N )C(O), wherein each R N is independently hydrogen or C1-6alkyl; and each G is independently C1-10alkyl, each of which is optionally substituted with 1 or 2 R groups; ( c) q is 0, 1, 2, or 3 (e.g., q is 0, 1,
- each L 2 is a bond; and each G is independently C1-10alkyl, each of which is optionally substituted with 1 or 2 R groups.
- -L’- is -C2-30alkyl-*, wherein * is the bond to ZZ, such as -C5- 20alkyl-* or -C10-20alkyl-*.
- -L’- is -C(O)-C2-30alkyl-*, wherein * is the bond to ZZ, such as -C(O)- C5-20alkyl-* or -C(O)-C10-20alkyl-*.
- L’-R T Embodiments In some embodiments, - , wherein 10 * is the bond to ZZ; L 1 is a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); and R T1 is as defined for Formula (X). In some embod 15 wherein * is the bond to ZZ; L 1 is a bond, C(O), C(S), S(O) 2 , P(O)(OH), or P(S)(OH); and R T1 is as defined for Formula (X).
- L 1 is a bond, C(O), C(S), S(O) 2 , P(O)(OH), or P(S)(OH); R is -OH or -C 1-6 alkyl-OH; and R T1 is as defined for Formula (X).
- * is the bond to ZZ; L 1 is a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); 142 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- ALN-529-WO R is -OH or -C1-6alkyl-OH; and R T1 is as defined for Formula (X).
- each L 2 is ( i) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(R N )C(O)-, -OC(O)O-, -OC(O)N(R N )-, -N(R N )C(O)O-, -N(R N )C(O)N(R N )-, -OP(O)(OH)O- ,- OP(S)(OH)O-, -O-, and -N(R N )-, wherein each R N is independently hydrogen or C 1-6 alkyl; or ( ii) independently selected from the group consisting of -C(O)O-, -
- -L’-R T is 143 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein * is the bond to ZZ; 5 q is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 (e.g., an integer from 1 to 8, an integer from 1 to 5, or an integer from 1 to 3); each L 2 is ( i) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(R N )C(O)-, -OC(O)O-, -OC(O)N(R N )-, -N(R N )C(O)O-, -N(R N )C(O)N(R N )-, -OP(O)(OH)O- ,- 10 OP(S)(OH)O-, -O-, and -N(R
- -L’-R T is , , or , wherein * is the bond to ZZ; 30 q is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 (e.g., an integer from 1 to 8, an integer from 1 to 5, or an integer from 1 to 3); each L 2 is 144 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- ALN-529-WO ( i) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(R N )C(O)-, -OC(O)O-, -OC(O)N(R N )-, -N(R N )C(O)O-, -N(R N )C(O)N(R N )-, -OP(O)(OH)O- ,- OP(S)(OH)O-, -O-, and -N(R N )-, wherein each R N is independently hydrogen or C1-6alkyl; or ( ii) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, 5 -N(R N )C(O)-, -OC(O)N(R N )-, -N(R N
- each L 2 is ( i) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(R N )C(O)-, -OC(O)O-, -OC(O)N(R N )-, -N(R N )C(O)O-, -N(R N )C(O)N(R N )-, -OP(O)(OH)O- ,- 25 OP(S)(OH)O-, -O-, and -N(R N )-, wherein each R N is independently hydrogen or C 1-6 alkyl; or ( ii) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(R N )C(O)-, -OC(O)O-, -OC(O)N(R N )-
- ALN-529-WO ( vi) independently selected from the group consisting of -C(O)N(RN)- and -N(RN)C(O), wherein each R N is independently hydrogen or C1-6alkyl; L 1 is a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); R is -OH or -C1-6alkyl-OH; and R T1 is as defined for Formula (X).
- each L 2 is ( i) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(R N )C(O)-, -OC(O)O-, -OC(O)N(R N )-, -N(R N )C(O)O-, -N(R N )C(O)N(R N )-, -OP(O)(OH)O- ,- OP(S)(OH)O-, -O-, and -N(R N )-, wherein each R N is independently hydrogen or C1-6alkyl; or 15 (ii) independently selected from the group consisting of -C(O)O-,
- -L’-R T is 146 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein* is the bond to ZZ; q is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 (e.g., an integer from 1 to 8, an integer from 1 to 5, or an integer from 1 to 3); 5 each L 2 is ( i) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(R N )C(O)-, -OC(O)O-, -OC(O)N(R N )-, -N(R N )C(O)O-, -N(R N )C(O)N(R N )-, -OP(O)(OH)O- ,- OP(S)(OH)O-, -O-, and -N(R
- each L 2 is ( i) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(R N )C(O)-, -OC(O)O-, -OC(O)N(R N )-, -N(R N )C(O)O-, -N(R N )C(O)N(R N )-, -OP(O)(OH)O- ,- OP(S)(OH)O-, -O-, and -N(R N )-, wherein each R N is independently hydrogen or C1-6alkyl; or 5 (ii) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(R N )C(O)-, -OC(O)N(R N )-, -N(R N )-,
- R is -O(R a ) or -C 1-6 alkyl-O(R a ), wherein R a is hydrogen; and 25 R T1 is as defined for Formula (X).
- R L Embodiments, Formula (X)
- R L is -N(R 3 )(R 4 ), -O(R 5 ), -S(R 5 ), or -R 5 , wherein R 5 is according to one Formulae (x-a) through (x-ab): ( x-a) (x-b) 148 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 149 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- R P3 is hydrogen and L, ZZ, L’ and R T1 are as defined for Formula (X) or any embodiment herein.
- R L is according to one of Formulae (xi-a) through (xi-m): 150 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO (xi-k) (xi-l) 151 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein R P3 is hydrogen, and L, ZZ, L’ and R T1 are as defined for Formula (X) or any embodiment herein.
- R L is according to one of Formulae (xi-n) through (xi-z): (xi-w) (xi-x) (xi-y) 152 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO (xi-z) wherein R P3 is hydrogen, and L, ZZ, L’ and R T1 are as defined for Formula (X) or any embodiment herein.
- R L is -N(R 3 )(R 4 ), wherein R 3 is hydrogen or C1-6alkyl and R 4 is R 5 .
- R L is -N(R 3 )(R 4 ), wherein R 3 is hydrogen and R 4 is R 5 . 5 In some embodiments, R L is -N(R 3 )(R 4 ), wherein R 3 is C1-3alkyl and R 4 is R 5 . In some embodiments, R L is -N(R 3 )(R 4 ), wherein R 3 is methyl and R 4 is R 5 . In some embodiments, R L is --N(R 3 )(R 4 ), wherein R 3 and R 4 taken together with the nitrogen atom to which they are attached form a 4 – 8 membered monocyclic heterocyclyl group that is substituted with R 5 .
- R L is --N(R 3 )(R 4 ), wherein R 3 and R 4 taken together with the nitrogen atom to which they are attached form a 4 – 8 membered monocyclic heterocyclyl group that is substituted with R 5 , provided that R 3 and R 4 taken together with the nitrogen atom to which they are attached do not form a morpholino group.
- R L is --N(R 3 )(R 4 ), wherein R 3 and R 4 taken together with the nitrogen 15 atom to which they are attached form a group that is piperidinyl, piperazinyl, pyrrolidinyl, imidazolidinyl, pyrazolidinyl, oxazolidinyl, thiazolidinyl, azetidinyl, pyrrolinyl, imidazolinyl, or pyrazolinyl, each substituted with R 5 .
- R L is -N(R 3 )(R 4 ).
- R L is -N(R 3 )(R 4 ), wherein R 3 and R 4 taken together with the nitrogen atom to which they are attached form a 4 – 8 membered monocyclic heterocyclyl group that is substituted with R 5 .
- R L is -O(R 5 ).
- R L is -R 5 .
- 24 e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6).
- 153 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- RL is , wherein * is a bond to a ZZ group; t is 0 to 10 (e.g., 1-5; or 1-3; or 1; or 2; or 3).
- L Embodiments, Formula (X) In some embodiments of any one of Formula (X) and any embodiments thereof, L is -L 1 -[G- 5 L 2 ] q -G-L 3 -*, wherein * is the bond to ZZ. In another embodiment, wherein L is -L 1 -[G-L 2 ] q -G-L 3 -*, wherein q is 0, 1, 2, 3, 4, or 5.
- L is -L 1 -[G-L 2 ] q -G-L 3 -*, wherein q is 0, 1, 2, 3, or 4
- L is -L 1 -[G-L 2 ] q -G-L 3 -*, wherein q is 0, 1, 2, or 3.
- L is -L 1 -[G-L 2 ] q -G-L 3 -*, wherein q is 0, 1, or 2.
- L is -L 1 -[G-L 2 ] q -G-L 3 -*, wherein q is 1, 2, 3, 4, or 5.
- L is -L 1 -[G-L 2 ] q -G-L 3 -*, wherein q is 1, 2, 3, or 4.
- L is -L 1 -[G-L 2 ] q -G-L 3 -*, wherein q is 1, 2, or 3.
- L is -L 1 -[G-L 2 ] q -G-L 3 -*, wherein q is 1 or 2.
- L is -L 1 -[G-L 2 ] q -G-L 3 -*, wherein q is 4.
- L 15 is -L 1 -[G-L 2 ] q -G-L 3 -*, wherein q is 3.
- L is -L 1 -[G-L 2 ] q -G-L 3 -*, wherein q is 2.
- L is -L 1 -G-L 2 -G-L 3 -*.
- L is -L 1 -G-L 3 -*.
- L is -G-L 3 -*.
- L is -L 1 -G-*.
- L is -G-*.
- L is -[G-L 2 ] q -G-*, wherein q is 1, 2, 3, 4, or 5 (e.g., q is 2; or 20 q is 3; or q is 4; or q is 5).
- each instance of A-B-A- is independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(R N )-, -N(R N )C(O)-, -OC(O)O-, -OC(O)N(R N )-, - N(R N )C(O)O-, -N(R N )C(O)N(R N )-, -OP(O)(OH)O- ,-OP(S)(OH)O-, -O-, and -N(R N )-, wherein each R N is independently hydrogen or C 1-6 alkyl.
- each instance of A-B-A- is independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(R N )-, -N(R N )C(O)-, -OC(O)N(R N )-, -N(R N )C(O)O-,- N(R N )C(O)N(R N )-, -O-, and -N(R N )-, wherein each R N is independently hydrogen or C 1-6 alkyl.
- each instance of A-B-A- is independently selected from the group consisting of -C(O)N(R N )-, -N(R N )C(O)-, -OC(O)N(R N )-, -N(R N )C(O)O-, -N(R N )C(O)N(R N )-, -O-, 30 and -N(R N )-, wherein each R N is independently hydrogen or C 1-6 alkyl.
- each instance of A-B-A- is independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(R N )-, -N(R N )C(O)-, -O-, and -N(R N )-, wherein each R N is independently hydrogen or C 1-6 alkyl.
- each instance of A-B-A- is independently selected from the group 35 consisting of -C(O)N(R N )-, -N(R N )C(O)-, -O-, and -N(R N )-, wherein each R N is independently hydrogen or C 1-6 alkyl.
- 154 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO D and F are each independently a bond, C1-10alkyl, C2-10alkenyl, or C2-10alkynyl, each optionally substituted with 1, 2, 3, or 4 R groups; and E is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups.
- D and F are each independently a bond or C1-10alkyl optionally substituted with 1, 2, 3, or 4 R groups; and E is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups.
- each G is independently C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3- 10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups.
- each G is independently C1-10alkyl, optionally substituted with 1, 2, or 3 R groups. In some embodiments, each G is independently C 1-10 alkyl. 15 In some embodiments, each G is independently C1-10alkyl, optionally substituted with 1 or 2 R groups. In some embodiments, each G is independently C1-10alkyl, optionally substituted with one R group..
- L is -L 1 -G-L 3 -*, wherein * is the bond to ZZ ;
- 20 G is -D-E-F-, wherein D, E, and F are independently a bond, C1-10alkyl, C2-10alkenyl, C2- 10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups;
- L 1 is -B-A-;
- L 3 is a bond or -A-B-A-;
- 25 each A is independently a bond, -O-, -S-, or -N(R N )-, wherein each R N is independently hydrogen or C1-6alkyl.
- each B is independently a bond, CH2, C(O), S(O)2, P(O)(OH), or P(S)(OH); and
- L is -L 1 -G-L 3 -*, wherein * is the bond to ZZ;
- G is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, 30 or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups;
- L 1 is -B-;
- L 3 is a bond or -A-B-A-; each A is independently a bond, -O-, -S-, or -N(R N )-, wherein each R N is independently hydrogen or C1-6alkyl; and 35 each B is independently a bond, CH2, C(O), S(O)2, P(O)(OH), or P(S)(OH; and
- L is -L 1
- ALN-529-WO L 1 is -B-A-, wherein, A is a bond, -O-, -S-, or -N(R N )-, wherein each R N is independently hydrogen or C1-6alkyl; and B is a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH).
- L is -L 1 -G-*, wherein * is the bond to ZZ;
- G is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, each of which is optionally substituted with 1 or 2 R groups;
- L 1 is -B-A-, wherein A is a bond, -O-, -S-, or -N(R N )-, each R N is independently hydrogen or C1-6alkyl; and 10 B is a bond, C(O), S(O)2, P(O)(OH), or P(S)(OH).
- L is -L 1 -G-*, wherein * is the bond to ZZ; G is C1-10alkyl or C2-10alkenyl, each of which is optionally substituted with 1 or 2 R groups; L 1 is bond, C(O), S(O)2, P(O)(OH), or P(S)(OH); and R N is hydrogen or C1-6alkyl.
- L is wherein * is the bond to ZZ; k is an integer from 1 to 10; L 1 is bond, C(O), C(S), C(NR N ), S(O) 2 , P(O)(OH), or P(S)(OH); and R N is hydrogen or C 1- 6 alkyl.
- L is wherein * is the bond to ZZ; k is an integer from 1 to 10; L 1 is bond, C(O), P(O) 20 In some embodiments, wherein * is the bond to ZZ; k is an integer from 1 to 10; or an integer from 2 to 10; or an integer from 3 to 10; or an integer from 4 to 10; or an integer from 5 to 10; or an integer from 5 to 9; or an integer from 5 to 8; or an integer from 5 to 7.
- each G is independently C 1-10 alkyl and L 2 is O, S, or N(H). 25
- L is -[G-L 2 ] q -G-*, wherein q is 1, 2, 3, 4, or 5 (e.g., q is 2; or q is 3; or q is 4; or q is 5)
- each G is independently C 1-10 alkyl and L 2 is O.
- L is -[CH 2 CH 2 O] q -G-*, wherein q is 1, 2, 3, 4, or 5 (e.g., q is 2; or q is 3; or q is 4; or q is 5), G is independently C 1-10 alkyl.
- L is , wherein * is the bond to ZZ; t is an integer from 0 to 10 (e.g., an integer from 1 to 5; or 1; or 2; or 3).
- I n some embodiments, L is , wherein * is the bond to ZZ. 156 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- L is , wherein * is the bond to ZZ; t is 1 to 10 (e.g., 1-5; or 1-3; or 1; or 2; or 3); and z is 1-10 (e.g., 1-6; or 1-4; or 1; or 2; or 3 or 4 or 5 or 6).
- * is the bond to ZZ, and t is an integer from 1 to 5 (e.g., 1; or 2; or 3).
- t is an integer from 0 to 10 (e.g., an integer from 1 to 5 or 1; or 2; or 3); a is an integer from 1 to 3; and s and s’ are each independently an integer from 1 to 24 (e.g., an integer from 1 to 16; an integer from 1 to 10; an integer from 3 to 10; an integer from 3 to 7; or an 10 integer from 4 to 6).
- * is the bond to ZZ; a is 1, 2 or 3; and each s, s’, and s” independently is an integer from 1 to 24 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7, or an integer from 4 to 6).
- L is wherein * is the bond to ZZ; and s, s’, 15 and s’’ are independently is an integer from 1 to 24 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7, or an integer from 4 to 6).
- * is the bond to ZZ and each s, s’, and s” independently is an integer from 1 to 24(e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7, or an integer from 4 to 6) 20
- L is wherein * is the bond to ZZ; s and k are independently is an integer from 1 to 20 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6); and w is an integer from 1 to 10 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6).
- L is wherein * is the bond to ZZ and w is an integer from 1 to 20 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6).
- L is C1-20 alkyl.
- L is C2-20 alkyl.
- L is C6-20 alkyl.
- L is C8-12 alkyl.
- L is C10 alkyl.
- RP3 when present, is hydrogen.
- the compound of Formula (X) is according to one of Formulae (X-b) 10 through (X-e) and (X-x) through (X-y): 158 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO or a salt thereof, wherein R P is hydrogen or a nitrogen protecting group (e.g., a nitrogen protecting group), wherein R and the remaining variables are as defined in Formula (X).
- R 1 is hydrogen. In another embodiment of Formulae (X-b) through (X-e) and (X-x) through (X-y), R 1 is C 1-6 alkyl (e.g., methyl or 5 t-butyl). In another embodiment of Formulae (X-b) through (X-e) and (X-x) through (X-y), R 1 is hydrogen and R P is hydrogen. In another embodiment of Formulae (X-b) through (X-e) and (X-x) through (X-y), R 1 is hydrogen and a nitrogen protecting group.
- R 1 is C 1-6 alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- R 1 is C 1-6 alkyl (e.g., 10 methyl or t-butyl) and a nitrogen protecting group.
- -L-ZZ-L’-R T Embodiments
- -L-ZZ-L’-R T is 159 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO (x-a).
- -L-ZZ-L’-R T is (x-b).
- -L-ZZ-L’-R T is (x-c). 5
- -L-ZZ-L’-R T is In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) through (X-y), -L-ZZ-L’-R T is In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) through (X-y), -L-ZZ-L’-R T is In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) 10 through (X-y), -L-ZZ-L’-R T is In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) through (X-y), -L-ZZZ-L’-R T is In an embodiment, of any one of Formula (X) and Formula
- -L-ZZ-L’-R T is (x-h). In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) through (X-y), -L-ZZ-L’-R T is (x-i). 5 In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) through (X-y), -L-ZZ-L’-R T is (x-j).
- -L-ZZ-L’-R T is (x-k). In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) 10 through (X-y), -L-ZZ-L’-R T is (x-l). 161 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- -L-ZZ-L’-R T is (x-m). In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) through (X-y), -L-ZZ-L’-R T is (x-n). 5 In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) through (X-y), -L-ZZ-L’-R T is (x-o).
- -L-ZZ-L’-R T is In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) through (X-y), -L-ZZ-L’-R T is (x-q). In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) through (X-y), -L-ZZ-L’-R T is 162 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- R T1 is -L L -oligonucleotide, wherein L L is a divalent linker that connects to the 3’-end of the 10 oligonucleotide, the 5’-end of the oligonucleotide, or an internal 2’- or 3’ position on an internal nucleotide (i.e., a nucleotide that is not the 5’-terminus
- L L is a bond.
- R T1 is -L L -oligonucleotide, wherein L L is a divalent linker that connects to the 3’-end of the oligonucleotide, such as one of: 15 directly to the 3’-carbon of the 3’-terminal nucleoside; directly to the 3’-O of the 3’-terminal nucleoside; directly to the 4’-carbon of the 3’-terminal nucleoside; directly to the 2’-carbon of the 3’-terminal nucleoside; or directly to the 2’-O of the 3’-terminal nucleoside.
- R T1 is -L L -oligonucleotide, wherein L L is a divalent linker that connects to the 5'-end of the oligonucleotide, such as one of: directly to the 5’-carbon of the 5’-terminal nucleoside; directly to the 5’-O of the 5’-terminal nucleoside; directly to the 4’-carbon of the 5’-terminal nucleoside; 25 directly to the 2’-carbon of the 5’-terminal nucleoside; or directly to the 2’-O of the 5’-terminal nucleoside.
- L L is a divalent linker that connects to the 5'-end of the oligonucleotide, such as one of: directly to the 5’-carbon of the 5’-terminal nucleoside; directly to the 5’-O of the 5’-terminal nucleoside; directly to the 4’-carbon of the 5’-terminal nucleoside; 25 directly to the 2’-carbon of the
- R T1 is -L L -oligonucleotide, wherein L L is a divalent linker that connects to an internal 2’- or 3’ position on an internal nucleotide.
- L L is a divalent linker that connects to an internal 2’- or 3’ position on an internal nucleotide.
- R T is R T1 , wherein R T1 is -L L -oligonucleotide, wherein L L is a divalent linker that connects to an internucleotide linkage (i.e., to an oxygen atom in a phosphodiester linkage 5 to form a phosphotriester; or to a nitrogen when the internucleotide linkage is a phosphoroamidate).
- L L is a divalent linker that connects to an internucleotide linkage (i.e., to an oxygen atom in a phosphodiester linkage 5 to form a phosphotriester; or to a nitrogen when the internucleotide linkage is a phosphoroamidate).
- L L when L L connects to a carbon atom on a nucleoside, then L L is -B 3 -A 3 -, wherein B 3 is -P(O)(OH)-, -P(S)(OH)-, or -P(S)(SH)-; and A 3 is -O-, -S-, or -N(H)- . 10
- L L when L L connects to a carbon atom on a nucleoside, then L L is -B 3 - A 3 -, wherein B 3 is -P(O)(OH)- or-P(S)(OH)-; and A 3 is -O-.
- L L when L L connects to a oxygen atom on a nucleoside, then L L is - 15 P(O)(OH)-, -P(S)(OH)-, or -P(S)(SH). In another embodiment, when L L connects to a oxygen atom on a nucleoside, then L L is - P(O)(OH)- or -P(S)(OH)-. In another embodiment, when L L connects to a oxygen atom on a nucleoside, then L L is - P(O)(OH)-. 20 In another embodiment, when L L connects to a oxygen atom on a nucleoside, then L L is - P(S)(OH)-.
- L L when L L connects to a oxygen atom on a nucleoside, then L L is -B3-A3-LL1-A3-B3-, wherein B 3 is a bond, -C(O)-, C(S)-, C(NH), S(O), S(O)2, -P(O)(OH)-, -P(S)(OH)-, or -P(S)(SH); 25 A 3 is a bond, -O-, -S-, or -N(H)- ; and L L1 is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl.
- L L when LL connects to a oxygen atom on a nucleoside, then LL is -B3- L L1 -B 3 -, wherein B 3 is -C(O)-; and L L1 is C1-10alkyl. 30 In another embodiment, when L L connects to a oxygen atom on a nucleoside, then L L is-a bond.
- R T is R T1 wherein R T1 is is -L L -oligonucleotide, when L L connects to a oxygen atom on a nucleoside, and L L is a bond, the nucleoside is of Formula (X-f), 164 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein B is an optionally modified nucleobase (e.g., adenine, cytosine, uracil, guanine, 5- methylcytosine, or-5-methyluracil); L’ is according any of the preceding embodiments; and * represent the bond to ZZ.
- R T1 is is -L L -oligonucleotide, when L L connects to a oxygen atom on a nucleoside, and L L is a bond, the nucleoside is of Formula (X-f), 164 ME1 ⁇ 53453057.v1 Attorney Docke
- -L’- is -L 1 -G-L 3 -*, wherein * is the bond to ZZ. 5
- -L’- is -C2-30alkyl-*, wherein the alkyl is optionally substituted with one or two R groups, and * is the bond to ZZ.
- -L’- is -C2-30alkyl-*, wherein the alkyl is optionally substituted with one or two groups selected from the group consisting of halogen, hydroxy, C1-6alkoxy, amino, Cl-6alkylamino, di(C1-6alkylamino), cyano, carboxy , and * is the bond to ZZ.
- -L’- is -C2-30alkyl-*, wherein the alkyl is optionally substituted with one group 10 selected from the group consisting of halogen, hydroxy, C1-6alkoxy, amino, Cl-6alkylamino, di(C1- 6alkylamino), cyano, carboxy , and * is the bond to ZZ.
- -L’- is -C2-30alkyl-*, wherein the alkyl is optionally substituted with one group selected from the group consisting of hydroxy, amino, and carboxy , and * is the bond to ZZ.
- -L’- is -C2-30alkyl-*, wherein the alkyl is optionally substituted with hydroxy, and * is the bond to ZZ.
- -L’- is -C2-30alkyl-*, wherein * is the bond to ZZ.
- -L’- is -C2-16alkyl-*, wherein * is the bond to ZZ.
- -L’- is -C4-12alkyl-*, wherein * is the bond to ZZ.
- -L’- is -C4-10alkyl-*, wherein * is the bond to ZZ.
- -L’- is -C5-10alkyl-*, wherein * is the bond to ZZ. In some embodiments, -L’- is -C6alkyl- *, wherein * is the bond to ZZ. In some embodiments, -L’- is -C8alkyl-*, wherein * is the bond to ZZ. 20 In some embodiments, -L’- is -C10alkyl-*, wherein * is the bond to ZZ.
- -L’- is -L 1 -[G-L 2 ]q-G-L 3 -*, wherein * is the bond to ZZ; q is 0, 1, 2, 3, 4, or 5; L 1 is a bond or -B-A-; 25 each L 2 is independently -A-B-A-; L 3 is a bond or -A-B-A-; each A is independently a bond, -O-, -S-, or -N(R N )-; each B is independently a bond, CH2, C(O), C(S), C(NR N ), S(O)2, P(O)(OH), or P(S)(OH); each R N is independently hydrogen or C1-6alkyl; and 30 each G is independently C1-10alkyl, C2-10alkenyl, C2-10alkynyl, each of which is optionally substituted with 1, 2, 3, or 4 R groups.
- -L’- is -L 1 -[G-L 2 ]q-G-*, wherein * is the bond to ZZ, q is 0, 1, 2, or 3;
- each L2 is independently a bond, C(O)O, OC(O), C(O)(NRN), N(RN)C(O), OP(O)(OH)O, or OP(S)(OH)O, wherein each R N is independently hydrogen or C1-6alkyl; and each G is independently C1-10alkyl or C2-10alkenyl, each of which is optionally substituted with 1 or 2 R groups.
- -L’- is -[G-L 2 ]q-G-*, wherein * is the bond to ZZ, q is 0, 1, 2, or 3 (e.g., 5 q is 0, 1, or 2; or 0 or 1; or 0; or 1; or 2); each G is independently C1-10alkyl, each of which is optionally substituted with 1 or 2 R groups, and one of: ( a) each L2 is independently C(O)O or OC(O); (b) each L2 is independently C(O)(NRN) or N(RN)C(O), wherein each RN is independently hydrogen or C1-6alkyl 10 (c) each L2 is independently OP(O)(OH)O, or OP(S)(OH)O (e.g., each is OP(O)(OH)O); or ( d) each L2 is a bond.
- the compound of Formula (X) is according to one of Formulae (X-g) through (X-q): 166 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO B is an optionally modified nucleobase (e.g., adenine, cytosine, uracil, guanine, 5- methylcytosine, or-5-methyluracil); each n is independently 0 or an integer selected from 1-10; (e.g., 1-5, or 1-3, or 3, or 2, or 1); 5 each m is independently integer selected from 1-20 (e.g., 2-12, or 2-10; or 2-6; or 2; or 3; or 4; or 5; or 6).
- nucleobase e.g., adenine, cytosine, uracil, guanine, 5- methylcytosine, or-5-methyluracil
- each n is independently 0 or an integer selected from 1-10
- the compound of Formula (X) is according to one of Formulae (X-r) through (X-w): 167 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 5 L and ZZ are as defined in Formula (X) or in any embodiment preceding or below;
- B is an optionally modified nucleobase (e.g., adenine, cytosine, uracil, guanine, 5- methylcytosine, or-5-methyluracil); 10 each m is independently integer selected from 1-20 (e.g., 2-12, or 2-10; or 2-6; or 2; or 3; or 4; or 5; or 6); each n is independently 0 or an integer selected from 1-10; (e.g., 1-5, or 1-3, or 3, or 2, or 1); R P is hydrogen or a nitrogen protecting group (e.g., a nitrogen protecting group); and R 1 is hydrogen or C 1-6 alkyl (e
- R 1 is hydrogen. In another embodiment of Formulae (X-r) through (X-w), R 1 is C 1-6 alkyl (e.g., methyl or t-butyl). In another embodiment of Formulae (X-r) through (X-w), R 1 is hydrogen and R P is hydrogen. In another embodiment of Formulae (X-r) through (X-w), R 1 is hydrogen and a nitrogen protecting group.
- R 1 is C 1-6 alkyl (e.g., methyl or t-butyl) and R P 168 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO is hydrogen.
- R 1 is C1-6alkyl (e.g., methyl or t-butyl) and a nitrogen protecting group.
- two adjacent nucleosides in the oligonucleotide have one of the 5 oligonucleotide, L’ is according any of the preceding embodiments; and B is an optionally modified nucleobase.
- each nucleoside of the two adjacent nucleosides is independently according to 10 any one of Formula (X-f) through (X-q).
- each nucleoside is according to the same Formula.
- three adjacent nucleosides in the oligonucleotide have the formula 169 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- each Y is independently O or S (or O; or S; or O then S or S then O, 5’ followed by 3’); represents the remainder for the oligonucleotide, L’ is according any of the preceding 5 embodiments; and B is an optionally modified nucleobase; e.g., each Y is O.
- each nucleoside of the three adjacent nucleosides is independently according to any one of Formula (X-f) through (X- q). In certain embodiments, each nucleoside is according to the same Formula.
- each nucleoside of the four adjacent nucleosides is independently according to any one of Formula (X-f) through (X-q).
- each nucleoside is according to the same Formula.
- each nucleoside is according to the same Formula (X-u) or (X-w).
- R T is R T1 , wherein R T1 is -L L -oligonucleotide, and when L L connects to an oxygen atom or nitrogen atom in an internucleotide linkage, the internucleotide linkage can be of the formula, including the 3’ and 5’ oxygen atoms of the preceding and following nucelosides, respectively, (X-pa) (X-pb) (X-pc) wherein L’ can be, for example a bond, -S(O)2- or, in for Formula (X-pc), a 5 -8 membered 10 heterocyclyl ring optionally substituted with 1 or 2 R groups, as defined herein; and * represent the bond to ZZ.
- the preceding includes, (X-pd) (X-pe) (X-pf) wherein * represent the bond to ZZ; and R N5 is hydrogen or C1-10 alkyl.
- the preceding includes, (X-pg) (X-ph) (X-pi) 15 wherein * represent the bond to ZZ; m is an integer selected from 1 – 20 (e.g., 1-10, or 2-20, or 2-10, or 4-10, or 4-8; or 6-12; or 5; or 6; or 7; or 8; or 9; or 10), and R N5 is hydrogen or C1-10 alkyl.
- the compound of Formula (X-pd) is 171 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein Y’ is O or S, and R Y , Y, R 1 , L, L’, and ZZ are as defined for Formula (X).
- R 1 is hydrogen.
- R 1 is C 1-6 alkyl (e.g., methyl or t-butyl).
- the compound is 5 172 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- each m is an integer selected from 1 – 20 (e.g., 2-20, 2-10, 1-10, 2-16, 4-16, 4-8, or 6-12), each n is independently 0 or an integer selected from 1-10; (e.g., 1-5, or 1-3, or 3, or 2, or 1); Y’ is O or S, and R 1 , L, L’, and ZZ are as defined for Formula (X). 10
- the compound of Formula (X-pe) is 174 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- Y’ is O or S, and R Y , Y, R 1 , L, L’, and ZZ are as defined for Formula (X).
- Y’ is O.
- Y’ is S.
- R 1 is hydrogen.
- R 1 is C1-6alkyl (e.g., methyl or t- 5 butyl).
- R P is hydrogen.
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O and R 1 is hydrogen.
- Y’ is O and R 1 is C1- 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R 1 is hydrogen. In one embodiment, 10 Y’ is S and R 1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and R P is hydrogen. In one embodiment, Y’ is O and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and R P is hydrogen .
- Boc t-butoxycarbonyl
- Cbz benzyloxycarbonyl
- pac phenoxyacetyl
- Y’ is S and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl 15 (pac)).
- R P is a nitrogen protecting group
- Y’ is O, R 1 is hydrogen and R P is hydrogen.
- Y’ is S, R 1 is hydrogen and R P is hydrogen.
- Y’ is O, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl 20 (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl 20 (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen .
- Y’ is S, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is a 25 nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- the compound is 175 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 5 176 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO w herein Y’ is O or S, and RP, R1, L, L’, and ZZ are as defined for Formula (X). In one embodiment, Y’ is O. In another embodiment, Y’ is S. In one embodiment, R 1 is hydrogen. In another embodiment, R 1 is C1-6alkyl (e.g., methyl or t- butyl). 5 In one embodiment, R P is hydrogen.
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O and R 1 is hydrogen.
- R 1 is C1- 6alkyl (e.g., methyl or t-butyl).
- Y’ is S and R 1 is hydrogen.
- Y’ is S and R 1 is C1-6alkyl (e.g., methyl or t-butyl). 10
- Y’ is O and R P is hydrogen.
- Y’ is O and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S and R P is hydrogen .
- Y’ is S and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O, R 1 is hydrogen and R P is hydrogen.
- Y’ is S, R 1 is hydrogen and R P is hydrogen.
- Y’ is O, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- R P is a nitrogen protecting group
- Y’ is S
- R 1 is hydrogen
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O, R 1 is C1-6alkyl 20 (e.g., methyl or t-butyl) and R P is hydrogen .
- Y’ is S, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen .
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S
- R 1 is C1-6alkyl (e.g., methyl or t-butyl)
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl 25 (pac)).
- t-butoxycarbonyl Boc
- benzyloxycarbonyl Cbz
- phenoxyacetyl 25 pac
- ALN-529-WO 5 wherein each m is an integer selected from 1 – 20 (e.g., 2-20, 2-10, 1-10, 2-16, 4-16, 4-8, or 6-12), Y’ is O or S, and R P , R 1 , L, L’, and ZZ are as defined for Formula (X). 178 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
- Y’ is O.
- Y’ is S.
- R 1 is hydrogen.
- R 1 is C1-6alkyl (e.g., methyl or t- butyl).
- R P is hydrogen.
- R P is a nitrogen protecting group 5 (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O and R 1 is hydrogen.
- R 1 is C1-6alkyl (e.g., methyl or t-butyl).
- Y’ is S and R 1 is hydrogen.
- Y’ is S and R 1 is C1-6alkyl (e.g., methyl or t-butyl).
- Y’ is O and R P is hydrogen.
- Y’ is O and R P is a 10 nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S and R P is hydrogen .
- Y’ is S and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O, R 1 is hydrogen and R P is hydrogen.
- Y’ is S, 15 R 1 is hydrogen and R P is hydrogen.
- Y’ is O, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- R P is a nitrogen protecting group
- Y’ is S
- R 1 is hydrogen
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen .
- Y’ is S, R 1 is C1-6alkyl (e.g., methyl 20 or t-butyl) and R P is hydrogen .
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S
- R 1 is C1-6alkyl (e.g., methyl or t-butyl)
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- R T1 when R T1 is -L L -oligonucleotide and is conjugated at the 5’-end of the oligonucleotide, in one embodiment, R T1 can be represented as Formula (X-5’) wherein L L is -P(Y)(OH)-, wherein Y is O or S (e.g., S); and * represents the bond to remainder of the compound of Formula (X).
- R T1 when R T1 is -L L -oligonucleotide and is conjugated at the 5’-end of the oligonucleotide, in one embodiment, R T1 can be represented as Formula (X-5’o) or Formula (X-5’s), wherein * represents the bond to remainder of the compound of Formula (X). 179 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In an embodiment of Formula (X-5’), (X-5’o), and Formula (X-5’s), -L-ZZ-L’-R T represents any one of Formulae (x-a) through (x-s) .
- -L-ZZ-L’-R T represents Formula ( In other embodiments-L-ZZ-L’-R T represents one of the following formulae: ( x-n) (x-o) (x-s) 5 In other embodiments of Formula (X-5’), (X-5’o), and Formula (X-5’s), L-ZZ-L’-R T represents, (x-m) In other embodiments of Formula (X-5’), (X-5’o), and Formula (X-5’s), L-ZZ-L’-R T 10 represents, (x-s).
- the compound of Formula (X) is 180 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- R T1 when R T1 is -L L -oligonucleotide and is conjugated at the 3’-end of the 5 oligonucleotide, in one embodiment, R T1 can be represented as Formula (X-3’) wherein L L is -P(Y)(OH)-, wherein Y is O or S (e.g., S); and * represents the bond to remainder of the compound of Formula (X).
- R T1 when R T1 is -L L -oligonucleotide and is conjugated at 10 the 3’-end of the oligonucleotide, in one embodiment, R T1 can be represented as Formula (X-3’o) or Formula (X-3’s), wherein * represents the bond to remainder of the compound of Formula (X).
- -L-ZZ-L’-R T represents 15 any one of Formulae (x-a) through (x-ab).
- -L-ZZ-L’-R T represents Formula (x-e), .
- -L-ZZ-L’-R T represents one of the following formulae: ( x-a) (x-b) (x-c) 181 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- L-ZZ-L’-R T represents, In other embodiments of Formula (X-3’), (X-3’o), and Formula (X-3’s), L-ZZ-L’-R T 5 represents, 182 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In other embodiments of Formula (X-3’), (X-3’o), and Formula (X-3’s), L-ZZ-L’-R T represents, (x-p).
- L-ZZ-L’-R T 5 represents, (x-ab).
- L-ZZ-L’-R T represents, (x-r).
- R L is 10
- the compound of Formula (X) is 183 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein Y' is O or S, and R Y , R 1 , Y, L’, ZZ, and L are as defined for Formula (X) or any embodiment thereof.
- R 1 is hydrogen. In another embodiment, R 1 is C1-6alkyl (e.g., 5 methyl or t-butyl).
- the compound of Formula (X) is 184 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein Y’ is O or S, and R Y , Y, R 1 , L’, ZZ, and L are as defined for Formula (X) or any embodiment thereof. In another embodiment, the compound of Formula (X) is 5 wherein Y’ is O or S, and R P , R 1 , L’, ZZ, and L are as defined for Formula (X) or any embodiment thereof.
- Y’ is O. In another embodiment, Y’ is S.
- R 1 is hydrogen. In another embodiment, R 1 is C1-6alkyl (e.g., methyl or t- 10 butyl). In another embodiment, -COOR1 is replaced with a carboxylic acid mimic, such as a tetrazolyl group (e.g., 1,2,3,4-tetrazol-5-yl).
- R P is hydrogen. In another embodiment, R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O and R 1 is hydrogen.
- Y’ is O and R 1 is C1- 15 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R 1 is hydrogen. In one embodiment, Y’ is S and R 1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and R P is hydrogen . In one embodiment, Y’ is O and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and R P is hydrogen .
- Boc t-butoxycarbonyl
- Cbz benzyloxycarbonyl
- pac phenoxyacetyl
- Y’ is S and R P is a 20 nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- R P is a 20 nitrogen protecting group
- e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac) 185 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
- Y’ is O, R 1 is hydrogen and R P is hydrogen.
- Y’ is S, R 1 is hydrogen and R P is hydrogen.
- Y’ is O, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- R P is a nitrogen protecting group
- Y’ is S
- R 1 is hydrogen
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl 5 (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is S, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S
- R 1 is C1-6alkyl (e.g., methyl or t-butyl)
- R P is a 10 nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- the compound of Formula (X) is 15 wherein Y’ is O or S, and R P , R 1 , L’, ZZ, and L are as defined for Formula (X) or any embodiment thereof.
- Y’ is O.
- Y’ is S.
- R 1 is hydrogen.
- R 1 is C1-6alkyl (e.g., methyl or t- butyl).
- R P is hydrogen.
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O and R 1 is hydrogen.
- R 1 is C1- 6alkyl (e.g., methyl or t-butyl).
- Y’ is S and R 1 is hydrogen. In one embodiment, Y’ is S and R 1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and R P is hydrogen. In one embodiment, Y’ is O and R P is a 5 nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and R P is hydrogen.
- Boc t-butoxycarbonyl
- Cbz benzyloxycarbonyl
- pac phenoxyacetyl
- Y’ is S and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- R P is a nitrogen protecting group
- Y’ is O, R 1 is hydrogen and R P is hydrogen.
- Y’ is S, 10 R 1 is hydrogen and R P is hydrogen.
- Y’ is O, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen .
- Y’ is S, R 1 is C1-6alkyl (e.g., methyl 15 or t-butyl) and R P is hydrogen.
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- the compound of Formula (X) is 187 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO , wherein Y’ is O or S, and R P , R 1 , L’, and L are as defined for Formula (X) or any embodiment thereof.
- Y’ is O.
- Y’ is S. 5
- R 1 is hydrogen.
- R 1 is C1-6alkyl (e.g., methyl or t- butyl).
- R P is hydrogen.
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O and R 1 is hydrogen.
- R 1 is C1- 10 6alkyl (e.g., methyl or t-butyl).
- Y’ is S and R 1 is hydrogen.
- Y’ is S and R 1 is C1-6alkyl (e.g., methyl or t-butyl).
- Y’ is O and R P is hydrogen.
- Y’ is O and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S and R P is hydrogen.
- Y’ is S and R P is a 15 nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O, R 1 is hydrogen and R P is hydrogen.
- Y’ is S, R 1 is hydrogen and R P is hydrogen.
- Y’ is O, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- R P is a nitrogen protecting group
- Y’ is S
- R 1 is hydrogen
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen .
- Y’ is S, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen .
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or 25 phenoxyacetyl (pac)).
- Y’ is S
- R 1 is C1-6alkyl (e.g., methyl or t-butyl)
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- the compound of Formula (X) is 188 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- each m is independently an integer selected from 1-10; each n is independently 0 or an integer selected from 1-10; (e.g., 1-5, or 1-3, or 3, or 2, or 1); Y’ is O or S, and R P and R 1 are 5 as defined for Formula (X) or any embodiment thereof.
- each m is independently an integer selected from 2-10; or 2-8, or 2-6.
- Y’ is O.
- Y’ is S.
- R 1 is hydrogen.
- R 1 is C 1-6 alkyl (e.g., methyl or t- butyl). 10
- R P is hydrogen.
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O and R 1 is hydrogen.
- R 1 is C 1- 6 alkyl (e.g., methyl or t-butyl).
- Y’ is S and R 1 is hydrogen.
- Y’ is S and R 1 is C 1-6 alkyl (e.g., methyl or t-butyl).
- Y’ is O and R P is hydrogen.
- Y’ is O and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- R P is a nitrogen protecting group
- Y’ is S and R P is hydrogen .
- Y’ is S and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- 189 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- Y’ is O, R 1 is hydrogen and R P is hydrogen. In one embodiment, Y’ is S, R 1 is hydrogen and R P is hydrogen. In one embodiment, Y’ is O, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl 5 (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Boc t-butoxycarbonyl
- Cbz benzyloxycarbonyl
- pac phenoxyacetyl
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is S, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S
- R 1 is C1-6alkyl (e.g., methyl or t-butyl)
- R P is a 10 nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- the compound of Formula (X) is 15 wherein Y’ is O or S, and R P and R 1 are as defined for Formula (X) or any embodiment thereof.
- Y’ is O.
- Y’ is S.
- R 1 is hydrogen.
- R 1 is C1-6alkyl (e.g., methyl or t- butyl).
- R P is hydrogen.
- R P is a nitrogen protecting group 20 (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O and R 1 is hydrogen.
- Y’ is O and R 1 is C1- 6alkyl (e.g., methyl or t-butyl).
- Y’ is S and R 1 is hydrogen.
- Y’ is S and R 1 is C1-6alkyl (e.g., methyl or t-butyl).
- Y’ is O and R P is hydrogen.
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S and R P is hydrogen.
- Y’ is S and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl 5 (pac)).
- Y’ is O, R 1 is hydrogen and R P is hydrogen. In one embodiment, Y’ is S, R 1 is hydrogen and R P is hydrogen. In one embodiment, Y’ is O, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl 10 (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Boc t-butoxycarbonyl
- Cbz benzyloxycarbonyl
- pac phenoxyacetyl
- Y’ is O, R 1 is C1- 6alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is S, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t- butyl) and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S
- R 1 is C1-6alkyl (e.g., methyl or t-butyl)
- R P is 15 a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- the compound of Formula (X) is 191 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein Y’ is O or S, and R P , R 1 , L’, ZZ, and L are as defined for Formula (X) or any embodiment thereof.
- Y’ is O.
- Y’ is S.
- R 1 is hydrogen.
- R 1 is C1-6alkyl (e.g., methyl or t- 5 butyl).
- R P is hydrogen.
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O and R 1 is hydrogen.
- Y’ is O and R 1 is C1- 6alkyl (e.g., methyl or t-butyl).
- Y’ is S and R 1 is hydrogen.
- 10 Y’ is S and R 1 is C1-6alkyl (e.g., methyl or t-butyl).
- Y’ is O and R P is hydrogen.
- Y’ is O and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S and R P is hydrogen .
- Y’ is S and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl 15 (pac)).
- Y’ is O, R 1 is hydrogen and R P is hydrogen. In one embodiment, Y’ is S, R 1 is hydrogen and R P is hydrogen. In one embodiment, Y’ is O, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl 20 (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Boc t-butoxycarbonyl
- Cbz benzyloxycarbonyl
- pac phenoxyacetyl
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is S, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S
- R 1 is C1-6alkyl (e.g., methyl or t-butyl)
- R P is a 25 nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- the compound of Formula (X) is 192 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein Y’ is O or S, and R P , R 1 , L’, and L are as defined for Formula (X) or any embodiment thereof. 5 In one embodiment, Y’ is O.
- Y’ is S.
- R 1 is hydrogen.
- R 1 is C1-6alkyl (e.g., methyl or t- butyl).
- R P is hydrogen.
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O and R 1 is hydrogen.
- Y’ is O and R 1 is C1- 6alkyl (e.g., methyl or t-butyl).
- Y’ is S and R 1 is hydrogen.
- Y’ is S and R 1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and R P is hydrogen. In one embodiment, Y’ is O and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl 15 (pac)). In one embodiment, Y’ is S and R P is hydrogen. In one embodiment, Y’ is S and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Boc t-butoxycarbonyl
- Cbz benzyloxycarbonyl
- pac phenoxyacetyl
- Y’ is O, R 1 is hydrogen and R P is hydrogen. In one embodiment, Y’ is S, R 1 is hydrogen and R P is hydrogen. In one embodiment, Y’ is O, R 1 is hydrogen and R P is a nitrogen 20 protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl 193 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- Boc t-butoxycarbonyl
- Cbz benzyloxycarbonyl
- pac phenoxyacetyl
- Y’ is O, R 1 is C1- 6alkyl (e.g., methyl or t-butyl) and R P is hydrogen . In one embodiment, Y’ is S, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen .
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t- butyl) and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) 5 or phenoxyacetyl (pac)).
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) 5 or phenoxyacetyl (pac)).
- Y’ is S, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- the compound of Formula (X) is 10 , wherein each m is independently an integer selected from 1-10; each n is independently 0 or an integer selected from 1-10; (e.g., 1-5, or 1-3, or 3, or 2, or 1); Y’ is O or S, and RP and R1 are as defined for Formula (X) or any embodiment thereof.
- each m is independently an integer selected from 2-10; or 2-8, or 2-6.
- Y’ is O.
- Y’ is S.
- R 1 is hydrogen.
- R 1 is C1-6alkyl (e.g., methyl or t- butyl).
- R P is hydrogen.
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O and R 1 is hydrogen.
- R 1 is C1- 6alkyl (e.g., methyl or t-butyl).
- Y’ is S and R 1 is hydrogen.
- Y’ is S and R 1 is C1-6alkyl (e.g., methyl or t-butyl). 194 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- Y’ is O and R P is hydrogen .
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S and R P is hydrogen.
- Y’ is S and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl 5 (pac)).
- Y’ is O, R 1 is hydrogen and R P is hydrogen.
- Y’ is S, R 1 is hydrogen and R P is hydrogen.
- Y’ is O, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl 10 (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O, R 1 is C1- 6alkyl (e.g., methyl or t-butyl) and R P is hydrogen .
- Y’ is S, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t- butyl) and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S
- R 1 is C1-6alkyl (e.g., methyl or t-butyl)
- R P 15 is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- the compound of Formula (X) is 20 wherein Y’ is O or S, and R P and R 1 are as defined for Formula (X) or any embodiment thereof.
- Y’ is O.
- Y’ is S. 195 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- R 1 is hydrogen. In another embodiment, R 1 is C1-6alkyl (e.g., methyl or t- butyl). In one embodiment, R P is hydrogen. In another embodiment, R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). 5 In one embodiment, Y’ is O and R 1 is hydrogen. In one embodiment, Y’ is O and R 1 is C1- 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R 1 is hydrogen.
- Y’ is S and R 1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and R P is hydrogen . In one embodiment, Y’ is O and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl 10 (pac)). In one embodiment, Y’ is S and R P is hydrogen. In one embodiment, Y’ is S and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Boc t-butoxycarbonyl
- Cbz benzyloxycarbonyl
- pac phenoxyacetyl
- Y’ is O, R 1 is hydrogen and R P is hydrogen. In one embodiment, Y’ is S, R 1 is hydrogen and R P is hydrogen. In one embodiment, Y’ is O, R 1 is hydrogen and R P is a nitrogen 15 protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- a nitrogen 15 protecting group e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)
- Y’ is S, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxy
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is S, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t-butyl) 20 and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S
- R 1 is C1-6alkyl (e.g., methyl or t-butyl)
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- the compound of Formula (X) is 25 , wherein Y’ is O or S, and R P , R 1 , L’, ZZ, and L are as defined for Formula (X) or any embodiment thereof.
- Y’ is O.
- Y’ is S.
- R 1 is hydrogen. In another embodiment, R 1 is C1-6alkyl (e.g., methyl or t- butyl). In one embodiment, R P is hydrogen. In another embodiment, R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). 5 In one embodiment, Y’ is O and R 1 is hydrogen. In one embodiment, Y’ is O and R 1 is C1- 6alkyl (e.g., methyl or t-butyl).
- Y’ is S and R 1 is hydrogen. In one embodiment, Y’ is S and R 1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and R P is hydrogen. In one embodiment, Y’ is O and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl 10 (pac)). In one embodiment, Y’ is S and R P is hydrogen.
- Boc t-butoxycarbonyl
- Cbz benzyloxycarbonyl
- pac phenoxyacetyl 10
- Y’ is S and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- R P is a nitrogen protecting group
- Y’ is O, R 1 is hydrogen and R P is hydrogen.
- Y’ is S, R 1 is hydrogen and R P is hydrogen.
- Y’ is O, R 1 is hydrogen and R P is a nitrogen 15 protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O, R 1 is C1- 6alkyl (e.g., methyl or t-butyl) and R P is hydrogen .
- Y’ is S, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t- 20 butyl) and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- the compound of Formula (X) is 25 wherein Y’ is O or S, and R P , R 1 , L’, and L are as defined for Formula (X) or any embodiment thereof.
- Y’ is O.
- Y’ is S. 197 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
- R 1 is hydrogen.
- R 1 is C1-6alkyl (e.g., methyl or t- butyl).
- R P is hydrogen.
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O and R 1 is hydrogen.
- R 1 is C1- 6alkyl (e.g., methyl or t-butyl).
- Y’ is S and R 1 is hydrogen.
- Y’ is S and R 1 is C1-6alkyl (e.g., methyl or t-butyl).
- Y’ is O and R P is hydrogen .
- Y’ is O and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl 10 (pac)).
- Y’ is S and R P is hydrogen.
- Y’ is S and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O, R 1 is hydrogen and R P is hydrogen.
- Y’ is S, R 1 is hydrogen and R P is hydrogen.
- Y’ is O, R 1 is hydrogen and R P is a nitrogen 15 protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- each m is independently an integer selected from 2-10; or 2-8, or 2-6.
- Y’ is O. In another embodiment, Y’ is S. 5
- R 1 is hydrogen. In another embodiment, R 1 is C1-6alkyl (e.g., methyl or t- butyl).
- R P is hydrogen. In another embodiment, R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O and R 1 is hydrogen.
- Y’ is O and R 1 is C1- 10 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R 1 is hydrogen. In one embodiment, Y’ is S and R 1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and R P is hydrogen . In one embodiment, Y’ is O and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and R P is hydrogen.
- Boc t-butoxycarbonyl
- Cbz benzyloxycarbonyl
- pac phenoxyacetyl
- Y’ is S and R P is a 15 nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- R P is a 15 nitrogen protecting group
- Y’ is O
- R 1 is hydrogen and R P is hydrogen.
- Y’ is S, R 1 is hydrogen and R P is hydrogen.
- Y’ is O, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O, R 1 is C1- 6alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is S, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen .
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t- butyl) and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) 25 or phenoxyacetyl (pac)).
- R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- the compound of Formula (X) is 199 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein Y’ is O or S, and R P and R 1 are as defined for Formula (X) or any embodiment thereof.
- Y’ is O.
- Y’ is S.
- R 1 is hydrogen.
- R 1 is C1-6alkyl (e.g., methyl or t- 5 butyl).
- R P is hydrogen.
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O and R 1 is hydrogen.
- Y’ is O and R 1 is C1- 6alkyl (e.g., methyl or t-butyl).
- Y’ is S and R 1 is hydrogen.
- 10 Y’ is S and R 1 is C1-6alkyl (e.g., methyl or t-butyl).
- Y’ is O and R P is hydrogen .
- Y’ is O and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S and R P is hydrogen.
- Y’ is S and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl 15 (pac)).
- Y’ is O, R 1 is hydrogen and R P is hydrogen.
- Y’ is S, R 1 is hydrogen and R P is hydrogen.
- Y’ is O, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- R P is a nitrogen protecting group
- Y’ is S
- R 1 is hydrogen
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl20 (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O, R 1 is C1- 6alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is S, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen .
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t- butyl) and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S. 5
- R 1 is hydrogen.
- R 1 is C 1-6 alkyl (e.g., methyl or t- butyl).
- R P is hydrogen.
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O and R 1 is hydrogen.
- Y’ is O and R 1 is C 1- 10 6 alkyl (e.g., methyl or t-butyl).
- Y’ is S and R 1 is hydrogen.
- Y’ is O, R 1 is hydrogen and R P is hydrogen. In one embodiment, Y’ is S, R 1 is hydrogen and R P is hydrogen. In one embodiment, Y’ is O, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In 20 one embodiment, Y’ is S, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- a nitrogen protecting group e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)
- Y’ is O, R 1 is C 1- 6 alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is S, R 1 is C 1-6 alkyl (e.g., methyl or t-butyl) and R P is hydrogen .
- Y’ is O, R 1 is C 1-6 alkyl (e.g., methyl or t- butyl) and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) 25 or phenoxyacetyl (pac)).
- Y’ is S
- R 1 is C 1-6 alkyl (e.g., methyl or t-butyl)
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- the compound of Formula (X) is 201 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein Y’ is O or S, and R P , R 1 , L’, and L are as defined for Formula (X) or any embodiment thereof.
- Y’ is O.
- Y’ is S. 5
- R 1 is hydrogen.
- R 1 is C 1-6 alkyl (e.g., methyl or t- butyl).
- R P is hydrogen.
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O and R 1 is hydrogen.
- Y’ is O and R 1 is C 1- 10 6 alkyl (e.g., methyl or t-butyl).
- Y’ is S and R 1 is hydrogen.
- Y’ is S and R 1 is C 1-6 alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and R P is hydrogen. In one embodiment, Y’ is O and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and R P is hydrogen. In one embodiment, Y’ is S and R P is a 15 nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Boc t-butoxycarbonyl
- Cbz benzyloxycarbonyl
- pac phenoxyacetyl
- Y’ is O, R 1 is hydrogen and R P is hydrogen. In one embodiment, Y’ is S, R 1 is hydrogen and R P is hydrogen. In one embodiment, Y’ is O, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In 20 one embodiment, Y’ is S, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- a nitrogen protecting group e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)
- Y’ is S
- R 1 is C 1-6 alkyl (e.g., methyl or t-butyl)
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- the compound of Formula (X) is 202 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein each m is independently an integer selected from 1-10; Y’ is O or S, and R P and R 1 , are as defined for Formula (X) or any embodiment thereof.
- each m is independently an integer selected from 2-10; or 2-8, or 2-6. 5
- Y’ is O.
- Y’ is S.
- R 1 is hydrogen.
- R 1 is C1-6alkyl (e.g., methyl or t- butyl).
- R P is hydrogen.
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O and R 1 is hydrogen.
- Y’ is O and R 1 is C1- 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R 1 is hydrogen. In one embodiment, Y’ is S and R 1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and R P is hydrogen. In one embodiment, Y’ is O and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl 15 (pac)). In one embodiment, Y’ is S and R P is hydrogen.
- Boc t-butoxycarbonyl
- Cbz benzyloxycarbonyl
- pac phenoxyacetyl 15
- Y’ is S and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- R P is a nitrogen protecting group
- Y’ is O, R 1 is hydrogen and R P is hydrogen.
- Y’ is S, R 1 is hydrogen and R P is hydrogen.
- Y’ is O, R 1 is hydrogen and R P is a nitrogen 20 protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O, R 1 is C1- 6alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is S, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is O
- R 1 is C1-6alkyl (e.g., methyl or t- 25 butyl)
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S
- R 1 is C1-6alkyl (e.g., methyl or t-butyl)
- R P 203 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- ALN-529-WO is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- the compound of Formula (X) is 5 wherein Y’ is O or S, and R P and R 1 are as defined for Formula (X) or any embodiment thereof.
- Y’ is O.
- Y’ is S.
- R 1 is hydrogen.
- R 1 is C1-6alkyl (e.g., methyl or t- butyl).
- R P is hydrogen.
- R P is a nitrogen protecting group 10 (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O and R 1 is hydrogen.
- R 1 is C1- 6alkyl (e.g., methyl or t-butyl).
- Y’ is S and R 1 is hydrogen.
- Y’ is S and R 1 is C1-6alkyl (e.g., methyl or t-butyl).
- Y’ is O and R P is hydrogen.
- Y’ is O and R P is a 15 nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S and R P is hydrogen.
- Y’ is S and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O, R 1 is hydrogen and R P is hydrogen.
- Y’ is S, 20 R 1 is hydrogen and R P is hydrogen.
- Y’ is O, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- R P is a nitrogen protecting group
- Y’ is S
- R 1 is hydrogen
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is S, R 1 is C1-6alkyl (e.g., methyl 25 or t-butyl) and R P is hydrogen.
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S
- R 1 is C1-6alkyl (e.g., methyl or t-butyl)
- R P is a 204 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- the compound of Formula (X) is , 5 wherein Y’ is O or S, and R P , R 1 , L’, ZZ, and L are as defined for Formula (X) or any embodiment thereof.
- Y’ is O.
- Y’ is S.
- R 1 is hydrogen.
- R 1 is C1-6alkyl (e.g., methyl or t- butyl).
- R P is hydrogen.
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O and R 1 is hydrogen.
- Y’ is O and R 1 is C1- 6alkyl (e.g., methyl or t-butyl).
- Y’ is S and R 1 is hydrogen.
- Y’ is S and R 1 is C1-6alkyl (e.g., methyl or t-butyl). 15 In one embodiment, Y’ is O and R P is hydrogen. In one embodiment, Y’ is O and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and R P is hydrogen. In one embodiment, Y’ is S and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Boc t-butoxycarbonyl
- Cbz benzyloxycarbonyl
- pac phenoxyacetyl
- Y’ is O, R 1 is hydrogen and R P is hydrogen. In one embodiment, Y’ is S, R 1 is hydrogen and R P is hydrogen. In one embodiment, Y’ is O, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- a nitrogen protecting group e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)
- Y’ is O, R 1 is C1-6alkyl 25 (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is S, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S
- R 1 is C1-6alkyl (e.g., methyl or t-butyl)
- R P is a 205 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- the compound of Formula (X) is , 5 wherein Y’ is O or S, and R P , R 1 , L’, and L are as defined for Formula (X) or any embodiment thereof.
- Y’ is O.
- Y’ is S.
- R 1 is hydrogen.
- R 1 is C 1-6 alkyl (e.g., methyl or t- butyl).
- R P is hydrogen.
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O and R 1 is hydrogen.
- Y’ is O and R 1 is C 1- 6 alkyl (e.g., methyl or t-butyl).
- Y’ is S and R 1 is hydrogen.
- Y’ is S and R 1 is C 1-6 alkyl (e.g., methyl or t-butyl). 15 In one embodiment, Y’ is O and R P is hydrogen. In one embodiment, Y’ is O and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and R P is hydrogen. In one embodiment, Y’ is S and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Boc t-butoxycarbonyl
- Cbz benzyloxycarbonyl
- pac phenoxyacetyl
- Y’ is O, R 1 is hydrogen and R P is hydrogen. In one embodiment, Y’ is S, R 1 is hydrogen and R P is hydrogen. In one embodiment, Y’ is O, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- a nitrogen protecting group e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)
- Y’ is O, R 1 is C 1- 25 6 alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is S, R 1 is C 1-6 alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is O, R 1 is C 1-6 alkyl (e.g., methyl or t- butyl) and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S
- R 1 is C 1-6 alkyl (e.g., methyl or t-butyl)
- R P 206 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- the compound of Formula (X) is , 5 wherein each m is independently an integer selected from 1-10; Y’ is O or S, and R P and R 1 are as defined for Formula (X) or any embodiment thereof.
- each m is independently an integer selected from 2-10; or 2-8, or 2-6.
- Y’ is O.
- Y’ is S.
- R 1 is hydrogen.
- R 1 is C1-6alkyl (e.g., methyl or t- 10 butyl).
- R P is hydrogen.
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O and R 1 is hydrogen.
- Y’ is O and R 1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R 1 is hydrogen. In one 15 embodiment, Y’ is S and R 1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and R P is hydrogen. In one embodiment, Y’ is O and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and R P is hydrogen.
- Boc t-butoxycarbonyl
- Cbz benzyloxycarbonyl
- pac phenoxyacetyl
- Y’ is S and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl 20 (pac)).
- R P is a nitrogen protecting group
- Y’ is O, R 1 is hydrogen and R P is hydrogen.
- Y’ is S, R 1 is hydrogen and R P is hydrogen.
- Y’ is O, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl 25 (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl 25 (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O, R 1 is C1- 6alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is S, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is O
- R 1 is C1-6alkyl (e.g., methyl or t- butyl)
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) 207 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO or phenoxyacetyl (pac)).
- Y’ is S
- R 1 is C1-6alkyl (e.g., methyl or t-butyl)
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- the compound of Formula (X) is 5 , wherein Y’ is O or S, and R P and R 1 are as defined for Formula (X) or any embodiment thereof.
- Y’ is O.
- Y’ is S.
- R 1 is hydrogen.
- R 1 is C 1-6 alkyl (e.g., methyl or t- butyl).
- R P is hydrogen.
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O and R 1 is hydrogen.
- Y’ is O and R 1 is C 1- 6 alkyl (e.g., methyl or t-butyl).
- Y’ is S and R 1 is hydrogen.
- Y’ is S and R 1 is C 1-6 alkyl (e.g., methyl or t-butyl).
- Y’ is O and R P is hydrogen.
- Y’ is O and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S and R P is hydrogen.
- Y’ is S and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O, R 1 is hydrogen and R P is hydrogen.
- Y’ is S, R 1 is hydrogen and R P is hydrogen.
- Y’ is O, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- R P is a nitrogen protecting group
- Y’ is S
- R 1 is hydrogen
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O, R 1 is C 1- 25 6 alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is S, R 1 is C 1-6 alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is O, R 1 is C 1-6 alkyl (e.g., methyl or t- butyl) and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S
- R 1 is C 1-6 alkyl (e.g., methyl or t-butyl)
- R P is 208 ME1 ⁇ 53453057.v1
- a nitrogen protecting group e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)
- Formula (X) 5 In embodiments of Formula (X), Formula (X-a) through (X-w), including embodiments of Formulae (x-a) through (x-s) and (xi-a) through (xi-z) ZZ is a linking group formed by a reactive 209 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- ZZ comprises Group(1). In some embodiments, ZZ comprises 5 Group(2). In some embodiments, ZZ comprises Group(3). In some embodiments, ZZ comprises Group(4). In some embodiments, ZZ comprises Group(5). In some embodiments, ZZ comprises Group(6).
- ZZ comprises Group(7). In some embodiments, ZZ comprises Group(8). In some embodiments, ZZ comprises Group(9). In some embodiments, ZZ comprises Group(10). In some embodiments, ZZ comprises Group(11). In some embodiments, ZZ comprises 10 Group(12). In some embodiments, wherein ZZ is -A’-B’-A’-.
- ZZ is -A’-B’-A’-, wherein each A’ is independently a bond, -O-, -S-, or -N(R N3 )-, wherein R N3 is independently hydrogen or C1-6alkyl and 15 each B’ is independently CH2, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH).
- ZZ is CH2, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH).
- ZZ is C(O), C(S), or S(O)2.
- ZZ is P(O)(OH), or P(S)(OH).
- ZZ is –C(O)-. 20 In some embodiments, ZZ is -A’-B’- or -B’-A’- wherein each A’ is independently -O-, -S-, or -N(R N3 )-; each B’ is independently CH2, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); and each R N3 is independently hydrogen or C1-6alkyl. In some embodiments, ZZ is -A’-B’- or -B’-A’- wherein 25 each A’ is independently -O- or -N(R N3 )-, wherein R N3 is independently hydrogen or C1- 6alkyl.
- each B’ is independently CH2, C(O), S(O)2, P(O)(OH), or P(S)(OH); and 210 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO each R N3 is independently hydrogen or C1-6alkyl.
- R N3 is independently hydrogen or C1-6alkyl.
- ZZ is -CH2O- or -OCH2-.
- ZZ is -S-S-.
- ZZ is -C(O)N(R N3 )-, -N(R N3 )C(O)-, -C(O)O-, -OC(O)-, - OC(O)N(R N3 )-, -N(R N3 )C(O)O-, -N(R N3 )C(O)N(R N3 )-, -S(O)2N(R N3 )-, or -N(R N3 )S(O)2-, wherein R N3 is independently hydrogen or C1-6alkyl.
- ZZ is -C(O)N(R N3 )- or -N(R N3 )C(O)-, wherein R N3 is independently 15 hydrogen or C1-6alkyl. In some embodiments, ZZ is -C(O)O- or -OC(O)-. In some embodiments, ZZ is -OC(O)N(R N3 )-, -N(R N3 )C(O)O-, or -N(R N3 )C(O)N(R N3 )-, wherein R N3 is independently hydrogen or C1-6alkyl.
- ZZ is -N(R N3 )C(O)N(R N3 )-, wherein R N3 is independently hydrogen 20 or C1-6alkyl. In some embodiments, ZZ is -OC(O)N(R N3 )- or -N(R N3 )C(O)O-, wherein R N3 is independently hydrogen or C1-6alkyl. In some embodiments, ZZ is -OP(O)(OH)O-, -OP(S)(OH)O-, -OP(O)(OH)-, -OP(S)(OH)-, - P(O)(OH)O-, or -P(S)(OH)O-.
- ZZ is -OP(O)(OH)O- or -OP(S)(OH)O-. In some embodiments, ZZ is -OP(S)(OH)O-. In some embodiments, ZZ is -OP(O)(OH)O-. In some embodiments, ZZ is -OP(O)(OH)-, -OP(S)(OH)-, -P(O)(OH)O-, or -P(S)(OH)O-. In some embodiments, ZZ is -OP(S)(OH)- or -P(S)(OH)O-. 30 In some embodiments, ZZ is -OP(O)(OH)- or -P(O)(OH)O-.
- the compound of Formula (X) is selected from the group consisting of: (X-a) (X-b) (X-c) (X-d) (X-e) (X-f) 212 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- the compound of Formula (X) is selected from the group consisting of: 213 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 214 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 215 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 216 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- the compound of Formula (X) is selected from the group consisting of: 217 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein * represents the bond to the remainder of the dsRNA agent.
- the compound of Formula (X) is selected from the group 218 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 219 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- the alpha-v-beta-6 ( ⁇ v ⁇ 6) integrin targeting ligand may be conjugated to the dsRNA agent of the disclosure, e.g., to at least one strand of the dsRNA agent of the disclosure, via a branched carrier group, e.g., a b.
- the alpha-v-beta-6 ( ⁇ v ⁇ 6) integrin targeting ligand conjugated to the dsRNA agent of the disclosure is represented by a compound of Formula (XV): 10 ( ⁇ -ZZ-)x ⁇ -T-R T (XV) or a salt thereof, wherein x is 2, 3, 4, 5, 6, 7, or 8; T is a divalent linking group; ⁇ is a branching group; 15 each ZZ is independently -A’-B’-A’- or a linking group formed by a first reactive pair, wherein 220 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- ALN-529-WO and R 5 is -L-* wherein L is -L 1 -[G-L 2 ]q-G-L 3 -*, * is the bond to a ZZ; and q is 0 or an integer selected from 1 – 25; (e.g., 1-20, or 1-15); 5 L 1 is a bond or -B-A-; each L 2 is independently -A-B-A-; L 3 is a bond or -A-B-A-; each G is independently -D-E-F-, wherein D, E, and F are independently a bond, C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3- 10 10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups; each A is independently a bond, -O-, -S-, or -N(R N )-; each B
- embodiments for the variable ZZ are each as described above for Formula (X); embodiments for the variable R T and L are each as described above 20 for Formula (X).
- T is a bond or **-L 6 -G 1 -[L 5 -G 1 ] q1 -L 4 -, wherein ** is the bond to R T ; q1 is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10; each L 4 , L 5 , and L 6 are independently a bond, -A 1 -B 1 -A 1 - or ZZ 1 ; 222 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- ALN-529-WO ZZ 1 is a group formed by reaction of a reactive pair (e.g., a reaction between an azide and an alkyne or a cycloalkyne); each G 1 is independently -D 1 -E 1 -F 1 -, wherein D 1 , E 1 , and F 1 are independently a bond, C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, 5 each of which is optionally substituted with 1, 2, or 3 R groups; each A 1 is independently a bond, -O-, -S-, or -N(R N1 )-; each B 1 is independently a bond, C(O), C(S), C(NR N1 ), S(O), S(O)2, P(O)(OH), P(S)(OH), or P(S)(SH); each R N1 is independently hydrogen or C
- T is **-L 6 -G 1 -L 5 -G 1 -L 4 -, wherein ** is the bond to R T ;
- L 4 and L 6 are independently -A 1 -B 1 -A 1 -;
- each L 5 is a bond or - A 1 -B 1 -A 1 - (e.g., a bond, -B 1 -A 1 - or -A 1 -B 1 -; or a bond);
- each G 1 is independently C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 15 membered heterocyclyl, aryl, or heteroaryl (e.g., C1-10alkyl or C2-10alkenyl);
- each A 1 is independently a bond, -O-, -S-, or -N(R N1 )-, wherein R N1 is independently hydrogen or C1-6alkyl; and each B 1 is
- T is **-L 6 -G 1 -[L 5 -G 1 ]q1-L 4 -, wherein ** is the bond to R T ; q1 is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10; each L 4 , L 5 , and L 6 are independently a bond or -A 1 -B 1 -A 1 -, or ZZ 1 ; ZZ 1 is a group formed by reaction of an azide and alkyne or cycloalkyne; 25 each G 1 is independently C1-10alkyl, each A 1 is independently a bond, -O-, -S-, or -N(R N1 )-; each B 1 is independently a bond, C(O), C(S), C(NR N1 ), S(O), S(O)2, P(O)(OH), P(S)(OH), or P(S)(SH); and each R N1 is independently hydrogen or C1-6alkyl.
- one L 5 is ZZ 1 .
- ZZ 1 comprises: 223 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO .
- T is **-L 6 -G 1 -L 5 -G 1 -L 4 -, wherein ** is the bond to R T ;
- L 4 and L 6 are independently -A 1 -B 1 - or -B 1 -A 1 -; 5 each L 5 is a bond or - A 1 -B 1 -A 1 - (e.g., a bond, -B 1 -A 1 - or -A 1 -B 1 -; or a bond);
- each G 1 is independently C 1-10 alkyl, C 2-10 alkenyl, C 2-10 alkynyl, C 3-10 cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl (e.g., C 1-10 alkyl or C 2-10 alkenyl);
- each A 1 is independently a bond, -O-, -S-, or -N(R N1 )-, wherein R N1 is independently hydrogen or C 1-6 alky
- T is **-B 1 -G 1 -L 5 -G 1 -B 1 -, wherein ** is the bond to R T ; each L 5 is a bond or - A 1 -B 1 -A 1 - (e.g., a bond, -B 1 -A 1 - or -A 1 -B 1 -; or a bond); each G 1 is independently C 1-10 alkyl, C 2-10 alkenyl, C 2-10 alkynyl, C 3-10 cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl (e.g., C 1-10 alkyl or C 2-10 alkenyl); 15 each A 1 is independently a bond, -O-, -S-, or -N(R N1 )-, wherein R N1 is independently hydrogen or C 1-6 alkyl; and each B 1 is independently a bond, C(O), C(S), S(O) 2 , P(O)
- T is **-L 6 -G 1 -L 5 -G 1 -L 4 -, wherein ** is the bond to R T ;
- L 4 and L 6 are independently -A 1 -B 1 -A 1 -;
- each L 5 is a bond or - A 1 -B 1 -A 1 - (e.g., a bond, -B 1 -A 1 - or -A 1 -B 1 -; or a bond);
- each G 1 is independently C 1-10 alkyl or C 2-10 alkenyl;
- each A 1 is independently a bond, -O-, -S-, or -N(R N1 )-, wherein R N1 is independently hydrogen or C 1-6 alkyl; and
- each B 1 is independently a bond, C(O), C(S), S(O) 2 , P(O)(OH), or P(S)(OH).
- T is **-L 6 -G 1 -L 5 -G 1 -L 4 -, wherein ** is the bond to R T ;
- L 4 and L 6 are independently -B 1 -A 1 - or -A 1 -B 1 -; each L 5 is a bond or - A 1 -B 1 -A 1 - (e.g., a bond, -B 1 -A 1 - or -A 1 -B 1 -; or a bond);
- each G 1 is independently C 1-10 alkyl or C 2-10 alkenyl;
- each A 1 is independently a bond, -O-, -S-, or -N(R N1 )-, wherein R N1 is independently 30 hydrogen or C 1-6 alkyl; and
- each B 1 is independently a bond, C(O), C(S), S(O) 2 , P(O)(OH), or P(S)(OH).
- T is **-B 1 -G 1 -L 5 -G 1 -B 1 -, wherein ** is the bond to R T ; each L 5 is a bond or - A 1 -B 1 -A 1 - (e.g., a bond, -B 1 -A 1 - or -A 1 -B 1 -; or a bond); each G 1 is independently C 1-10 alkyl or C 2-10 alkenyl; 224 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- each A 1 is independently a bond, -O-, -S-, or -N(R N1 )-, wherein R N1 is independently hydrogen or C1-6alkyl; and each B 1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH).
- T is **-B 1 -C1-10alkyl-L 5 -C1-10alkyl-B 1 -, wherein 5 ** is the bond to R T ; each L 5 is a bond or - A 1 -B 1 -A 1 - (e.g., a bond, -B 1 -A 1 - or -A 1 -B 1 -; or a bond); each A 1 is independently a bond, -O-, -S-, or -N(R N1 )-, wherein R N1 is independently hydrogen or C1-6alkyl; and each B 1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH).
- T is -L 4 -G 1 -L 6 -**, wherein ** is the bond to R T ;
- L 4 and L 6 are independently -A 1 -B 1 -A 1 -;
- each G 1 is independently C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, or 3 R groups;
- 15 each A 1 is independently a bond, -O-, -S-, or -N(R N1 )-, wherein R N1 is hydrogen or C1- 6alkyl; and
- each B 1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH).
- T is -L 4 -G 1 -L 6 -**, wherein ** is the bond to R T ; 20 L 4 is -C(O)O- or C(O)N(R N1 )-, wherein R N1 is hydrogen or C1-6alkyl; L 6 is -OP(O)(OH)O- or -OP(S)(OH)O-; and each G 1 is independently C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, or 3 R groups.
- T is one of: (d) **-L 6 -G 1 -ZZ 1 -L 5 -G 1 -L 4 -, 30 (e) **-L 6 -G 1 -L 5 -G 1 -ZZ 1 -G 1 -L 4 -; or (f) **-L 6 -G 1 -ZZ 1 -G 1 -L 4 -, wherein the sum of q2 and q3 is less than q1 In certain embodiments, q2 and q3 are independently 0, 1, 2, 3 or 4.
- each G 1 is independently C 1-20 alkyl (e.g., C 2-15 alkyl; or C 2- 12 alkyl; or C 2-10 alkyl; or C 2-8 alkyl; or C 2-6 alkyl).
- each L 5 is independently -C(O)O-, -OC(O)-, -C(O)N(H)-, - N(H)C(O)-, -OC(O)O-, -OC(O)N(H)-, -N(H)C(O)O-, -N(H)C(O)N(H)-, -P(O)(OH)O-, -OP(S)(OH)-, -OP(O)(OH)O, -OP(S)(OH)O, -P(O)(OH)O-, or -P(S)(OH)O-.
- each L 5 is 225 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO independently -C(O)O-, -OC(O)-, -C(O)N(H)- or -N(H)C(O)-. In certain embodiments, each L 5 is independently -C(O)N(H)- or -N(H)C(O)-.
- each G 1 is independently C 1-20 alkyl (e.g., C 2-15 alkyl; or C 2-12 alkyl; or C 2-10 alkyl); and each L 5 is independently -C(O)O-, -OC(O)-, -C(O)N(H)-, -N(H)C(O)-, -OC(O)O-, - 5 OC(O)N(H)-, -N(H)C(O)O-, -N(H)C(O)N(H)-, -P(O)(OH)O-, -OP(S)(OH)-, -OP(O)(OH)O, - OP(S)(OH)O, -P(O)(OH)O-, or -P(S)(OH)O-.
- each L 5 is independently -C(O)O-, -OC(O)-, -C(O)N(H)-, -N(H)C(
- each G 1 is independently C 1-20 alkyl (e.g., C 2-15 alkyl; or C 2-12 alkyl; or C 2-10 alkyl); and each L 5 is independently -C(O)O-, -OC(O)-, -C(O)N(H)- or -N(H)C(O)-.
- L 6 is a bond.
- L 6 is -C(O)-, -S(O) 2 -, - 10 P(O)(OH)-, or -P(S)(OH)-.
- L 6 is -P(O)(OH)- or -P(S)(OH)-.
- L 6 is -P(O)(OH)-. In certain embodiments, L 6 is -P(S)(OH)-. In certain embodiments, L 6 is -C(O)-. In certain embodiments, L 4 is -C(O)O-, -OC(O)-, -C(O)N(H)-, -N(H)C(O)-, -OC(O)O-, - OC(O)N(H)-, -N(H)C(O)O-, -N(H)C(O)N(H)-, -P(O)(OH)O-, -OP(S)(OH)-, -OP(O)(OH)O, -15 OP(S)(OH)O, -P(O)(OH)O-, or -P(S)(OH)O-.
- L 4 is -P(O)(OH)O-, - OP(S)(OH)-, -OP(O)(OH)O, -OP(S)(OH)O, -P(O)(OH)O-, or -P(S)(OH)O-.
- L 4 is -C(O)O-, -OC(O)-, -C(O)N(H)-, or -N(H)C(O)-.
- T is one of: 20 (d) **-L 6 -G 1 -ZZ 1 -L 5 -G 1 -L 4 -, (e) **-L 6 -G 1 -L 5 -G 1 -ZZ 1 -G 1 -L 4 -; or (f) **-L 6 -G 1 -ZZ 1 -G 1 -L 4 -, wherein the sum of q2 and q3 is less than q1; and ZZ 1 is selected from the group consisting of: 226 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- each G 1 is independently C 1-20 alkyl (e.g., C 2-15 alkyl; or C 2-12 alkyl; or C 2-10 alkyl; or C 2-8 alkyl; or C 2- 6 alkyl).
- each L 5 is independently -C(O)O-, -OC(O)-, -C(O)N(H)-, - N(H)C(O)-, -OC(O)O-, -OC(O)N(H)-, -N(H)C(O)O-, -N(H)C(O)N(H)-, -P(O)(OH)O-, -OP(S)(OH)-, -OP(O)(OH)O, -OP(S)(OH)O, -P(O)(OH)O-, or -P(S)(OH)O-.
- each L 5 is 10 independently -C(O)O-, -OC(O)-, -C(O)N(H)- or -N(H)C(O)-. In certain embodiments, each L 5 is independently -C(O)N(H)- or -N(H)C(O)-.
- each G 1 is independently C1-20 alkyl (e.g., C2-15alkyl; or C2-12alkyl; or C2-10alkyl); and each L 5 is independently -C(O)O-, -OC(O)-, -C(O)N(H)-, -N(H)C(O)-, -OC(O)O-, - OC(O)N(H)-, -N(H)C(O)O-, -N(H)C(O)N(H)-, -P(O)(OH)O-, -OP(S)(OH)-, -OP(O)(OH)O, - 15 OP(S)(OH)O, -P(O)(OH)O-, or -P(S)(OH)O-.
- each L 5 is independently -C(O)O-, -OC(O)-, -C(O)N(H)-, -N(H)C(
- each G 1 is independently C1-20 alkyl (e.g., C2-15alkyl; or C2-12alkyl; or C2-10alkyl); and each L 5 is independently -C(O)O-, -OC(O)-, -C(O)N(H)- or -N(H)C(O)-.
- L 6 is a bond.
- L 6 is -C(O)-, -S(O)2-, - P(O)(OH)-, or -P(S)(OH)-.
- L 6 is -P(O)(OH)- or -P(S)(OH)-.
- L 6 is -P(O)(OH)-. In certain embodiments, L 6 is -P(S)(OH)-. In certain embodiments, L 6 is -C(O)-. In certain embodiments, L 4 is -C(O)O-, -OC(O)-, -C(O)N(H)-, -N(H)C(O)-, -OC(O)O-, - OC(O)N(H)-, -N(H)C(O)O-, -N(H)C(O)N(H)-, -P(O)(OH)O-, -OP(S)(OH)-, -OP(O)(OH)O, - OP(S)(OH)O, -P(O)(OH)O-, or -P(S)(OH)O-.
- L 4 is -P(O)(OH)O-, - 25 OP(S)(OH)-, -OP(O)(OH)O, -OP(S)(OH)O, -P(O)(OH)O-, or -P(S)(OH)O-.
- L 4 is -C(O)O-, -OC(O)-, -C(O)N(H)-, or -N(H)C(O)-.
- T is one of: (a) **-L 6 -C2-12alkyl-[L 5 -C2-12alkyl]q2-ZZ 1 -[L 5 -C2-12alkyl]q3-L 4 -; (c) **-L 6 - C2-12alkyl-L 5 -C2-12alkyl-ZZ 1 -L 5 -C2-12alkyl-L 4 -; 30 (d) **-L 6 -C 2-12 alkyl-ZZ 1 -L 5 -C 2-12 alkyl-L 4 -, (e) **-L 6 -C 2-12 alkyl-L 5 -C 2-12 alkyl-ZZ 1 -C 2-12 alkyl-L 4 -; or (f) **-L 6 -C2-12alkyl-ZZ 1 -C2-12alkyl-L 4 -, 227 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alny
- each L 5 is independently -C(O)O-, -OC(O)-, -C(O)N(H)-, - N(H)C(O)-, -OC(O)O-, -OC(O)N(H)-, -N(H)C(O)O-, -N(H)C(O)N(H)-, -P(O)(OH)O-, -OP(S)(OH)-, 5 -OP(O)(OH)O, -OP(S)(OH)O, -P(O)(OH)O-, or -P(S)(OH)O-.
- each L 5 is independently -C(O)O-, -OC(O)-, -C(O)N(H)- or -N(H)C(O)-. In certain embodiments, each L 5 is independently -C(O)N(H)- or -N(H)C(O)-. In certain embodiments, L 6 is a bond. In certain embodiments, L 6 is -C(O)-, -S(O) 2 -, - P(O)(OH)-, or -P(S)(OH)-. In certain embodiments, L 6 is -P(O)(OH)- or -P(S)(OH)-.
- L 6 is -P(O)(OH)-. In certain embodiments, L 6 is -P(S)(OH)-. In certain embodiments, L 6 is -C(O)-. In certain embodiments, L 4 is -C(O)O-, -OC(O)-, -C(O)N(H)-, -N(H)C(O)-, -OC(O)O-, - OC(O)N(H)-, -N(H)C(O)O-, -N(H)C(O)N(H)-, -P(O)(OH)O-, -OP(S)(OH)-, -OP(O)(OH)O, - OP(S)(OH)O, -P(O)(OH)O-, or -P(S)(OH)O-.
- L 4 is -P(O)(OH)O-, - 15 OP(S)(OH)-, -OP(O)(OH)O, -OP(S)(OH)O, -P(O)(OH)O-, or -P(S)(OH)O-.
- L 4 is -C(O)O-, -OC(O)-, -C(O)N(H)-, or -N(H)C(O)-.
- T is selected from the following, wherein ** is the bond to R T : ( q) **-C(O)-C1-10alkyl-L5-C1-10alkylC(O)-, (r) **-C(O)-C2-10alkyl-L5-C2-10alkyl-C(O)-, 20 (s) **-C(O)-C4-10alkyl-L5-C4-10alkyl-C(O)-, (t) **-C(O)-C6-10alkyl-L5-C6-10alkyl-C(O)-, (u) **-C(O)-C2-8alkyl-L5-C2-8alkyl-C(O)-, (v) **-C(O)-C2-6alkyl-L5-C2-6alkyl-C(O)-, (w) **-C(O)-C2-4alkyl-L5-C2-4alkyl-C(O)- 25 (x
- T is selected from the following, wherein ** is the bond to R T : 228 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO ( ff) **- N(H)C(O)-C6-12alkyl-C(O)-, (gg) **- N(H)C(O)-C10alkyl-C(O)-, (hh) **-C(O)-C2-20alkyl-C(O)N(H)-, (ii) **-C(O)-C6-20alkyl-C(O)N(H)-, 5 (jj) **-C(O)-C6-12alkyl-C(O)N(H)-, (kk) **-C(O)-C10alkyl-C(O)N(H)-, (ll) **-N(H)C(O)-C2-20alkyl-C(O)N(H)
- T is -L 4 -G 1 -L 6 -**, wherein ** is the bond to R T ;
- L 4 is -C(O)O- or C(O)N(R N1 )-, wherein R N1 is hydrogen or C1-6alkyl;
- L 6 is -OP(O)(OH)O- or -OP(S)(OH)O-; and 15 each G 1 is independently C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with one R group.
- T is -L 4 -G 1 -L 6 -**, wherein ** is the bond to R T ;
- L 4 is -C(O)O- or C(O)N(R N1 )-, wherein R N1 is hydrogen or C1-6alkyl;
- L 6 is -OP(O)(OH)O- or -OP(S)(OH)O-; and 20 each G 1 is independently C3-10cycloalkyl or 3-10 membered heterocyclyl.
- T is -L 4 -G 1 -L 6 -**, wherein ** is the bond to R T ;
- L 4 is -C(O)O- or C(O)N(R N1 )-, wherein R N1 is hydrogen or C1-6alkyl;
- L 6 is -OP(O)(OH)O- or -OP(S)(OH)O-; and each G 1 is independently C3-10cycloalkyl or 3-10 membered heterocyclyl.
- X is O or S (e.g., S).
- T is **-L 6 -[G 5 -O]q5-G 5 -L 4 -, wherein ** is the bond to R T ;
- q5 is an integer selected from 1 to 20;
- L 4 and L 6 are independently -A 1 -B 1 -A 1 -, wherein 30 each A 1 is independently a bond, -O-, -S-, or -N(R N1 )-, wherein R N1 is hydrogen or C1-6alkyl;
- each B 1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH);
- T is **-C(O)-[CH2CH2-O]q5-G 5 -L 4 -, wherein ** is the bond to R T ; 35 q5 is an integer selected from 1 to 20; L 4 is -A 1 -B 1 -A 1 -, wherein 229 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- each A 1 is independently a bond, -O-, -S-, or -N(R N1 )-, wherein R N1 is hydrogen or C1-6alkyl; each B 1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); G 5 is C1-10alkyl.
- T is **-C(O)-[CH2CH2-O]q5-G 5 -L 4 -, wherein ** is the bond to R T ;
- 5 q5 is an integer selected from 1 to 20;
- L 4 is -A 1 -B 1 or -B 1 -A 1 -, wherein each A 1 is independently -O- or -N(H)-, each B 1 is independently C(O),
- G 5 is C1-10alkyl (e.g., C2-10alkyl or C2-6alkyl).
- T is **-C(O)-[CH2CH2-O]q5- C2-10alkyl-C(O)N(H)-, wherein ** is the bond to R T , wherein q5 is an integer selected from 1 to 20 (e.g., 1 to 10, or 2 to 10; or 2 – 8; or 1; or 2; or 3; or 4.)
- Formula (XV) is according to one of Formulae (XVa) through (XVc), respectively: (XVc).
- ⁇ is #–[G 2 -L 7 ]q2-* or #–G 3 -([L 7 -G 4 ]q3-*)y, wherein 20 # is the bond to T; y is 1, 2, 3, 4, or 5; q2 is 1, 2, 3, 4, 5, 6, 7, or 8; q3 is 0, 1, 2, 3, 4, 5, 6, 7, or 8; each G 2 , G 3 , and G 4 is independently -D 2 -E 2 -F 2 -, wherein 25 D 2 , E 2 , and F 2 are independently a bond, C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, 4, or 5 R B groups, and wherein each G 2 and G 4 optionally contains at least one bond to a ZZ (e.g.,
- each L 7 is independently -A 2 -B 2 -A 2 -; wherein each A 2 is independently a bond, -O-, -S-, or -N(R N2 )-; each B 2 is independently a bond, C(O), C(S), C(NR N2 ), S(O), S(O)2, P(O)(OH), P(S)(OH), or P(S)(SH); and 5 each R N2 is independently hydrogen, C1-6alkyl, a bond to a ZZ, or two R N2 within an -A 2 -B 2 - A 2 - group taken together with the atoms to which they are connected from a 4-8 membered heterocyclyl; and each R B is independently halogen, cyano, azido, nitro, -N(R 10 )2, -O(R 10 ), -S(R 10 ), -C(O)OR 10 , 10 -C(O)R 10 , -
- ⁇ is #–[G2-L7]q2-* wherein # is the bond to T; q2 is 1, 2, 3, 4, 5, 6, 7, or 8; q3 is 0, 1, 2, 3, 4, 5, 6, 7, or 8; 20 each G 2 , G 3 , and G 4 is independently -D 2 -E 2 -F 2 -, wherein D 2 , E 2 , and F 2 are independently a bond, C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, 4, or 5 R B groups, and wherein each G 2 optionally contains at least one bond to ZZ; 25 each L 7 is independently -A 2 -B 2 -A 2 -; each A 2 is independently a bond, -O-, -S-, or -N(R N2 )-; each B 2 is independently a bond,
- - ⁇ - is #–[G 2 -L 7 ]q2-*, where # is the bond to T and * is a bond to a ZZ group.
- such embodiments include the following, wherein each * is a bond to a ZZ; # is the bond to T, each G 2 is independently C 1-10 alkyl, C 2-10 alkenyl, C 3-10 cycloalkyl, 3-10 membered 5 heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, 4, or 5 R B groups; and each L 7 is independently -A 2 -B 2 -A 2 -, wherein each A 2 is independently a bond, -O-, -S-, or - N(R N2 )-; each B 2 is independently a bond, C(O), S(O) 2 , P(O)(OH), or P(S)(OH).
- each G 2 is independently C 1-10 alkyl, each optionally substituted with 1 or 2 R B groups. In one embodiment, each G 2 is independently C 1-10 alkyl. 10 In one embodiment, each L 7 is independently -A 2 -B 2 -A 2 -, wherein each A 2 is independently a bond, -O-, -S-, or -N(R N2 )-; and each B 2 is independently a bond, C(O) or S(O) 2, provided that at least one A 2 is not a bond.
- each L 7 is independently -A 2 -B 2 - or - B 2 -A 2 -, wherein each A 2 is independently, -O-, -S-, or -N(R N2 )-; and each B 2 is independently a bond, C(O) or S(O) 2.
- such embodiments include each of the following, wherein # is the bond to T and each * is a bond to a ZZ group. ; and each G 2 is independently C 1-10 alkyl.
- such embodiments include each of the following, wherein # is the bond to T and each * is a bond to a ZZ; 232 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein # is the bond to T and each * is a bond to a ZZ group.
- # is the bond to T and each * is a bond to a ZZ group.
- -#–G 3 -([L 7 -G 4 ] q3 -*) y where # is the bond to T and * is a bond to a ZZ group.
- such embodiments include each of the following, 5 wherein # is the bond to T, each * is a bond to a ZZ group, and each L 7 is selected from the group consisting of -O-, -S-, -N(H)-, -C(O)O-, -OC(O)-, - C(O)N(H)-, -OC(O)O-, -N(H)C(O)O-, -OC(O)N(H)-, -OP(O)(OH)O-, or -OP(S)(OH)O-; and each G 4 is independently -D 2 -E 2 -F 2 -, wherein each D 2 and F 2 are independently a bond or C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3- 10 10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, 4,
- each L 7 is selected from the group consisting of -O-, -S-, -N(H)-, -N(H)C(O)-, -C(O)N(H)-, - OP(O)(OH)O-, and -OP(S)(OH)O-; and each G 4 is independently -D 2 -E 2 -F 2 -, wherein each D 2 and F 2 are independently a bond or C1-10alkyl; 233 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- each E 2 is independently C1-10alkyl, C2-10alkenyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, 4, or 5 R B groups.
- each L 7 is selected from the group consisting of -O-, -S-, -N(H)-, -N(H)C(O)-,-C(O)N(H)-, - 5 OP(O)(OH)O-, and -OP(S)(OH)O-; and each G 4 is independently C1-10alkyl, C2-10alkenyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, 4, or 5 R B .
- each L 7 is selected from the group consisting of -O-, -S-, -N(H)-, -N(H)C(O)-, -C(O)N(H)-, - 10 OP(O)(OH)O-, and -OP(S)(OH)O-; and each G 4 is independently C1-10alkyl which is optionally substituted with 1 or, 2 5 R B groups.
- each L 7 is selected from the group consisting of -O-, -S-, -N(H)-, --N(H)C(O)-, C(O)N(H)-, - 15 OP(O)(OH)O-, and -OP(S)(OH)O-; and each G 4 is independently C1-10alkyl.
- each L 7 is selected from the group consisting of --N(H)C(O)- and C(O)N(H)-; and each G 4 is independently C1-10alkyl.
- such embodiments include each of the following, wherein each * is a bond to a wherein # is the bond to T and each * is a bond to a ZZ group.
- 234 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO ZZ Embodiments, Formulae (XV) and (XVa) through (XVc)
- ZZ is a linking group formed by a reactive pair.
- ZZ comprises a group selected from the group consisting of 235 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
- ZZ comprises Group(1).
- ZZ comprises Group(2).
- ZZ comprises Group(3).
- ZZ comprises Group(4).
- ZZ comprises Group(5).
- ZZ comprises Group(6).
- ZZ comprises Group(7).
- ZZ comprises 5 Group(8).
- ZZ comprises Group(9).
- ZZ comprises Group(10).
- ZZ comprises Group(11).
- ZZ comprises Group(12). In some embodiments, wherein ZZ is -A’-B’-A’-. In some embodiments, ZZ is -A’-B’-A’-, wherein 10 each A’ is independently a bond, -O-, -S-, or -N(R N3 )-, wherein R N3 is independently hydrogen or C 1-6 alkyl and each B’ is independently CH 2 , C(O), C(S), S(O) 2 , P(O)(OH), or P(S)(OH). In some embodiments, ZZ is CH 2 , C(O), C(S), S(O) 2 , P(O)(OH), or P(S)(OH).
- ZZ is C(O), C(S), or S(O) 2 . 15 In some embodiments, ZZ is P(O)(OH), or P(S)(OH). In some embodiments, ZZ is –C(O)-. In some embodiments, ZZ is -A’-B’- or -B’-A’- wherein each A’ is independently -O-, -S-, or -N(R N3 )-; each B’ is independently CH 2 , C(O), C(S), S(O) 2 , P(O)(OH), or P(S)(OH); and 20 each R N3 is independently hydrogen or C 1-6 alkyl.
- ZZ is -A’-B’- or -B’-A’- wherein each A’ is independently -O- or -N(R N3 )-, wherein R N3 is independently hydrogen or C 1- 6 alkyl.
- each B’ is independently CH 2 , C(O), S(O) 2 , P(O)(OH), or P(S)(OH); and 25 each R N3 is independently hydrogen or C 1-6 alkyl.
- ZZ is -C(O)N(R N3 )-, -N(R N3 )C(O)-, -C(O)O-, -OC(O)-, - OC(O)N(R N3 )-, -N(R N3 )C(O)O-, -N(R N3 )C(O)N(R N3 )-, -S(O)2N(R N3 )-, or -N(R N3 )S(O)2-, wherein R N3 10 is independently hydrogen or C1-6alkyl.
- ZZ is -C(O)N(R N3 )- or -N(R N3 )C(O)-, wherein R N3 is independently hydrogen or C1-6alkyl. In some embodiments, ZZ is -C(O)O- or -OC(O)-. In some embodiments, ZZ is -OC(O)N(R N3 )-, -N(R N3 )C(O)O-, or -N(R N3 )C(O)N(R N3 )-, 15 wherein R N3 is independently hydrogen or C1-6alkyl.
- ZZ is -N(R N3 )C(O)N(R N3 )-, wherein R N3 is independently hydrogen or C1-6alkyl. In some embodiments, ZZ is -OC(O)N(R N3 )- or -N(R N3 )C(O)O-, wherein R N3 is independently hydrogen or C1-6alkyl. 20 In some embodiments, ZZ is -OP(O)(OH)O-, -OP(S)(OH)O-, -OP(O)(OH)-, -OP(S)(OH)-, - P(O)(OH)O-, or -P(S)(OH)O-. 25 and .
- R T is R T1 and is as defined for Formula (X).
- R T is -G 0 -OR T1 , wherein R T1 is as defined for Formula (X) and G 0 is selected from: 5 (c) G0 is -D0-E0-F0-, wherein D 0 and F 0 are independently a bond or C1-10alkyl optionally substituted with 1, 2, 3, or 4 R groups; and E 0 is C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups; 10 (d) G0 is -D0-E0-F0-, wherein D 0 and F 0 are independently a bond or C1-10alkyl optionally substituted with 1, 2, 3, or 4 R groups; and E 0 is 3-10 membered heterocyclyl optionally substituted with 1, 2, 3, or 4 R groups; and ( e) G0 is 3-10 membered heterocyclyl optionally substituted with 1 or 2 R groups; 15 ( f)
- G0 is C1-10alkyl or C2-10alkenyl, each of which is optionally substituted with 1 or 2 R groups;
- G0 is C1-10alkyl optionally substituted with 1 or 2 R groups;
- 5 G0 is C1-10alkyl, optionally substituted with -O(Ra), wherein Ra is independently hydrogen, C 1-6 alkyl, or a hydroxyl protecting group; e.g., , ( l) G0 is C1-10alkyl, and ( m) G0 is absent (a bond); 10 wherein * represents the bond to T, the broken bond represents the bond to OR T1 , and R is - C 1-6 alkyl-OR a or -OR a , wherein R a is independently hydrogen or C 1-6 alkyl.
- R Y is defined in the structure of Formula (XII) according to any one of 15 the R Y Embodiments of Formula (IV).
- Formula (XII) has the structure described above for any embodiment of Formula (IV), where the variable Z is replaced by a bond to a ZZ group.
- Formula (XII) has the structure of any one of Formula (XII-a) through (XII-h) and (XII-t): 20 (XII-e) (XII-f) 239 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- L Embodiments Formula and (XII-a) through (XII-h) and (XII-r) In some embodiments of any one of Formula (XII) and Formulae (XII-a) through (XII-h) and 10 (XII-r), L is -L 1 -[G-L 2 ]q-G-L 3 -*, wherein * is the bond to a ZZ group.
- L is -L 1 -[G-L 2 ]q-G-L 3 -*, wherein q is 0, 1, 2, 3, 4, or 5.
- L is -L 1 -[G-L 2 ]q-G-L 3 -*, wherein q is 0, 1, 2, 3, or 4
- L is -L 1 -[G-L 2 ]q-G-L 3 -*, wherein q is 0, 1, 2, or 3.
- L is -L 1 -[G-L 2 ]q-G-L 3 -*, wherein q is 0, 1, or 2.
- L is -L 1 -[G-L 2 ]q-G-L 3 -*, wherein q is 1, 2, 3, 4, or 5.
- L is -L 1 -[G-L 2 ]q-G-L 3 -*, wherein q is 1, 2, 3, or 4.
- L is -L 1 -[G-L 2 ]q-G-L 3 -*, wherein q is 1, 2, or 3.
- L is -L 1 -[G-L 2 ]q-G-L 3 -*, wherein q is 1 or 2.
- L is -L 1 -[G-L 2 ]q-G-L 3 -*, wherein q is 4.
- L 20 is -L 1 -[G-L 2 ]q-G-L 3 -*, wherein q is 3.
- L is -L 1 -[G-L 2 ]q-G-L 3 -*, wherein q is 2.
- 240 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
- L is -L 1 -G-L 2 -G-L 3 -*.
- L is -L 1 -G-L 3 -*. In another embodiment, L is -G-L 3 -*. In another embodiment , L is -L 1 -G-*. In another embodiment, L is -G-*. In another embodiment, wherein L is -[G-L 2 ] q -G-*, wherein q is 1, 2, 3, 4, or 5 (e.g., q 5 is 2; or q is 3; or q is 4; or q is 5).
- each instance of A-B-A- is independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(R N )-, -N(R N )C(O)-, -OC(O)O-, -OC(O)N(R N )-, - N(R N )C(O)O-, -N(R N )C(O)N(R N )-, -OP(O)(OH)O- ,-OP(S)(OH)O-, -O-, and -N(R N )-, wherein each R N is independently hydrogen or C1-6alkyl.
- each instance of A-B-A- is independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(R N )-, -N(R N )C(O)-, -OC(O)N(R N )-, -N(R N )C(O)O-,- N(R N )C(O)N(R N )-, -O-, and -N(R N )-, wherein each R N is independently hydrogen or C1-6alkyl.
- each instance of A-B-A- is independently selected from the group consisting of -C(O)N(R N )-, -N(R N )C(O)-, -OC(O)N(R N )-, -N(R N )C(O)O-, -N(R N )C(O)N(R N )-, -O-, 15 and -N(R N )-, wherein each R N is independently hydrogen or C1-6alkyl.
- each instance of A-B-A- is independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(R N )-, -N(R N )C(O)-, -O-, and -N(R N )-, wherein each R N is independently hydrogen or C1-6alkyl.
- each instance of A-B-A- is independently selected from the group 20 consisting of -C(O)N(R N )-, -N(R N )C(O)-, -O-, and -N(R N )-, wherein each R N is independently hydrogen or C1-6alkyl.
- D and F are each independently a bond, C1-10alkyl, C2-10alkenyl, or C2-10alkynyl, each optionally substituted with 1, 2, 3, or 4 R groups; and 25 E is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups.
- D and F are each independently a bond or C1-10alkyl optionally substituted with 1, 2, 3, or 4 R groups; and 30 E is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups.
- each G is independently C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3- 10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups.
- each G is independently C1-10alkyl, optionally substituted with 1, 2, or 3 R groups. In some embodiments, each G is independently C1-10alkyl, optionally substituted with 1 or 2 R groups. 241 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- each G is independently C1-10alkyl, optionally substituted with one R group
- L is -L 1 -G-L 3 -*, wherein * is the bond to a ZZ group ;
- G is -D-E-F-, wherein D, E, and F are independently a bond, C1-10alkyl, C2-10alkenyl, C2- 5 10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups;
- L 1 is -B-A-;
- L 3 is a bond or -A-B-A-;
- each A is independently a bond, -O-, -S-, or -N(R N )-, wherein each R N is independently 10 hydrogen or C1-6alkyl.
- each B is independently a bond, CH2, C(O), S(O)2, P(O)(OH), or P(S)(OH); and
- L is -L 1 -G-L 3 -*, wherein * is the bond to a ZZ group; G is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups; 15 L 1 is -B-; L 3 is a bond or -A-B-A-; each A is independently a bond, -O-, -S-, or -N(R N )-, wherein each R N is independently hydrogen or C1-6alkyl; and each B is independently a bond, CH2, C(O), S(O)2, P(O)(OH), or P(S)(OH; and 20 In some embodiments, L is -L 1
- L is -L 1 -G-*, wherein * is the bond to a ZZ group; G is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, each of which is optionally substituted with 1 or 2 R groups; 30 L 1 is -B-A-, wherein A is a bond, -O-, -S-, or -N(R N )-, each R N is independently hydrogen or C1-6alkyl; and B is a bond, C(O), S(O)2, P(O)(OH), or P(S)(OH).
- L is -L 1 -G-*, wherein * is the bond to a ZZ group; G is C1-10alkyl or C2-10alkenyl, each of which is optionally substituted with 1 or 2 R groups; 35 L 1 is bond, C(O), S(O)2, P(O)(OH), or P(S)(OH); and R N is hydrogen or C1-6alkyl.
- L is wherein * is the bond to a ZZ group; k is an integer from 1 to 10; L 1 is bond, C(O), C(S), C(NR N ), S(O) 2 , P(O)(OH), or P(S)(OH); and R N is hydrogen or C 1-6 alkyl.
- L is wherein * is the bond to a ZZ group; k is an 5 integer from 1 to 10; L 1 is bond, C(O), P(O)(OH), or P(S)(OH).
- L is , wherein * is the bond to a ZZ group; k is an integer from 1 to 10; or an integer from 2 to 10; or an integer from 3 to 10; or an integer from 4 to 10; or an integer from 5 to 10; or an integer from 5 to 9; or an integer from 5 to 8; or an integer from 5 to 7. 10 In some embodiments, L is , wherein * is the bond to a ZZ group; t is an integer from 0 to 10 (e.g., an integer from 1 to 5; or 1; or 2; or 3).
- t is an integer from 0 to 10 (e.g., an integer from 1 to 5 or 1; or 2; or 3); a is an integer from 1 to 3; and s and s’ are each independently an integer from 1 to 15 24 (e.g., an integer from 1 to 16; an integer from 1 to 10; an integer from 3 to 10; an integer from 3 to 7; or an integer from 4 to 6).
- * is the bond to a ZZ group; a is 1, 2 or 3; and each s, s’, and s” independently is an integer from 1 to 24 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7, or an integer20 from 4 to 6).
- L is wherein * is the bond to a ZZ group; and s, s’, and s’’ are independently is an integer from 1 to 24 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7, or an integer from 4 to 6).
- each s, s’, and s independently is an integer from 1 to 24(e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7, or an integer from 4 to 6).
- L is wherein * is the bond to ZZ; s and 5 k are independently is an integer from 1 to 20 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6); and w is an integer from 1 to 10 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6).
- L is wherein * is the bond to ZZ 10 and w is an integer from 1 to 20 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6).
- L is C1-20 alkyl. In some embodiments, L is C2-20 alkyl. In some embodiments, L is C6-20 alkyl. In some embodiments, L is C8-12 alkyl. In some embodiments, L is C10 alkyl. 15 In another embodiment, wherein L is -[G-L 2 ]q-G-*, wherein q is 1, 2, 3, 4, or 5 (e.g., q is 2; or q is 3; or q is 4; or q is 5), each G is indepdently C 1-10 alkyl and L 2 is O, S, or N(H).
- each G is indepdently C1-10alkyl and L 2 is O.
- L is -[CH 2 CH 2 O] q -G-*, wherein q is 1, 2, 3, 4, or 520 (e.g., q is 2; or q is 3; or q is 4; or q is 5)
- G is indepdently C 1-10 alkyl.
- L is , wherein * is the bond to ZZ; t is an integer from 0 to 10 (e.g., an integer from 1 to 5; or 1; or 2; or 3). I n some embodiments, L is , wherein * is the bond to ZZ. In some embodiments, L is , wherein * is the bond to ZZ; t is 1 to 10 25 (e.g., 1-5; or 1-3; or 1; or 2; or 3); and z is 1-10 (e.g., 1-6; or 1-4; or 1; or 2; or 3 or 4 or 5 or 6). 244 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- L is , wherein * is the bond to ZZ, and t is an integer from 1 to 5 (e.g., 1; or 2; or 3). I n some embodiments, , wherein * is the bond to ZZ.
- R L Embodiments, Formulae (XII) and (XII-a) through (XII-h) and (XII-r) 5 In some embodiments of any one of Formula (XII) and Formulae (XII-a) through (XII-h) and (XII-r), R L is -N(R 3 )(R 4 ), wherein R 3 is hydrogen or C1-6alkyl and R 4 is R 5 .
- R L is -N(R 3 )(R 4 ), wherein R 3 is hydrogen and R 4 is R 5 . In some embodiments, R L is -N(R 3 )(R 4 ), wherein R 3 is C1-3alkyl and R 4 is R 5 . In some embodiments, R L is -N(R 3 )(R 4 ), wherein R 3 is methyl and R 4 is R 5 . 10 In some embodiments, R L is --N(R 3 )(R 4 ), wherein R 3 and R 4 taken together with the nitrogen atom to which they are attached form a 4 – 8 membered monocyclic heterocyclyl group that is substituted with R 5 .
- R L is --N(R 3 )(R 4 ), wherein R 3 and R 4 taken together with the nitrogen atom to which they are attached form a 4 – 8 membered monocyclic heterocyclyl group that 15 is substituted with R 5 , provided that R 3 and R 4 taken together with the nitrogen atom to which they are attached do not form a morpholino group.
- R L is --N(R 3 )(R 4 ), wherein R 3 and R 4 taken together with the nitrogen atom to which they are attached form a group that is piperidinyl, piperazinyl, pyrrolidinyl, imidazolidinyl, pyrazolidinyl, oxazolidinyl, thiazolidinyl, azetidinyl, pyrrolinyl, imidazolinyl, or 20 pyrazolinyl, each substituted wi In some embodiments, .
- R L is 25 2, 3, 4, 5, 6, 7, 8, 9 or 10; a is an integer from 1 to 3 and s and s’ are each independently an integer from 1 to 24 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6). 245 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- R L is 10 wherein * is a bond to a ZZ group; s, s’, and s’’ are independently an integer from 1 to 24 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6); and t is an integer from 1 to 10 (e.g., an integer from 1 to 8, an integer from 1 to 5, an integer from 1 to 3, or 1, or 2, or 3).
- R L is , wherein * is a bond to a ZZ group; s is an integer from 1 to 24 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 t 20 , wherein * is a bond to a ZZ group; s is an integer from 1 to 24 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6); and t is an integer from 0 to 10 (e.g., an integer from 1 to 8, an integer from 1 to 5, an integer from 1 to 3, or 1, or 2, or 3). 25 In some embodiments, R L is -R 5 .
- RL is , wherein * is a bond to a ZZ group; t 5 is 0 to 10 (e.g., 1-5; or 1-3; or 1 I n some embodiments, wherein * is a bond to a ZZ group; s and k are independently is an integer from 1 to 20 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6); and w is an integer from 1 to 10 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to10 10, an integer from 3 to 7 or an integer from 4 to 6).
- R L is wherein * is a bond to a ZZ group.
- R L is 247 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein * is a bond to a ZZ group and w is an integer selected from 1-10 (e.g., 2-10, 2-8, 4-8). . 5
- the compound of Formula (XII) is according to one of Formulae (XII-i) through (XII-j) 248 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- each R 21 is independently selected from group consisting of R and a nitrogen protecting group, 5 and L is defined according to Formula (XII), or according to any of the preceding embodiments of L.
- R 1 is hydrogen.
- R 1 is C 1-6 alkyl (e.g., methyl or t- butyl).
- the compound of Formula (XII) is according to one of Formulae (XII- m) through (XII-q) and (XII-t): 249 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO or a salt thereof, wherein * is a bond to a ZZ group, p is 0, 1 or 2; each R 21 is independently selected from group consisting of R; R P is hydrogen or a nitrogen protecting group (e.g., a nitrogen protecting group), 5 and L is defined according to Formula (XII), or according to any of the preceding embodiments of L, wherein R and the remaining variables are as defined in Formula (XII).
- the compound of Formula (XII) is according to one of Formulae (XII-u) through (XII-z): (XII-u) (XII-v) 250 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- R 21 is independently selected from group consisting of R;
- R P is hydrogen or a nitrogen protecting group (e.g., a nitrogen protecting group), and L is defined according to Formula (XII), or according to any of the preceding 5 embodiments of L, wheren R and the remaining variables are as defined in Formula (XII).
- R 1 is hydrogen.
- R 1 is C 1-6 alkyl (e.g., methyl or t-butyl).
- R N3 is independently hydrogen or C 1-6 alkyl; ⁇ is selected from, 251 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein # is the bond to T and each * is a bond to a ZZ group; and wherein ** represents the bond to T, and the remaining variables are as defined in Formula (XV), and any embodiment thereof.
- ⁇ is selected from Formula (XII) and any one of Formula (XII-a) through (XII-q) and (XII-t) through (XII-z);
- ZZ is - C(O)N(R N3 )-, -N(R N3 )C(O)-, -C(O)O-, -OC(O)-, wherein R N3 is independently hydrogen or C 1-6 alkyl;
- 10 ⁇ is selected from, wherein # is the bond to T and each * is a bond to a ZZ group. 15 and the remaining variables are as defined in Formula (XV), and any embodiment thereof.
- R N3 is independently hydrogen or C1-6alkyl
- ⁇ is selected from, ⁇ wherein # is the bond to T and each * is a bond to a ZZ group, G 3 is C1-10alkyl; 10 each G 4 is independently C1-10alkyl; and , wherein ** represents the bond to T, and the remaining variables are as defined in Formula (XV), and any embodiment thereof.
- 15 ⁇ is selected from Formula (XII) and any one of Formula (XII-a) through (XII-q) and (XII-t) through (XII-z); ZZ is -C(O)-, -C(O)N(R N3 )-, -N(R N3 )C(O)-, -C(O)O-, -OC(O)-, wherein R N3 is independently hydrogen or C1-6alkyl; ⁇ is selected from, , , , 253 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- ⁇ is selected from Formula (XII) and any one of Formula (XII-i) through (XII-q) and (XII-t) through (XII-z);
- ZZ is -OP(O)(OH)O-, -OP(S)(OH)O-, -C(O)N(R N3 )-, -N(R N3 )C(O)-, -C(O)O-, -OC(O)-, wherein R N3 is independently hydrogen or C1-6alkyl;
- 10 T is **-L 6 -G 1 -L 5 -G 1 -L 4 -, wherein ** is the bond to R T ;
- L 4 and L 6 are independently -B 1 -A 1 - or -A 1 -B 1 -; 254 ME1 ⁇ 53453057.v1
- each L 5 is a bond or - A 1 -B 1 -A 1 - (e.g., a bond, -B 1 -A 1 - or -A 1 -B 1 -; or a bond); each G 1 is independently C1-10alkyl or C2-10alkenyl; each A 1 is independently a bond, -O-, -S-, or -N(R N1 )-, wherein R N1 is independently hydrogen or C1-6alkyl; and 5 each B 1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); and wherein ** represents the bond to T, and the remaining variables are as defined in Formula (XV), and any embodiment thereof.
- 10 ⁇ is selected from Formula (XII) and any one of Formula (XII-m) through (XII-q) and (XII-t) through (XII-z);
- ZZ is -OP(O)(OH)O-, -OP(S)(OH)O-, -C(O)N(R N3 )-, -N(R N3 )C(O)-, -C(O)O-, -OC(O)-, wherein R N3 is independently hydrogen or C1-6alkyl;
- 15 T is **-L 6 -G 1 -L 5 -G 1 -L 4 -, wherein ** is the bond to R T ;
- L 4 and L 6 are independently -B 1 -A 1 - or -A 1 -B 1 -; each L 5 is a bond or - A 1 -B 1 -A 1 - (e.g., a bond, -B 1 -A 1 - (e.
- ⁇ is selected from Formula (XII) and any one of Formula (XII-m) through (XII-q) and (XII-t) through (XII-z); ZZ is -C(O)N(H)- or -N(H)C(O)-; 5 ⁇ is T is **-L 6 -G 1 -L 5 -G 1 -L 4 -, wherein ** is the bond to R T ; L 4 is -A 1 -B 1 -; L 6 is -B 1 -; L 5 is a bond, -B 1 -A 1 -, or -A 1 -B 1 -; 10 each G 1 is independently C1-10alkyl; each A 1 is independently a bond, -O- or -N(H); bond t ,
- R P3 is hydrogen; 256 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO ⁇ is selected from Formula (XII) and any one of Formula (XII-m) through (XII-q) and (XII- t); ZZ is -C(O)N(H)- or -N(H)C(O)-; and T is **-L 6 -G 1 -L 5 -G 1 -L 4 -, wherein ** is the bond to R T ; L 4 is -A 1 -B 1 -; 5 L 6 is -B 1 -; L 5 is a bond, -B 1 -A 1 -, or -A 1 -B 1 -; each G 1 is independently C1-10alkyl; each A 1 is independently a bond, -O- or -N(H); each
- ⁇ is selected from Formula (XII) and any one of Formula (XII-m) through (XII-q) and (XII-t) through (XII-z);
- ZZ is -OP(O)(OH)O-, -OP(S)(OH)O-, -C(O)N(R N3 )-, -N(R N3 )C(O)-, -C(O)O-, -OC(O)-, 15 wherein R N3 is independently hydrogen or C1-6alkyl;
- T is ***-L 6 -[G 5 -O] q5 -G 5 -L 4 -, wherein q5 is an integer selected from 1 to 20;
- L 4 and L 6 are independently -A 1 -B 1 -A 1 -, wherein 20 each A 1 is independently a bond, -O-, -S-, or -N(R N1 )-, wherein R N1 is
- ⁇ is selected from Formula (XII) and any one of Formula (XII-m) through (XII-q) and (XII-t) 5 through (XII-z), wherein L is wherein * is the bond to ZZ; s and k are independently is an integer from 1 to 20 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6); and w is an integer from 1 to 10 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6); ; 10 ZZ is -C(O)N(H)-, -N(H)C(O)-; T is ***-L 6
- ⁇ is selected from Formula (XII) and any one of Formula (XII-m) through (XII-q) and (XII-t) t hrough (XII-z), wherein L is wherein * is the bond to ZZ and w is an integer from 1 to 20 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6; 258 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- ALN-529-WO ZZ is -C(O)N(H)-, -N(H)C(O)-; T is **-C(O)-[CH2CH2-O]q5- C2-10alkyl-C(O)N(H)-, wherein ** is the bond to the pyrrolidine ring and q5 is an integer selected from 1 to 20 (e.g., 1 to 10, or 2 to 10; or 2 – 8; or 1; or 2; or 3; or 4); and the remaining variables are as defined in Formula (XV), and any embodiment thereof.
- R T1 is -L L -oligonucleotide, wherein L L is a divalent linker that connects to the 3’-end of the 10 oligonucleotide, the 5’-end of the oligonucleotide, or an internal 2’- or 3’ position on a internal nucleotide (i.e., a nucleotide that is not the 5’-terminal or 3’-terminal nucleoside).
- L L is a divalent linker that connects to the 3’-end of the 10 oligonucleotide, the 5’-end of the oligonucleotide, or an internal 2’- or 3’ position on a internal nucleotide (i.e., a nucleotide that is not the 5’-terminal or 3’-terminal nucleoside).
- R T1 is -L L -oligonucleotide, wherein L L is a divalent linker that connects to the 3’-end of the oligonucleotide, such as one of : directly to the 3’-carbon of the 3’-terminal nucleoside; 15 directly to the 3’-O of the 3’-terminal nucleoside; directly to the 4’-carbon of the 3’-terminal nucleoside; directly to the 2’-carbon of the 3’-terminal nucleoside; or directly to the 2’-O of the 3’-terminal nucleoside.
- L L is a divalent linker that connects to the 3’-end of the oligonucleotide, such as one of : directly to the 3’-carbon of the 3’-terminal nucleoside; 15 directly to the 3’-O of the 3’-terminal nucleoside; directly to the 4’-carbon of the 3’-terminal nucleoside; directly to the 2’-carbon
- R T1 is -L L -oligonucleotide, wherein L L is a divalent linker that 20 connects to the 5'-end of the oligonucleotide, such as one of: directly to the 5’-carbon of the 5’-terminal nucleoside; directly to the 5’-O of the 5’-terminal nucleoside; directly to the 4’-carbon of the 5’-terminal nucleoside; directly to the 2’-carbon of the 5’-terminal nucleoside; or 25 directly to the 2’-O of the 5’-terminal nucleoside.
- L L is a divalent linker that 20 connects to the 5'-end of the oligonucleotide, such as one of: directly to the 5’-carbon of the 5’-terminal nucleoside; directly to the 5’-O of the 5’-terminal nucleoside; directly to the 4’-carbon of the 5’-terminal nucleoside; directly to the 2’-carbon of
- R T1 is -L L -oligonucleotide, wherein L L is a divalent linker that connects to an internal 2’- or 3’ position on an internal nucleotide. In some embodiments, R T1 is -L L -oligonucleotide, wherein L L is a divalent linker that connects to an internal 2’- position on a internal nucleotide.
- L L when L L connects to a carbon aton on a nucleoside, then L L is -B 3 -A 3 -, wherein B 3 is -P(O)(OH)-, -P(S)(OH)-, or -P(S)(SH)-; and A 3 is -O-, -S-, or -N(H)- .
- L L when L L connects to a carbon atom on a nucleoside, then L L is -B 3 - 35 A 3 -, wherein B 3 is -P(O)(OH)- or-P(S)(OH)-; and A 3 is -O-.
- L L when L L connects to a oxygen atom on a nucleoside, then L L is - P(O)(OH)-, -P(S)(OH)-, or -P(S)(SH). In another embodiment, when L L connects to a oxygen atom on a nucleoside, then L L is - P(O)(OH)- or -P(S)(OH)-. 5 In another embodiment, when L L connects to a oxygen atom on a nucleoside, then L L is - P(O)(OH)-.
- L L when L L connects to a oxygen atom on a nucleoside, then L L is - P(S)(OH)-. In another embodiment, when L L connects to a oxygen atom on a nucleoside, then 10 LL is -B3-A3-LL1-A3-B3-, wherein B 3 is a bond, -C(O)-, C(S)-, C(NH), S(O), S(O)2, -P(O)(OH)-, -P(S)(OH)-, or -P(S)(SH); A 3 is a bond, -O-, -S-, or -N(H)- ; and L L1 is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl.
- LL when LL connects to a oxygen atom on a nucleoside, then LL is -B3- L L1 -B 3 -, wherein B 3 is -C(O)-; and L L1 is C1-10alkyl.
- R T is R T1
- R T1 is -L L -oligonucleotide
- the nucleoside is of Formula (XV-f), (XV-f) wherein B is an optionally modified nucleobase (e.g., adenine, cytosine, uracil, guanine, 5- 20 methylcytosine, or-5-methyluracil); Tis according any of the preceding embodiments; and * represent the bond to ZZ.
- -T- is -L 1 -G-L 3 -*, wherein * is the bond to ZZ.
- -T- is -C2-30alkyl-*, wherein the alkyl is optionally substituted with one or two R groups, and * is the bond to ZZ.
- -T- is -C2-30alkyl-*, wherein the alkyl 25 is optionally substituted with one or two groups selected from the group consisting of halogen, hydroxy, C1-6alkoxy, amino, Cl-6alkylamino, di(C1-6alkylamino), cyano, carboxy , and * is the bond to ZZ.
- -T- is -C2-30alkyl-*, wherein the alkyl is optionally substituted with one group selected from the group consisting of halogen, hydroxy, C1-6alkoxy, amino, Cl-6alkylamino, di(C1- 6alkylamino), cyano, carboxy , and * is the bond to ZZ.
- -T- is -C2-30alkyl-*, 30 wherein the alkyl is optionally substituted with one group selected from the group consisting of hydroxy, amino, and carboxy , and * is the bond to ZZ.
- -T- is -C2-30alkyl-*, wherein the alkyl is optionally substituted with hydroxy, and * is the bond to ZZ.
- 260 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
- -T- is -C2-30alkyl-*, wherein * is the bond to ZZ.
- -T- is -C2-16alkyl-*, wherein * is the bond to ZZ.
- -T- is -C4-12alkyl-*, wherein * is the bond to ZZ.
- -T- is -C4-10alkyl-*, wherein * is the bond to ZZ. In some embodiments, -T- is -C5-10alkyl-*, wherein * is the bond to ZZ. In some embodiments, -T- is -C6alkyl- 5 *, wherein * is the bond to ZZ. In some embodiments, -T- is -C8alkyl-*, wherein * is the bond to ZZ. In some embodiments, -T- is -C10alkyl-*, wherein * is the bond to ZZ.
- -T- is -L 1 -[G-L 2 ]q-G-L 3 -*, wherein * is the bond to ZZ; q is 0, 1, 2, 3, 4, or 5; 10 L 1 is a bond or -B-A-; each L 2 is independently -A-B-A-; L 3 is a bond or -A-B-A-; each A is independently a bond, -O-, -S-, or -N(R N )-; each B is independently a bond, CH2, C(O), C(S), C(NR N ), S(O)2, P(O)(OH), or P(S)(OH); 15 each R N is independently hydrogen or C1-6alkyl; and each G is independently C1-10alkyl, C2-10alkenyl, C2-10alkynyl, each of which is optionally substituted with 1, 2, 3, or 4 R groups.
- -T- is -L 1 -[G-L 2 ]q-G-*, wherein * is the bond to ZZ, q is 0, 1, 2, or 3;
- -T- is -[G-L 2 ]q-G-*, wherein * is the bond to ZZ, q is 0, 1, 2, or 3 (e.g., q is 0, 1, or 2; or 0 or 1; or 0; or 1; or 2); each G is independently C1-10alkyl, each of which is optionally 30 substituted with 1 or 2 R groups.
- each L2 is independently C(O)O or OC(O);
- each L2 is independently C(O)(NRN) or N(RN)C(O), wherein each RN is independently hydrogen or C1-6alkyl
- each L2 is independently OP(O)(OH)O, or OP(S)(OH)O (e.g., each is OP(O)(OH)O); 35 or ( f) each L2 is a bond.
- the compound of Formula (XV) is according to one of Formulae (XV- g) through (XV-q): 261 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- ALN-529-WO B is an optionally modified nucleobase (e.g., adenine, cytosine, uracil, guanine, 5- methylcytosine, or-5-methyluracil); each n is independently 0 or an integer selected from 1-10; (e.g., 1-5, or 1-3, or 3, or 2, or 1); 5 each m is independently integer selected from 1-20 (e.g., 2-12, or 2-10; or 2-6; or 2; or 3; or 4; or 5; or 6). 262 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- nucleobase e.g., adenine, cytosine, uracil, guanine, 5- methylcytosine, or-5-methyluracil
- each n is independently 0 or an integer selected from 1-10; (e.g., 1-5, or 1-3, or 3, or 2, or 1); 5 each m is
- the compound of Formula (XV) is according to one of Formulae (XV- r) through (XV-w): 263 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- ALN-529-WO or a salt thereof wherein L and ZZ are as defined in Formula (XV) or in any embodiment preceding or below;
- B is an optionally modified nucleobase (e.g., adenine, cytosine, uracil, guanine, 5- 5 methylcytosine, or-5-methyluracil); each m is independently integer selected from 1-20 (e.g., 2-12, or 2-10; or 2-6; or 2; or 3; or 4; or 5; or 6); 264 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- ALN-529-WO R P is hydrogen or a nitrogen protecting group (e.g., a nitrogen protecting group); and R 1 is hydrogen or C1-6alkyl (e.g., methyl or t-butyl).
- R 1 is hydrogen.
- R 1 is C1-6alkyl (e.g., methyl or t-butyl).
- R 1 is hydrogen and R P is hydrogen.
- R 1 is hydrogen and a nitrogen protecting group.
- R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- R 1 is C1-6alkyl (e.g., methyl or t-butyl) and a nitrogen protecting group.
- R T is R T1 , wherein R T1 is -L L -oligonucleotide
- the internucleotide linkage can be of the formula, including the 3’ and 5’ oxygen atoms of the preceding and following nucelosides, respectively, (XV-pa) (XV-pb) (XV-pc) wherein T can be, for example a bond, -S(O)2- or, in for Formula (XV-i), a 5 -8 membered 15 heterocyclyl ring optionally substituted with 1 or 2 R groups, as defined herein ; and * represent the bond to ⁇ .
- the preceding includes, (XV-pd) (XV-pe) (XV-pf) wherein * represent the bond to ⁇ ; and R N5 is hydrogen or C1-10 alkyl.
- the preceding includes, (XV-pg) (XV-ph) (XV-pi) 20 wherein * represent the bond to ⁇ ; m is an integer selected from 1 – 20 (e.g., 1-10, or 2-20, or 2-10, or 4-10, or 4-8; or 6-12; or 5; or 6; or 7; or 8; or 9; or 10), and R N5 is hydrogen or C1-10 alkyl.
- the compound of Formula (XV-pd) is 265 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein Y’ is O or S, and R Y , Y, R 1 , L, T, ⁇ , and ZZ are as defined for Formula (XV).
- R 1 is hydrogen.
- R 1 is C1-6alkyl (e.g., methyl or t-butyl). 5 266 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- ALN-529-WO wherein Y’ is O or S, and R 1 , T, ⁇ , R P , L, and ZZ are as defined for Formula (XV).
- the compound is 267 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein each m is an integer selected from 1 – 20 (e.g., 2-20, 2-10, 1-10, 2-16, 4-16, 4-8, or 6-12), Y’ is O or S, and R 1 , ⁇ , R P and ZZ are as defined for Formula (XV).
- the compound of Formula (XV-pe) is 268 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein Y’ is O or S, and R Y , Y, R 1 , L, T , ⁇ , and ZZ are as defined for Formula (XV).
- Y’ is O.
- Y’ is S.
- R 1 is hydrogen.
- R 1 is C 1-6 alkyl (e.g., methyl or t- 5 butyl).
- R P is hydrogen.
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O and R 1 is hydrogen.
- Y’ is O and R 1 is C 1- 6 alkyl (e.g., methyl or t-butyl).
- Y’ is S and R 1 is hydrogen.
- 10 Y’ is S and R 1 is C 1-6 alkyl (e.g., methyl or t-butyl).
- Y’ is O and R P is hydrogen .
- Y’ is O and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S and R P is hydrogen .
- Y’ is S and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl 15 (pac)).
- Y’ is O, R 1 is hydrogen and R P is hydrogen.
- Y’ is S, R 1 is hydrogen and R P is hydrogen.
- Y’ is O, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- R P is a nitrogen protecting group
- Y’ is S
- R 1 is hydrogen
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl 20 (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O, R 1 is C 1-6 alkyl (e.g., methyl or t-butyl) and R P is hydrogen .
- Y’ is S, R 1 is C 1-6 alkyl (e.g., methyl or t-butyl) and R P is hydrogen .
- Y’ is O, R 1 is C 1-6 alkyl (e.g., methyl or t-butyl) and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S
- R 1 is C 1-6 alkyl (e.g., methyl or t-butyl)
- R P is a 25 nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- the compound is 269 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 270 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- ALN-529-WO 271 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein Y’ is O or S, and R 1 , L, T, ⁇ , R P , and ZZ are as defined for Formula (XV).
- Y’ is O.
- Y’ is S. 5
- R 1 is hydrogen.
- R 1 is C 1-6 alkyl (e.g., methyl or t- butyl).
- R P is hydrogen.
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O and R 1 is hydrogen.
- R 1 is C 1- 10 6 alkyl (e.g., methyl or t-butyl).
- Y’ is S and R 1 is hydrogen.
- Y’ is S and R 1 is C 1-6 alkyl (e.g., methyl or t-butyl).
- Y’ is O and R P is hydrogen .
- Y’ is O and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S and R P is hydrogen .
- Y’ is S and R P is a 15 nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O, R 1 is hydrogen and R P is hydrogen.
- Y’ is S, R 1 is hydrogen and R P is hydrogen.
- Y’ is O
- R 1 is hydrogen
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S
- R 1 is hydrogen
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen .
- Y’ is S, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen .
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t-butyl) 5 and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S
- R 1 is C1-6alkyl (e.g., methyl or t-butyl)
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- the compound is 10 273 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- ALN-529-WO 5 wherein each m is an integer selected from 1 – 20 (e.g., 2-20, 2-10, 1-10, 2-16, 4-16, 4-8, or 6-12), Y’ is O or S, and R 1 , ⁇ , R P , and ZZ are as defined for Formula (XV).
- Y’ is O.
- Y’ is S. 274 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
- R 1 is hydrogen.
- R 1 is C1-6alkyl (e.g., methyl or t- butyl).
- R P is hydrogen.
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O and R 1 is hydrogen.
- R 1 is C1- 6alkyl (e.g., methyl or t-butyl).
- Y’ is S and R 1 is hydrogen.
- Y’ is S and R 1 is C1-6alkyl (e.g., methyl or t-butyl).
- Y’ is O and R P is hydrogen .
- Y’ is O and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl 10 (pac)).
- Y’ is S and R P is hydrogen .
- Y’ is S and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O, R 1 is hydrogen and R P is hydrogen.
- Y’ is S, R 1 is hydrogen and R P is hydrogen.
- Y’ is O, R 1 is hydrogen and R P is a nitrogen 15 protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen .
- Y’ is S, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen .
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t-butyl) 20 and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S
- R 1 is C1-6alkyl (e.g., methyl or t-butyl)
- R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- L L when L L connects to a oxygen atom on a nucleoside, then L L is-a 25 bond.
- R T1 when R T1 is -L L -oligonucleotide and is conjugated at the 5’-end of the oligonucleotide, in one embodiment, R T1 can be represented as Formula (XV-5’) (XV-5’) wherein L L is -P(Y)(OH)-, wherein Y is O or S (e.g., S); and * represents the bond to 30 remainder of the compound of Formula (XV).
- R T1 when R T1 is -L L -oligonucleotide and is conjugated at the 5’-end of the oligonucleotide, in one embodiment, R T1 can be represented as Formula (XV-5’o) or Formula ( 35 wherein * represents the bond to remainder of the compound of Formula (XV).
- a compound of Formula (XV) can be represented by, 275 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- R T1 when R T1 is -L L -oligonucleotide and is conjugated at the 3’-end of the 5 oligonucleotide, in one embodiment, R T1 can be represented as Formula (XV-3’) wherein L L is -P(Y)(OH)-, wherein Y is O or S (e.g., S); and * represents the bond to remainder of the compound of Formula (XV).
- R T1 when R T1 is -L L -oligonucleotide and is conjugated 10 at the 3’-end of the oligonucleotide, in one embodiment, R T1 can be represented as Formula (XV-3’o) or Formula ( wherein * represents the bond to remainder of the compound of Formula (XV).
- a compound of Formula (XV) can be represented by, 15 , wherein Y’ is O or S, x is an integer selected from 2 to 8, and ⁇ , R Y , Y, R 1 , L, T, and ZZ are as defined for Formula (XV) or any embodiment thereof.
- R 1 is hydrogen.
- R 1 is C1-6alkyl (e.g., methyl or t-butyl).
- the compound of Formula (XV) is 276 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- ALN-529-WO 5 wherein m is an integer selected from 1 – 10; n in an integer selected from 1 – 6; L 4 and L 6 are independently -B 1 -A 1 - or -A 1 -B 1 -; each L 5 is a bond or - A 1 -B 1 -A 1 - (e.g., a bond, -B 1 -A 1 - or -A 1 -B 1 -; or a bond); each G 1 is independently C1-10alkyl or C2-10alkenyl; each A 1 is independently a bond, -O-, -S-, or -N(R N1 )-, wherein R N1 is independently 10 hydrogen or C1-6alkyl; and each B 1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH).
- each ⁇ is , wherein m is an integer selected from 1 – 10. 277 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
- each ⁇ is , wherein m is an integer selected from 1 – 10;
- each 5 wherein m is an integer selected from 1 – 10;
- each , wherein m is an integer selected from 1 – 10.
- each ⁇ is 10 , wherein m is an integer selected from 1 – 10; 278 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein m is an integer selected from 1 – 10; and n is an integer selected from 1 – 6. 5 wherein m is an integer selected from 1 – 10; and n is an integer selected from 1 – 6. I n another embodiment of Formula (XV-x), each . In another embodiment of Formula (XV-x), each .
- L 4 and L 6 are independently -B 1 -A 1 - or -A 1 -B 1 -; 279 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- ALN-529-WO L 5 is a bond, -B 1 -A 1 - or -A 1 -B 1 -; each G 1 is independently C1-10alkyl; each A 1 is independently a bond, -O-, -S-, or -N(R N1 )-, wherein R N1 is independently hydrogen or C1-6alkyl; and 5 each B 1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH).
- L 4 is -B 1 -A 1 - or -A 1 -B 1 -;
- L 6 is B 1 ;
- L 5 is a bond, -B 1 -A 1 - or -A 1 -B 1 -;
- each G 1 is independently C1-10alkyl;
- each A 1 is independently -O- or -N(H)-, and
- each B 1 is independently C(O), S(O)2, P(O)(OH), or P(S)(OH).
- L 5 is a bond, -B 1 -A 1 - or -A 1 -B 1 -; each A 1 is independently -O- or -N(H)-, and each B 1 is independently C(O), S(O)2, P(O)(OH), or P(S)(OH).
- -L 4 -G 1 -L 5 -G 1 -L 4 - is -C(O)-C1-10alkyl-L 5 -C1-10alkyl-C(O)N(H)-, wherein L 5 is a bond, -B 1 -A 1 - 20 or -A 1 -B 1 -, wherein A 1 is -O- or -N(H)-, and B 1 is C(O), S(O)2, P(O)(OH), or P(S)(OH).
- the compound of Formula (XV) is 25 wherein Y’ is O or S; each ZZ is N(H)C(O) or C(O)N(H); 280 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- each G 1 is independently C1-10alkyl; 5 each A 1 is independently a bond, -O-, -S-, or -N(R N1 )-, wherein R N1 is independently hydrogen or C1-6alkyl; and wherein m is an integer selected from 1 – 10 R 1 is hydrogen or C 1-6 alkyl (e.g., hydrogen); and R P is 10 hydrogen or a nitrogen protecting group (e.g., hydrogen).
- each ⁇ is , wherein m is an integer selected from 1 – 10 ; R 1 is hydrogen or C1-6alkyl (e.g., hydrogen); and R P is hydrogen or a nitrogen protecting group (e.g., 15 hydrogen). ; 281 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
- R 1 is hydrogen or C1-6alkyl (e.g., hydrogen); and R P is hydrogen or a nitrogen protecting group (e.g., hydrogen).
- R 1 is hydrogen or C1-6alkyl (e.g., hydrogen); and R P is hydrogen or a nitrogen protecting group (e.g., hydrogen).
- the compound of Formula (XV) is wherein Y’ is O or S; e 10 wherein m is an integer selected from 1 – 10; n is an integer selected from 1-6; L 5 is a bond or - A 1 -B 1 -A 1 - (e.g., a bond, -B 1 -A 1 - or -A 1 -B 1 -; or a bond); each G 1 is independently C 1-10 alkyl; each A 1 is independently a bond, -O-, -S-, or -N(R N1 )-, wherein R N1 is independently hydrogen or C 1-6 alkyl; and 15 each B 1 is independently a bond, C(O), C(S), S(O) 2 , P(O)(OH), or P(S)(OH).
- each ⁇ is hydrogen).
- each ⁇ is , wherein m is an integer selected from 1 – 10; ; R 1 is hydrogen or C 1-6 alkyl (e.g., hydrogen); and R P is hydrogen or a nitrogen protecting group (e.g., hydrogen).
- each ⁇ is , wherein m is an integer selected from 1 – 10; R 1 is hydrogen or C1-6alkyl (e.g., hydrogen); and R P is hydrogen or a nitrogen protecting group (e.g.,15 hydrogen). 285 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
- each ⁇ is , wherein m is an integer selected from 1 – 10 R 1 is hydrogen or C 1-6 alkyl (e.g., hydrogen); and R P is hydrogen or a nitrogen protecting group (e.g., hydrogen).
- each ⁇ is 5 hydrogen).
- each , wherein m is an integer selected from 1 – 10; and n is an integer selected from 1 – 6; R 1 is hydrogen or10 C 1-6 alkyl (e.g., hydrogen); and R P is hydrogen or a nitrogen protecting group (e.g., hydrogen).
- each ⁇ is 10 , wherein R 1 is hydrogen or C 1-6 alkyl (e.g., hydrogen); and R P is hydrogen or a nitrogen protecting group (e.g., hydrogen) .
- R 1 is hydrogen or C 1-6 alkyl (e.g., hydrogen); and R P is hydrogen or a nitrogen protecting group (e.g., hydrogen) .
- Y’ is O.
- Y’ is S.
- R 1 is hydrogen.
- R 1 is C1-6alkyl (e.g., methyl or t-butyl).
- R P is hydrogen.
- R P is a nitrogen protecting group (e.g., t- butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). 287 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
- Y’ is O and R 1 is hydrogen.
- Y’ is O and R 1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R 1 is hydrogen. In one embodiment, Y’ is S and R 1 is C1-6alkyl (e.g., methyl or t-butyl). 5 In one embodiment of Formula (XV-x), (XV-x1), and (XV-x2), and each of the preceding embodiments thereof, Y’ is O and R P is hydrogen .
- Y’ is O and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S and R P is hydrogen.
- Y’ is S and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- R 1 is hydrogen and R P is hydrogen.
- Y’ is S, R 1 is hydrogen and R P is hydrogen.
- Y’ is O, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S, R 1 is hydrogen and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl 15 (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is O, R 1 is C1- 6alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is S, R 1 is C1-6alkyl (e.g., methyl or t-butyl) and R P is hydrogen.
- Y’ is O, R 1 is C1-6alkyl (e.g., methyl or t- butyl) and R P is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- Y’ is S
- R 1 is C1-6alkyl (e.g., methyl or t-butyl)
- R P is 20 a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)).
- the compound is of the structure: wherein each 25 1-10; 2-10; 2-6; 4; 3; 2; or 1) ; and 288 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- the compound is of the structure: 5 10
- the compound is of the structure: 289 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 5
- the compound is of the structure: 290 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO , wherein * represents the bond to the remainder of the dsRNA agent.
- the compound of Formula (XV) is 5 291 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein * represents the bond to the remainder of the dsRNA agent.
- the compound of Formula (XV) is, 5 wherein * represents the bond to the remainder of the dsRNA agent.
- the compound of Formula (XV) is, 10 292 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein * represents the bond to the remainder of the dsRNA agent.
- the compound of Formula (XV) is, 5 wherein * represents the bond to the remainder of the dsRNA agent. 293 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
- the compound of Formula (XV) is, wherein B is an optionally modified nucleobase (e.g., cytosine, uracil, 5-methylcytosine, 5- 5 wherein * represents the bond to the remainder of the dsRNA agent. 10 VI.
- RNAi agent of the disclosure Delivery of an RNAi Agent of the Disclosure
- a cell e.g., a cell within a subject, such as a human subject (e.g., a subject in need thereof, such as a subject having a target gene-associated (i.e., DMPK-associated) disorder
- delivery 15 may be performed by contacting a cell with an RNAi agent of the disclosure either in vitro or in vivo.
- In vivo delivery may also be performed directly by administering a composition comprising an RNAi agent, e.g., a dsRNA, to a subject.
- in vivo delivery may be performed indirectly by administering one or more vectors that encode and direct the expression of the RNAi agent.
- any method of delivering a nucleic acid molecule in vitro or in vivo can be adapted for use with a RNAi agent of the disclosure.
- factors to consider in order to deliver an RNAi agent include, for example, biological stability of the delivered agent, prevention of non-specific effects, and accumulation of the delivered agent in the target tissue.
- the RNA can be modified or alternatively 25 delivered using a drug delivery system; both methods act to prevent the rapid degradation of the 294 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO dsRNA by endo- and exo-nucleases in vivo.
- RNAi agents can be modified by chemical conjugation to lipophilic groups such as cholesterol to enhance cellular uptake and prevent degradation.
- the RNAi agent can be delivered using drug delivery systems such as a nanoparticle, a dendrimer, a polymer, liposomes, or a cationic delivery system.
- a RNAi agent forms a complex with cyclodextrin for systemic administration.
- Certain aspects of the instant disclosure relate to a method of reducing the expression of a target gene, i.e., DMPK, in a cell, comprising contacting said cell with the double-stranded RNAi agent of the disclosure.
- the cell is a skeletal muscle.
- the cell is a cardiac muscle cell.
- the cell is an adipocyte.
- the RNAi agent is taken up on one or more tissue or cell types present in organs, e.g., liver, skeletal muscle, cardiac muscle, adipose tissue.
- Another aspect of the disclosure relates to a method of reducing the expression and/or activity of a target gene in a subject, comprising administering to the subject the double-stranded RNAi agent of the disclosure.
- Another aspect of the disclosure relates to a method of treating a subject having a target gene- associated disorder or at risk of having or at risk of developing a target gene-associated disorder, comprising administering to the subject a therapeutically effective amount of the double-stranded RNAi agent of the disclosure, thereby treating the subject.
- the double-stranded RNAi agent is administered subcutaneously. 25 In one embodiment, the double-stranded RNAi agent is administered intramuscularly. In one embodiment, the double-stranded RNAi agent is administered by intravenously.
- modified siRNA compounds e.g., modified siRNA compounds
- a composition that includes a RNAi agent can be delivered to a subject by a variety of routes.
- Exemplary routes include pulmonary system, intravenous, subcutaneous, oral, topical, rectal, anal, vaginal, nasal, and ocular.
- the RNAi agents of the disclosure can be incorporated into pharmaceutical compositions suitable for administration.
- Such compositions typically include one or more species of RNAi agent 35 and a pharmaceutically acceptable carrier.
- pharmaceutically acceptable carrier is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration.
- the use of such media and agents for pharmaceutically active 295 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- compositions of the present disclosure may be administered in a number 5 of ways depending upon whether local or systemic treatment is desired and upon the area to be treated. Administration may be intratracheal, intranasal, topical (including ophthalmic, vaginal, rectal, intranasal, transdermal), oral, parenteral, or pulmonary, e.g., by inhalation or insufflation of powders or aerosols, including by nebulizer.
- Parenteral administration includes intravenous drip, subcutaneous, intraperitoneal, or intramuscular injection administration. 10
- 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 RNAi agent in powder or aerosol form.
- the vascular endothelial cells could be targeted by coating a balloon catheter with the RNAi agent and mechanically introducing the RNA.
- Aqueous compositions may be sterile and may optionally contain buffers, diluents, absorption enhancers and other suitable additives. Such administration permits both systemic and local delivery of the double stranded RNAi agents of the disclosure.
- Formulations for topical administration may include transdermal patches, ointments, lotions, creams, gels, drops, suppositories, sprays, liquids, and powders.
- Conventional pharmaceutical 20 carriers, aqueous, powder or oily bases, thickeners and the like may be necessary or desirable.
- Coated condoms, gloves, and the like may also be useful.
- Compositions for oral administration include powders or granules, suspensions or solutions in water, syrups, elixirs or non-aqueous media, tablets, capsules, lozenges, or troches.
- carriers that can be used include lactose, sodium citrate and salts of phosphoric acid.
- the administration of the siRNA compound is parenteral, e.g., intravenous (e.g., as a bolus or as a diffusible infusion), 35 intradermal, intraperitoneal, intramuscular, subcutaneous, transmucosal, buccal, sublingual, endoscopic, rectal, oral, vaginal, topical, pulmonary system, intranasal, urethral, or ocular.
- Administration can be provided by the subject or by another person, e.g., a health care provider.
- the 296 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No.
- ALN-529-WO medication can be provided in measured doses or in a dispenser which delivers a metered dose. Selected modes of delivery are discussed in more detail below.
- Vector encoded RNAi agents of the Disclosure 5 RNAi agents targeting the target gene can be expressed from transcription units inserted into DNA or RNA vectors (see, e.g., Couture, A, et al., TIG. (1996), 12:5-10; WO 00/22113, WO 00/22114, and US 6,054,299). Expression can be sustained (months or longer), depending upon the specific construct used and the target tissue or cell type.
- transgenes can be introduced as a linear construct, a circular plasmid, or a viral vector, which can be an integrating or non-integrating 10 vector.
- the transgene can also be constructed to permit it to be inherited as an extrachromosomal plasmid (Gassmann, et al., (1995) Proc. Natl. Acad. Sci. USA 92:1292).
- the individual strand or strands of a RNAi agent can be transcribed from a promoter on an expression vector. Where two separate strands are to be expressed to generate, for example, a dsRNA, two separate expression vectors can be co-introduced (e.g., by transfection or infection) into a target 15 cell.
- each individual strand of a dsRNA can be transcribed by promoters both of which are located on the same expression plasmid.
- a dsRNA is expressed as inverted repeat polynucleotides joined by a linker polynucleotide sequence such that the dsRNA has a stem and loop structure.
- RNAi agent expression vectors are generally DNA plasmids or viral vectors. Expression 20 vectors compatible with eukaryotic cells, such as those compatible with vertebrate cells, can be used to produce recombinant constructs for the expression of a RNAi agent as described herein.
- RNAi agent expressing vectors can be systemic, such as by intravenous or intramuscular administration, by administration to target cells ex-planted from the patient followed by reintroduction into the patient, or by any other means that allows for introduction into a desired target cell.
- Viral vector systems which can be utilized with the methods and compositions described herein include, but are not limited to, (a) adenovirus vectors; (b) retrovirus vectors, including but not limited to lentiviral vectors, moloney murine leukemia virus, etc.; (c) adeno- associated virus vectors; (d) herpes simplex virus vectors; (e) SV 40 vectors; (f) polyoma virus vectors; (g) papilloma virus vectors; (h) picornavirus vectors; (i) pox virus vectors such as an orthopox, e.g., vaccinia virus vectors 30 or avipox, e.g.
- RNAi agent canary pox or fowl pox; and (j) a helper-dependent or gutless adenovirus. Replication- defective viruses can also be advantageous.
- Different vectors will or will not become incorporated into the cells’ genome.
- the constructs can include viral sequences for transfection, if desired.
- the construct can be incorporated into vectors capable of episomal replication, e.g. EPV and EBV vectors.
- Constructs for the recombinant expression of a RNAi agent will generally require 35 regulatory elements, e.g., promoters, enhancers, etc., to ensure the expression of the RNAi agent in target cells.
- Other aspects to consider for vectors and constructs are known in the art. VII.
- compositions 297 ME1 ⁇ 53453057.v1 Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
- the present disclosure also includes pharmaceutical compositions and formulations which include the RNAi agents of the disclosure.
- pharmaceutical compositions containing an RNAi agent, as described herein, and a pharmaceutically acceptable carrier are useful for treating a subject 5 who would benefit from inhibiting or reducing the expression of a target gene, e.g., a subject having a DMPK–associated disorder, e.g., DM1.
- Such pharmaceutical compositions are formulated based on the mode of delivery.
- compositions that are formulated for systemic administration via parenteral delivery, e.g., by intravenous (IV), intramuscular (IM), or for subcutaneous (subQ) delivery.
- IV intravenous
- IM intramuscular
- subQ subcutaneous
- the pharmaceutical compositions of the disclosure are pyrogen free or non-pyrogenic.
- the delivery vehicle can deliver an iRNA compound, e.g., a double- stranded iRNA compound, or ssiRNA compound, (e.g., a precursor thereof, e.g., a larger siRNA compound which can be processed into a ssiRNA compound, or a DNA which encodes an siRNA 15 compound, e.g., a double-stranded siRNA compound, or ssiRNA compound, or precursor thereof) to a cell by a topical route of administration.
- the delivery vehicle can be microscopic vesicles.
- the microscopic vesicles are liposomes.
- the liposomes are cationic liposomes.
- the microscopic vesicles are micelles.
- the disclosure features a pharmaceutical composition including an siRNA compound, e.g., a double-stranded siRNA 20 compound, or ssiRNA compound, (e.g., a precursor thereof, 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) in an injectable dosage form.
- the injectable dosage form of the pharmaceutical composition includes sterile aqueous solutions or dispersions and sterile powders.
- the sterile 25 solution can include a diluent such as water; saline solution; fixed oils, polyethylene glycols, glycerin, or propylene glycol.
- a pharmaceutical composition including an siRNA compound, e.g., a double-stranded siRNA compound, or ssiRNA compound, (e.g., a precursor thereof, e.g., a larger siRNA compound which can be processed into a ssiRNA compound, or a DNA 30 which encodes an siRNA compound, e.g., a double-stranded siRNA compound, or ssiRNA compound, or precursor thereof) in oral dosage form.
- siRNA compound e.g., a double-stranded siRNA compound, or ssiRNA compound, or precursor thereof
- a pharmaceutical composition including an siRNA compound, e.g., a double-stranded siRNA compound, or ssiRNA compound, (e.g., a precursor thereof, e.g.
- the oral dosage form is selected from the group consisting of tablets, capsules and gel capsules.
- the pharmaceutical composition includes an enteric material that substantially prevents dissolution of the tablets, capsules or gel capsules in a mammalian stomach.
- the enteric material 35 is a coating.
- the coating can be acetate phthalate, propylene glycol, sorbitan monoleate, cellulose acetate trimellitate, hydroxy propyl methyl cellulose phthalate or cellulose acetate phthalate.
- the oral dosage form of the pharmaceutical composition includes a penetration enhancer, e.g., a penetration enhancer described herein.
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Abstract
The disclosure relates to double stranded ribonucleic acid (dsRNA) agents and compositions targeting a dystrophy myotonic protein kinase (DMPK) gene, as well as methods of inhibiting expression of a DMPK gene and methods of treating subjects having a DMPK-associated disease or disorder, e.g., myotonic dystrophy (DM), using such dsRNA agents and compositions.
Description
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO DYSTROPHY MYOTONIC PROTEIN KINASE (DMPK) IRNA COMPOSITIONS AND METHODS OF USE THEREOF RELATED APPLICATION 5 This application claims the benefit of priority to U.S. Provisional Application Nos. 63/659,098, filed on June 12, 2024, and 63/760,695, filed on February 20, 2025. The entire contents of each of the foregoing applications are incorporated herein by reference. SEQUENCE LISTING 10 The instant application contains a Sequence Listing which has been submitted electronically in XML format and is hereby incorporated by reference in its entirety. Said XML copy, created on June 9, 2025, is named 121301_24020_SL.xml and is 1,027,775 bytes in size. BACKGROUND OF THE DISCLOSURE 15 The dystrophy myotonic protein kinase (DMPK) protein, also known as myotonin-protein kinase (MT-PK) is a serine-threonine kinase with homology to other kinases that interact with members of the Rho family of small GTPases. Substrates for this enzyme include myogenin, the beta- subunit of the L-type calcium channels, and phospholemman. Although the specific function of this protein is unknown, it plays an important role in muscle, heart, and brain cells. 20 Myotonic dystrophy (DM) type 1 (DM1) is an autosomal RNA dominant disease caused by expression of an expansion of a heterozygous cytosine thymine guanine (CTG) repeat located in the 3′ untranslated region of the DM protein kinase (DMPK) gene located on chromosome 19q13.3. DM1 is a multisystem disorder characterized by myotonia, muscular dystrophy, cataracts, hypogonadism, frontal balding, cardiac conduction defects, endocrine abnormalities, and iridescent cataracts, 25 although the clinical features of DM1 and the severity of disease vary with the number of repeats: normal individuals have 5 to 37 repeats, mildly affected persons have 50 to 150 repeats, patients with classic DM1 have 100 to 1,000 repeats, and those with onset at birth can have more than 2,000 repeats. Effective therapies and treatments for DM1 are currently not available and, instead, 30 treatments and therapies focus on managing symptoms and improving quality of life. In addition, despite significant advances in the field of RNAi, there remains a need for an agent that can selectively and efficiently silence the DMPK gene using the cell's own RNAi machinery that has both high biological activity and in vivo stability, and that can effectively inhibit expression of a target DMPK gene. 35 SUMMARY OF THE DISCLOSURE The present disclosure provides iRNA compositions which effect the RNA-induced silencing complex (RISC)-mediated cleavage of RNA transcripts of a target gene encoding dystrophy myotonic 1 ME1\53453057.v1 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO protein kinase (DMPK). The DMPK gene may be within a cell, e.g., a cell within a subject, such as a human subject. The present disclosure also provides methods of using the iRNA compositions of the disclosure for inhibiting the expression of a DMPK gene, and/or for treating a subject who would benefit from inhibiting or reducing the expression of an DMPK gene, e.g., a subject suffering or prone 5 to suffering from an DMPK-associated disorder, e.g., Myotonic dystrophy (DM) type 1 (DM1). Accordingly, in an aspect, the disclosure provides a double stranded ribonucleic acid (dsRNA) agent for inhibiting expression of a dystrophy myotonic protein kinase (DMPK) gene in a cell, or a pharmaceutically acceptable salt thereof, comprising a sense strand and an antisense strand forming a double stranded region, wherein the antisense strand comprises at least 15, e.g., 15, 16, 18, 10 18, 19, 20, 21, 22, or 23, contiguous nucleotides differing by no more than three nucleotides from any one of the antisense strand nucleotide sequences in any one of Tables 2-3. In one aspect, the disclosure provides a double stranded ribonucleic acid (dsRNA) agent for inhibiting expression of a dystrophy myotonic protein kinase (DMPK) gene in a cell, or a pharmaceutically acceptable salt thereof, comprising a sense strand and an antisense strand forming a 15 double stranded region; wherein the sense strand comprises at least 15, e.g., 15, 16, 18, 18, 19, 20, or 21, contiguous nucleotides differing by no more than three, e.g., 3, 2, 1, or 0, nucleotides from the nucleotide sequence of SEQ ID NO:1 and the antisense strand comprises at least 15, e.g., 15, 16, 18, 18, 19, 20, 21, 22, or 23, contiguous nucleotides differing by no more than three, e.g., 3, 2, 1, or 0, nucleotides from the corresponding portion of the nucleotide sequence of SEQ ID NO:2; at least one 20 alpha-v-beta-6 (αvβ6) integrin targeting ligand that mediates delivery to muscle tissue conjugated to at least one strand; and at least one in vivo delivery enhancing moiety conjugated to one or more internal positions on at least one strand. In another aspect, the present disclosure provides a double stranded ribonucleic acid (dsRNA) agent for inhibiting expression of a dystrophy myotonic protein kinase (DMPK) gene in a cell, or a 25 pharmaceutically acceptable salt thereof, comprising a sense strand and an antisense strand forming a double stranded region; wherein the antisense strand comprises at least 15, e.g., 15, 16, 18, 18, 19, 20, 21, 22, or 23, contiguous nucleotides differing by no more than three, e.g., 3, 2, 1, or 0, nucleotides from any one of the antisense strand nucleotide sequences in any one of Tables 2-3; at least one alpha- v-beta-6 (αvβ6) integrin targeting ligand that mediates delivery to muscle tissue conjugated to at least 30 one strand; and at least one in vivo delivery enhancing moiety conjugated to one or more internal positions on at least one strand. In one embodiment, the sense strand comprises at least 15, e.g., 15, 16, 18, 18, 19, 20, or 21, contiguous nucleotides differing by no more than three, e.g., 3, 2, 1, or 0, nucleotides from any one of the sense strand nucleotide sequences in any one of Tables 2-3. 35 In another embodiment, the sense strand comprises at least 15, e.g., 15, 16, 18, 18, 19, 20, or 21, contiguous nucleotides differing by no more than two nucleotides from any one of the sense strand nucleotide sequences in any one of Tables 2-3 and the antisense strand comprises at least 15, e.g., 15, 2 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 16, 18, 18, 19, 20, 21, 22, or 23, contiguous nucleotides differing by no more than two nucleotides from any one of the antisense strand nucleotide sequences in any one of Tables 2-3. In one embodiment, the sense strand comprises at least 15, e.g., 15, 16, 18, 18, 19, 20, or 21, contiguous nucleotides differing by no more than one nucleotide from any one of the sense strand 5 nucleotide sequences in any one of Tables 2-3 and the antisense strand comprises at least 15, e.g., 15, 16, 18, 18, 19, 20, 21, 22, or 23, contiguous nucleotides differing by no more than one nucleotide from any one of the antisense strand nucleotide sequences in any one of Tables 2-3. In a further embodiment, the sense strand comprises a nucleotide sequence selected from the group consisting of any one of the sense strand nucleotide sequences in any one of Tables 2-3 and the 10 antisense strand comprises a nucleotide sequence selected from the group consisting of any one of the antisense strand nucleotide sequences in any one of Tables 2-3. In one embodiment, the dsRNA agent, or a pharmaceutically acceptable salt thereof, comprises at least one nucleotide comprising a nucleotide modification. In another embodiment, all of the nucleotides of the sense strand comprise a nucleotide 15 modification; all of the nucleotides of the antisense strand comprise a nucleotide modification; or all of the nucleotides of the sense strand and all of the nucleotides of the antisense strand comprise a nucleotide modification. In one embodiment, at least one of the nucleotide modifications is selected from the group consisting of a deoxy-nucleotide modification, a 3’-terminal deoxythimidine (dT) nucleotide 20 modification, a 2'-O-methyl nucleotide modification, a 2'-fluoro nucleotide modification, a 2'-deoxy nucleotide modification, a locked nucleotide modification, an unlocked nucleotide modification, a conformationally restricted nucleotide modification, a constrained ethyl nucleotide modification, an abasic nucleotide modification, a 2’-amino nucleotide modification, a 2’-O-allyl nucleotide modification, 2’-C-alkyl nucleotide modification, 2’-hydroxly nucleotide modification, a 2’- 25 methoxyethyl nucleotide modification, a 2’-O-alkyl nucleotide modification, a morpholino nucleotide modification, a phosphoramidate modification, a non-natural base comprising nucleotide modification, a tetrahydropyran nucleotide modification, a 1,5-anhydrohexitol nucleotide modification, a cyclohexenyl nucleotide modification, a nucleotide comprising a phosphorothioate group modification, a nucleotide comprising a methylphosphonate group modification, a nucleotide 30 comprising a 5’-phosphate modification, a nucleotide comprising a 5’-phosphate mimic modification, a thermally destabilizing nucleotide modification, a glycol modified nucleotide (GNA) modification, a nucleotide comprising a 2’ phosphate, and a 2-O-(N-methylacetamide) nucleotide modification; and combinations thereof. In one embodiment, at least one of the modified nucleotides is selected from the group35 consisting of LNA, HNA, CeNA, 2’-methoxyethyl, 2’-O-alkyl, 2’-O-allyl, 2’-C- allyl, 2’-fluoro, 2’- deoxy, 2’-hydroxyl, and glycol; and combinations thereof. In another embodiment, at least one of the modified nucleotides is selected from the group consisting of a deoxy-nucleotide, a 2'-O-methyl modified nucleotide, a 2'-fluoro modified nucleotide, 3 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO a 2'-deoxy-modified nucleotide, a glycol modified nucleotide (GNA), a nucleotide comprising a 2’ phosphate, a nucleotide comprising a phosphorothioate group, and a vinyl-phosphonate nucleotide; and combinations thereof. In one embodiment, at least one of the modified nucleotides is a nucleotide modified with a 5 thermally destabilizing nucleotide modification, e.g., selected from the group consisting of an abasic modification; a mismatch with the opposing nucleotide in the duplex; a destabilizing sugar modification, a 2’-deoxy modification, an acyclic nucleotide, an unlocked nucleic acid (UNA), and a glycerol nucleic acid (GNA). In one embodiment, the dsRNA agent, or a pharmaceutically acceptable salt thereof, further 10 comprises a phosphate or phosphate mimic at the 5’-end of the antisense strand, e.g., a 5’-vinyl phosphonate (VP). In one embodiment, the 3’ end of the sense strand is protected via an end cap which is a cyclic group having an amine, said cyclic group being selected from the group consisting of pyrrolidinyl, pyrazolinyl, pyrazolidinyl, imidazolinyl, imidazolidinyl, piperidinyl, piperazinyl, 15 [1,3]dioxolanyl, oxazolidinyl, isoxazolidinyl, morpholinyl, thiazolidinyl, isothiazolidinyl, quinoxalinyl, pyridazinonyl, tetrahydrofuranyl, and decalinyl. In some embodiments, the double stranded region may be 19-30 nucleotide pairs in length; 19-25 nucleotide pairs in length; 19-23 nucleotide pairs in length; 23-27 nucleotide pairs in length; or 21-23 nucleotide pairs in length. 20 In some embodiments, each strand is independently no more than 30 nucleotides in length. In one embodiment, the sense strand is 21 nucleotides in length and the antisense strand is 23 nucleotides in length. In one embodiment, the dsRNA agent, or a pharmaceutically acceptable salt thereof, comprises at least one single-stranded overhang, e.g., a single-stranded overhang that is 1, 2 or 3 25 nucleotides in length. In one embodiment, at least one end of the dsRNA agent, or a pharmaceutically acceptable salt thereof, is blunt-ended. In some embodiments, the dsRNA agent, or a pharmaceutically acceptable salt thereof, further comprises at least one phosphorothioate or methylphosphonate internucleotide linkage. 30 In one embodiment, the phosphorothioate or methylphosphonate internucleotide linkage is at the 3’-terminus of one strand. In another embodiment, the phosphorothioate or methylphosphonate internucleotide linkage is at the 5’-terminus of one strand. In one embodiment, the phosphorothioate or methylphosphonate internucleotide linkage is at 35 both the 5’- and 3’-terminus of one strand. In one embodiment, the dsRNA agent, or a pharmaceutically acceptable salt thereof, comprises 6-10, e.g., 6, 7, 8, 9, or 10, phosphorothioate or methylphosphonate internucleotide linkages. 4 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In one embodiment, the dsRNA agent, or a pharmaceutically acceptable salt thereof, comprises 7 phosphorothioate or methylphosphonate internucleotide linkages. In one embodiment, the αvβ6 integrin targeting ligand the αvβ6 integrin targeting ligand comprises a structure represented by Formula (X):
5 or a salt thereof, wherein: or CH2;
, wherein m is 0, 1, 2, 3, or 4; and each R2 is independently R, or two R2 groups on adjacent carbon atoms taken together with the atoms 10 to which they are bound form a fused 4 – 8 membered ring that is optionally substituted by 1, 2, 3 or 4 groups independently selected from group consisting of R and a nitrogen protecting group; A is an 5-membered heteroaryl optionally substituted with 1 or 2 substituents independently selected from methyl, ethyl, fluoro, hydroxymethyl, 2-hydroxypropan-2-yl, trifluoromethyl, difluoromethyl, and fluoromethyl; 15 Q is -COOR1 or tetrazolyl (e.g., 1,2,3,4-tetrazol-5-yl), wherein R1 is hydrogen or C1-6alkyl (e.g., methyl) ; and RL is -N(R3)(R4), -O(R5), -S(R5), or -R5, wherein R3 and R4 are either 20 (i) R3 is hydrogen or C1-6alkyl and R4 is R5; or (ii) R3 and R4 taken together with the nitrogen atom to which they are attached form a 4 – 8 membered monocyclic heterocyclyl group that is substituted with R5; and R5 is -L-ZZ-L’-RT wherein 25 L and L’ are independently -L1-[G-L2]q-G-L3-*, wherein * is the bond to ZZ; q is 0 or an integer selected from 1 to 25; L1 is a bond or -B-A-; each L2 is independently -A-B-A-; 30 L3 is a bond or -A-B-A-; 5 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO each G is independently -D-E-F-, wherein D, E, and F are independently a bond, C1-10alkyl, C2- 10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups; each A is independently a bond, -O-, -S-, or -N(RN)-; 5 each B is independently a bond, CH2, C(O), C(S), C(NRN), S(O), S(O)2, P(O)(OH), P(S)(OH), or P(S)(SH); each RN is independently hydrogen or C1-6alkyl, or two RN within an -A-B-A- group taken together with the atoms to which they are connected from a 4-8 membered heterocyclyl; and 10 ZZ is -A’-B’-A’- or a linking group formed by a reactive pair, wherein each A’ is independently a bond, -O-, -S-, or -N(RN3)-; each B’ is independently a bond, CH2, C(O), C(S), C(NRN3), -C=N-, S(O), S(O)2, P(O)(OH), P(S)(OH), or P(S)(SH); and each RN3 is independently hydrogen or C1-6alkyl, or two RN3 within the -A’-B’-A’- group taken 15 together with the atoms to which they are connected from a 4-8 membered heterocyclyl; RT is RT1 or -G0-ORT1, wherein G0 is absent or -D0-E0-F0-, wherein D0, E0, and F0 are independently a bond, C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups; 20 RT1 is LL-oligonucleotide, wherein LL is an oligonucleotide linking group connecting the αvβ6 integrin targeting ligand to oligonucleotide comprised in the dsRNA agent; and each R group is independently selected from the group consisting of R’, C1-6alkyl, C1-6haloalkyl, C2- 6alkenyl, C2-6alkynyl, C3-8cycloalkyl, heterocyclyl, aryl, heteroaryl, C3-8cycloalkylC1-6alkyl, heterocyclylC1-6alkyl, aryl C1-6alkyl, heteroarylC1-6alkyl, each of which, other than R’, is optionally 25 substituted with 1, 2, or 3 R’ groups, wherein each R’ is independently halogen, cyano, azido, nitro, -N(Rb)2, -O(Ra), -S(R0), -C(O)OR0, C(O)R0, -C(O)N(R0)2, -C(NR0)OR0, -C(NR0)R0, -C(NR0)N(R0)2, -C(S)OR0, -C(S)R0, -C(S)N(R0)2, -S( O)2R0, -S(O)2OR0, -S(O)2N(R0)2, -N(R0)C(O)OR0, -N(R0)C(O)R0, -N(R0)C(O)N(R0)2, -N(R0)S(O)2R0, -N(R0)S(O)2OR0, -N(R0)S(O)2N(R0)2, -OC(O)OR0, -OC(O)R0, -OC(O)N(R0)2, -OS(O)2R0, - 30 OS(O)2OR0, -OS(O)2N(R0)2, or -SC(O)R0, wherein each R0 is independently hydrogen or C1-6alkyl; each Ra is independently hydrogen or C1-6alkyl; and each Rb is independently hydrogen, C1-6alkyl, or a nitrogen protecting group provided that in each -D-E-F- group, at least one of D, E, and F is not a bond; and RL is not N- morpholinyl. 35 In one embodiment, the αvβ6 integrin targeting ligand of Formula (X) is 6 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
, wherein Y’ is O or S, and RP and R1 are as defined for Formula (X) or any embodiment thereof. In one embodiment, Y’ is O. In one embodiment, Y’ is S. 5 In one embodiment, R1 is hydrogen. In one embodiment, R1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, RP is hydrogen. In one embodiment, RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). 10 In one embodiment, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1-6alkyl. In one embodiment, Y’ is S and R1 is hydrogen. In one embodiment, Y’ is S and R1 is C1-6alkyl. In one embodiment, Y’ is O and RP is hydrogen. 15 In one embodiment, Y’ is O and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and RP is hydrogen In one embodiment, Y’ is S and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). 20 In one embodiment, Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen protecting group. In one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group. In one embodiment, Y’ is O, R1 is C1-6alkyl and RP is hydrogen. 25 In one embodiment, Y’ is S, R1 is C1-6alkyl and RP is hydrogen. In one embodiment, Y’ is O, R1 is C1-6alkyl and RP is a nitrogen protecting group. In one embodiment, Y’ is S, R1 is C1-6alkyl and RP is a nitrogen protecting group. 7 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 56. In one embodiment, the αvβ6 integrin targeting ligand is
wherein a broken bond represents a bond to the remainder of the dsRNA, or a pharmaceutically acceptable salt thereof. 5 In one embodiment, the in vivo delivery enhancing moiety comprises at least one C10-C26 hydrocarbon chain. In one embodiment, the in vivo delivery enhancing moiety comprises at least one C22 hydrocarbon chain. In one embodiment, the at least one C22 hydrocarbon chains is an aliphatic, alicyclic, or 10 polyalicyclic compound. In one embodiment, the at least one C22 hydrocarbon chains contains a functional group selected from the group consisting of hydroxyl, amine, carboxylic acid, sulfonate, phosphate, thiol, azide, and alkyne. In one embodiment, the at least one C22 hydrocarbon chains is a C22 acid. 15 In one embodiment, the C22 acid is selected from the group consisting of docosanoic acid, 6- octyltetradecanoic acid, 10-hexylhexadecanoic acid, all-cis-7,10,13,16,19-docosapentaenoic acid, all- cis-4,7,10,13,16,19-docosahexaenoic acid, all-cis-13,16-docosadienoic acid, all-cis-7,10,13,16- docosatetraenoic acid, all-cis-4,7,10,13,16-docosapentaenoic acid, and cis-13-docosenoic acid. In one embodiment, the at least one C22 hydrocarbon chains is a C22 alcohol. 20 In one embodiment, the C22 alcohol is selected from the group consisting of 1-docosanol, 6- octyltetradecan-1-ol, 10-hexylhexadecan-1-ol, cis-13-docosen-1-ol, docosan-9-ol, docosan-2-ol, docosan-10-ol, docosan-11-ol, andcis-4,7,10,13,16,19-docosahexanol. In one embodiment, the at least one C22 hydrocarbon chains is a C22 amide. In one embodiment, the C22 amide is selected from the group consisting of (E)-Docos-4- 25 enamide, (E)-Docos-5-enamide, (Z)-Docos-9-enamide, (E)-Docos-11-enamide,12-Docosenamide, 8 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO (Z)-Docos-13-enamide, (Z)-N-Hydroxy-13-docoseneamide, (E)-Docos-14-enamide, 6-cis- Docosenamide, 14-Docosenamide Docos-11-enamide, (4E,13E)-Docosa-4,13-dienamide, and (5E,13E)-Docosa-5,13-dienamide. In one embodiment, the at least one C10-C26 hydrocarbon chain is unsubstituted or 5 substituted with at least one functional group selected from the group consisting of hydroxyl, amine, carboxylic acid, sulfonate, phosphate, thiol, azide, and alkyne. In one embodiment, the at least one C10-C26 hydrocarbon chains is substituted with a carboxylic acid group. In one embodiment, the in vivo delivery enhancing moiety is attached to the dsRNA agent, or 10 a pharmaceutically acceptable salt thereof, via a linker or via a carrier or via an internucleotide phosphate linkage. In one embodiment, the in vivo delivery enhancing moiety is attached to the dsRNA agent via a linker. In one embodiment, the linker comprises an ether, a thioether, a urea, a carbonate, an amine, 15 an amide, a maleimide-thioether, a disulfide, a phosphodiester, a sulfonamide linkage, a product of a click reaction, or carbamate. In one embodiment, the linker is selected from the group consisting of -(CH2)nNH-; - C(O)(CH2)nNH-; -NR’’’’(CH2)nNH-, -C(O)-(CH2)n-C(O)-; -C(O)-(CH2)n-C(O)O-; -C(O)-O-; -C(O)- (CH2)n-NH-C(O)-; -C(O)-(CH2)n-; -C(O)-NH-; -C(O)-; -(CH2)n-C(O)-; -(CH2)n-C(O)O-; -(CH2)n-; and 20 -(CH2)n-NH-C(O)-; wherein n is a number from 1 to 20; and R’’’’ is C1-C6 alkyl. In one embodiment, the linker comprises –(CH2)n-NH-C(O)- or –(CH2)n-NH-C(O)-(CH2)2- C(COOH)-NH-C(O)-, wherein n is a number from 1 to 20. In one embodiment, the linker comprises –(CH)2-O-(CH2CH2)-(O)-(CH2CH2)-NH-C(O)-. In one embodiment, the in vivo delivery enhancing moiety is represented by the following structure: 25 , 30
, 9 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 5
wherein a broken bond represents a bond to the remainder of the dsRNA agent, or a pharmaceutically 10 acceptable salt thereof. In one embodiment, the in vivo delivery enhancing moiety is represented by the following structure:
, 15 wherein a broken bond represents a bond to the remainder of the dsRNA, or a pharmaceutically acceptable salt thereof. In one embodiment, the at least one αvβ6 integrin targeting ligand is conjugated to the sense strand. In one embodiment, the at least one αvβ6 integrin targeting ligand is conjugated to the 3’-end 20 of the sense strand. In another embodiment, the at least one αvβ6 integrin targeting ligand is 10 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO conjugated to the 5’-end of the sense strand. In one embodiment, the at least one αvβ6 integrin targeting ligand is conjugated to both the 5’-end and the 3’-end of the sense strand. In one embodiment, the at least one αvβ6 integrin targeting ligand is conjugated to an internal position of the sense strand. 5 In one embodiment, the at least one αvβ6 integrin targeting ligand is conjugated to the antisense strand. In one embodiment, the at least one αvβ6 integrin targeting ligand is conjugated to the 3’ end antisense strand. In another embodiment, the at least one αvβ6 integrin targeting ligand is conjugated to the 5’ end of the antisense strand. In one embodiment, the at least one αvβ6 integrin targeting ligand is conjugated to both the 5’-end and the 3’-end of the antisense strand. 10 In one embodiment, the at least one αvβ6 integrin targeting ligand is conjugated to an internal position of the antisense strand. In one embodiment, the at least one in vivo delivery enhancing moiety is conjugated to an internal position of the sense strand. In one embodiment, the at least one in vivo delivery enhancing moiety is conjugated to one or 15 more of the following internal positions: positions 4-8 and 13-18 on the sense strand, counting from the 5’ end. In one embodiment, the at least one in vivo delivery enhancing moiety is conjugated to one or more of the following internal positions: positions 5, 6, 7, 15, 16 and 17 on the sense strand, counting from the 5’-end. 20 In one embodiment, the at least one in vivo delivery enhancing moiety is conjugated to position 6 on the sense strand, counting from the 5’-end. In one embodiment, the at least one in vivo delivery enhancing moiety is conjugated to an internal position of the antisense strand. In one embodiment, the at least one in vivo delivery enhancing moiety is conjugated to one or 25 more of the following internal positions: positions 6-10 and 15-18 on the antisense strand, counting from the 5’-end. In one embodiment, the at least one in vivo delivery enhancing moiety is conjugated to one or more of the following internal positions: positions 15, 16 and 17 on the antisense strand, counting from the 5’-end. 30 In one embodiment, the at least one αvβ6 integrin targeting ligand and the at least one in vivo delivery enhancing moiety are both conjugated to the sense strand. In one embodiment, the at least one αvβ6 integrin targeting ligand and the at least one in vivo delivery enhancing moiety are both conjugated to the antisense strand. In one embodiment, the at least one αvβ6 integrin targeting ligand is conjugated to the sense 35 strand and the at least one in vivo delivery enhancing moiety is conjugated to the antisense strand. In one embodiment, the at least one αvβ6 integrin targeting ligand is conjugated to the antisense strand and the at least one in vivo delivery enhancing moiety is conjugated to the sense strand. 11 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In one embodiment, the dsRNA agent is selected from the group consisting of AD-2702386, AD-2702387, AD-2814835, AD-2814836, AD-2814837, AD-2814838, AD-2814839, or AD- 3100656. The present disclosure also provides cells and pharmaceutical compositions, e.g., a dsRNA, or 5 a pharmaceutically acceptable salt thereof, of the disclosure and a pharmaceutically acceptable carrier, comprising a dsRNA agent, or a pharmaceutically acceptable salt thereof, as described herein. In the pharmaceutical compositions of the disclosure, the dsRNA agent may in an unbuffered solution, e.g., saline or water, or a buffer solution, e.g., a buffer solution comprises acetate, citrate, prolamine, carbonate, or phosphate or any combination thereof, or phosphate buffered saline (PBS). 10 In one aspect, the present disclosure provides a method of inhibiting expression of a dystrophy myotonic protein kinase (DMPK) gene in a cell. The method includes contacting the cell with the dsRNA agent, or a pharmaceutically acceptable salt thereof, of the disclosure, or the pharmaceutical composition of the disclosure, thereby inhibiting expression of the DMPK gene in the cell. 15 In one embodiment, the cell is a muscle cell, e.g., a skeletal muscle cell, a cardiac muscle cell, and/or a smooth muscle cell. In one embodiment, the cell is within a subject, e.g., a human, such as a subject having an DMPK-associated disorder, e.g., myotonic dystrophy type 1 (DM1). In one embodiment, contacting the cell with the dsRNA agent inhibits the expression of the 20 DMPK gene by at least 50%, 60%, 70%, 80%, 90%, or 95%. In one embodiment, inhibiting expression of the DMPK gene decreases DMPK protein level in serum of the subject by at least 50%, 60%, 70%, 80%, 90%, or 95%. In one aspect, the present disclosure provides a method of treating a subject having a disorder that would benefit from reduction in dystrophy myotonic protein kinase (DMPK) expression. The 25 method includes administering to the subject a therapeutically effective amount of the dsRNA agent, or a pharmaceutically acceptable salt thereof, of the disclosure, or the pharmaceutical composition of the disclosure, thereby treating the subject having the disorder that would benefit from reduction in DMPK expression. In another aspect, the present disclosure provides a method of preventing at least one 30 symptom in a subject having a disorder that would benefit from reduction in dystrophy myotonic protein kinase (DMPK) expression. The method includes administering to the subject a prophylactically effective amount of the dsRNA agent, or a pharmaceutically acceptable salt thereof, of the disclosure, or the pharmaceutical composition of the disclosure, thereby preventing at least one symptom in the subject having the disorder that would benefit from reduction in DMPK expression. 35 In one embodiment, treating comprises amelioration of at least on sign or symptom of the disease. In another embodiment, treating comprises prevention of progression of the disease. 12 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In one embodiment, the disorder is an DMPK-associated disorder, e.g., myotonic dystrophy type 1 (DM1). In one embodiment, the subject is a human. In one embodiment, the dsRNA agent is administered to the subject subcutaneously. 5 In another embodiment, the dsRNA agent, or a pharmaceutically acceptable salt thereof, is administered to the subject intramuscularly. In one embodiment, the method further comprises administering to the subject an additional therapeutic agent for treatment of a DMPK-associated disorder. The present disclosure further provides a kit, a vial, or a syringe comprising the dsRNA agent, 10 or a pharmaceutically acceptable salt thereof, of the disclosure or the pharmaceutical composition of the disclosure. In one embodiment, the present disclosure provides an RNA-induced silencing complex (RISC) comprising an antisense strand of any of the dsRNA agents, or a pharmaceutically acceptable salt thereof, of the disclosure. 15 BRIEF DESCRIPTION OF THE DRAWINGS FIG.1 is a graph showing the precent of DMPK remaining at Day 85 in non-human primates (NHP) that were administered a single dose of PBS or 3 mg/kg of AD-2814835, AD-2814836, AD- 2814837, AD-2814838, or AD-2814839 DMPK-targeting siRNA duplexes in muscle tissue. 20 FIG.2 is a graph showing NHP DMPK knockdown mediated by AD-3100656 in heart, gastrocnemius, and quadriceps of non-human primates at Day 32 following a single subcutaneous dose of 3 mg/kg. The control group was the average of animals treated with non-DMPK targeting siRNAs. The DMPK mRNA % remaining is relative to two housekeeping genes (PPIB and ADD1). 25 DETAILED DESCRIPTION OF THE DISCLOSURE The present disclosure provides iRNA compositions which effect the RNA-induced silencing complex (RISC)-mediated cleavage of RNA transcripts of a dystrophy myotonic protein kinase (DMPK) gene. The gene may be within a cell, such as an adipocyte and/or a liver cell, e.g., a cell within a subject, such as a human subject. The use of these iRNAs enables the targeted degradation 30 of mRNAs of the corresponding DMPK gene in a mammal, e.g., a human. The iRNAs of the disclosure have been designed to target the human DMPK gene, including portions of the gene that are conserved in orthologs of other mammalian species. Without intending to be limited by theory, it is believed that a combination or sub-combination of the foregoing properties and the specific target sites or the specific modifications in these iRNAs confer to the 35 iRNAs of the disclosure improved efficacy, stability, potency, durability, and safety. Accordingly, the present disclosure provides methods for treating and preventing a DMPK- associated disorder, e.g., myotonic dystrophy type 1 (DM1), using dsRNA compositions which effect 13 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO the RNA-induced silencing complex (RISC)-mediated cleavage of RNA transcripts of a DMPK gene. The iRNAs of the disclosure include an RNA strand (the antisense strand) having a region which is up to about 30 nucleotides or less in length, e.g., 19-30, 19-29, 19-28, 19-27, 19-26, 19-25, 19-24, 5 19-23, 19-22, 19-21, 19-20, 20-30, 20-29, 20-28, 20-27, 20-26, 20-25, 20-24,20-23, 20-22, 20-21, 21- 30, 21-29, 21-28, 21-27, 21-26, 21-25, 21-24, 21-23, or 21-22 nucleotides in length, which region is substantially complementary to at least part of an mRNA transcript of a DMPK gene. In certain embodiments, one or both of the strands of the double stranded RNA agents of the disclosure is up to 66 nucleotides in length, e.g., 36-66, 26-36, 25-36, 31-60, 22-43, 27-53 nucleotides 10 in length, with a region of at least 19 contiguous nucleotides that is substantially complementary to at least a part of an mRNA transcript of a metabolic disorder-associated target gene, i.e., DMPK. In some embodiments, such dsRNA agents having longer length antisense strands may, for example, include a second RNA strand (the sense strand) of 20-60 nucleotides in length wherein the sense and antisense strands form a duplex of 18-30 contiguous nucleotides. 15 The use of iRNAs of the disclosure enables the targeted degradation of the DMPK mRNAs in mammals. Using in vitro and in vivo assays, the present inventors have demonstrated that iRNAs targeting the gene can potently mediate RNAi, resulting in significant inhibition of expression of the DMPK gene. Thus, methods and compositions including these iRNAs are useful for treating a subject having a DMPK-associated disorder, e.g., myotonic dystrophy type 1 (DM1), or for treating a 20 subject at risk of developing a DMPK-associated disorder. Accordingly, the present disclosure provides methods and combination therapies for treating a subject having a disorder that would benefit from inhibiting or reducing the expression of a DMPK gene, e.g., a DMPK-associated disorder, e.g., myotonic dystrophy type 1 (DM1), using iRNA compositions which effect the RNA-induced silencing complex (RISC)-mediated cleavage of RNA 25 transcripts of a DMPK gene. The present disclosure also provides methods for preventing at least one symptom in a subject having a disorder that would benefit from inhibiting or reducing the expression of a DMPK gene, e.g., a DMPK-associated disorder, e.g., myotonic dystrophy type 1 (DM1). The following detailed description discloses how to make and use compositions containing 30 iRNAs to inhibit the expression of DMPK, as well as compositions, uses, and methods for treating subjects that would benefit from inhibition and/or reduction of the expression of DMPK, e.g., subjects susceptible to or diagnosed with a DMPK-associated disorder, e.g., myotonic dystrophy type 1 (DM1). 35 I. Definitions In order that the present disclosure may be more readily understood, certain terms are first defined. In addition, it should be noted that whenever a value or range of values of a parameter are 14 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO recited, it is intended that values and ranges intermediate to the recited values are also intended to be part of this disclosure. The articles “a” and “an” are used herein to refer to one or to more than one (i.e., to at least one) of the grammatical object of the article. By way of example, “an element” means one element or 5 more than one element, e.g., a plurality of elements. The term "including" is used herein to mean, and is used interchangeably with, the phrase "including but not limited to". The term "or" is used herein to mean, and is used interchangeably with, the term "and/or," unless context clearly indicates otherwise. For example, “sense strand or antisense strand” is 10 understood as “sense strand or antisense strand or sense strand and antisense strand.” The term “about” is used herein to mean within the typical ranges of tolerances in the art. For example, “about” can be understood as about 2 standard deviations from the mean. In certain embodiments, about means +10%. In certain embodiments, about means +5%. When about is present before a series of numbers or a range, it is understood that “about” can modify each of the 15 numbers in the series or range. The term “at least”, “no less than”, or “or more” prior to a number or series of numbers is understood to include the number adjacent to the term “at least”, and all subsequent numbers or integers that could logically be included, as clear from context. For example, the number of nucleotides in a nucleic acid molecule must be an integer. For example, “at least 19 nucleotides of a 20 21 nucleotide nucleic acid molecule” means that 19, 20, or 21 nucleotides have the indicated property. When at least is present before a series of numbers or a range, it is understood that “at least” can modify each of the numbers in the series or range. As used herein, “no more than” or “or less” is understood as the value adjacent to the phrase and logical lower values or integers, as logical from context, to zero. For example, a duplex with an 25 overhang of “no more than 2 nucleotides” has a 2, 1, or 0 nucleotide overhang. When “no more than” is present before a series of numbers or a range, it is understood that “no more than” can modify each of the numbers in the series or range. As used herein, ranges include both the upper and lower limit. As used herein, methods of detection can include determination that the amount of analyte present is below the level of detection of the method. 30 In the event of a conflict between an indicated target site and the nucleotide sequence for a sense or antisense strand, the indicated sequence takes precedence. In the event of a conflict between a sequence and its indicated site on a transcript or other sequence, the nucleotide sequence recited in the specification takes precedence. As used herein, “dystrophy myotonic protein kinase,” used interchangeably with the terms 35 “DMPK,” refers to the serine-threonine kinase that is closely related to other kinases that interact with members of the Rho family of small GTPases. Substrates for this enzyme include myogenin, the beta- subunit of the L-type calcium channels, and phospholemman. The 3' untranslated region of this gene contains 5-38 copies of a CTG trinucleotide repeat. Expansion of this unstable motif to 50-5,000 15 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO copies causes myotonic dystrophy type I, which increases in severity with increasing repeat element copy number. Repeat expansion is associated with condensation of local chromatin structure that disrupts the expression of genes in this region. An exemplary sequence of a human DMPK mRNA transcript can be found at, for example, 5 GenBank Accession No. NM_004409.5 (GI: 1677499213, SEQ ID NO:1; reverse complement, SEQ ID NO:2). An exmplary sequence of mouse DMPK mRNA can be found at, for example, GenBank Accession No. NM_032418.3 (SEQ ID NO:3; reverse complement, SEQ ID NO:4). An exemplary sequence of rat DMPK mRNA can be found at, for example, GenBank Accession No. NM_001415847 (SEQ ID NO:5; reverse complement, SEQ ID NO:6). An exemplary sequence of 10 Macaca mulatta DMPK mRNA can be found at, for example, GenBank Accession No. NM_001260568 (SEQ ID NO:7; reverse complement, SEQ ID NO:8). Exemplary sequences for Macaca fascicularis DMPK mRNA can be found at GenBank Acession No. XM_005589613.2 and XM_045381179.1. Additional examples of DMPK mRNA sequences are readily available through publicly 15 available databases, e.g., GenBank, UniProt, OMIM, the UCSC Genome Browser, and the Macaca genome project web site. Further information on DMPK can be found, for example, at www.ncbi.nlm.nih.gov/gene/?term= DMPK. The term DMPK, as used herein, also refers to variations of the DMPK gene including 20 variants provided in the SNP database. Numerous sequence variations within the DMPK gene have been identified and may be found at, for example, NCBI dbSNP and UniProt (see, e.g., www.ncbi.nlm.nih.gov/snp/?term= DMPK, the entire contents of which is incorporated herein by reference as of the date of filing this application). The entire contents of each of the foregoing GenBank Accession numbers and the Gene 25 database numbers are incorporated herein by reference as of the date of filing this application. As used herein, “target sequence” or “target nucleic acid” refers to a contiguous portion of the nucleotide sequence of an mRNA molecule formed during the transcription of a DMPK gene, including mRNA that is a product of RNA processing of a primary transcription product. In one embodiment, the target portion of the sequence will be at least long enough to serve as a substrate for 30 RNAi-directed cleavage at or near that portion of the nucleotide sequence of an mRNA molecule formed during the transcription of a DMPK gene. In one embodiment, the target sequence is within the protein coding region of the DMPK gene. In another embodiment, the target sequence is within the 3’ UTR of the DMPK gene. The target nucleic acid can be a cellular gene (or mRNA transcribed from the gene) whose expression is associated with a particular disorder or disease state. 35 The target sequence may be from about 19-36 nucleotides in length, e.g., about 19-30 nucleotides in length. For example, the target sequence can be about 19-30 nucleotides, 19-30, 19-29, 19-28, 19-27, 19-26, 19-25, 19-24, 19-23, 19-22, 19-21, 19-20, 20-30, 20-29, 20-28, 20-27, 20-26, 20- 25, 20-24, 20-23, 20-22, 20-21, 21-30, 21-29, 21-28, 21-27, 21-26, 21-25, 21-24, 21-23, or 21-22 16 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO nucleotides in length. In certain embodiments, the target sequence is 19-23 nucleotides in length, optionally 21-23 nucleotides in length. Ranges and lengths intermediate to the above recited ranges and lengths are also contemplated to be part of the disclosure. As used herein, the term “strand comprising a sequence” refers to an oligonucleotide 5 comprising a chain of nucleotides that is described by the sequence referred to using the standard nucleotide nomenclature. “G,” “C,” “A,” “T,” and “U” each generally stand for a nucleotide that contains guanine, cytosine, adenine, thymidine, and uracil as a base, respectively. However, it will be understood that the term “ribonucleotide” or “nucleotide” can also refer to a modified nucleotide, as further detailed 10 below, or a surrogate replacement moiety (see, e.g., Table 1). The skilled person is well aware that guanine, cytosine, adenine, and uracil can be replaced by other moieties without substantially altering the base pairing properties of an oligonucleotide comprising a nucleotide bearing such replacement moiety. For example, without limitation, a nucleotide comprising inosine as its base can base pair with nucleotides containing adenine, cytosine, or uracil. Hence, nucleotides containing uracil, 15 guanine, or adenine can be replaced in the nucleotide sequences of dsRNA featured in the disclosure by a nucleotide containing, for example, inosine. In another example, adenine and cytosine anywhere in the oligonucleotide can be replaced with guanine and uracil, respectively to form G-U Wobble base pairing with the target mRNA. Sequences containing such replacement moieties are suitable for the compositions and methods featured in the disclosure. 20 The terms “iRNA”, “RNAi agent,” “iRNA agent,”, “RNA interference agent” as used interchangeably herein, refer to an agent that contains RNA as that term is defined herein, and which mediates the targeted cleavage of an RNA transcript via an RNA-induced silencing complex (RISC) pathway. iRNA directs the sequence-specific degradation of mRNA through a process known as RNA interference (RNAi). The iRNA modulates, e.g., inhibits, the expression of a DMPK gene in a 25 cell, e.g., a muscle cell , within a subject, such as a mammalian subject. The “RNAi agent” and “dsRNA agent” may be used interchangeably herein. The terms “RNAi agent” and “dsRNA agent” may be used interchangeably herein. In one embodiment, an RNAi agent of the disclosure includes a single stranded RNA that interacts with a target RNA sequence, e.g., a DMPK mRNA sequence, to direct the cleavage of the 30 target RNA. Without wishing to be bound by theory it is believed that long double stranded RNA introduced into cells is broken down into siRNA by a Type III endonuclease known as Dicer (Sharp et al. (2001) Genes Dev.15:485). Dicer, a ribonuclease-III-like enzyme, processes the dsRNA into 19- 23 base pair short interfering RNAs with characteristic two base 3' overhangs (Bernstein, et al., (2001) Nature 409:363). The siRNAs are then incorporated into an RNA-induced silencing complex 35 (RISC) where one or more helicases unwind the siRNA duplex, enabling the complementary antisense strand to guide target recognition (Nykanen, et al., (2001) Cell 107:309). Upon binding to the appropriate target mRNA, one or more endonucleases within the RISC cleave the target to induce silencing (Elbashir, et al., (2001) Genes Dev.15:188). Thus, in one aspect the disclosure relates to a 17 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO single stranded RNA (siRNA) generated within a cell and which promotes the formation of a RISC complex to effect silencing of the DMPK gene. Accordingly, the term “siRNA” is also used herein to refer to an iRNA as described above. In certain embodiments, the RNAi agent may be a single-stranded siRNA (ssRNAi) that is 5 introduced into a cell or organism to inhibit a target mRNA. Single-stranded RNAi agents bind to the RISC endonuclease, Argonaute 2, which then cleaves the target mRNA. The single-stranded siRNAs are generally 15-30 nucleotides and are chemically modified. The design and testing of single- stranded siRNAs are described in U.S. Patent No.8,101,348 and in Lima et al., (2012) Cell 150:883- 894, the entire contents of each of which are hereby incorporated herein by reference. Any of the 10 antisense nucleotide sequences described herein may be used as a single-stranded siRNA as described herein or as chemically modified by the methods described in Lima et al., (2012) Cell 150:883-894. In certain embodiments, an “iRNA” for use in the compositions, uses, and methods of the disclosure is a double stranded RNA and is referred to herein as a “double stranded RNA agent,” “double stranded RNA (dsRNA) molecule,” “dsRNA agent,” or “dsRNA”. The term “dsRNA”, refers to a 15 complex of ribonucleic acid molecules, having a duplex structure comprising two anti-parallel and substantially complementary nucleic acid strands, referred to as having “sense” and “antisense” orientations with respect to a target RNA, i.e., a DMPK mRNA sequence. In some embodiments of the disclosure, a double stranded RNA (dsRNA) triggers the degradation of a target RNA, e.g., an mRNA, through a post-transcriptional gene-silencing mechanism referred to herein as RNA 20 interference or RNAi. In general, the majority of nucleotides of each strand of a dsRNA molecule are ribonucleotides, but as described in detail herein, each or both strands can also include one or more non-ribonucleotides, e.g., a deoxyribonucleotide or a modified nucleotide. In addition, as used in this specification, an “iRNA” may include ribonucleotides with chemical modifications; an iRNA may 25 include substantial modifications at multiple nucleotides. As used herein, the term “modified nucleotide” refers to a nucleotide having, independently, a modified sugar moiety, a modified internucleotide linkage, or modified nucleobase, or any combination thereof. Thus, the term modified nucleotide encompasses substitutions, additions or removal of, e.g., a functional group or atom, to internucleoside linkages, sugar moieties, or nucleobases. The modifications suitable for use in the 30 agents of the disclosure include all types of modifications disclosed herein or known in the art. Any such modifications, as used in a siRNA type molecule, are encompassed by “iRNA” or “RNAi agent” for the purposes of this specification and claims. In certain embodiments of the instant disclosure, inclusion of a deoxy-nucleotide if present within an RNAi agent can be considered to constitute a modified nucleotide. 35 The duplex region may be of any length that permits specific degradation of a desired target RNA through a RISC pathway, and may range from about 19 to 36 base pairs in length, e.g., about 19-30 base pairs in length, for example, about 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, or 36 base pairs in length, such as about 19-30, 19-29, 18 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 19-28, 19-27, 19-26, 19-25, 19-24, 19-23, 19-22, 19-21, 19-20, 20-30, 20-29, 20-28, 20-27, 20-26, 20- 25, 20-24,20-23, 20-22, 20-21, 21-30, 21-29, 21-28, 21-27, 21-26, 21-25, 21-24, 21-23, or 21-22 base pairs in length. In certain embodiments, the duplex region is 19-21 base pairs in length, e.g., 21 base pairs in length. Ranges and lengths intermediate to the above recited ranges and lengths are also 5 contemplated to be part of the disclosure. The two strands forming the duplex structure may be different portions of one larger RNA molecule, or they may be separate RNA molecules. Where the two strands are part of one larger molecule, and therefore are connected by an uninterrupted chain of nucleotides between the 3’-end of one strand and the 5’-end of the respective other strand forming the duplex structure, the connecting 10 RNA chain is referred to as a “hairpin loop.” A hairpin loop can comprise at least one unpaired nucleotide. In some embodiments, the hairpin loop can comprise at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 23 or more unpaired nucleotides. In some embodiments, the hairpin loop can be 10 or fewer nucleotides. In some embodiments, the hairpin loop can be 8 or fewer unpaired nucleotides. In some embodiments, the hairpin loop can be 4-10 unpaired nucleotides. In some embodiments, the hairpin 15 loop can be 4-8 nucleotides. In certain embodiment, the two strands of double-stranded oligomeric compound can be linked together. The two strands can be linked to each other at both ends, or at one end only. By linking at one end is meant that 5'-end of first strand is linked to the 3'-end of the second strand or 3'- end of first strand is linked to 5'-end of the second strand. When the two strands are linked to each 20 other at both ends, 5'-end of first strand is linked to 3'-end of second strand and 3'-end of first strand is linked to 5'-end of second strand. The two strands can be linked together by an oligonucleotide linker including, but not limited to, (N)n; wherein N is independently a modified or unmodified nucleotide and n is 3-23. In some embodiemtns, n is 3-10, e.g., 3, 4, 5, 6, 7, 8, 9, or 10. In some embodiments, the oligonucleotide linker is selected from the group consisting of GNRA, (G)4, (U)4, and (dT)4, 25 wherein N is a modified or unmodified nucleotide and R is a modified or unmodified purine nucleotide. Some of the nucleotides in the linker can be involved in base-pair interactions with other nucleotides in the linker. The two strands can also be linked together by a non-nucleosidic linker, e.g. a linker described herein. It will be appreciated by one of skill in the art that any oligonucleotide chemical modifications or variations describe herein can be used in the oligonucleotide linker. 30 Hairpin and dumbbell type oligomeric compounds will have a duplex region equal to or at least 14, 15, 15, 16, 17, 18, 19, 29, 21, 22, 23, 24, or 25 nucleotide pairs. The duplex region can be equal to or less than 200, 100, or 50, in length. In some embodiments, ranges for the duplex region are 15-30, 17 to 23, 19 to 23, and 19 to 21 nucleotides pairs in length. The hairpin oligomeric compounds can have a single strand overhang or terminal unpaired 35 region, in some embodiments at the 3', and in some embodiments on the antisense side of the hairpin. In some embodiments, the overhangs are 1-4, more generally 2-3 nucleotides in length. The hairpin oligomeric compounds that can induce RNA interference are also referred to as "shRNA" herein. 19 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO Where the two substantially complementary strands of a dsRNA are comprised by separate RNA molecules, those molecules need not be, but can be covalently connected. Where the two strands are connected covalently by means other than an uninterrupted chain of nucleotides between the 3’-end of one strand and the 5’-end of the respective other strand forming the duplex structure, the connecting 5 structure is referred to as a “linker.” The RNA strands may have the same or a different number of nucleotides. The maximum number of base pairs is the number of nucleotides in the shortest strand of the dsRNA minus any overhangs that are present in the duplex. In addition to the duplex structure, an RNAi may comprise one or more nucleotide overhangs. In one embodiment of the RNAi agent, at least one strand comprises a 3’ overhang of at least 1 nucleotide. In another embodiment, at least one 10 strand comprises a 3’ overhang of at least 2 nucleotides, e.g., 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, or 15 nucleotides. In other embodiments, at least one strand of the RNAi agent comprises a 5’ overhang of at least 1 nucleotide. In certain embodiments, at least one strand comprises a 5’ overhang of at least 2 nucleotides, e.g., 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, or 15 nucleotides. In still other embodiments, both the 3’ and the 5’ end of one strand of the RNAi agent comprise an overhang of at least 1 15 nucleotide. In certain embodiments, an iRNA agent of the disclosure is a dsRNA, each strand of which comprises 19-23 nucleotides, that interacts with a target RNA sequence, e.g., a DMPK mRNA sequence, to direct cleavage of the target RNA. In some embodiments, an iRNA of the disclosure is a dsRNA of 24-30 nucleotides that 20 interacts with a target RNA sequence, e.g., a DMPK mRNA sequence, to direct the cleavage of the target RNA. As used herein, the term “nucleotide overhang” refers to at least one unpaired nucleotide that protrudes from the duplex structure of a double stranded iRNA. For example, when a 3'-end of one strand of a dsRNA extends beyond the 5'-end of the other strand, or vice versa, there is a nucleotide 25 overhang. A dsRNA can comprise an overhang of at least one nucleotide; alternatively the overhang can comprise at least two nucleotides, at least three nucleotides, at least four nucleotides, at least five nucleotides or more. A nucleotide overhang can comprise or consist of a nucleotide/nucleoside analog, including a deoxynucleotide/nucleoside. The overhang(s) can be on the sense strand, the antisense strand, or any combination thereof. Furthermore, the nucleotide(s) of an overhang can be 30 present on the 5'-end, 3'-end, or both ends of either an antisense or sense strand of a dsRNA. In one embodiment, the antisense strand of a dsRNA has a 1-10 nucleotide, e.g., a 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotide, overhang at the 3’-end or the 5’-end. In one embodiment, the sense strand of a dsRNA has a 1-10 nucleotide, e.g., a 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotide, overhang at the 3’-end or the 5’-end. In another embodiment, one or more of the nucleotides in the overhang is 35 replaced with a nucleoside thiophosphate. In certain embodiments, the antisense strand of a dsRNA has a 1-10 nucleotide, e.g., 0-3, 1-3, 2-4, 2-5, 4-10, 5-10, e.g., a 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotide, overhang at the 3’-end or the 5’- end. In one embodiment, the sense strand of a dsRNA has a 1-10 nucleotide, e.g., a 1, 2, 3, 4, 5, 6, 7, 20 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 8, 9, or 10 nucleotide, overhang at the 3’-end or the 5’-end. In another embodiment, one or more of the nucleotides in the overhang is replaced with a nucleoside thiophosphate. In certain embodiments, the antisense strand of a dsRNA has a 1-10 nucleotides, e.g., a 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotide, overhang at the 3’-end or the 5’-end. In certain embodiments, the 5 overhang on the sense strand or the antisense strand, or both, can include extended lengths longer than 10 nucleotides, e.g., 1-30 nucleotides, 2-30 nucleotides, 10-30 nucleotides, 10-25 nucleotides, 10-20 nucleotides, or 10-15 nucleotides in length. In certain embodiments, an extended overhang is on the sense strand of the duplex. In certain embodiments, an extended overhang is present on the 3’ end of the sense strand of the duplex. In certain embodiments, an extended overhang is present on the 5’ end 10 of the sense strand of the duplex. In certain embodiments, an extended overhang is on the antisense strand of the duplex. In certain embodiments, an extended overhang is present on the 3’end of the antisense strand of the duplex. In certain embodiments, an extended overhang is present on the 5’end of the antisense strand of the duplex. In certain embodiments, one or more of the nucleotides in the extended overhang is replaced with a nucleoside thiophosphate. In certain embodiments, the overhang 15 includes a self-complementary portion such that the overhang is capable of forming a hairpin structure that is stable under physiological conditions. “Blunt” or “blunt end” means that there are no unpaired nucleotides at that end of the double stranded RNA agent, i.e., no nucleotide overhang. A “blunt ended” double stranded RNA agent is double stranded over its entire length, i.e., no nucleotide overhang at either end of the molecule. The20 RNAi agents of the disclosure include RNAi agents with no nucleotide overhang at one end (i.e., agents with one overhang and one blunt end) or with no nucleotide overhangs at either end. Most often such a molecule will be double-stranded over its entire length. The term “antisense strand” or "guide strand" refers to the strand of an iRNA, e.g., a dsRNA, which includes a region that is substantially complementary to a target sequence, e.g., a DMPK 25 mRNA. As used herein, the term “region of complementarity” refers to the region on the antisense strand that is substantially complementary to a sequence, for example a target sequence, e.g., a DMPK nucleotide sequence, as defined herein. Where the region of complementarity is not fully complementary to the target sequence, the mismatches can be in the internal or terminal regions of the 30 molecule. Generally, the most tolerated mismatches are in the terminal regions, e.g., within 5, 4, or 3 nucleotides of the 5’- or 3’-end of the iRNA. In some embodiments, a double stranded RNA agent of the disclosure includes a nucleotide mismatch in the antisense strand. In some embodiments, the antisense strand of the double stranded RNA agent of the disclosure includes no more than 4 mismatches with the target mRNA, e.g., the antisense strand includes 4, 3, 2, 1, or 0 mismatches with 35 the target mRNA. In some embodiments, the antisense strand double stranded RNA agent of the disclosure includes no more than 4 mismatches with the sense strand, e.g., the antisense strand includes 4, 3, 2, 1, or 0 mismatches with the sense strand. In some embodiments, a double stranded RNA agent of the disclosure includes a nucleotide mismatch in the sense strand. In some 21 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO embodiments, the sense strand of the double stranded RNA agent of the disclosure includes no more than 4 mismatches with the antisense strand, e.g., the sense strand includes 4, 3, 2, 1, or 0 mismatches with the antisense strand. In some embodiments, the nucleotide mismatch is, for example, within 5, 4, 3 nucleotides from the 3’-end of the iRNA. In another embodiment, the nucleotide mismatch is, for 5 example, in the 3’-terminal nucleotide of the iRNA agent. In some embodiments, the mismatch(s) is not in the seed region. Thus, an RNAi agent as described herein can contain one or more mismatches to the target sequence. In one embodiment, an RNAi agent as described herein contains no more than 3 mismatches (i.e., 3, 2, 1, or 0 mismatches). In one embodiment, an RNAi agent as described herein 10 contains no more than 2 mismatches. In one embodiment, an RNAi agent as described herein contains no more than 1 mismatch. In one embodiment, an RNAi agent as described herein contains 0 mismatches. In certain embodiments, if the antisense strand of the RNAi agent contains mismatches to the target sequence, the mismatch can optionally be restricted to be within the last 5 nucleotides from either the 5’- or 3’-end of the region of complementarity. For example, in such embodiments, for 15 a 23 nucleotide RNAi agent, the strand which is complementary to a region of DMPK, generally does not contain any mismatch within the central 13 nucleotides. The methods described herein or methods known in the art can be used to determine whether an RNAi agent containing a mismatch to a target sequence is effective in inhibiting the expression of a target gene. Consideration of the efficacy of RNAi agents with mismatches in inhibiting expression of a DMPK gene is important, especially if the 20 particular region of complementarity in the target gene is known to have polymorphic sequence variation within the population. The term “sense strand” or "passenger strand" as used herein, refers to the strand of an iRNA that includes a region that is substantially complementary to a region of the antisense strand as that term is defined herein. 25 As used herein, “substantially all of the nucleotides are modified” are largely but not wholly modified and can include not more than 5, 4, 3, 2, or 1 unmodified nucleotides. As used herein, the term “cleavage region” refers to a region that is located immediately adjacent to the cleavage site. The cleavage site is the site on the target at which cleavage occurs. In some embodiments, the cleavage region comprises three bases on either end of, and immediately 30 adjacent to, the cleavage site. In some embodiments, the cleavage region comprises two bases on either end of, and immediately adjacent to, the cleavage site. In some embodiments, the cleavage site specifically occurs at the site bound by nucleotides 10 and 11 of the antisense strand, and the cleavage region comprises nucleotides 11, 12 and 13. As used herein, and unless otherwise indicated, the term “complementary,” when used to 35 describe a first nucleotide sequence in relation to a second nucleotide sequence, refers to the ability of an oligonucleotide or polynucleotide comprising the first nucleotide sequence to hybridize and form a duplex structure under certain conditions with an oligonucleotide or polynucleotide comprising the second nucleotide sequence, as will be understood by the skilled person. Such conditions can, for 22 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO example, be stringent conditions, where stringent conditions can include: 400 mM NaCl, 40 mM PIPES pH 6.4, 1 mM EDTA, 50oC or 70oC for 12-16 hours followed by washing (see, e.g., “Molecular Cloning: A Laboratory Manual, Sambrook, et al. (1989) Cold Spring Harbor Laboratory Press). Other conditions, such as physiologically relevant conditions as can be encountered inside an 5 organism, can apply. The skilled person will be able to determine the set of conditions most appropriate for a test of complementarity of two sequences in accordance with the ultimate application of the hybridized nucleotides. Complementary sequences within an iRNA, e.g., within a dsRNA as described herein, include base-pairing of the oligonucleotide or polynucleotide comprising a first nucleotide sequence to an 10 oligonucleotide or polynucleotide comprising a second nucleotide sequence over the entire length of one or both nucleotide sequences. Such sequences can be referred to as “fully complementary” with respect to each other herein. However, where a first sequence is referred to as “substantially complementary” with respect to a second sequence herein, the two sequences can be fully complementary, or they can form one or more, but generally not more than 5, 4, 3, or 2 mismatched 15 base pairs upon hybridization for a duplex up to 30 base pairs, while retaining the ability to hybridize under the conditions most relevant to their ultimate application, e.g., inhibition of gene expression, in vitro or in vivo. However, where two oligonucleotides are designed to form, upon hybridization, one or more single stranded overhangs, such overhangs shall not be regarded as mismatches with regard to the determination of complementarity. For example, a dsRNA comprising one oligonucleotide 20 21 nucleotides in length and another oligonucleotide 23 nucleotides in length, wherein the longer oligonucleotide comprises a sequence of 21 nucleotides that is fully complementary to the shorter oligonucleotide, can yet be referred to as “fully complementary” for the purposes described herein. “Complementary” sequences, as used herein, can also include, or be formed entirely from, non- Watson-Crick base pairs or base pairs formed from non-natural and modified nucleotides, in so far as 25 the above requirements with respect to their ability to hybridize are fulfilled. Such non-Watson-Crick base pairs include, but are not limited to, G:U Wobble or Hoogsteen base pairing. The terms “complementary,” “fully complementary” and “substantially complementary” herein can be used with respect to the base matching between the sense strand and the antisense strand of a dsRNA, or between two oligonucletoides or polynucleotides, such as the antisense strand of a 30 double stranded RNA agent and a target sequence, as will be understood from the context of their use. As used herein, a polynucleotide that is “substantially complementary to at least part of” a messenger RNA (mRNA) refers to a polynucleotide that is substantially complementary to a contiguous portion of the mRNA of interest (e.g., an mRNA encoding DMPK). For example, a polynucleotide is complementary to at least a part of a DMPK mRNA if the sequence is substantially 35 complementary to a non-interrupted portion of an mRNA encoding DMPK. Accordingly, in some embodiments, the antisense strand polynucleotides disclosed herein are fully complementary to the target gene, i.e., DMPK sequence. 23 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In some embodiments, the antisense strand polynucleotides disclosed herein are substantially complementary to the target gene sequence and comprise a contiguous nucleotide sequence which is at least about 80% complementary over its entire length to the equivalent region of the nucleotide sequence of SEQ ID NOs: 1, 3, 5, and 7, for DMPK, or a fragment of SEQ ID NOs: 1, 3, 5, and 7, 5 such as about 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or about 99% complementary. In other embodiments, the antisense polynucleotides disclosed herein are substantially complementary to the target DMPK sequence and comprise a contiguous nucleotide sequence which is at least about 80% complementary over its entire length to any one of the sense strand nucleotide 10 sequences in any one of Tables 2-3, or a fragment of any one of the sense strand nucleotide sequences in any one of Tables 2-3, such as about 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or about 99% complementary. In one embodiment, an RNAi agent of the disclosure includes a sense strand that is substantially complementary to an antisense polynucleotide which, in turn, is the same as a target 15 DMPK sequence, and wherein the sense strand polynucleotide comprises a contiguous nucleotide sequence which is at least about 80% complementary over its entire length to the equivalent region of the nucleotide sequence of SEQ ID NOs: 2, 4, 6, and 8, or a fragment of any one of SEQ ID NOs: 2, 4, 6, and 8, 10, such as about 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or about 99% complementary. 20 In some embodiments, an iRNA of the disclosure includes a sense strand that is substantially complementary to an antisense polynucleotide which, in turn, is complementary to a target DMPK sequence, and wherein the sense strand polynucleotide comprises a contiguous nucleotide sequence which is at least about 80% complementary over its entire length to any one of the antisense strand nucleotide sequences in any one of any one of Tables 2-3, or a fragment of any one of the antisense 25 strand nucleotide sequences in any one of Tables 2-3, such as about 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or about 99% complementary. In some embodiments, the double-stranded region of a double-stranded iRNA agent is equal to or at least, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 23, 24, 25, 26, 27, 28, 29, 30 or more nucleotide pairs in length. 30 In some embodiments, the antisense strand of a double-stranded iRNA agent is equal to or at least 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length. In some embodiments, the sense strand of a double-stranded iRNA agent is equal to or at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length. 35 In one embodiment, the sense and antisense strands of the double-stranded iRNA agent are each independently 15 to 30 nucleotides in length. In one embodiment, the sense and antisense strands of the double-stranded iRNA agent are each independently 19 to 25 nucleotides in length. 24 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In one embodiment, the sense and antisense strands of the double-stranded iRNA agent are each independently 21 to 23 nucleotides in length. In one embodiment, the sense strand of the iRNA agent is 21-nucleotides in length, and the antisense strand is 23-nucleotides in length, wherein the strands form a double-stranded region of 21 5 consecutive base pairs having a 2-nucleotide long single stranded overhang at the 3'-end. In general, an “iRNA” includes ribonucleotides with chemical modifications. Such modifications may include all types of modifications disclosed herein or known in the art. Any such modifications, as used in a dsRNA molecule, are encompassed by “iRNA” for the purposes of this specification and claims. 10 In certain embodiments of the instant disclosure, inclusion of a deoxy-nucleotide if present within an RNAi agent can be considered to constitute a modified nucleotide. In an aspect of the disclosure, an agent for use in the methods and compositions of the disclosure is a single-stranded antisense oligonucleotide molecule that inhibits a target mRNA via an antisense inhibition mechanism. The single-stranded antisense oligonucleotide molecule is 15 complementary to a sequence within the target mRNA. The single-stranded antisense oligonucleotides can inhibit translation in a stoichiometric manner by base pairing to the mRNA and physically obstructing the translation machinery, see Dias, N. et al., (2002) Mol Cancer Ther 1:347- 355. The single-stranded antisense oligonucleotide molecule may be about 14 to about 30 nucleotides in length and have a sequence that is complementary to a target sequence. For example, the single- 20 stranded antisense oligonucleotide molecule may comprise a sequence that is at least about 14, 15, 16, 17, 18, 19, 20, or more contiguous nucleotides from any one of the antisense sequences described herein. In some embodiments, a dsRNA agent of the disclosure comprises: (a) a sense strand having: (i) a length of 21 nucleotides; (ii) an in vivo delivery enhancing moiety, (iii) an αvβ6 integrin targeting25 ligand, and (iv) 2’-fluoro modifications at positions 1, 3, 5, 7, 9 to 11, 13, 17, 19, and 21, and 2’-O- methyl modifications at positions 2, 4, 6, 8, 12, 14 to 16, 18, and 20 (counting from the 5’ end); and (b) an antisense strand having: (i) a length of 23 nucleotides; (ii) 2’-O-methyl modifications at positions 1, 3, 5, 9, 11 to 13, 15, 17, 19, 21, and 23, and 2’-fluoro modifications at positions 2, 4, 6 to 8, 10, 14, 16, 18, 20, and 22 (counting from the 5’ end); and (iii) phosphorothioate linkages between 30 nucleotide positions 21 and 22, and between nucleotide positions 22 and 23 (counting from the 5’ end); wherein the dsRNA agent has a two-nucleotide overhang at the 3’-end of the antisense strand, and a blunt end at the 5’-end of the antisense strand. In some embodiments, a dsRNA agent of the disclosure comprises: (a) a sense strand having: (i) a length of 21 nucleotides; (ii) an in vivo delivery enhancing moiety, (iii) an αvβ6 integrin targeting35 ligand; (iv) 2’-fluoro modifications at positions 1, 3, 5, 7, 9 to 11, 13, 15, 17, 19, and 21, and 2’-O- methyl modifications at positions 2, 4, 6, 8, 12, 14, 16, 18, and 20 (counting from the 5’ end); and (v) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, and between nucleotide positions 2 and 3 (counting from the 5’ end); and (b) an antisense strand having: (i) a 25 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO length of 23 nucleotides; (ii) 2’-O-methyl modifications at positions 1, 3, 5, 7, 9, 11 to 13, 15, 17, 19, and 21 to 23, and 2’-fluoro modifications at positions 2, 4, 6, 8, 10, 14, 16, 18, and 20 (counting from the 5’ end); and (iii) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, between nucleotide positions 2 and 3, between nucleotide positions 21 and 22, and between 5 nucleotide positions 22 and 23 (counting from the 5’ end); wherein the dsRNA agent has a two- nucleotide overhang at the 3’-end of the antisense strand, and a blunt end at the 5’-end of the antisense strand. In some embodiments, a dsRNA agent of the disclosure comprises: (a) a sense strand having: (i) a length of 21 nucleotides; (ii) an in vivo delivery enhancing moiety, (iii) an αvβ6 integrin targeting 10 ligand; (iv) 2’-O-methyl modifications at positions 1 to 6, 8, 10, and 12 to 21, 2’-fluoro modifications at positions 7 and 9, and a deoxy-nucleotide (e.g. dT) at position 11 (counting from the 5’ end); and (v) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, and between nucleotide positions 2 and 3 (counting from the 5’ end); and (b) an antisense strand having: (i) a length of 23 nucleotides; (ii) 2’-O-methyl modifications at positions 1, 3, 7, 9, 11, 13, 15, 17, and 19 15 to 23, and 2’-fluoro modifications at positions 2, 4 to 6, 8, 10, 12, 14, 16, and 18 (counting from the 5’ end); and (iii) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, between nucleotide positions 2 and 3, between nucleotide positions 21 and 22, and between nucleotide positions 22 and 23 (counting from the 5’ end); wherein the dsRNA agent has a two- nucleotide overhang at the 3’-end of the antisense strand, and a blunt end at the 5’-end of the antisense 20 strand. In some embodiments, a dsRNA agent of the disclosure comprises: (a) a sense strand having: (i) a length of 21 nucleotides; (ii) an in vivo delivery enhancing moiety, (iii) an αvβ6 integrin targeting ligand; (iv) 2’-O-methyl modifications at positions 1 to 6, 8, 10, 12, 14, and 16 to 21, and 2’-fluoro modifications at positions 7, 9, 11, 13, and 15 (counting from the 5’ end); and (v) phosphorothioate 25 internucleotide linkages between nucleotide positions 1 and 2, and between nucleotide positions 2 and 3 (counting from the 5’ end); and (b) an antisense strand having: (i) a length of 23 nucleotides; (ii) 2’- O-methyl modifications at positions 1, 5, 7, 9, 11, 13, 15, 17, 19, and 21 to 23, and 2’-fluoro modifications at positions 2 to 4, 6, 8, 10, 12, 14, 16, 18, and 20 (counting from the 5’ end); and (iii) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, between nucleotide 30 positions 2 and 3, between nucleotide positions 21 and 22, and between nucleotide positions 22 and 23 (counting from the 5’ end); wherein the dsRNA agent has a two-nucleotide overhang at the 3’-end of the antisense strand, and a blunt end at the 5’-end of the antisense strand. In some embodiments, a dsRNA agent of the disclosure comprises: (a) a sense strand having: (i) a length of 21 nucleotides; (ii) an in vivo delivery enhancing moiety, (iii) an αvβ6 integrin targeting 35 ligand; (iv) 2’-O-methyl modifications at positions 1 to 9, and 12 to 21, and 2’-fluoro modifications at positions 10, and 11 (counting from the 5’ end); and (v) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, and between nucleotide positions 2 and 3 (counting from the 5’ end); and (b) an antisense strand having: (i) a length of 23 nucleotides; (ii) 2’-O-methyl modifications 26 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO at positions 1, 3, 5, 7, 9, 11 to 13, 15, 17, 19, and 21 to 23, and 2’-fluoro modifications at positions 2, 4, 6, 8, 10, 14, 16, 18, and 20 (counting from the 5’ end); and (iii) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, between nucleotide positions 2 and 3, between nucleotide positions 21 and 22, and between nucleotide positions 22 and 23 (counting from the 5’ 5 end); wherein the dsRNA agent has a two-nucleotide overhang at the 3’-end of the antisense strand, and a blunt end at the 5’-end of the antisense strand. In some embodiments, a dsRNA agent of the disclosure comprises: (a) a sense strand having: (i) a length of 21 nucleotides; (ii) an in vivo delivery enhancing moiety, (iii) an αvβ6 integrin targeting ligand; (iv) 2’-fluoro modifications at positions 1, 3, 5, 7, 9 to 11, and 13, and 2’-O-methyl 10 modifications at positions 2, 4, 6, 8, 12, and 14 to 21 (counting from the 5’ end); and (v) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, and between nucleotide positions 2 and 3 (counting from the 5’ end); and (b) an antisense strand having: (i) a length of 23 nucleotides; (ii) 2’-O-methyl modifications at positions 1, 3, 5 to 7, 9, 11 to 13, 15, 17 to 19, and 21 to 23, and 2’-fluoro modifications at positions 2, 4, 8, 10, 14, 16, and 20 (counting from 15 the 5’ end); and (iii) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, between nucleotide positions 2 and 3, between nucleotide positions 21 and 22, and between nucleotide positions 22 and 23 (counting from the 5’ end); wherein the dsNRA agent has a two- nucleotide overhang at the 3’-end of the antisense strand, and a blunt end at the 5’-end of the antisense strand. 20 In some embodiments, a dsRNA agent of the disclosure comprises: (a) a sense strand having: (i) a length of 21 nucleotides; (ii) an in vivo delivery enhancing moiety, (iii) an αvβ6 integrin targeting ligand; (iv) 2’-O-methyl modifications at positions 1 to 6, 8, and 12 to 21, and 2’-fluoro modifications at positions 7, and 9 to 11 (counting from the 5’ end); and (v) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, and between nucleotide positions 2 and 3 (counting 25 from the 5’ end); and (b) an antisense strand having: (i) a length of 23 nucleotides; (ii) 2’-O-methyl modifications at positions 1, 3 to 5, 7, 8, 10 to 13, 15, and 17 to 23, and 2’-fluoro modifications at positions 2, 6, 9, 14, and 16 (counting from the 5’ end); and (iii) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, between nucleotide positions 2 and 3, between nucleotide positions 21 and 22, and between nucleotide positions 22 and 23 (counting from the 5’ 30 end); wherein the dsRNA agent has a two-nucleotide overhang at the 3’-end of the antisense strand, and a blunt end at the 5’-end of the antisense strand. In some embodiments, a dsRNA agent of the disclosure comprises: (a) a sense strand having: (i) a length of 21 nucleotides; (ii) an in vivo delivery enhancing moiety, (iii) an αvβ6 integrin targeting ligand; (iv) 2’-O-methyl modifications at positions 1 to 6, 8, and 12 to 21, and 2’-fluoro modifications 35 at positions 7, and 9 to 11; and (v) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, and between nucleotide positions 2 and 3 (counting from the 5’ end); and (b) an antisense strand having: (i) a length of 23 nucleotides; (ii) 2’-O-methyl modifications at positions 1, 3 to 5, 7, 10 to 13, 15, and 17 to 23, and 2’-fluoro modifications at positions 2, 6, 8, 9, 14, and 16 27 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO (counting from the 5’ end); and (iii) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, between nucleotide positions 2 and 3, between nucleotide positions 21 and 22, and between nucleotide positions 22 and 23 (counting from the 5’ end); wherein the dsRNA agent has a two-nucleotide overhang at the 3’-end of the antisense strand, and a blunt end at the 5’-end of the 5 antisense strand. In some embodiments, a dsRNA agent of the disclosure comprises: (a) a sense strand having: (i) a length of 19 nucleotides; (ii) an in vivo delivery enhancing moiety, (iii) an αvβ6 integrin targeting ligand; (iv) 2’-O-methyl modifications at positions 1 to 4, 6, and 10 to 19, and 2’-fluoro modifications at positions 5, and 7 to 9; and (v) phosphorothioate internucleotide linkages between nucleotide 10 positions 1 and 2, and between nucleotide positions 2 and 3 (counting from the 5’ end); and (b) an antisense strand having: (i) a length of 21 nucleotides; (ii) 2’-O-methyl modifications at positions 1, 3 to 5, 7, 10 to 13, 15, and 17 to 21, and 2’-fluoro modifications at positions 2, 6, 8, 9, 14, and 16 (counting from the 5’ end); and (iii) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, between nucleotide positions 2 and 3, between nucleotide positions 19 and 20, and 15 between nucleotide positions 20 and 21 (counting from the 5’ end); wherein the dsRNA agent has a two-nucleotide overhang at the 3’-end of the antisense strand, and a blunt end at the 5’-end of the antisense strand. In some embodiments, a dsRNA agent of the disclosure comprises: (a) a sense strand having: (i) a length of 21 nucleotides; (ii) an in vivo delivery enhancing moiety, (iii) an αvβ6 integrin targeting 20 ligand; (iv) 2’-O-methyl modifications at positions 1 to 8, and 12 to 21, and 2’-fluoro modifications at positions 9 to 11; and (v) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, and between nucleotide positions 2 and 3 (counting from the 5’ end); and (b) an antisense strand having: (i) a length of 23 nucleotides; (ii) 2’-O-methyl modifications at positions 1, 3, 4, 6, 8 to 11, 13, 15 to 23, and a 2’-fluoro modification at position 14 (counting from the 5’ end), and 2’- 25 deoxy-modified nucleotides at positions 2, 5, 7, and 12; and (iii) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, between nucleotide positions 2 and 3, between nucleotide positions 21 and 22, and between nucleotide positions 22 and 23 (counting from the 5’ end); wherein the dsRNA agent has a two-nucleotide overhang at the 3’-end of the antisense strand, and a blunt end at the 5’-end of the antisense strand. 30 In some embodiments, a dsRNA agent of the disclosure comprises: (a) a sense strand having: (i) a length of 21 nucleotides; (ii) an in vivo delivery enhancing moiety, (iii) an αvβ6 integrin targeting ligand; (iv) 2’-O-methyl modifications at positions 1 to 6, 8, and 12 to 21, and 2’-fluoro modifications at positions 7, and 9 to 11; and (v) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, and between nucleotide positions 2 and 3 (counting from the 5’ end); and (b) an 35 antisense strand having: (i) a length of 23 nucleotides; (ii) 2’-O-methyl modifications at positions 1, 3 to 4, 6, 8 to 13, 15, and 17 to 23, 2’-fluoro modifications at positions 2, 14, and 16, a 2’-deoxy- modified nucleotide at position 5, and a GNA at position 7 (counting from the 5’ end); and (iii) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, between nucleotide 28 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO positions 2 and 3, between nucleotide positions 21 and 22, and between nucleotide positions 22 and 23 (counting from the 5’ end); wherein the dsRNA agent has a two-nucleotide overhang at the 3’-end of the antisense strand, and a blunt end at the 5’-end of the antisense strand. In some embodiments, a dsRNA agent of the disclosure comprises: (a) a sense strand having: 5 (i) a length of 21 nucleotides; (ii) an in vivo delivery enhancing moiety at position 5, 6, 16 or 17 (counting from the 5’ end), (iii) an αvβ6 integrin targeting ligand on the 3’ end; (iv) 2’-O-methyl modifications at positions 1 to 6, 8, and 12 to 21, and 2’-fluoro modifications at positions 7 and 9 to 11 (counting from the 5’ end); and (v) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, between nucleotide positions 2 and 3, between positions 20 and 21, and between 10 position 21 and the αvβ6 integrin targeting ligand (counting from the 5’ end); and (b) an antisense strand having: (i) a length of 23 nucleotides; (ii) 2’-O-methyl modifications at positions 1, 3 to 4, 6, 8 to 13, 15, and 17 to 23, 2’-fluoro modifications at positions 2, 14, and 16, a 2’-deoxy-modified nucleotide at position 5, and a GNA at position 7 (counting from the 5’ end); (iii) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, between nucleotide positions 2 and 3, 15 between nucleotide positions 21 and 22, and between nucleotide positions 22 and 23 (counting from the 5’ end); and (iv) a 5’-VP; wherein the dsRNA agent has a two-nucleotide overhang at the 3’-end of the antisense strand, and a blunt end at the 5’-end of the antisense strand. In some embodiments, a dsRNA agent of the disclosure comprises: (a) a sense strand having: (i) a length of 21 nucleotides; (ii) an in vivo delivery enhancing moiety at position 5, 6, 16 or 17 20 (counting from the 5’ end), (iii) an αvβ6 integrin targeting ligand on the 3’ end; (iv) 2’-O-methyl modifications at positions 1 to 6, 8, and 12 to 21, and 2’-fluoro modifications at positions 7, and 9 to 11 (counting from the 5’ end); and (v) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, between nucleotide positions 2 and 3, between positions 20 and 21, and between position 21 and the αvβ6 integrin targeting ligand (counting from the 5’ end); and (b) an antisense 25 strand having: (i) a length of 23 nucleotides; (ii) 2’-O-methyl modifications at positions 1, 3 to 5, 7 to 13, 15, and 17 to 23, and 2’-fluoro modifications at positions 2, 6, 9, 14, and 16 (counting from the 5’ end); (iii) phosphorothioate internucleotide linkages between nucleotide positions 1 and 2, between nucleotide positions 2 and 3, between nucleotide positions 21 and 22, and between nucleotide positions 22 and 23 (counting from the 5’ end); and (iv) a 5’-VP; wherein the dsRNA agent has a two- 30 nucleotide overhang at the 3’-end of the antisense strand, and a blunt end at the 5’-end of the antisense strand. In some embodiments, the sense strand of the dsRNA agent has 2’-F modifications at positions 7, 9, 10 and 11 (counting from the 5’ end). In some embodiments, the sense strand of the dsRNA agent has 2’-F modifications at positions 9 to 11 (counting from the 5’ end). In some 35 embodiments, the sense strand of the dsRNA agent has 2’-F modifications at positions 7 to 9 (counting from the 5’ end). In some embodiments, the sense strand of the dsRNA agent has 2’-F modifications at positions 5, 7, 8, and 9 (counting from the 5’ end). In some embodiments, the sense strand of the dsRNA agent has 2’-F modifications at positions 9, 11, and 13 (counting from the 5’ 29 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO end). In some embodiments, the sense strand of the dsRNA agent has 2’-F modifications at positions 9, 11, and 12 (counting from the 5’ end). In some embodiments, the sense strand of the dsRNA agent has 2’-F modifications at positions 2, 4, 6, 8, 10, 12, 14, 16, 18, and 20 (counting from the 5’ end). In some embodiments, the antisense strand of the dsRNA agent has 2’-F modifications at 5 positions 1, 2, 6, 14, and 16 (counting from the 5’ end). In some embodiments, the antisense strand of the dsRNA agent has 2’-F modifications at positions 2, 4, 6, 8, 10, 12, 14, 16, 18, and 20 (counting from the 5’ end). In some embodiments, the antisense strand of the dsRNA agent has 2’-F modifications at positions 2, 4, 6, 12, 14, 16, 18, and 19 (counting from the 5’ end). In some embodiments, the antisense strand of the dsRNA agent has 2’-F modifications at positions 2, 3, 5, 10, 10 12, 14, and 16 (counting from the 5’ end). In some embodiments, the antisense strand of the dsRNA agent has 2’-F modifications at positions 2, 4, 12, 14 and 16 (counting from the 5’ end). In some embodiments, the antisense strand of the dsRNA agent has 2’-F modifications at positions 2, 12, 14, and 16 (counting from the 5’ end). In some embodiments, the antisense strand of the dsRNA agent has 2’-F modifications at positions 2, 6, 14, and 16 (counting from the 5’ end). In some embodiments, the 15 antisense strand of the dsRNA agent has 2’-F modifications at positions 2, 14, and 16 (counting from the 5’ end). In some embodiments, the antisense strand of the dsRNA agent has 2’-F modifications at positions 2 and 14 (counting from the 5’ end). In some embodiments, the antisense strand of the dsRNA agent has a 2’-F modification at only position 14 (counting from the 5’ end). In some embodiments, the antisense strand of the dsRNA agent has 2’-deoxy-modified 20 nucleotides at positions 2, 5, 7, and 12 (counting from the 5’ end). In some embodiments, the antisense strand of the dsRNA agent comprises a 2’-deoxy-modified nucleotide at position 5 (counting from the 5’ end). In some embodiments, the antisense strand of the dsRNA agent comprises a GNA modified nucleotide at position 7 (counting from the 5’ end). 25 A “pharmaceutically acceptable salt” of the dsRNA agents of the disclosure includes any salt which is pharmaceutically acceptable, e.g., a sodium salt of the dsRNA agent. An “alpha-v-beta-6 (αvβ6) integrin targeting ligand”, as used herein, includes any moiety (e.g., peptides and small molecules) which bind an αvβ6 integrin and are able to mediate delivery of a dsRNA agent to which they are attached to skeletal muscle (e.g., a skeletal muscle cell or skeletal 30 muscle tissue) and/or cardiac muscle (e.g., a cardiac muscle cell or cardiac muscle tissue). The αvβ6 integrin targeting ligands bind αvβ6 integrin or the αvβ6 integrin receptor on skeletal muscle/cardiac myocytes (cells). Exemplary αvβ6 integrin targeting ligands are described below. Exemplary αvβ6 integrin targeting ligands are also described in WO2024/086633, the entire contents of which are incorporated by reference herein. 35 The phrase “contacting a cell with an iRNA,” such as a dsRNA, as used herein, includes contacting a cell by any possible means. Contacting a cell with an iRNA includes contacting a cell in vitro with the iRNA or contacting a cell in vivo with the iRNA. The contacting may be done directly or indirectly. Thus, for example, the iRNA may be put into physical contact with the cell by the 30 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO individual performing the method, or alternatively, the iRNA may be put into a situation that will permit or cause it to subsequently come into contact with the cell. Contacting a cell in vitro may be done, for example, by incubating the cell with the iRNA. Contacting a cell in vivo may be done, for example, by injecting the iRNA into or near the tissue 5 where the cell is located, or by injecting the iRNA into another area, e.g., the bloodstream or the subcutaneous space, such that the agent will subsequently reach the tissue where the cell to be contacted is located. For example, the iRNA may contain or be coupled to alpha-v-beta-6 (αvβ6) integrin targeting ligand that mediates delivery to muscle tissue and at least one in vivo delivery enhancing moiety. 10 Combinations of in vitro and in vivo methods of contacting are also possible. For example, a cell may also be contacted in vitro with an RNAi agent and subsequently transplanted into a subject. In certain embodiments, contacting a cell with an iRNA includes “introducing” or “delivering the iRNA into the cell” by facilitating or effecting uptake or absorption into the cell. Absorption or uptake of an iRNA can occur through unaided diffusion or active cellular processes, or by auxiliary 15 agents or devices. Introducing an iRNA into a cell may be in vitro or in vivo. For example, for in vivo introduction, iRNA can be injected into a tissue site or administered systemically. In vitro introduction into a cell includes methods known in the art such as electroporation and lipofection. Further approaches are described herein below or are The term “lipid nanoparticle” or “LNP” is a vesicle comprising a lipid layer encapsulating a 20 pharmaceutically active molecule, such as a nucleic acid molecule, e.g., an iRNA or a plasmid from which an iRNA is transcribed. LNPs are described in, for example, U.S. Patent Nos.6,858,225, 6,815,432, 8,158,601, and 8,058,069, the entire contents of which are hereby incorporated herein by reference. As used herein, a “subject” is an animal, such as a mammal, including a primate (such as a 25 human, a non-human primate, e.g., a monkey, and a chimpanzee), a non-primate (such as a cow, a pig, a horse, a goat, a rabbit, a sheep, a hamster, a guinea pig, a cat, a dog, a rat, or a mouse), or a bird that expresses the target gene, either endogenously or heterologously. In an embodiment, the subject is a human, such as a human being treated or assessed for a disease or disorder that would benefit from reduction in DMPK expression; a human at risk for a disease or disorder that would benefit from 30 reduction in DMPK expression; a human having a disease or disorder that would benefit from reduction in DMPK expression; or human being treated for a disease or disorder that would benefit from reduction in DMPK expression as described herein. In some embodiments, the subject is a female human. In other embodiments, the subject is a male human. In one embodiment, the subject is an adult subject. In another embodiment, the subject is a pediatric subject. 35 As used herein, the terms “treating” or “treatment” refer to a beneficial or desired result, such as reducing at least one sign or symptom associated with DMPK expression or DMPK protein production, e.g., a DMPK-associated disease, e.g., myotonic dystrophy type 1 (DM1), in a subject. Treatment also includes a reduction of one or more sign or symptoms associated with unwanted 31 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO DMPK expression; diminishing the extent of unwanted DMPK activation or stabilization; amelioration or palliation of unwanted DMPK activation or stabilization. “Treatment” can also mean prolonging survival as compared to expected survival in the absence of treatment. The term “lower” in the context of the level of DMPK in a subject or a disease marker or 5 symptom refers to a statistically significant decrease in such level. The decrease can be, for example, at least 10%, 15%, 20%, 25%, 30%, %, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or more. In certain embodiments, a decrease is at least 20%. In certain embodiments, the decrease is at least 50% in a disease marker, e.g., protein or gene expression level. “Lower” in the context of the level of DMPK in a subject is a decrease to a level accepted as within the range of 10 normal for an individual without such disorder. In certain embodiments, “lower” is the decrease in the difference between the level of a marker or symptom for a subject suffering from a disease and a level accepted within the range of normal for an individual. The term “lower” can also be used in association with normalizing a symptom of a disease or condition, i.e. decreasing the difference between a level in a subject suffering from a DMPK- 15 associated disorder towards or to a level in a normal subject not suffering from a DMPK-associated disorder. As used herein, if a disease is associated with an elevated value for a symptom, “normal” is considered to be the upper limit of normal. If a disease is associated with a decreased value for a symptom, “normal” is considered to be the lower limit of normal. As used herein, “prevention” or “preventing,” when used in reference to a disease, disorder or 20 condition thereof, may be treated or ameliorated by a reduction in expression of a DMPK gene or production of a DMPK protein, refers to a reduction in the likelihood that a subject will develop a symptom associated with such a disease, disorder, or condition, e.g., a symptom of a DMPK- associated disorder, e.g., DM1. The failure to develop a disease, disorder or condition, or the reduction in the development of a symptom associated with such a disease, disorder or condition (e.g., 25 by at least about 10% on a clinically accepted scale for that disease or disorder), or the exhibition of delayed symptoms delayed (e.g., by days, weeks, months or years) is considered effective prevention. As used herein, the term “DMPK-associated disorder” or “DMPK-associated disease” is a disease or disorder that would benefit from reduction in the mRNA expression or activity of DMPK. The term “DMPK-associated disease,” is a disease or disorder that is caused by, or associated with, 30 DMPK mRNA expression or DMPK protein production. The term “DMPK-associated disease” includes a disease, disorder or condition that would benefit from a decrease in DMPK mRNA expression or DMPK protein activity. In some embodiments, the DMPK-associated disease is a myotonic dystrophy. Myotonic dystrophy, as used herein, refers to a part of a group of inherited disorders called 35 muscular dystrophies. It is the most common form of muscular dystrophy that begins in adulthood. Myotonic dystrophy is characterized by progressive muscle wasting and weakness. People with this disorder often have prolonged muscle contractions (myotonia) and are not able to relax certain muscles after use. Other signs and symptoms of myotonic dystrophy include clouding of the lens of 32 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO the eye (cataracts) and abnormalities of the electrical signals that control the heartbeat (cardiac conduction defects). Some affected individuals develop a condition called diabetes mellitus, in which blood sugar levels can become dangerously high. The features of myotonic dystrophy often develop during a person's twenties or thirties, although they can occur at any age. The severity of the condition 5 varies widely among affected people, even among members of the same family. There are two major types of myotonic dystrophy: type 1 and type 2. Their signs and symptoms overlap, although type 2 tends to be milder than type 1. The muscle weakness associated with type 1 particularly affects muscles farthest from the center of the body (distal muscles), such as those of the lower legs, hands, neck, and face. Muscle weakness in type 2 primarily involves muscles close to the center of the body 10 (proximal muscles), such as the those of the neck, shoulders, elbows, and hips. The two types of myotonic dystrophy are caused by mutations in different genes. Myotonic dystrophy type 1 is caused by mutations in the DMPK gene, while type 2 results from mutations in the CNBP gene. The protein produced from the DMPK gene likely plays a role in communication within cells. It appears to be important for the correct functioning of cells in the heart, 15 brain, and skeletal muscles (which are used for movement). The protein produced from the CNBP gene is found primarily in the heart and in skeletal muscles, where it helps regulate the function of other genes. Similar changes in the structure of the DMPK and CNBP genes cause myotonic dystrophy type 1 and type 2. In each case, a segment of DNA is abnormally repeated many times, forming an unstable region in the gene. The gene with the abnormal segment produces an unusually 20 long messenger RNA, which is a molecular blueprint of the gene that guides the production of proteins. The unusually long messenger RNA forms clumps inside the cell that interfere with the production of many other proteins. These changes prevent muscle cells and cells in other tissues from functioning normally, which leads to the signs and symptoms of myotonic dystrophy. If these changes affect the DMPK gene, the result is myotonic dystrophy type 1, if the CNBP gene is affected, the 25 result is myotonic dystrophy type 2. In some embodiments, the DMPK-associated disease is myotonic dystrophy type 1 (DM1). "Therapeutically effective amount," as used herein, is intended to include the amount of an RNAi agent that, when administered to a subject having a DMPK-associated disorder, is sufficient to effect treatment of the disease (e.g., by diminishing, ameliorating, or maintaining the existing disease 30 or one or more symptoms of disease). The "therapeutically effective amount" may vary depending on the RNAi agent, how the agent is administered, the disease and its severity and the history, age, weight, family history, genetic makeup, the types of preceding or concomitant treatments, if any, and other individual characteristics of the subject to be treated. “Prophylactically effective amount,” as used herein, is intended to include the amount of an 35 RNAi agent that, when administered to a subject having a DMPK-associated disorder, is sufficient to prevent or ameliorate the disease or one or more symptoms of the disease. Ameliorating the disease includes slowing the course of the disease or reducing the severity of later-developing disease. The "prophylactically effective amount" may vary depending on the RNAi agent, how the agent is 33 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO administered, the degree of risk of disease, and the history, age, weight, family history, genetic makeup, the types of preceding or concomitant treatments, if any, and other individual characteristics of the patient to be treated. A "therapeutically-effective amount" or “prophylactically effective amount” also includes an 5 amount of an RNAi agent that produces some desired effect at a reasonable benefit/risk ratio applicable to any treatment. The iRNA employed in the methods of the present disclosure may be administered in a sufficient amount to produce a reasonable benefit/risk ratio applicable to such treatment. The phrase "pharmaceutically acceptable" is employed herein to refer to those compounds, 10 materials, compositions, or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human subjects and animal subjects without excessive 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- 15 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, involved in carrying 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 compatible with the other ingredients of the formulation and not injurious to the 20 subject being treated. Such carriers are known in the art. Pharmaceutically acceptable carriers include carriers for administration by injection. The term “sample,” as used herein, includes a collection of similar fluids, cells, or tissues isolated from a subject, as well as fluids, cells, or tissues present within a subject. Examples of biological fluids include blood, serum and serosal fluids, plasma, cerebrospinal fluid, ocular fluids, 25 lymph, urine, saliva, and the like. Tissue samples may include samples from tissues, organs, or localized regions. For example, samples may be derived from particular organs, parts of organs, or fluids or cells within those organs. In certain embodiments, samples may be derived from the liver (e.g., whole liver or certain segments of liver or certain types of cells in the liver, such as, e.g., hepatocytes). In some embodiments, a “sample derived from a subject” refers to urine obtained from 30 the subject. A “sample derived from a subject” can refer to blood or blood derived serum or plasma from the subject. Terms used herein may be preceded and/or followed by a single dash, or a double dash, "=", to indicate the bond order of the bond between the named substituent and its parent moiety; a single dash indicates a single bond and a double dash indicates a double bond or a pair of single bonds in the 35 case of a spiro-substituent. In the absence of a single or double dash it is understood that a single bond is formed between the substituent and its parent moiety; further, substituents are intended to be read "left to right" unless a dash indicates otherwise. For example, C1-6alkoxycarbonyloxy and - 34 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO OC(O)C1-66alkyl indicate the same functionality; similarly arylalkyl, arylalkyl-, and -alkylaryl indicate the same functionality. Further, certain terms herein may be used as both monovalent and divalent linking radicals as would be familiar to those skilled in the art, and by their presentation linking between two other 5 moieties. For example, an alkyl group can be both a monovalent radical or divalent radical; in the latter case, it would be apparent to one skilled in the art that an additional hydrogen atom is removed from a monovalent alkyl radical to provide a suitable divalent moiety. Throughout the disclosure,
used to represent an oligonucleotide; such oligonucleotides may be an RNA, a DNA, a single-stranded RNA, such as an 10 antisense oligonucleotide (ASO), a sense or an antisense strand of an siRNA, and oligonucleotide derivatives such as phosphorodiamidate morpholino oligomers (PMOs). The term “conjugated”, as used herein in reference, e.g., to a moiety conjugated to a dsRNA agent of the disclosure, e.g., at least one αvβ6 integrin targeting ligand conjugated to at least one strand of a dsRNA agent of the disclosure, or at least one in vivo delivery enhancing moiety 15 conjugated to at least one strand of a dsRNA agent of the disclosure, means that the moiety is covalently attached to a dsRNA agent directly or via a linker or via a carrier or via an internucleotide phosphate linkage. The term "alkenyl" as used herein, means a straight or branched chain hydrocarbon containing from 2 to 10 carbons, unless otherwise specified, and containing at least one carbon-carbon double20 bond. Representative examples of alkenyl include, but are not limited to, ethenyl, 2-propenyl, 2- methyl-2-propenyl, 3-butenyl, 4-pentenyl, 5-hexenyl, 2-heptenyl, 2-methyl-1-heptenyl, 3-decenyl, and 3,7-dimethylocta-2,6-dienyl. The term “alkynyl” as used herein means a straight or branched hydrocarbon chain containing from 2 to 10 carbons, unless otherwise specified, and containing at least one carbon-carbon triple25 bond. Representative examples of alkynyl include, but are not limited to, 1-butynyl, 2-butynyl, 1- propynyl and the like. The term "alkoxy" as used herein, means an alkyl group, as defined herein, appended to the parent molecular moiety through an oxygen atom. Representative examples of alkoxy include, but are not limited to, methoxy, ethoxy, n-propoxy, 2-propoxy, n-butoxy, tert-butoxy, n-pentyloxy, and n- 30 hexyloxy. The term "alkyl" as used herein, means a straight or branched chain hydrocarbon containing from 1 to 10 carbon atoms, unless otherwise specified. Representative examples of alkyl include, but are not limited to, methyl, ethyl, n-propyl, iso-propyl, n-butyl, sec -butyl, iso-butyl, tert-butyl, n- pentyl, isopentyl, neopentyl, n-hexyl, 3-methylhexyl, 2,2-dimethylpentyl, 2,3-dimethylpentyl, n- 35 heptyl, n-octyl, n-nonyl, and n-decyl. When an "alkyl" group is a divalent linking group between two other moieties, then it may also be a straight or branched chain; examples include, but are not limited to -CH2-, -CH2CH2-, -CH2CH2CHC(CH3)-, -CH2CH(CH2CH3)CH2-. 35 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO The term "aryl," as used herein, means a phenyl (i.e., monocyclic aryl); naphthyl or azulenyl; a bicyclic ring system containing a phenyl fused to a cycloalkyl, cycloalkenyl, or heterocyclyl ring. Representative examples of the bicyclic aryls include, but are not limited to, azulenyl, naphthyl, 2,3- dihydroinden-1-yl, 2,3-dihydroinden-2-yl, 2,3-dihydroinden-3-yl, 2,3-dihydroinden-4-yl, 2,3- 5 dihydroinden-5-yl, 2,3-dihydroindol-1-yl, indolin-2-yl, indolin-3-yl, indolin-4-yl, indolin-5-yl, indolin-6-yl, indolin-7-yl, inden-1-yl, inden-2-yl, inden-3-yl, inden-4-yl, dihydronaphthalen-2-yl, dihydronaphthalen-3-yl, dihydronaphthalen-4-yl, dihydronaphthalen-1-yl, 5,6,7,8- tetrahydronaphthalen-1-yl, 5,6,7,8-tetrahydronaphthalen-2-yl, 2,3-dihydrobenzofuran-2-yl, 2,3- dihydrobenzofuran-3-yl, 2,3-dihydrobenzofuran-4-yl, 2,3-dihydrobenzofuran-5-yl, 2,3-10 dihydrobenzofuran-6-yl, 2,3-dihydrobenzofuran-7-yl, 2,3-dihydrobenzothien-2-yl, 2,3- dihydrobenzothien-3-yl, 2,3-dihydrobenzothien-4-yl, 2,3-dihydrobenzothien-5-yl, 2,3- dihydrobenzothien-6-yl, 2,3-dihydrobenzothien-7-yl, 2,3-dihydrobenzothien-8-yl, benzo[d][1,3]dioxol-4-yl, benzo[d][1,3]dioxol-5-yl, 2H-chromen-2-on-3-yl, 2H-chromen-2-on-4-yl, 2H-chromen-2-on-5-yl, 2H-chromen-2-on-6-yl, 2H-chromen-2-on-7-yl, 2H-chromen-2-on-8-yl,15 isoindoline-1,3-dion-2-yl,isoindoline-1,3-dion-4-yl, isoindoline-1,3-dion-5-yl, inden-1-on-2-yl, inden- 1-on-3-yl, inden-1-on-4-yl, inden-1-on-5-yl, inden-1-on-6-yl, inden-1-on-7-yl, 2,3- dihydrobenzo[b][1,4]dioxan-2-yl, 2,3-dihydrobenzo[b][1,4]dioxan-5-yl, 2,3- dihydrobenzo[b][1,4]dioxan-6-yl, 2H-benzo[b][1,4]oxazin-3(4H)-on-5-yl, 2H-benzo[b][1,4]oxazin- 3(4H)-on-6-yl, 2H-benzo[b][1,4]oxazin-3(4H)-on-7-yl, 2H-benzo[b][1,4]oxazin3(4H)-on-8-yl,20 quinazolin-4(3H)-on-5-yl, quinazolin-4(3H)-on-6-yl, quinazolin-4(3H)-on-7-yl, quinazolin-4(3H)-on- 8-yl, quinoxalin-2(1H)-on-5-yl, quinoxalin-2(1H)-on-6-yl, quinoxalin-2(1H)-on-7-yl, quinoxalin- 2(1H)-on-8-yl, benzo[d]thiazol-2(3H)-on-3-yl, benzo[d]thiazol-2(3H)-on-4-yl, benzo[d]thiazol- 2(3H)-on-5-yl, benzo[d]thiazol-2(3H)-on-6-yl, and, benzo[d]thiazol-2(3H)-on-7-yl. In certain embodiments, the bicyclic aryl is (i) naphthyl or (ii) a phenyl ring fused to either a 5 25 or 6 membered monocyclic cycloalkyl, a 5 or 6 membered monocyclic cycloalkenyl, or a 5 or 6 membered monocyclic heterocyclyl, wherein the fused cycloalkyl, cycloalkenyl, and heterocyclyl groups are optionally substituted with one or two groups which are independently oxo or thia. The term "arylalkyl," “aralkyl”, "-alkylaryl," and "arylalkyl-" as used herein, means an aryl group, as defined herein, appended to the parent molecular moiety through an alkyl group, as defined30 herein. Representative examples of arylalkyl include, but are not limited to, benzyl, 2-phenylethyl, 3- phenylpropyl, and 2-naphth-2-ylethyl. The term “azido” means a -N3 group. The term “carboxy” means a -COOH group. The terms "cyano" and "nitrile" as used herein, mean a -CN group. 35 The term "cycloalkyl" as used herein, means a monocyclic or a bicyclic cycloalkyl ring system. Monocyclic ring systems are cyclic hydrocarbon groups containing from 3 to 10 carbon atoms, where such groups are saturated. Examples of monocyclic cycloalkyls include cyclopropyl, 36 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, and cyclooctyl. Bicyclic cycloalkyl ring systems are bridged monocyclic rings or fused bicyclic rings. Bridged monocyclic rings contain a monocyclic cycloalkyl ring where two non-adjacent carbon atoms of the monocyclic ring are linked by an alkylene bridge of between one and three additional carbon atoms (i.e., a bridging group of the form - 5 (CH2)w-, where w is 1, 2, or 3). Representative examples of bridged bicyclic ring systems include, but are not limited to, bicyclo[3.1.1]heptane, bicyclo[2.2.1]heptane, bicyclo[2.2.2]octane, bicyclo[3.2.2]nonane, bicyclo[3.3.1]nonane, and bicyclo[4.2.1]nonane. Fused bicyclic cycloalkyl ring systems contain a monocyclic cycloalkyl ring fused to a monocyclic cycloalkyl. Representative examples of fused bicyclic ring systems include, but are not limited to, decaliyl. Cycloalkyl groups 10 are optionally substituted with one or two groups which are independently oxo or thia. In certain embodiments, the fused bicyclic cycloalkyl is a 5 or 6 membered monocyclic cycloalkyl ring fused to a 5 or 6 membered monocyclic cycloalkyl, wherein the fused bicyclic cycloalkyl is optionally substituted by one or two groups which are independently oxo or thia. "Cycloalkenyl" as used herein refers to a monocyclic or a bicyclic cycloalkenyl ring system. 15 Monocyclic ring systems are cyclic hydrocarbon groups containing from 3 to 8 carbon atoms, where such groups are unsaturated (i.e., containing at least one annular carbon-carbon double bond), but not aromatic. Examples of monocyclic ring systems include cyclopentenyl and cyclohexenyl. Bicyclic cycloalkenyl rings are bridged monocyclic rings or a fused bicyclic rings. Bridged monocyclic rings contain a monocyclic cycloalkenyl ring where two non-adjacent carbon atoms of the monocyclic ring 20 are linked by an alkylene bridge of between one and three additional carbon atoms (i.e., a bridging group of the form -(CH2)w-, where w is 1, 2, or 3). Representative examples of bicyclic cycloalkenyls include, but are not limited to, norbornenyl and bicyclo[2.2.2]oct-2-enyl. Fused bicyclic cycloalkenyl ring systems contain a monocyclic cycloalkenyl ring fused to either a monocyclic cycloalkyl or a monocyclic cycloalkenyl. Cycloalkenyl groups are optionally substituted with one or two groups 25 which are independently oxo or thia. The term “monocyclic ring”, as used herein, comprises monocyclic aryl, monocyclic cycloalkyl, monocyclic cycloalkenyl and monocyclic heterocyclyl. The term "halo" or "halogen" as used herein, means -CI, -Br, -I or -F. The term “H” means hydrogen. 30 The term "haloalkyl" as used herein, means at least one halogen, as defined herein, appended to the parent molecular moiety through an alkyl group, as defined herein. Representative examples of haloalkyl include, but are not limited to, chloromethyl, 2-fluoroethyl, trifluoromethyl, pentafluoroethyl, and 2-chloro-3-fluoropentyl. The term "heteroaryl," as used herein, means a monocyclic heteroaryl or a bicyclic ring 35 system containing at least one heteroaromatic ring (i.e., a monocyclic or bicyclic aromatic ring system containing at least one heteroatom within the aromatic system). The monocyclic heteroaryl can be a 5 or 6 membered ring. The 5 membered ring consists of two double bonds and one, two, three or four nitrogen atoms and optionally one oxygen or sulfur atom. The 6 membered ring consists of three 37 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO double bonds and one, two, three or four nitrogen atoms. The 5 or 6 membered heteroaryl is connected to the parent molecular moiety through any carbon atom or any nitrogen atom contained within the heteroaryl. Representative examples of monocyclic heteroaryl include, but are not limited to, furyl, imidazolyl, isoxazolyl, isothiazolyl, oxadiazolyl, oxazolyl, pyridinyl, pyridazinyl, 5 pyrimidinyl, pyrazinyl, pyrazolyl, pyrrolyl, tetrazolyl, thiadiazolyl, thiazolyl, thienyl, triazolyl, and triazinyl. The bicyclic heteroaryl consists of a monocyclic heteroaryl fused to a phenyl, a monocyclic cycloalkyl, a monocyclic cycloalkenyl, a monocyclic heterocyclyl, or a monocyclic heteroaryl. The fused cycloalkyl or heterocyclyl portion of the bicyclic heteroaryl group is optionally substituted with one or two groups which are independently oxo or thia. Representative examples of bicyclic 10 heteroaryl include, but are not limited to, benzimidazolyl, benzofuranyl, benzothienyl, benzoxadiazolyl, benzoxathiadiazolyl, benzothiazolyl, cinnolinyl, 5 ,6-dihydroquinolin-2-yl, 5,6- dihydroquinolin-8-yl, 5,6-dihydroisoquinolin-1-yl, furopyridinyl, indazolyl, indolyl, isoquinolinyl, naphthyridinyl, quinolinyl, purinyl, 5,6,7,8-tetrahydroquinolin-2-yl, 5,6,7,8-tetrahydroquinolin-3-yl, 5,6,7,8-tetrahydroquinolin-4-yl, 5,6,7,8-tetrahydroquinolin-5-yl, 5,6,7,8-tetrahydroquinolin-6-yl, 15 5,6,7,8-tetrahydroquinolin-7-yl, 5,6,7,8-tetrahydroquinolin-8-yl, 5,6,7,8-tetrahydroisoquinolin-1-yl, thienopyridinyl, 4,5,6,7-tetrahydrobenzo[c][1,2,5]oxadiazol-4-yl, and 6,7- dihydrobenzo[c][1,2,5]oxadiazol-4(5H)-onyl. In certain embodiments, the fused bicyclic heteroaryl is a 5 or 6 membered monocyclic heteroaryl ring fused to either a phenyl ring, a 5 or 6 membered monocyclic cycloalkyl, a 5 or 6 membered monocyclic cycloalkenyl, a 5 or 6 membered monocyclic 20 heterocyclyl, or a 5 or 6 membered monocyclic heteroaryl, wherein the fused cycloalkyl, cycloalkenyl, and heterocyclyl groups are optionally substituted with one or two groups which are independently oxo or thia. The term "heteroarylalkyl" and "-alkylheteroaryl" as used herein, means a heteroaryl, as defined herein, appended to the parent molecular moiety through an alkyl group, as defined herein.25 Representative examples of heteroarylalkyl include, but are not limited to, fur-3-ylmethyl, 1H- imidazol-2-ylmethylm 1H-imidazol-4-ylmethyl, 1-(pyridin-4-yl)ethyl, pyridin-3-ylmethyl, pyridin-4- ylmethyl, pyrimidin-5-ylmethyl, 2-(pyrimidin-2-yl)propyl, thien-2-ylmethyl, and thien-3-ylmethyl. The term "heterocyclyl" as used herein, means a monocyclic heterocycle or a bicyclic heterocycle. The monocyclic heterocycle is a 3, 4, 5, 6, or 7 membered ring containing at least one 30 heteroatom independently selected from the group consisting of O, N, and S where the ring is saturated or unsaturated, but not aromatic. The 3 or 4 membered ring contains 1 heteroatom selected from the group consisting of O, N and S. The 5 membered ring can contain zero or one double bond and one, two or three heteroatoms selected from the group consisting of O, N and S. The 6 or 7 membered ring contains zero, one, or two double bonds and one, two or three heteroatoms selected 35 from the group consisting of O, N and S. Representative examples of monocyclic heterocycles include, but are not limited to, azetidinyl, azepanyl, aziridinyl, diazepanyl, 1,3-dioxan-2-yl, 1,3- dioxolan-2-yl, 1,3-dithiolan-2-yl, 1,2-dithiolan-3-yl, 1,2-dithiolan-4-yl, 1,3-dithian-2-yl, 1,2-dithian-3- yl, 1,2-dithian-4-yl, imidazolinyl, imidazolidinyl, isothiazolinyl, isothiazolidinyl, isoxazolinyl, 38 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO isoxazolidinyl, morpholinyl, oxadiazolinyl, oxadiazolidinyl, oxazolinyl, oxazolidinyl, piperazinyl, piperidinyl, pyranyl, pyrazolinyl, pyrazolidinyl, pyrrolinyl, pyrrolidinyl, tetrahydrofuranyl, tetrahydrothienyl, thiadiazolinyl, thiadiazolidinyl, thiazolinyl, thiazolidinyl, thiomorpholinyl, 1,1- dioxidothiomorpholinyl (thiomorpholine sulfone), thiopyranyl, and trithianyl. The bicyclic 5 heterocycle is a monocyclic heterocycle fused to either a monocyclic cycloalkyl, a monocyclic cycloalkenyl, or a monocyclic heterocycle. Representative examples of bicyclic heterocyclyls include, but are not limited to, decahydroquinolinyl, decahydroisoquinolinyl, octahydro-1H-indolyl, and octahydrobenzofuranyl. Heterocyclyl groups are optionally substituted with one or two groups which are independently oxo or thia. In certain embodiments, the bicyclic heterocyclyl is a 5 or 6 10 membered monocyclic heterocyclyl ring fused to a 5 or 6 membered monocyclic cycloalkyl, a 5 or 6 membered monocyclic cycloalkenyl, or a 5 or 6 membered monocyclic heterocyclyl, wherein the bicyclic heterocyclyl is optionally substituted by one or two groups which are independently oxo or thia. The term "hydroxy" or “hydroxyl” as used herein means an -OH group. The term “thiol” as 15 used herein means an –SH group. The term "hydroxyl protecting group," as used herein, refers to a labile chemical moiety which protects a hydroxyl group against undesired reactions during synthetic procedure(s). After the synthetic procedure(s), the hydroxy protecting group may be selectively removed. Hydroxy protecting groups as known in the art are described generally in T. H. Greene and P. G. M. Wuts, Protective 20 Groups in Organic Synthesis, 3rd edition, John Wiley & Sons, New York (1999). Examples of hydroxyl protecting groups include, but are not limited to, benzyloxycarbonyl, 4- nitrobenzyloxycarbonyl, 4-bromobenzyloxycarbonyl, 4-methoxybenzyloxycarbonyl, methoxycarbonyl, tert-butoxycarbonyl, isopropoxycarbonyl, diphenylmethoxycarbonyl, 2,2,2- trichloroethoxycarbonyl, 2-(trimethylsilyl) ethoxycarbonyl, 2-furfuryloxycarbonyl, allyloxycarbonyl, 25 acetyl, formyl, chloroacetyl, trifluoroacetyl, methoxyacetyl, phenoxyacetyl, benzoyl, methyl, t-butyl, 2,2,2-trichloroethyl, 2-trimethylsilyl ethyl, l,l-dimethyl-2-propenyl, 3-methyl-3-butenyl, allyl, benzyl, para-methoxybenzyldiphenylmethyl, triphenylmethyl (trityl), tetrahydrofuryl, methoxymethyl, methylthiomethyl, benzyloxymethyl, 2,2,2-trichloroethoxymethyl, 2-(trimethylsilyl)ethoxymethyl, methanesulfonyl, para-toluenesulfonyl, tert-butyldimethylsilyl (TBDMS), trimethylsilyl, triethylsilyl, 30 and triisopropylsilyl. In certain embodiments, hydroxyl protecting groups can be selected from acetyl (Ac or — C(O)CH3), benzoyl (Bz or —C(O)C6H5), and trimethylsilyl (TMS or -Si(CH3)3). The term "nitro" as used herein means a -NO2 group. The term "oxo" as used herein means a =O group. The term "saturated" as used herein means the referenced chemical structure does not contain 35 any multiple carbon-carbon bonds. For example, a saturated cycloalkyl group as defined herein includes cyclohexyl, cyclopropyl, and the like. The term "thia" as used herein means a =S group. 39 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO The term “amine” or “amino” encompasses compounds where a nitrogen atom is covalently bonded to at least one carbon or heteroatom. The term “alkyl amino” includes groups and compounds wherein the nitrogen is bound to at least one additional alkyl group. The term “dialkyl amino” includes groups wherein the nitrogen atom is bound to at least two additional alkyl groups. 5 The term "unsaturated" as used herein means the referenced chemical structure contains at least one multiple carbon-carbon bond (i.e., double or triple bond, or both), but is not aromatic. For example, an unsaturated cycloalkyl group as defined herein includes cyclohexenyl, cyclopentenyl, cyclohexadienyl, and the like. The term “leaving group” as used herein means an atom or group (charged or uncharged) that 10 becomes detached from an atom in what is considered to be the residual or main part of the substrate in a specified reaction. For example, the specified reaction herein, unless otherwise noted, is an SN1 or an SN2 reaction as is understood by one skilled in the art. In certain embodimentns, the specified reaction herein, is an SN2 reaction. The term“substituted” as used herein, whether preceded by the term“optionally” or not, 15 means that at least one hydrogen present on a group (e.g., a carbon or nitrogen atom) is replaced with a permissible substituent, e.g., a substituent which upon substitution results in a stable compound, e.g., a compound which does not spontaneously undergo transformation such as by rearrangement, cyclization, elimination, or other reaction. Unless otherwise indicated, a“substituted” group has a substituent at one or more substitutable positions of the group, and when more than one position in 20 any given structure is substituted, the substituent is either the same or different at each position. Suitable substituents include, but are not limited to, halogen, hydroxy, thiol, nitro, alkoxy, azido, carboxy, cyano, amino, C1-6alkyl, C2-6alkenyl, C1-6alkoxy, C1-6alkylamino.The term “support linking group as used herein means a divalent chemical moiety that covalent connects a surface-bound functional group of a solid support (e.g., an amino group of an amino-modified solid support) to 25 another chemical moiety. The term “reactive pair” as used herein means two functional groups known by one skilled in the art to be capable of reacting, alone or in the presence of other reagents, to form a covalent linkage between the two chemical entities which each contain one of member of the reactive pair, respectively; the latter, herein, is referred to as “linking group formed by a reactive pair”. In some 30 embodiments, a reactive pair is a click pair, i.e., two functional groups capable of reacting in a click reaction to form a covalent linkage. The term “Michael acceptor” as used herein means an alpha, beta-unsaturated compound capable of reacting with a nucleophile at the beta-carbon of the electrophilic alkene of the alpha, beta -unsaturated compound. Examples of alpha, beta-unsaturated compound include, but are not limited 35 to, such as an alpha, beta-unsaturated aldehyde, ester, amide, sulfonyl, ketone, nitrile, or nitro. “Alpha, beta-unsaturated” refers to the carbon-carbon multiple bond that connects the carbon atom that is immediately adjacent to the referenced aldehyde, ester, amide, sulfonyl, ketone, nitrile, or nitro group, to its adjacent carbon atom. Examples of Michael acceptor group include, but are not limited 40 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO to, N-maleimide, acrylaldehyde, acrylonitrile, acrylic acid, acrylamide (e.g., N-isoproprylacrylamide), acrylate esters (e.g., methyl acrylate), vinyl sulfones, vinylsulfonates, and vinylsulfonamides. The term “nitrogen protecting group” as used herein means those functional groups that are well known in the art and include those described in detail, for example, in Protecting Groups in 5 Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3rd edition, John Wiley & Sons, 1999, the entirety of which is incorporated herein by reference. Suitable nitrogen protecting groups include but are not limited to, allyl (Alloc), acetyl (Ac), Adpoc (1-(1-Adamantyl)-1-methylethoxycarbonyl), Boc (tert-butyloxy carbonyl), Dde
Dnp (2,4-dinitrophenyl), Mmt (4-methoxytrityl), Mtt (4-methyltrityl), Teoc (2-trimethylsilylethoxycarbonyl, Tfa (trifluoroacetyl),10 optionally substituted trityl (e.g., trityl (Trt), 2-chlorotrityl (Clt), 4-methoxytrityl (Mmt), 4- methyltrityl (Mtt), 4,4’-dimethoxytrityl (DMT)), and 4,4’,4’’-trimethoxytrityl), optionally substituted benzyloxycarbonyl (e.g., benzyloxycarbonyl (Z) or 2-chlorobenzyloxycarbonyl (2ClZ)), fluorenylmethoxycarbonyl (Fmoc), methoxyacetyl (mac), phenoxyacetyl (pac), 2- chlorophenoxyacetyl, 3-chlorophenoxyacetyl, 4-chlorophenoxyacetyl, 2,4-dichlorophenoxyacetyl, 2-15 methylphenoxyacetyl, 3-methylphenoxyacetyl, 4-methylphenoxyacetyl, 4-chloro-2- methylphenoxyacetyl, 2-nitrophenoxyacetyl, 3-nitrophenoxyacetyl, 4-nitrophenoxyacetyl, 2- isopropylphenoxyacetyl, 3-isopropylphenoxyacetyl, 4-isopropylphenoxyacetyl, 2-(t- butyl)phenoxyacetyl, 3-(t-butyl)phenoxyacetyl, 4-(t-butyl)phenoxyacetyl, 2-fluorophenoxyacetyl, 3- fluorophenoxyacetyl, 4-fluorophenoxyacetyl, 2,4-difluorophenoxyacetyl, 4- 20 (trifluoromethoxy)phenoxyacetyl, 2-phenoxypropanoyl, 2-(4-chloro-2-methylphenoxy)propanoyl, and 2-(4-chlorophenoxy)propanoyl. As used herein, the term “remainder of the dsRNA agent”, refers to an oligonucleotide strand (i.e. the sense strand or the antisense strand) that forms a dsRNA agent and any intervening linking group that connects the parent moiety (e.g., one or more αvβ6 integrin targeting ligand or one or more 25 in vivo delivery enhancing moieties) to the oligonucleotide strand. The terms “linker”, “linking group”, “carrier” and “carrier group”, in some embodiments, each refer to a chemical moiety connecting at least one αvβ6 integrin targeting ligand or at least one in vivo delivery enhancing moiety to at least one strand of the dsRNA agent of the disclosure. 30 II. iRNAs of the Disclosure Described herein are iRNAs for use in the methods of the present disclosure. The iRNAs are double stranded ribonucleic acid (dsRNA) molecules. In one embodiment, the dsRNA agent targets an DMPK gene and inhibits the expression of the DMPK gene. In one embodiment, the iRNA agent 41 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO includes dsRNA molecules for inhibiting the expression of an DMPK gene in a cell, such as a liver cell, such as a muscle cell within a subject, e.g., a mammal, such as a human having DM1. The iRNA agents provided herein comprise a sense strand and an antisense strand and at least one of the strands is modified for targeting delivery to extrahepatic tissue, e.g., muscle tissue, e.g., 5 skeletal muscle tissue and/or cardiac muscle tissue. In one embodiment, the iRNA agents are modified by conjugation to at least one alpha-v-beta-6 (αvβ6) integrin ligand and conjugation to at least one in vivo delivery enhancing moiety. By “integrin ligand” is meant any ligand that binds to an integrin or an integrin receptor. Integrin ligands comprise binding sequences that are recognized and bound by integrins or ntegrin 10 receptors. Various ligands, including peptides and small molecules, which bind αvβ6 integrins or αvβ6 integrin receptors (αvβ6 integrin targeting ligands) have been designed and synthesized herein and in, e.g., U.S. Patent 6,410,526, the entire contents of which are incorporated herein by reference. An exemplary linker to conjugate a αvβ6 integrin targeting ligand to the dsRNA agent is: 15
42 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 5
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. In one embodiment, at least one of the strands of the iRNA agent is conjugated to at least one αvβ6 integrin targeting ligand and at least one in vivo delivery enhancing moiety. For example, the 5 iRNA agent may be conjugated to one, two, three, four, or more αvβ6 integrin targeting ligands and one, two, three, four or more in vivo delivery enhancing moieties. In some embodiments, the αvβ6 integrin targeting ligand is conjugated to the sense strand. The αvβ6 integrin targeting ligand may be conjugated to an extrernal position of sense strand, e.g., the 3’-end of the sense strand, to the 5’-end of the sense strand, or to both the 5-end and the 3’-end of the 10 sense strand. In some embodiments, the αvβ6 integrin targeting ligand may be conjugated to an internal position of the sense strand. In other embodiments, the αvβ6 integrin targeting ligand is conjugated to the antisense strand. The αvβ6 integrin targeting ligand may be conjugated to an external position of the antisense strand, e.g., the 3’-end of the antisense strand, to the 5’-end of the antisense strand, or to both the 5-end and 15 the 3’-end of the antisense strand. In some embodiments, the αvβ6 integrin targeting ligand may be conjugated to an internal position of the antisense strand. In some embodiments, the in vivo delivery enhancing moiety is conjugated to the sense strand. The in vivo delivery enhancing moiety may be conjugated to an extrernal position of sense strand, e.g., the 3’-end of the sense strand, to the 5’-end of the sense strand, or to both the 5-end and 20 the 3’-end of the sense strand. In some embodiments, the in vivo delivery enhancing moiety may be conjugated to an internal position of the sense strand. In some embodiments, the in vivo delivery enhancing moiety is not conjugated to an external position of the sense strand. In other embodiments, the αvβ6 integrin targeting ligand is conjugated to the antisense strand. The in vivo delivery enhancing moiety may be conjugated to an external position of the antisense25 strand, e.g., the 3’-end of the antisense strand, to the 5’-end of the antisense strand, or to both the 5- end and the 3’-end of the antisense strand. In some embodiments, the in vivo delivery enhancing 44 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO moiety may be conjugated to an internal position of the antisense strand. In some embodiments, the in vivo delivery enhancing moiety is not conjugated to an external position of the antisense strand. In some embodiments, the αvβ6 integrin targeting ligand and the in vivo delivery enhancing moiety are both conjugated to the sense strand of the dsRNA agent. For example, the αvβ6 integrin 5 targeting ligand is conjugated to an external position of the sense strand, e.g., the 3’-end of the sense strand or the 5’-end of the sense strand, and the in vivo delivery enhancing moiety is conjugated to an internal position of the sense strand. In some embodiments, the αvβ6 integrin targeting ligand and the in vivo delivery enhancing moiety are both conjugated to the antisense strand of the dsRNA agent. For example, the αvβ6 10 integrin targeting ligand is conjugated to an external position of the antisense strand, e.g., the 3’-end of the sense strand or the 5’-end of the antisense strand, and the in vivo delivery enhancing moiety is conjugated to an internal position of the antisense strand. In some embodiments, the αvβ6 integrin targeting ligand is conjugated to a sense strand, and the in vivo delivery enhancing moiety is conjugated to an antisense strand. In other embodiments, the 15 αvβ6 integrin targeting ligand is conjugated to an antisense strand, and the in vivo delivery enhancing moiety is conjugated to a sense strand. The dsRNA agent includes an antisense strand having a region of complementarity which is complementary to at least a part of an mRNA formed in the expression of a DMPK gene. The region of complementarity is about 19-30 nucleotides in length (e.g., about 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, or 19 nucleotides in length). 20 Upon contact with a cell expressing the DMPK gene, the iRNA inhibits the expression of the DMPK gene (e.g., a human, a primate, a non-primate, or a rat gene) by at least about 50% as assayed by, for example, a PCR or branched DNA (bDNA)-based method, or by a protein-based method, such as by immunofluorescence analysis, using, for example, western blotting or flow cytometric techniques. In certain embodiments, inhibition of expression is determined by the qPCR method 25 provided in the examples herein with the siRNA at, e.g., a 10 nM concentration, in an appropriate organism cell line provided therein. In certain embodiments, inhibition of expression in vivo is determined by knockdown of the human gene in a rodent expressing the human gene, e.g., a mouse or an AAV-infected mouse expressing the human target gene, e.g., when administered as single dose, e.g., at 3 mg/kg at the nadir of RNA expression. 30 A dsRNA includes two RNA strands that are complementary and hybridize to form a duplex structure under conditions in which the dsRNA will be used. One strand of a dsRNA (the antisense strand) includes a region of complementarity that is substantially complementary, and generally fully complementary, to a target sequence. The target sequence can be derived from the sequence of an mRNA formed during the expression of a DMPK gene. The other strand (the sense strand) includes a 35 region that is complementary to the antisense strand, such that the two strands hybridize and form a duplex structure when combined under suitable conditions. As described elsewhere herein and as known in the art, the complementary sequences of a dsRNA can also be contained as self- 45 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO complementary regions of a single nucleic acid molecule, as opposed to being on separate oligonucleotides. Generally, the duplex structure is 15 to 30 base pairs in length, e.g., 15-29, 15-28, 15-27, 15- 26, 15-25, 15-24, 15-23, 15-22, 15-21, 15-20, 15-19, 15-18, 15-17, 18-30, 18-29, 18-28, 18-27, 18-26, 5 18-25, 18-24, 18-23, 18-22, 18-21, 18-20, 19-30, 19-29, 19-28, 19-27, 19-26, 19-25, 19-24, 19-23, 19- 22, 19-21, 19-20, 20-30, 20-29, 20-28, 20-27, 20-26, 20-25, 20-24,20-23, 20-22, 20-21, 21-30, 21-29, 21-28, 21-27, 21-26, 21-25, 21-24, 21-23, or 21-22 base pairs in length. In certain embodiments, the duplex structure is 18 to 25 base pairs in length, e.g., 18-25, 18-24, 18-23, 18-22, 18-21, 18-20, 19-25, 19-24, 19-23, 19-22, 19-21, 19-20, 20-25, 20-24,20-23, 20-22, 20-21, 21-25, 21-24, 21-23, 21-22, 22- 10 25, 22-24, 22-23, 23-25, 23-24 or 24-25 base pairs in length, for example, 19-21 basepairs in length. Ranges and lengths intermediate to the above recited ranges and lengths are also contemplated to be part of the disclosure. Similarly, the region of complementarity to the target sequence is 15 to 30 nucleotides in length, e.g., 15-29, 15-28, 15-27, 15-26, 15-25, 15-24, 15-23, 15-22, 15-21, 15-20, 15-19, 15-18, 15- 15 17, 18-30, 18-29, 18-28, 18-27, 18-26, 18-25, 18-24, 18-23, 18-22, 18-21, 18-20, 19-30, 19-29, 19-28, 19-27, 19-26, 19-25, 19-24, 19-23, 19-22, 19-21, 19-20, 20-30, 20-29, 20-28, 20-27, 20-26, 20-25, 20- 24,20-23, 20-22, 20-21, 21-30, 21-29, 21-28, 21-27, 21-26, 21-25, 21-24, 21-23, or 21-22 nucleotides in length, for example 19-23 nucleotides in length or 21-23 nucleotides in length. Ranges and lengths intermediate to the above recited ranges and lengths are also contemplated to be part of the disclosure. 20 In some embodiments, the duplex structure is 19 to 30 base pairs in length. Similarly, the region of complementarity to the target sequence is 19 to 30 nucleotides in length. In some embodiments, the dsRNA is about 19 to about 23 nucleotides in length, or about 25 to about 30 nucleotides in length. In general, the dsRNA is long enough to serve as a substrate for the Dicer enzyme. For example, it is well-known in the art that dsRNAs longer than about 21-23 25 nucleotides in length may serve as substrates for Dicer. As the ordinarily skilled person will also recognize, the region of an RNA targeted for cleavage will most often be part of a larger RNA molecule, often an mRNA molecule. Where relevant, a “part” of an mRNA target is a contiguous sequence of an mRNA target of sufficient length to allow it to be a substrate for RNAi-directed cleavage (i.e., cleavage through a RISC pathway). 30 One of skill in the art will also recognize that the duplex region is a primary functional portion of a dsRNA, e.g., a duplex region of about 19 to about 30 base pairs, e.g., about 19-30, 19-29, 19-28, 19-27, 19-26, 19-25, 19-24, 19-23, 19-22, 19-21, 19-20, 20-30, 20-29, 20-28, 20-27, 20-26, 20- 25, 20-24,20-23, 20-22, 20-21, 21-30, 21-29, 21-28, 21-27, 21-26, 21-25, 21-24, 21-23, or 21-22 base pairs. Thus, in one embodiment, to the extent that it becomes processed to a functional duplex, of 35 e.g., 15-30 base pairs, that targets a desired RNA for cleavage, an RNA molecule or complex of RNA molecules having a duplex region greater than 30 base pairs is a dsRNA. Thus, an ordinarily skilled artisan will recognize that in one embodiment, a miRNA is a dsRNA. In another embodiment, a 46 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO dsRNA is not a naturally occurring miRNA. In another embodiment, an iRNA agent useful to target DMPK gene expression is not generated in the target cell by cleavage of a larger dsRNA. A dsRNA as described herein can further include one or more single-stranded nucleotide overhangs, e.g., 1-4, 2-4, 1-3, 2-3, 1, 2, 3, or 4 nucleotides. dsRNAs having at least one nucleotide 5 overhang can have superior inhibitory properties relative to their blunt-ended counterparts. A nucleotide overhang can comprise or consist of a nucleotide/nucleoside analog, including a deoxynucleotide/nucleoside. The overhang(s) can be on the sense strand, the antisense strand, or any combination thereof. Furthermore, the nucleotide(s) of an overhang can be present on the 5'-end, 3'- end, or both ends of an antisense or sense strand of a dsRNA. 10 A dsRNA can be synthesized by standard methods known in the art. Double stranded RNAi compounds of the disclosure may be prepared using a two-step procedure. First, the individual strands of the double stranded RNA molecule are prepared separately. Then, the component strands are annealed. The individual strands of the siRNA compound can be prepared using solution-phase or solid-phase organic synthesis or both. Organic synthesis offers the advantage that the oligonucleotide15 strands comprising unnatural or modified nucleotides can be easily prepared. Similarly, single- stranded oligonucleotides of the disclosure can be prepared using solution-phase or solid-phase organic synthesis or both. In an aspect, a dsRNA of the disclosure includes at least two nucleotide sequences, a sense sequence and an anti-sense sequence. The sense strand is selected from the group of sequences 20 provided in any one of Tables 2-3, and the corresponding antisense strand of the sense strand is selected from the group of sequences of any one of Tables 2-3. In this aspect, one of the two sequences is complementary to the other of the two sequences, with one of the sequences being substantially complementary to a sequence of an mRNA generated in the expression of a-associated target gene. As such, in this aspect, a dsRNA will include two oligonucleotides, where one 25 oligonucleotide is described as the sense strand in any one of Tables 2-3, and the second oligonucleotide is described as the corresponding antisense strand of the sense strand in any one of Tables 2-3. In certain embodiments, the substantially complementary sequences of the dsRNA are contained on separate oligonucleotides. In other embodiments, the substantially complementary 30 sequences of the dsRNA are contained on a single oligonucleotide. It will be understood that, although the sequences in, for example, Table 2, are not described as modified or conjugated sequences, the RNA of the iRNA of the disclosure e.g., a dsRNA of the disclosure, may comprise any one of the sequences set forth in any one of Tables 2-3 that is un- modified, un-conjugated, or modified or conjugated differently than described therein. In other 35 words, the disclosure encompasses dsRNA of Tables 2-3 which are un-modified, un-conjugated, modified, or conjugated, as described herein. The skilled person is well aware that dsRNAs having a duplex structure of about 20 to 23 base pairs, e.g., 21, base pairs have been hailed as particularly effective in inducing RNA interference 47 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO (Elbashir et al., EMBO 2001, 20:6877-6888). However, others have found that shorter or longer RNA duplex structures can also be effective (Chu and Rana (2007) RNA 14:1714-1719; Kim et al. (2005) Nat Biotech 23:222-226). In the embodiments described above, by virtue of the nature of the oligonucleotide sequences provided in any one of Tables 2-3. dsRNAs described herein can include at 5 least one strand of a length of minimally 21 nucleotides. It can be reasonably expected that shorter duplexes having any one of the sequences in any one of Tables 2-3 minus only a few nucleotides on one or both ends can be similarly effective as compared to the dsRNAs described above. Hence, dsRNAs having a sequence of at least 19, 20, or more contiguous nucleotides derived from any one of the sequences of any one of Tables 2-3, and differing in their ability to inhibit the expression of a 10 DMPK gene by not more than about 5, 10, 15, 20, 25, or 30 % inhibition from a dsRNA comprising the full sequence, are contemplated to be within the scope of the present disclosure. In addition, the RNAs provided in Tables 2-3 identify a site(s) in a DMPK transcript that is susceptible to RISC-mediated cleavage. As such, the present disclosure further features iRNAs that target within one of these sites. As used herein, an iRNA is said to target within a particular site of an 15 RNA transcript if the iRNA promotes cleavage of the transcript anywhere within that particular site. Such an iRNA will generally include at least about 19 contiguous nucleotides from any one of the sequences provided in any one of Tables 2-3 coupled to additional nucleotide sequences taken from the region contiguous to the selected sequence in a DMPK gene. 20 III. Modifications for the RNAi Agents of the Disclosure In one embodiment, the iRNA for use in the methods of the disclosure e.g., a dsRNA, is un- modified, and does not comprise, e.g., chemical modifications and/or conjugations known in the art and described herein. In another embodiment, the iRNA for use in the methods of the disclosure, e.g., a dsRNA, is chemically modified to enhance stability or other beneficial characteristics. In certain 25 embodiments of the disclosure, substantially all of the nucleotides of an iRNA of the disclosure are modified. In other embodiments of the disclosure, all of the nucleotides of an iRNA of the disclosure are modified. iRNAs of the disclosure in which “substantially all of the nucleotides are modified” are largely but not wholly modified and can include not more than 5, 4, 3, 2, or 1 unmodified nucleotides. In some aspects of the disclosure, substantially all of the nucleotides of an iRNA of the disclosure 30 are modified and the iRNA agents comprise no more than 10 nucleotides comprising 2’-fluoro modifications (e.g., no more than 92^-fluoro modifications, no more than 82^-fluoro modifications, no more than 72^-fluoro modifications, no more than 62^-fluoro modifications, no more than 52^-fluoro modifications, no more than 42^-fluoro modifications, no more than 52^-fluoro modifications, no more than 42^-fluoro modifications, no more than 32^-fluoro modifications, or no more than 22^-fluoro 35 modifications). For example, in some embodiments, the sense strand comprises no more than 4 nucleotides comprising 2^-fluoro modifications (e.g., no more than 32^-fluoro modifications, or no more than 22^-fluoro modifications). In other embodiments, the antisense strand comprises no more than 6 nucleotides comprising 2^-fluoro modifications (e.g., no more than 52^-fluoro modifications, no more than 48 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 42^-fluoro modifications, no more than 42^-fluoro modifications, or no more than 22^-fluoro modifications). In other aspects of the disclosure, all of the nucleotides of an iRNA of the disclosure are modified and the iRNA agents comprise no more than 10 nucleotides comprising 2’-fluoro modifications (e.g., no 5 more than 92^-fluoro modifications, no more than 82^-fluoro modifications, no more than 72^-fluoro modifications, no more than 62^-fluoro modifications, no more than 52^-fluoro modifications, no more than 42^-fluoro modifications, no more than 52^-fluoro modifications, no more than 42^-fluoro modifications, no more than 32^-fluoro modifications, or no more than 22^-fluoro modifications). The nucleic acids featured in the disclosure can be synthesized and/or modified by methods well 10 established in the art, such as those described in “Current protocols in nucleic acid chemistry,” Beaucage, S.L. et al. (Edrs.), John Wiley & Sons, Inc., New York, NY, USA, which is hereby incorporated herein by reference. Modifications include, for example, end modifications, e.g., 5’-end modifications (phosphorylation, conjugation, inverted linkages) or 3’-end modifications (conjugation, DNA nucleotides, inverted linkages, etc.); base modifications, e.g., replacement with stabilizing bases, destabilizing bases, or 15 bases that base pair with an expanded repertoire of partners, removal of bases (abasic nucleotides), or conjugated bases; sugar modifications (e.g., at the 2’-position or 4’-position) or replacement of the sugar; and/or backbone modifications, including modification or replacement of the phosphodiester linkages. Specific examples of iRNA compounds useful in the embodiments described herein include, but are not limited to RNAs containing modified backbones or no natural internucleoside linkages. RNAs having 20 modified backbones include, among others, those that do not have a phosphorus atom in the backbone. For the purposes of this specification, and as sometimes referenced in the art, modified RNAs that do not have a phosphorus atom in their internucleoside backbone can also be considered to be oligonucleosides. In some embodiments, a modified iRNA will have a phosphorus atom in its internucleoside backbone. Modified RNA backbones include, for example, phosphorothioates, chiral phosphorothioates, 25 phosphorodithioates, phosphotriesters, aminoalkylphosphotriesters, methyl and other alkyl phosphonates including 3'-alkylene phosphonates and chiral phosphonates, phosphinates, phosphoramidates including 3'- amino phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, and boranophosphates having normal 3'-5' linkages, 2'-5'-linked analogs of these, and those having inverted polarity wherein the adjacent pairs of nucleoside units are linked 3'-5' to 5'-3' or 2'-5' 30 to 5'-2'. Various salts, mixed salts and free acid forms are also included. In some embodiments of the disclosure, the dsRNA agents of the disclosure are in a free acid form. In other embodiments of the disclosure, the dsRNA agents of the disclosure are in a salt form. In one embodiment, the dsRNA agents of the disclosure are in a sodium salt form. In certain embodiments, when the dsRNA agents of the disclosure are in the sodium salt form, sodium ions are present in the agent as counterions for substantially all of the phosphodiester and/or 35 phosphorothiotate groups present in the agent. Agents in which substantially all of the phosphodiester and/or phosphorothioate linkages have a sodium counterion include not more than 5, 4, 3, 2, or 1 phosphodiester and/or phosphorothioate linkages without a sodium counterion. In some embodiments, when the dsRNA 49 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO agents of the disclosure are in the sodium salt form, sodium ions are present in the agent as counterions for all of the phosphodiester and/or phosphorothiotate groups present in the agent. Representative U.S. patents that teach the preparation of the above phosphorus-containing linkages include, but are not limited to, U.S. Patent Nos.3,687,808; 4,469,863; 4,476,301; 5,023,243; 5 5,177,195; 5,188,897; 5,264,423; 5,276,019; 5,278,302; 5,286,717; 5,321,131; 5,399,676; 5,405,939; 5,453,496; 5,455,233; 5,466,677; 5,476,925; 5,519,126; 5,536,821; 5,541,316; 5,550,111; 5,563,253; 5,571,799; 5,587,361; 5,625,050; 6,028,188; 6,124,445; 6,160,109; 6,169,170; 6,172,209; 6, 239,265; 6,277,603; 6,326,199; 6,346,614; 6,444,423; 6,531,590; 6,534,639; 6,608,035; 6,683,167; 6,858,715; 6,867,294; 6,878,805; 7,015,315; 7,041,816; 7,273,933; 7,321,029; and US Pat RE39464, the entire 10 contents of each of which are hereby incorporated herein by reference. Modified RNA backbones that do not include a phosphorus atom therein have backbones that are formed by short chain alkyl or cycloalkyl internucleoside linkages, mixed heteroatoms and alkyl or cycloalkyl internucleoside linkages, or one or more short chain heteroatomic or heterocyclic internucleoside linkages. These include those having morpholino linkages (formed in part from the sugar 15 portion of a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfone backbones; formacetyl and thioformacetyl backbones; methylene formacetyl and thioformacetyl backbones; alkene containing backbones; sulfamate backbones; methyleneimino and methylenehydrazino backbones; sulfonate and sulfonamide backbones; amide backbones; and others having mixed N, O, S and CH2 component parts. Representative U.S. patents that teach the preparation of the above oligonucleosides include, but 20 are not limited to, U.S. Patent Nos.5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141; 5,235,033; 5,64,562; 5,264,564; 5,405,938; 5,434,257; 5,466,677; 5,470,967; 5,489,677; 5,541,307; 5,561,225; 5,596,086; 5,602,240; 5,608,046; 5,610,289; 5,618,704; 5,623,070; 5,663,312; 5,633,360; 5,677,437; and, 5,677,439, the entire contents of each of which are hereby incorporated herein by reference. In other embodiments, suitable RNA mimetics are contemplated for use in iRNAs, in which both 25 the sugar and the internucleoside linkage, i.e., the backbone, of the nucleotide units are replaced with novel groups. The base units are maintained for hybridization with an appropriate nucleic acid target compound. One such oligomeric compound, an RNA mimetic that has been shown to have excellent hybridization properties, is referred to as a peptide nucleic acid (PNA). In PNA compounds, the sugar backbone of an RNA is replaced with an amide containing backbone, in particular an aminoethylglycine 30 backbone. The nucleobases are retained and are bound directly or indirectly to aza nitrogen atoms of the amide portion of the backbone. Representative U.S. patents that teach the preparation of PNA compounds include, but are not limited to, U.S. Patent Nos.5,539,082; 5,714,331; and 5,719,262, the entire contents of each of which are hereby incorporated herein by reference. Additional PNA compounds suitable for use in the iRNAs of the disclosure are described in, for example, in Nielsen et al., Science, 1991, 254, 35 1497-1500. Some embodiments featured in the disclosure include RNAs with phosphorothioate backbones and oligonucleosides with heteroatom backbones, and in particular --CH2--NH--CH2-, --CH2--N(CH3)--O-- CH2--[known as a methylene (methylimino) or MMI backbone], --CH2--O--N(CH3)--CH2--, --CH2-- 50 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO N(CH3)--N(CH3)--CH2-- and --N(CH3)--CH2--CH2--[wherein the native phosphodiester backbone is represented as --O--P--O--CH2--] of the above-referenced U.S. Patent No.5,489,677, and the amide backbones of the above-referenced U.S. Patent No.5,602,240. In some embodiments, the RNAs featured herein have morpholino backbone structures of the above-referenced U.S. Patent No.5,034,506. 5 Modified RNAs can also contain one or more substituted sugar moieties. The iRNAs, e.g., dsRNAs, featured herein can include one of the following at the 2'-position: OH; F; O-, S-, or N-alkyl; O-, S-, or N-alkenyl; O-, S- or N-alkynyl; or O-alkyl-O-alkyl, wherein the alkyl, alkenyl and alkynyl can be substituted or unsubstituted C1 to C10 alkyl or C2 to C10 alkenyl and alkynyl. Exemplary suitable modifications include O[(CH2)nO] mCH3, O(CH2).nOCH3, O(CH2)nNH2, O(CH2) nCH3, O(CH2)nONH2, and 10 O(CH2)nON[(CH2)nCH3)]2, where n and m are from 1 to about 10. In other embodiments, dsRNAs include one of the following at the 2' position: C1 to C10 lower alkyl, substituted lower alkyl, alkaryl, aralkyl, O- alkaryl or O-aralkyl, SH, SCH3, OCN, Cl, Br, CN, CF3, OCF3, SOCH3, SO2CH3, ONO2, NO2, N3, NH2, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl, an RNA cleaving group, a reporter group, an intercalator, a group for improving the pharmacokinetic properties of 15 an iRNA, or a group for improving the pharmacodynamic properties of an iRNA, and other substituents having similar properties. In some embodiments, the modification includes a 2'-methoxyethoxy (2'-O-- CH2CH2OCH3, also known as 2'-O-(2-methoxyethyl) or 2'-MOE) (Martin et al., Helv. Chim. Acta, 1995, 78:486-504) i.e., an alkoxy-alkoxy group. Another exemplary modification is 2'-dimethylaminooxyethoxy, i.e., a O(CH2)2ON(CH3)2 group, also known as 2'-DMAOE, as described in examples herein below, and 2'- 20 dimethylaminoethoxyethoxy (also known in the art as 2'-O-dimethylaminoethoxyethyl or 2'-DMAEOE), i.e., 2'-O--CH2--O--CH2--N(CH2)2. Further exemplary modifications include : 5’-Me-2’-F nucleotides, 5’- Me-2’-OMe nucleotides, 5’-Me-2’-deoxynucleotides, (both R and S isomers in these three families); 2’- alkoxyalkyl; and 2’-NMA (N-methylacetamide). Other modifications include 2'-methoxy (2'-OCH3), 2'-aminopropoxy (2'-OCH2CH2CH2NH2) and 25 2'-fluoro (2'-F). Similar modifications can also be made at other positions on the RNA of an iRNA, particularly the 3' position of the sugar on the 3' terminal nucleotide or in 2'-5' linked dsRNAs and the 5' position of 5' terminal nucleotide. iRNAs can also have sugar mimetics such as cyclobutyl moieties in place of the pentofuranosyl sugar. Representative U.S. patents that teach the preparation of such modified sugar structures include, but are not limited to, U.S. Pat. Nos.4,981,957; 5,118,800; 5,319,080; 5,359,044; 30 5,393,878; 5,446,137; 5,466,786; 5,514,785; 5,519,134; 5,567,811; 5,576,427; 5,591,722; 5,597,909; 5,610,300; 5,627,053; 5,639,873; 5,646,265; 5,658,873; 5,670,633; and 5,700,920, certain of which are commonly owned with the instant application. The entire contents of each of the foregoing are hereby incorporated herein by reference. An iRNA of the disclosure can also include nucleobase (often referred to in the art simply as 35 “base”) modifications or substitutions. As used herein, “unmodified” or “natural” nucleobases include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) and uracil (U). Modified nucleobases include other synthetic and natural nucleobases such as 5-methylcytosine (5- me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl 51 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2- thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine, 5-propynyl uracil and cytosine, 6- azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8- thioalkyl, 8-hydroxyl anal other 8-substituted adenines and guanines, 5-halo, particularly 5-bromo, 5- 5 trifluoromethyl and other 5-substituted uracils and cytosines, 7-methylguanine and 7-methyladenine, 8- azaguanine and 8-azaadenine, 7-deazaguanine and 7-daazaadenine and 3-deazaguanine and 3- deazaadenine. Further nucleobases include those disclosed in U.S. Pat. No.3,687,808, those disclosed in Modified Nucleosides in Biochemistry, Biotechnology and Medicine, Herdewijn, P. ed. Wiley-VCH, 2008; those disclosed in The Concise Encyclopedia Of Polymer Science And Engineering, pages 858-859, 10 Kroschwitz, J. L, ed. John Wiley & Sons, 1990, these disclosed by Englisch et al., (1991) Angewandte Chemie, International Edition, 30:613, and those disclosed by Sanghvi, Y S., Chapter 15, dsRNA Research and Applications, pages 289-302, Crooke, S. T. and Lebleu, B., Ed., CRC Press, 1993. Certain of these nucleobases are particularly useful for increasing the binding affinity of the oligomeric compounds featured in the disclosure. These include 5-substituted pyrimidines, 6-azapyrimidines and N-15 2, N-6 and 0-6 substituted purines, including 2-aminopropyladenine, 5-propynyluracil and 5- propynylcytosine.5-methylcytosine substitutions have been shown to increase nucleic acid duplex stability by 0.6-1.2 °C (Sanghvi, Y. S., Crooke, S. T. and Lebleu, B., Eds., dsRNA Research and Applications, CRC Press, Boca Raton, 1993, pp.276-278) and are exemplary base substitutions, even more particularly when combined with 2'-O-methoxyethyl sugar modifications. 20 Representative U.S. patents that teach the preparation of certain of the above noted modified nucleobases as well as other modified nucleobases include, but are not limited to, the above noted U.S. Patent Nos.3,687,808, 4,845,205; 5,130,30; 5,134,066; 5,175,273; 5,367,066; 5,432,272; 5,457,187; 5,459,255; 5,484,908; 5,502,177; 5,525,711; 5,552,540; 5,587,469; 5,594,121, 5,596,091; 5,614,617; 5,681,941; 5,750,692; 6,015,886; 6,147,200; 6,166,197; 6,222,025; 6,235,887; 6,380,368; 6,528,640; 25 6,639,062; 6,617,438; 7,045,610; 7,427,672; and 7,495,088, the entire contents of each of which are hereby incorporated herein by reference. An iRNA of the disclosure can also be modified to include one or more locked nucleic acids (LNA). A locked nucleic acid is a nucleotide having a modified ribose moiety in which the ribose moiety comprises an extra bridge connecting the 2' and 4' carbons. This structure effectively "locks" the ribose in 30 the 3'-endo structural conformation. The addition of locked nucleic acids to siRNAs has been shown to increase siRNA stability in serum, and to reduce off-target effects (Elmen, J. et al., (2005) Nucleic Acids Research 33(1):439-447; Mook, OR. et al., (2007) Mol Canc Ther 6(3):833-843; Grunweller, A. et al., (2003) Nucleic Acids Research 31(12):3185-3193). An iRNA of the disclosure can also be modified to include one or more bicyclic sugar moities. A 35 “bicyclic sugar” is a furanosyl ring modified by the bridging of two atoms. A“bicyclic nucleoside” (“BNA”) is a nucleoside having a sugar moiety comprising a bridge connecting two carbon atoms of the sugar ring, thereby forming a bicyclic ring system. In certain embodiments, the bridge connects the 4′- carbon and the 2′-carbon of the sugar ring. Thus, in some embodiments an agent of the disclosure may 52 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO include one or more locked nucleic acids (LNA). A locked nucleic acid is a nucleotide having a modified ribose moiety in which the ribose moiety comprises an extra bridge connecting the 2' and 4' carbons. In other words, an LNA is a nucleotide comprising a bicyclic sugar moiety comprising a 4'-CH2-O-2' bridge. This structure effectively "locks" the ribose in the 3'-endo structural conformation. The addition of locked 5 nucleic acids to siRNAs has been shown to increase siRNA stability in serum, and to reduce off-target effects (Elmen, J. et al., (2005) Nucleic Acids Research 33(1):439-447; Mook, OR. et al., (2007) Mol Canc Ther 6(3):833-843; Grunweller, A. et al., (2003) Nucleic Acids Research 31(12):3185-3193). Examples of bicyclic nucleosides for use in the polynucleotides of the disclosure include without limitation nucleosides comprising a bridge between the 4′ and the 2′ ribosyl ring atoms. In certain 10 embodiments, the antisense polynucleotide agents of the disclosure include one or more bicyclic nucleosides comprising a 4′ to 2′ bridge. Examples of such 4′ to 2′ bridged bicyclic nucleosides, include but are not limited to 4′-(CH2)—O-2′ (LNA); 4′-(CH2)—S-2′; 4′-(CH2)2—O-2′ (ENA); 4′-CH(CH3)—O- 2′ (also referred to as “constrained ethyl” or “cEt”) and 4′-CH(CH2OCH3)—O-2′ (and analogs thereof; see, e.g., U.S. Pat. No.7,399,845); 4′-C(CH3)(CH3)—O-2′ (and analogs thereof; see e.g., US Patent No. 15 8,278,283); 4′-CH2—N(OCH3)-2′ (and analogs thereof; see e.g., US Patent No.8,278,425); 4′-CH2—O— N(CH3)-2′ (see, e.g.,U.S. Patent Publication No.2004/0171570); 4′-CH2—N(R)—O-2′, wherein R is H, C1-C12 alkyl, or a protecting group (see, e.g., U.S. Pat. No.7,427,672); 4′-CH2—C(H)(CH3)-2′ (see, e.g., Chattopadhyaya et al., J. Org. Chem., 2009, 74, 118-134); and 4′-CH2—C(═CH2)-2′ (and analogs thereof; see, e.g., US Patent No. 8,278,426). The entire contents of each of the foregoing are hereby 20 incorporated herein by reference. Additional representative U.S. Patents and US Patent Publications that teach the preparation of locked nucleic acid nucleotides include, but are not limited to, the following: U.S. Patent Nos.6,268,490; 6,525,191; 6,670,461; 6,770,748; 6,794,499; 6,998,484; 7,053,207; 7,034,133;7,084,125; 7,399,845; 7,427,672; 7,569,686; 7,741,457; 8,022,193; 8,030,467; 8,278,425; 8,278,426; 8,278,283; US 25 2008/0039618; and US 2009/0012281, the entire contents of each of which are hereby incorporated herein by reference. Any of the foregoing bicyclic nucleosides can be prepared having one or more stereochemical sugar configurations including for example α-L-ribofuranose and β-D-ribofuranose (see WO 99/14226). An iRNA of the disclosure can also be modified to include one or more constrained ethyl 30 nucleotides. As used herein, a "constrained ethyl nucleotide" or "cEt" is a locked nucleic acid comprising a bicyclic sugar moiety comprising a 4'-CH(CH3)-0-2' bridge. In one embodiment, a constrained ethyl nucleotide is in the S conformation referred to herein as “S-cEt.” An iRNA of the disclosure may also include one or more “conformationally restricted nucleotides” (“CRN”). CRN are nucleotide analogs with a linker connecting the C2’and C4’ carbons of 35 ribose or the C3 and -C5′ carbons of ribose. CRN lock the ribose ring into a stable conformation and increase the hybridization affinity to mRNA. The linker is of sufficient length to place the oxygen in an optimal position for stability and affinity resulting in less ribose ring puckering. 53 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO Representative publications that teach the preparation of certain of the above noted CRN include, but are not limited to, US Patent Publication No.2013/0190383; and PCT publication WO 2013/036868, the entire contents of each of which are hereby incorporated herein by reference. In some embodiments, an iRNA of the disclosure comprises one or more monomers that are UNA 5 (unlocked nucleic acid) nucleotides. UNA is unlocked acyclic nucleic acid, wherein any of the bonds of the sugar has been removed, forming an unlocked "sugar" residue. In one example, UNA also encompasses monomer with bonds between C1'-C4' have been removed (i.e. the covalent carbon-oxygen- carbon bond between the C1' and C4' carbons). In another example, the C2'-C3' bond (i.e. the covalent carbon-carbon bond between the C2' and C3' carbons) of the sugar has been removed (see Nuc. Acids 10 Symp. Series, 52, 133-134 (2008) and Fluiter et al., Mol. Biosyst., 2009, 10, 1039 hereby incorporated by reference). Representative U.S. publications that teach the preparation of UNA include, but are not limited to, US Patent No.8,314,227; and US Patent Publication Nos.2013/0096289; 2013/0011922; and 2011/0313020, the entire contents of each of which are hereby incorporated herein by reference. 15 Potentially stabilizing modifications to the ends of RNA molecules can include N- (acetylaminocaproyl)-4-hydroxyprolinol (Hyp-C6-NHAc), N-(caproyl-4-hydroxyprolinol (Hyp-C6), N- (acetyl-4-hydroxyprolinol (Hyp-NHAc), thymidine-2'-0-deoxythymidine (ether), N-(aminocaproyl)-4- hydroxyprolinol (Hyp-C6-amino), 2-docosanoyl-uridine-3"- phosphate, inverted base dT(idT) and others. Disclosure of this modification can be found in PCT Publication No. WO 2011/005861. 20 Other modifications of an iRNA of the disclosure include a 5’ phosphate or 5’ phosphate mimic, e.g., a 5’-terminal phosphate or phosphate mimic on the antisense strand of an RNAi agent. Suitable phosphate mimics are disclosed in, for example US Patent Publication No.2012/0157511, the entire contents of which are incorporated herein by reference. In certain embodiments, a dsRNA molecule can be optimized for RNA interference by 25 incorporating thermally destabilizing modifications in the seed region of the antisense strand. As used herein “seed region” means at positions 2-9 of the 5’-end of the referenced strand. For example, thermally destabilizing modifications can be incorporated in the seed region of the antisense strand to reduce or inhibit off-target gene silencing. The term “thermally destabilizing modification(s)” includes modification(s) that would result 30 with a dsRNA with a lower overall melting temperature (Tm) than the Tm of the dsRNA without having such modification(s). For example, the thermally destabilizing modification(s) can decrease the Tm of the dsRNA by 1 – 4 °C, such as one, two, three or four degrees Celsius. And, the term “thermally destabilizing nucleotide” refers to a nucleotide containing one or more thermally destabilizing modifications. 35 It has been discovered that dsRNAs with an antisense strand comprising at least one thermally destabilizing modification of the duplex within the first 9 nucleotide positions, counting from the 5’ end, of the antisense strand have reduced off-target gene silencing activity. Accordingly, in some embodiments, the antisense strand comprises at least one (e.g., one, two, three, four, five or more) 54 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO thermally destabilizing modification of the duplex within the first 9 nucleotide positions of the 5’ region of the antisense strand. In some embodiments, one or more thermally destabilizing modification(s) of the duplex is/are located in positions 2-9, or preferably positions 4-8, from the 5’- end of the antisense strand. In some further embodiments, the thermally destabilizing modification(s) 5 of the duplex is/are located at position 6, 7 or 8 from the 5’-end of the antisense strand. In still some further embodiments, the thermally destabilizing modification of the duplex is located at position 7 from the 5’-end of the antisense strand. In some embodiments, the thermally destabilizing modification of the duplex is located at position 2, 3, 4, 5 or 9 from the 5’-end of the antisense strand. The thermally destabilizing modifications can include, but are not limited to, abasic 10 modification; mismatch with the opposing nucleotide in the opposing strand; and sugar modification such as 2’-deoxy modification , a 2’-5’ linked nucleotide (“3’-RNA’), or acyclic nucleotide, e.g., unlocked nucleic acids (UNA) or glycol nucleic acid (GNA). Exemplified abasic modifications include, but are not limited to the following: 15
wherein B is a modified or unmodified nucleobase. Exemplified sugar modifications include, but are not limited to the following: 55 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
wherein B is a modified or unmodified nucleobase. In some embodiments the thermally destabilizing modification of the duplex is selected from 5 the group consisting of:
wherein B is a modified or unmodified nucleobase and the asterisk on each structure represents either R, S or racemic. 10 The term "acyclic nucleotide" refers to any nucleotide having an acyclic ribose sugar, for example, where any of bonds between the ribose carbons (e.g., C1’-C2’, C2’-C3’, C3’-C4’, C4’-O4’, or C1’-O4’) is absent or at least one of ribose carbons or oxygen (e.g., C1’, C2’, C3’, C4’ or O4’) are independently or in combination absent from the nucleotide. In some embodiments, acyclic nucleotide 56 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
is a modified or unmodified nucleobase, R1 and R2 independently are H, halogen, OR3, or alkyl; and R3 is H, alkyl, cycloalkyl, aryl, aralkyl, heteroaryl or sugar). The term “UNA” refers to unlocked acyclic nucleic acid, wherein any of the bonds of the sugar has been removed, forming an unlocked 5 "sugar" residue. In one example, UNA also encompasses monomers with bonds between C1'-C4' being removed (i.e. the covalent carbon-oxygen-carbon bond between the C1' and C4' carbons). In another example, the C2'-C3' bond (i.e. the covalent carbon-carbon bond between the C2' and C3' carbons) of the sugar is removed (see Mikhailov et. al., Tetrahedron Letters, 26 (17): 2059 (1985); and Fluiter et al., Mol. Biosyst., 10: 1039 (2009), which are hereby incorporated by reference in their10 entirety). The acyclic derivative provides greater backbone flexibility without affecting the Watson- Crick pairings. The acyclic nucleotide can be linked via 2’-5’ or 3’-5’ linkage. The term ‘GNA’ refers to glycol nucleic acid which is a polymer similar to DNA or RNA but differing in the composition of its “backbone” in that is composed of repeating glycerol units linked by phosphodiester bonds: 15
. The thermally destabilizing modification of the duplex can be mismatches (i.e., noncomplementary base pairs) between the thermally destabilizing nucleotide and the opposing nucleotide in the opposite strand within the dsRNA duplex. Exemplary mismatch base pairs include G:G, G:A, G:U, G:T, A:A, A:C, C:C, C:U, C:T, U:U, T:T, U:T, or a combination thereof. Other 20 mismatch base pairings known in the art are also amenable to the present disclosure. A mismatch can occur between nucleotides that are either naturally occurring nucleotides or modified nucleotides, i.e., the mismatch base pairing can occur between the nucleobases from respective nucleotides independent of the modifications on the ribose sugars of the nucleotides. In certain embodiments, the dsRNA molecule contains at least one nucleobase in the mismatch pairing that is a 2’-deoxy 25 nucleobase; e.g., the 2’-deoxy nucleobase is in the sense strand. 57 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In some embodiments, the thermally destabilizing modification of the duplex in the seed region of the antisense strand includes nucleotides with impaired W-C H-bonding to complementary base on the target mRNA, such as:
. 5 More examples of abasic nucleotide, acyclic nucleotide modifications (including UNA and GNA), and mismatch modifications have been described in detail in WO 2011/133876, which is herein incorporated by reference in its entirety. The thermally destabilizing modifications may also include universal base with reduced or abolished capability to form hydrogen bonds with the opposing bases, and phosphate modifications. 10 In some embodiments, the thermally destabilizing modification of the duplex includes nucleotides with non-canonical bases such as, but not limited to, nucleobase modifications with impaired or completely abolished capability to form hydrogen bonds with bases in the opposite strand. These nucleobase modifications have been evaluated for destabilization of the central region of the dsRNA duplex as described in WO 2010/0011895, which is herein incorporated by reference in its 15 entirety. Exemplary nucleobase modifications are:
58 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In some embodiments, the thermally destabilizing modification of the duplex in the seed region of the antisense strand includes one or more ^-nucleotide complementary to the base on the target mRNA, such as:
5 wherein R is H, OH, OCH3, F, NH2, NHMe, NMe2 or O-alkyl. Exemplary phosphate modifications known to decrease the thermal stability of dsRNA duplexes compared to natural phosphodiester linkages are:
The alkyl for the R group can be a C1-C6alkyl. Specific alkyls for the R group include, but are 10 not limited to methyl, ethyl, propyl, isopropyl, butyl, pentyl and hexyl. As the skilled artisan will recognize, in view of the functional role of nucleobases is defining specificity of an RNAi agent of the disclosure, while nucleobase modifications can be performed in the various manners as described herein, e.g., to introduce destabilizing modifications into an RNAi agent of the disclosure, e.g., for purpose of enhancing on-target effect relative to off-target effect, the 15 range of modifications available and, in general, present upon RNAi agents of the disclosure tends to be much greater for non-nucleobase modifications, e.g., modifications to sugar groups or phosphate backbones of polyribonucleotides. Such modifications are described in greater detail in other sections of the instant disclosure and are expressly contemplated for RNAi agents of the disclosure, either possessing native nucleobases or modified nucleobases as described above or elsewhere herein. 20 In some embodiments, the dsRNA agent further comprises a phosphate or phosphate mimic at the 5’-end of the sense or antisense strand. In one embodiment, there is a phosphate or phosphate mimic at the 5’-end of the sense strand. In one embodiment, there is a phosphate or phosphate mimic at the 5’-end of the antisense strand. In some embodiments, the phosphate mimic is 5’-end phosphorothioate (5’-PS), 5’- 25 end phosphorodithioate (5’-PS2), 5’ end vinylphosphonate (5’-VP), 5’-end methylphosphonate (MePhos), or 5’-deoxy-5’-C-malonyl
one embodiment, the phosphate mimic is a 5’-vinyl phosphonate (VP). In one embodiment, the phosphate mimic is a 5’-(E)-vinyl phosphonate (VP) isomer (i.e., trans-vinylphosphate), 5’-(Z)-VP isomer (i.e., cis-vinylphosphate), or mixtures thereof. 59 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In exemplary embodiments, a 5’-vinyl phosphonate modified nucleotide of the disclosure has the structure:
, wherein: X is O or S; R is hydrogen, hydroxy, fluoro, methoxy, 2-methoxyethoxy; 5 R5’ is =C(H)-P(O)(OH)2 and the double bond between the C5’ carbon and R5’ is in the E or Z orientation (e.g., E orientation); and B is a nucleobase or a modified nucleobase, optionally where B is adenine, guanine, cytosine, thymine, or uracil. In one embodiment, R5’ is =C(H)-P(O)(OH)2 and the double bond between the C5’ carbon10 and R5’ is in the E orientation. In another embodiment, R is methoxy and R5’ is =C(H)-P(O)(OH)2 and the double bond between the C5’ carbon and R5’ is in the E orientation. In another embodiment, X is S, R is methoxy, and R5’ is =C(H)-P(O)(OH)2 and the double bond between the C5’ carbon and R5’ is in the E orientation. In some embodiments, the -CH2OH group at the 4’-position of the 5’-terminal nucleotide is 15 replaced with a phosphate mimic of the formula -O-CH2-P(O)(OR)2, wherein each R is independently hydrogen or C1-4 alkyl (e.g., one R group is hydrogen and one R group is methyl; or both R groups are hydrogen). In one embodiment, the phosphate mimic is a 5’-cyclopropyl phosphonate (VP) (i.e., the CH2OH group at the 4’-position of the 5’-terminal nucleotide is replaced with a group of the formula -Cy- 20 P(O)(OR)2, wherein Cy is a cyclopropyl ring and each R is independently hydrogen or C1-4 alkyl (e.g., one R group is hydrogen or both R groups are hydrogen). In some exemplary embodiments, the 5’-end phosphate mimic i
,
salt (e.g., sodium salt) thereof, wherein B is an optionally modified nucleobase (e.g., U). 25 In some embodiments, the 5’-end phosphate mimic is part of a modified 5’-terminal nucleotide. For example, the phosphate mimic may be part of a modified 5’-terminal nucleotide 60 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO having the structure
, wherein B is an optionally modified nucleobase. In some embodiments, the 5’-end phosphate mimic can also include a 5’-phosphate prodrug or 5’-phosphonate prodrug. In some embodiments, the 5’-phosphate prodrug or 5’-phosphonate 5 prodrug has a structure of formulas disclosed in WO2022/147214, which is incorporated herein by reference. In some exemplary embodiments, the 5’-phosphate prodrug or 5’-phosphonate prodrug is: 10
-methoxyphenyl)-3,3-dimethyl-1,2-dithiolan-4-ol)
61 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In some exemplary embodiments, the 5’-phosphate prodrug or 5’-phosphonate prodrug is:
. The siRNA containing one of the above list of 5’ modified phosphate prodrugs generally has an activity comparable to that of the siRNA containing 5’-VP. In some exemplary embodiments, the 5’- 5 phosphate prodrug or 5’-phosphonate prodrug is:
. The siRNA containing one of the above list of 5’ modified phosphate prodrugs can have an improved stability than that of the siRNA containing 5’-VP and better or comparable activity than that of the siRNA containing 5’-VP. 10 In some embodiments, the 5’-end of the antisense strand of the dsRNA agent does not contain a 5’-vinyl phosphonate (VP). IV. In vivo Delivery Enhancing Moiety Conjugated to dsRNA agent The present disclosure provides dual conjugated dsRNA agents for inhibiting expression of a 15 target gene, i.e., a DMPK gene. In some embodiments, a dsRNA agent comprises an antisense strand and a sense strand; at least one αvβ6 integrin targeting ligand that mediates delivery to muscle tissue conjugated to at least one strand; and at least one in vivo delivery enhancing moiety conjugated to at least one strand. Suitable in vivo delivery enhancing moieties for use in the present disclosure are described in 20 International Application No. PCT/US2022/046668, filed on October 14, 2022, in U.S. Provisional Application No.63/659,097, entitled “Dual Conjugate Compounds for Extrahepatic Delivery,” filed on June 12, 2024, and in International Application No. PCT/US2025/XXXXXX, filed on June 11, 2025, entitled “Dual Conjugate Compounds for Extrahepatic Delivery”. The entire contents of each of the foregoing applications are incorporated herein by reference. 25 The at least one in vivo delivery enhancing moiety may be conjugated to any internal position of the antisense strand or the sense strand. In some embodiments, the at least one in vivo delivery enhancing moiety may be conjugated to a position that is not an external position of the antisense strand or the sense strand. In other embodiments, the at least one in vivo delivery enhancing moiety may be conjugated to an external positon of the antisense strand or the sense strand. 30 As used herein, the term “in vivo delivery enhancing moiety” refers to a moiety which, when conjugated to a dsRNA agent, enhances delivery of the dsRNA agent to a target tissue, e.g., muscle, 62 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO or a cell type, such as a muscle cell (e.g., a skeletal muscle cell or a cardiac muscle cell). In some embodiments, the in vivo delivery enhancing moiety has pharmacokinetic (PK) enhancing properties, such as increasing the residence time in the blood of the dsRNA agent, and/or increasing tissue PK, including increasing tissue exposure of the dsRNA agent. In some embodiments, the in vivo delivery 5 enhancing moiety can have a cooperative or synergistic effect with an αvβ6 compound in increasing tissue exposure when both elements are conjugated to the dsRNA agent. In some embodiments, the in vivo delivery enhancing moiety is lipophilic. Thus, when conjugated to one or more internal position(s) of the dsRNA agent of the disclosure, the in vivo delivery enhancing moiety increases lipophilicity of the dsRNA agent and provides optimal 10 hydrophobicity for the enhanced in vivo delivery of dsRNA to muscle tissue, e.g., skeletal muscle tissue or cardiac muscle tissue. One way to characterize lipophilicity is by the octanol-water partition coefficient, logKow, where Kow is the ratio of a chemical’s concentration in the octanol-phase to its concentration in the aqueous phase of a two-phase system at equilibrium. The octanol-water partition coefficient is a 15 laboratory-measured property of a substance. However, it may also be predicted by using coefficients attributed to the structural components of a chemical which are calculated using first-principle or empirical methods (see, for example, Tetko et al., J. Chem. Inf. Comput. Sci.41:1407-21 (2001), which is incorporated herein by reference in its entirety). It provides a thermodynamic measure of the tendency of the substance to prefer a non-aqueous or oily milieu rather than water (i.e. its 20 hydrophilic/lipophilic balance). In principle, a chemical substance is lipophilic in character when its logKow exceeds 0. Typically, the lipophilic moiety possesses a logKow exceeding 1, exceeding 1.5, exceeding 2, exceeding 3, exceeding 4, exceeding 5, or exceeding 10. For instance, the logKow of 6- amino hexanol, for instance, is predicted to be approximately 0.7. Using the same method, the logKow of cholesteryl N-(hexan-6-ol) carbamate is predicted to be 10.7. 25 The lipophilicity of a molecule can change with respect to the functional group it carries. For instance, adding a hydroxyl group or amine group to the end of a hydrocarbon chain, e.g., a C22 hydrocarbon chain, can increase or decrease the partition coefficient (e.g., logKow) value of the hydrocarbon chain. Alternatively, the hydrophobicity of the dsRNA agent conjugated to at least one in vivo 30 delivery enhancing moiety can be measured by its protein binding characteristics. For instance, the unbound fraction in the plasma protein binding assay of the dsRNA agent can be determined to positively correlate to the relative hydrophobicity of the dsRNA agent, which can positively correlate to the silencing activity of the dsRNA agent. In one embodiment, the plasma protein binding assay determined is an electrophoretic 35 mobility shift assay (EMSA) using human serum albumin protein. In some embodiments, the hydrophobicity of the dsRNA agent, measured by fraction of unbound dsRNA agent in the binding assay, exceeds 0.15, exceeds 0.2, exceeds 0.25, exceeds 0.3, exceeds 0.35, exceeds 0.4, exceeds 0.45, or exceeds 0.5 for an enhanced in vivo delivery of dsRNA agent. 63 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO The at least one in vivo delivery enhancing moiety may be attached to the dsRNA agent of the disclosure by any method known in the art, including via a functional grouping already present in the in vivo delivery enhancing moiety or introduced into the dsRNA agent, such as a hydroxy group (e.g., —CO—CH2—OH). The functional groups already present in the in vivo delivery enhancing moiety 5 or introduced into the dsRNA agent include, but are not limited to, hydroxyl, amine, carboxylic acid, sulfonate, phosphate, thiol, azide, and alkyne. Conjugation of the dsRNA agent and the in vivo delivery enhancing moiety may occur, for example, through formation of an ether or a carboxylic or carbamoyl ester linkage between the hydroxy and an alkyl group R—, an alkanoyl group RCO— or a substituted carbamoyl group 10 RNHCO—. The alkyl group R may be cyclic (e.g., cyclohexyl) or acyclic (e.g., straight-chained or branched; and saturated or unsaturated). Alkyl group R may be a butyl, pentyl, hexyl, heptyl, octyl, nonyl, decyl, undecyl, dodecyl, tridecyl, tetradecyl, pentadecyl, hexadecyl, heptadecyl or octadecyl group, or the like. In certain embodiments, more than one in vivo delivery enhancing moiety can be conjugated 15 to the dsRNA agent of the disclosure. In one embodiment, two or more in vivo delivery enhancing moieties are conjugated to the same strand of the dsRNA agent. In one embodiment, each strand of the dsRNA agent is conjugated to one or more in vivo delivery enhancing moieties. In one embodiment, two or more in vivo delivery enhancing moieties are conjugated to the same position (i.e., the same nucleobase, same sugar moiety, or same internucleosidic linkage) of the dsRNA agent. 20 This can be achieved by, e.g., conjugating the two or more in vivo delivery enhancing moieties via a carrier, and/or conjugating the two or more in vivo delivery enhancing moieties via a branched linker, and/or conjugating the two or more in vivo delivery enhancing moieties via one or more linkers, with one or more linkers linking the in vivo delivery enhancing moieties consecutively. In some embodiments, the in vivo delivery enhancing moiety may comprise at least one C10- 25 C26 hydrocarbon chain, e.g., a C10 hydrocarbon chain, a C11 hydrocarbon chain, a C12 hydrocarbon chain, a C13 hydrocarbon chain, a C14 hydrocarbon chain, a C15 hydrocarbon chain, a C16 hydrocarbon chain, a C17 hydrocarbon chain, a C18 hydrocarbon chain, a C19 hydrocarbon chain, a C20 hydrocarbon chain, a C21 hydrocarbon chain, a C22 hydrocarbon chain, a C23 hydrocarbon chain, a C24 hydrocarbon chain, a C25 hydrocarbon chain or a C26 hydrocarbon chain. In some embodiments, the C10-C2630 hydrocarbon chain may be a straight hydrocarbon chain. In other embodiments, the C10-C26 hydrocarbon chain may be a branched hydrocarbon chain. In some embodiments, the C10-C26 hydrocarbon chain may be a saturated hydrocarbon chain. In other embodiments, the C10-C26 hydrocarbon chain may be an unsaturated hydrocarbon chain, e.g., comprising one or more double bonds and/or one or more triple bonds. 35 In one embodiment, the in vivo delivery enhancing moiety may comprise at least one C11 hydrocarbon chain. In one embodiment, the at least one in vivo delivery enhancing moiety may comprise at least one C17 hydrocarbon chain. In one embodiment, the in vivo delivery enhancing moiety may comprise at least one C22 hydrocarbon chain. 64 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In some embodiments, the C10-C26 hydrocarbon chain may be unsubstituted. In other embodiments, the C10-C26 hydrocarbon chain may be substituted with at least one functional group selected from the group consisting of hydroxyl, amine, carboxylic acid, sulfonate, phosphate, thiol, azide, and alkyne. In one embodiment, the C10-C26 hydrocarbon chain is substituted with a carboxylic 5 acid group. In some embodiments, the C10-C26 hydrocarbon chain is represented by –(CH2)n-, wherein n is a number from 10 to 26, e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26; and – is a bond connecting the C10-C26 hydrocarbon chain to other portions of the in vivo delivery enhancing moiety. In this embodiment, the C10-C26 hydrocarbon chain is connected at both ends to the 10 remainder of the in vivo delivery enhancing moiety. In some embodiments, the C10-C26 hydrocarbon chain is represented by the following structure: –linker-(CH2)n(CH3), wherein n is a number from 10 to 25, e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or 25; the linker is as described hereinbelow; and – is a bond connecting the C10-C26 hydrocarbon chain to other portions of the in vivo delivery enhancing moiety. In this15 embodiment, the C10-C26 hydrocarbon chain is connected at one end to other portions of the in vivo delivery enhancing moiety. In some embodiments, the C10-C26 hydrocarbon chain is represented by the following structure: –linker-(CH2)n-A, wherein n is a number from 10 to 26, e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26; the linker as described hereinbelow and A is a functional group 20 selected from the group consisting of hydroxyl, amine, carboxylic acid, sulfonate, phosphate, thiol, azide, and alkyne; or A1 or A2 with a structure shown below:
In one embodiment, A is carboxylic acid. 25 In one embodiment, A is A1. In one embodiment, A is A2. Exemplary in vivo delivery enhancing moieties useful in the context of the present disclosure are described, e.g., in WO 2023/064530, the entire contents of which are incorporated herein by reference. 30 Lipophilic Moiety 65 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO As noted above, the in vivo delivery enhancing moiety an comprise at least one C10-C26 hydrocarbon chain. In some embodiments, the in vivo delivery enhancing moiety comprises a C22 hydrocarbon chain, e.g., one or more C22 hydrocarbon chains. In some embodiments, the C22 hydrocarbon chain is a C22 acid, e.g., a C22 acid selected from the group consisting of docosanoic acid, 5 6-octyltetradecanoic acid, 10-hexylhexadecanoic acid, all-cis-7,10,13,16,19-docosapentaenoic acid, all-cis-4,7,10,13,16,19-docosahexaenoic acid, all-cis-13,16-docosadienoic acid, all-cis-7,10,13,16- docosatetraenoic acid, all-cis-4,7,10,13,16-docosapentaenoic acid, and cis-13-docosenoic acid.
In one embodiment, the C22 hydrocarbon chain is a C22 alcohol, e.g. the C22 alcohol selected10 from the group consisting of 1-docosanol, 6-octyltetradecan-1-ol, 10-hexylhexadecan-1-ol, cis-13- docosen-1-ol, docosan-9-ol, docosan-2-ol, docosan-10-ol, docosan-11-ol, and cis-4,7,10,13,16,19- docosahexanol.
In one embodiment, the C22 hydrocarbon chain is a C22 amide, e.g., the C22 amide selected 15 from the group consisting of (E)-Docos-4-enamide, (E)-Docos-5-enamide, (Z)-Docos-9-enamide, (E)-Docos-11-enamide,12-Docosenamide, (Z)-Docos-13-enamide, (Z)-N-Hydroxy-13- docoseneamide, (E)-Docos-14-enamide, 6-cis-Docosenamide, 14-Docosenamide Docos-11-enamide, (4E,13E)-Docosa-4,13-dienamide, and (5E,13E)-Docosa-5,13-dienamide. In one embodiment, the C22 hydrocarbon chain includes, but are not limited to, docosan-2-yl, 20 docosan-3-yl, docosan-4-yl, docosan-5-yl, docosan-6-yl, docosan-7-yl, docosan-8-yl, docosan-9-yl, docosan-10-yl, docosan-11-yl, 2-(decyl)dodecan-1-yl, 2-(nonyl)tridecan-1-yl, 2-(octyl)tetradecan-1- yl, 2-(heptyl)pentadecan-1-yl, 2-(hexyl)hexadecan-1-yl, 2-(pentyl)heptadecan-1-yl, 2- 66 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO (butyl)octadecan-1-yl, 2-(propyl)nonadecan-1-yl, 2-(ethyl)eicosan-1-yl, 2-(methyl)henicosan-1-yl, 3- (nonyl)tridecan-1-yl, 3-(octyl)tetradecan-1-yl, 3-(heptyl)pentadecan-1-yl, 3-(hexyl)hexadecan-1-yl, 3- (pentyl)heptadecan-1-yl, 3-(butyl)octadecan-1-yl, 3-(propyl)nonadecan-1-yl, 3-(ethyl)eicosan-1-yl, 3- (methyl)henicosan-1-yl, 4-(octyl)tetradecan-1-yl, 4-(heptyl)pentadecan-1-yl, 4-(hexyl)hexadecan-1-yl, 5 4-(pentyl)heptadecan-1-yl, 4-(butyl)octadecan-1-yl, 4-(propyl)nonadecan-1-yl, 4-(ethyl)eicosan-1-yl, 4-(methyl)henicosan-1-yl, 5-(heptyl)pentadecan-1-yl, 5-(hexyl)hexadecan-1-yl, 5-(pentyl)heptadecan- 1-yl, 5-(butyl)octadecan-1-yl, 5-(propyl)nonadecan-1-yl, 5-(ethyl)eicosan-1-yl, 5-(methyl)henicosan- 1-yl, 6-(hexyl)hexadecan-1-yl, 6-(pentyl)heptadecan-1-yl, 6-(butyl)octadecan-1-yl, 6- (propyl)nonadecan-1-yl, 6-(ethyl)eicosan-1-yl, 6-(methyl)henicosan-1-yl, 7-(pentyl)heptadecan-1-yl, 10 7-(butyl)octadecan-1-yl, 7-(propyl)nonadecan-1-yl, 7-(ethyl)eicosan-1-yl, 7-(methyl)henicosan-1-yl, 8-(butyl)octadecan-1-yl, 8-(propyl)nonadecan-1-yl, 8-(ethyl)eicosan-1-yl, 8-(methyl)henicosan-1-yl, 9-(propyl)nonadecan-1-yl, 9-(ethyl)eicosan-1-yl, 9-(methyl)henicosan-1-yl, 10-(ethyl)eicosan-1-yl, 10-(methyl)henicosan-1-yl, and 11-(methyl)henicosan-1-yl, which is substituted at the 2’-oxygen of a nucleoside of an oligonucleotide herein. 15 In some embodiments, the at least one C10-C26 hydrocarbon chain comprised in the in vivo delivery enhancing moiety may be conjugated to the remainder of the dsRNA agent via a linker or via a carrier or via an internucleotide phosphate linkage. In one embodiment, the at least one C10-C26 hydrocarbon chain is conjugated to the remainder of the dsRNA agent via a linker. In some embodiments, the linker may be a cleavable linker, i.e., the linker comprises a portion that can be 20 cleavable chemically or enzymatically. For example, amide linkages can be enzymatically cleavable. In some embodiments, the linker comprises –(CH2)n-NH-C(O)- or –(CH2)n-NH-C(O)-(CH2)2- C(COOH)-NH-C(O)-, wherein n is a number from 1 to 20, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20. In one embodiment, the linker comprises –(CH)2-O-(CH2CH2)-(O)- (CH2CH2)-NH-C(O)-. 25 In some embodiments, the linker may comprise a group selected from the group consisting of an ether, a thioether, a urea, a carbonate, an amine, an amide, a maleimide-thioether, a disulfide, a phosphodiester, a sulfonamide linkage, a product of a click reaction, and a carbamate. In some embodiments, the linker may be selected from the group consisting of -(CH2)nNH-; -C(O)(CH2)nNH-; -NR’’’’(CH2)nNH-, -C(O)-(CH2)n-C(O)-; -C(O)-(CH2)n-C(O)O-; -C(O)-O-; -C(O)-(CH2)n-NH-C(O)-;30 -C(O)-(CH2)n-; -C(O)-NH-; -C(O)-; -(CH2)n-C(O)-; -(CH2)n-C(O)O-; -(CH2)n-; and -(CH2)n-NH- C(O)-; wherein n is a number from 1 to 20; and R’’’’ is C1-C6 alkyl, e.g., C1 alkyl, C2 alkyl, C3 alkyl, C4 alkyl, C5 alkyl or C6 alkyl. In some embodiments, n may be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19 or 20. In some embodiments, the αvβ6 integrin targeting ligand is linked to the remainder of the 35 dsRNA agent as shown in the exemplary schematics below, wherein “2’-N6” refers to attachment of a lipophilic moiety (e.g., C22) at the 2’ position on the nucleotide at position 6 on the sense strand (counting from the 5’ end): 67 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 68 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 5 10
In some embodiments, the in vivo delivery enhancing moiety that may be conjugated to the 15 dsRNA agent of the disclosure is represented by the following structure: , 20
, 69 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 5
wherein the broken bond represents the bond to the remainder of the dsRNA agent (e.g., to a 2’- 10 oxygen of a nucleoside). The in vivo delivery enhancing moiety may be attached to the remainder of the dsRNA agent at a 2’ position on an internal nucleotide. The at least one in vivo delivery enhancing moiety may be conjugated to the dsRNA agent via a direct attachment to the ribosugar of the dsRNA agent, e.g., an antisense strand or a sense strand. 15 Alternatively, the at least one in vivo delivery enhancing moiety may be conjugated to the dsRNA agent via a linker or a carrier. In certain embodiments, at least one in vivo delivery enhancing moiety may be conjugated to the iRNA agent via one or more linkers (tethers). In one embodiment, the at least one in vivo delivery enhancing moiety is conjugated to the20 dsRNA agent via a linker containing an ether, thioether, urea, carbonate, amine, amide, maleimide- thioether, disulfide, phosphodiester, sulfonamide linkage, a product of a click reaction (e.g., a triazole from the azide-alkyne cycloaddition), or carbamate. 70 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In some embodiments, the in vivo delivery enhancing moiety and the targeting moiety are independently present within: (a) an internally-modified nucleosides such as, 5
(b) a modified internucleotide linkage such as, -OP(Y)(X)O-, wherein Y is O or S (e.g., O),
(c) a 5’-terminal modification such as 10
C(O), S(O)2, or -P(Y’)(OH)-O-; or (ii) -P(Y)(OH)O-RL or -C(O)N(H)RL, wherein Y is O or S; (d) a 3’-terminal modification such as -P(Y)(OH)-R3, wherein Y is O or S; and R3 is
15 wherein: B is an optionally modified nucleobase; 71 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO B1 is a nucleobase modified with a lipophilic moiety or a targeting moiety (e.g., a pyrimidine nucleobase modified at the 5-position); RL, RL1, and RL2 are each a group containing a lipophilic moiety or a targeting moiety; R2’ or R3’ may be any functional group that is an acceptable 2’-modification for a ribose 5 sugar. Examples of suitable R2’ or R3’groups include, but are not limited to, hydrogen, halogen (e.g., 2’-fluoro), hydroxy, 2’-O-alkyl (e.g., 2’-OMethyl), 2’-O-methoxyalkyl (e.g., 2’-O-methoxymethyl, 2’-O-methoxyethyl, or 2’-O-2-methoxypropanyl) modification, 2’-O-allyl modification, 2’-C-allyl modification, 2'-O-N-methylacetamido (2'-O-NMA, i.e. -OCH2C(O)N(H)Me) modification, 2'-O- dimethylaminoethoxyethyl (2'-O-DMAEOE) modification, 2'-O-aminopropyl (2'-O-AP) modification, 10 or 2'-ara-F modification. For instance, R2’ or R3’ may be H, OH, F, OMe, O-methoxyalkyl, O-allyl, O-N-methylacetamido, O-dimethylaminoethoxyethyl, or O-aminopropyl. In one embodiment, RL, RL1, and RL2 are each a group containing a lipophilic moiety, such as a saturated or unsaturated C22-hydrocarbon chain. In one embodiment, when RL comprises a lipophilic moiety, then RL can be selected from the group consisting of:
15 wherein integer m is 0-8 (e.g., 0; or 1-8; or 0-6; or 1; or 2; or 3; or 4; or 5; or 6; or 7; or 8); integer n is 1-21 (e.g., 1-12, 1-10, 1-8, 1-6, 1-4, or 1-2; or 2 or 3 or 4 or 5 or 6); W is C1-C4 alkyl (e.g., methyl, ethyl, propyl, isopropyl, butyl, isobutyl, or t-butyl); R and R’ are each independently H or C1-C4 alkyl (e.g., methyl, ethyl, propyl, isopropyl, or t- butyl); 20 G is G1 or a saturated or unsaturated C21 hydrocarbon chain (i.e., G together with the carbonyl to which it is attached may form a group with 22 carbons) (for instance, G may be a linear or branched C21 alkyl group), wherein G is optionally substituted with one or two groups selected from 72 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO the group consisting of halogen, -ORG, -SRG, -N(RG)2, -C(O)ORG, -OC(O)RG, -C(O)N(RG) 2, - N(RG)C(O)RG, -N(RG)C(O)ORG, -N(RG)SO2(RG), or -SO2N(RG)2, wherein each RG is independently hydrogen or C1-C6 alkyl (for instance, G is optionally substituted with a -ORG, -C(O)ORG, or - N(RG)C(O)RG); and 5 G1 is a saturated or unsaturated C22 hydrocarbon chain (for instance, G1 may be a linear or branched C22 alkyl group), wherein G1 is optionally substituted with one or two groups selected from the group consisting of halogen, -ORG1, -SRG1, -N(RG1)2, -C(O)ORG1, -OC(O)RG1, -C(O)N(RG1)2, - N(RG1)C(O)RG1, -N(RG1)C(O)ORG1, -N(RG1)SO2(RG1), or -SO2N(RG1)2, wherein each RG1 is independently hydrogen or C1-C6 alkyl (for instance, G1 is optionally substituted with a -ORG1, - 10 C(O)ORG1, or -N(RG1)C(O)RG1). Examples of RL include, but are not limited to the following structures:
Further examples of RL include, but are not limited to the following structures:
, 73 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
, In another embodiment, RL1 can be selected from the group consisting of,
In another embodiment, RL2 can be selected from the group consisting of the following 5 structures: 74 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
wherein integer m is 0-8 (for instance, m is 0; or m is 1-8; or m is 0-6; or m is 1; or 2; or 3; or 4; or 5; or 6; or 7; or 8); integer n is 1-21 (for instance, 1-12, 1-10, 1-8, 1-6, 1-4, or 1-2; or 2 or 3 or 4 or 5 or 6); 5 R and R’ are each independently H or an alkyl group such as a C1-C4 alkyl (e.g., methyl, ethyl, propyl, isopropyl, t-butyl); G is G1 or a saturated or unsaturated C21 hydrocarbon chain (i.e., G together with the carbonyl to which it is attached may form a group with 22 carbons) (for instance, G may be a linear or branched C21 alkyl group), wherein G is optionally substituted with one or two groups selected from10 the group consisting of halogen, -ORG, -SRG, -N(RG)2, -C(O)ORG, -OC(O)RG, -C(O)N(RG) 2, - N(RG)C(O)RG, -N(RG)C(O)ORG, -N(RG)SO2(RG), or -SO2N(RG)2, wherein each RG is independently hydrogen or C1-C6 alkyl (for instance, G is optionally substituted with a -ORG, -C(O)ORG, or - N(RG)C(O)RG); and G1 is a saturated or unsaturated C22 hydrocarbon chain (for instance, G1 may be a linear or 15 branched C22 alkyl group), wherein G1 is optionally substituted with one or two groups selected from the group consisting of halogen, -ORG1, -SRG1, -N(RG1)2, -C(O)ORG1, -OC(O)RG1, -C(O)N(RG1)2, - N(RG1)C(O)RG1, -N(RG1)C(O)ORG1, -N(RG1)SO2(RG1), or -SO2N(RG1)2, wherein each RG1 is independently hydrogen or C1-C6 alkyl (for instance, G1 is optionally substituted with a -ORG1, - C(O)ORG1, or -N(RG1)C(O)RG1). 20 Examples of RL2 include, but are not limited to the following structures:
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In some embodiments, B1 is a nucleobase modified with a G or G1 group, wherein G and G1 are as defined above (e.g., a pyrimidine nucleobase modified at the 5’-position with a group comprising G or G1). Examples of B1 include, but are not limited to,
. 5 In some embodiments, in vivo delivery enhancing moiety is present within a modified nucleoside of the formula:
wherein: B is an optionally modified nucleobase; 10 G3 is a saturated or unsaturated C1-20 hydrocarbon group (e.g., C1-6 alkylene; C2-6 alkylene; or hexylene); LK is a linking group such as -O-, -N(H)-, -S-, -S-S-, -C(O)O-, OC(O)-, -C(O)N(H)-, - N(H)C(O), -OC(O)N(H)-, -N(H)C(O)O-, -S(O)2-, -S(O)2O-, -S(O)2N(H)-, -P(O)(OH)O-, - OP(O)(OH)-, -P(S)(OH)O-, -OP(S)(OH)-, -OP(O)(OH)O-, -OP(S)(OH)O-, 15 G2 is a saturated or unsaturated C21-C22 hydrocarbon group; and RG is hydrogen, hydroxy, amino, -COOH, or -C(O)NH2. For example, when LK contains a carbonyl attached to G2 (e.g., (-N(H)C(O)- or -OC(O)-), then G2 is a C21 hydrocarbon group; and when LK does not contain a carbonyl attached to G2, then G2 is a C22 hydrocarbon group. In one embodiment, RG is hydrogen. In another embodiment, RG is OH, 76 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In one embodiment, RG is COOH. In another embodiment, RG is CONH2. In one embodiment, RG is amino. In the above structures for the lipophilic monomers, the monomers may also contain one or more asymmetric centers and thus occur as racemates and racemic mixtures, single enantiomers, 5 individual diastereomers and diastereomeric mixtures. All such isomeric forms of the monomers are expressly included. Further, in the preceding and throughout the present application, where a modified internucleotide linkage is shown with substituent atoms fully described at the phosphorous atom, e.g.,
, where C’ is the 2’-carbon or 3’-carbon atom of a ribose ring, it is understood that the oxygen having the broken bond is the 5'-oxygen of the subsequent nucleotide. 10 In one embodiment, the in vivo delivery enhancing moiety is present within a modified nucleoside of the formula:
. In one embodiment, the in vivo delivery enhancing moiety is present within a modified nucleoside of the formula:
. In one embodiment, the in vivo delivery enhancing moiety is present within a modified 15 nucleoside of the formula:
. In one embodiment, the in vivo delivery enhancing moiety is present within a modified nucleoside of the formula:
. In some embodiments, the in vivo delivery enhancing moiety is present within a modified nucleoside of the formula:
20 1-10, 1-8, 1-6, 1-4, or 1-2, or 2 or 3 or 4 or 5 or 6); G is a C22 hydrocarbon chain, optionally substituted with one or two groups selected from the group consisting of halogen, -ORG, -SRG, - N(RG)2, -C(O)ORG, -OC(O)RG, -C(O)N(RG)2, -N(RG)C(O)RG, -N(RG)C(O)ORG, -N(RG)SO2(RG), or - 77 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO SO2N(RG)2, wherein each RG is independently hydrogen or C1-C6 alkyl; and nucleobase B is a modified or unmodified nucleobase. In one embodiment, n is 1. In one embodiment, n is 2-6. In one embodiment, n is 6. In one embodiment, G is C22 alkyl chain. In some embodiments, the in vivo delivery enhancing moiety is present within a modified 5 nucleoside of the formula:
, wherein n is an integer of 1-21, for instance, 1-12, 1- 10, 1-8, 1-6, 1-4, or 1-2, or 2 or 3 or 4 or 5 or 6); G is a C22 hydrocarbon chain, optionally substituted with one or two groups selected from the group consisting of halogen, -ORG, -SRG, -N(RG)2, - C(O)ORG, -OC(O)RG, -C(O)N(RG) 2, -N(RG)C(O)RG, -N(RG)C(O)ORG, -N(RG)SO2(RG), or - SO2N(RG)2, wherein each RG is independently hydrogen or C1-C6 alkyl; and nucleobase B is a 10 modified or unmodified nucleobase. In one embodiment, n is 1. In one embodiment, n is 2-6. In one embodiment, n is 6. In one embodiment, G is C22 alkyl chain. In one embodiment, the in vivo delivery enhancing moiety is present within a modified nucleoside of the formula:
. In one embodiment, the in vivo delivery enhancing moiety is present within a modified 15 nucleoside of the formula:
. In one embodiment, the in vivo delivery enhancing moiety is present within a modified nucleoside of the formula:
. In one embodiment, the in vivo delivery enhancing moiety is present within a modified
. 20 In some embodiments, the in vivo delivery enhancing moiety is present within a modified internucleotide linkage of the form, -OP(Y)(X)O-, wherein Y is O or S (e.g., O), and X is -N(H)(RL1), wherein RL1 is -G1 or S(O)2-G1, each as defined above, wherein the phosphorous atom in the internucleotide linkage is optionally enriched in the Sp or Rp isomer, or is racemic. 78 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In some embodiments, the in vivo delivery enhancing moiety is present within a modified internucleotide linkage of the form, -OP(O)(X)O-, wherein X is -N(H)(RL1), wherein RL1 is
, wherein the phosphorous atom in the internucleotide linkage is optionally enriched in the Sp or Rp isomer, or is racemic. 5 In some embodiments, the in vivo delivery enhancing moiety is present within a a modified internucleotide linkage of the form,
, wherein the 3’-O is from the preceding nucleoside and the 5’-O is from the subsequent nucleoside, and wherein the phosphorous atom in the internucleotide linkage is optionally enriched in the Sp or Rp isomer, or is racemic. In certain embodiments, the preceding nucleotide contains a 2’-fluoro modification. In certain 10 embodiments, the preceding nucleotide contains a 2’-O-methyl modification. In certain embodiments, the preceding nucleotide contains a 2’-H modification. In some embodiments, the in vivo delivery enhancing moiety is present within a a modified internucleotide linkage of the form,
, wherein the 3’-O is from the preceding nucleoside and the 5’-O is from the subsequent nucleoside, and wherein the phosphorous 15 atom in the internucleotide linkage is optionally enriched in the Sp or Rp isomer, or is racemic. In certain embodiments, the preceding nucleotide contains a 2’-fluoro modification. In certain embodiments, the preceding nucleotide contains a 2’-O-methyl modification. In certain embodiments, the preceding nucleotide contains a 2’-H modification. In some embodiments, the in vivo delivery enhancing moiety is present within a 20 a modified internucleotide linkage of the form, -OP(Y)(X)O-, whereinY is O or S and X is
, wherein G1 is defined above, such
. In some embodiments, in vivo delivery enhancing moiety is conjugated to the 3’-end or 5’- end of one of the sense and antisense strands via a direct bond or through a carrier or linker. In some embodiments, in vivo delivery enhancing moiety is conjugated to the 3’-end of the sense or antisense 25 strand via a direct bond or through a carrier or linker. In some embodiments, in vivo delivery enhancing moiety is conjugated to the 5’-end of the sense or antisense strand via a direct bond or through a carrier or linker. 79 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In some embodiments, in vivo delivery enhancing moiety is conjugated to the 5’-end of one of
the sense and antisense strands and is of the formula: , or a salt thereof, wherein X is O or S (e.g., S); L is a divalent linking group (e.g., C1-20 alkyl or C1-10 alkyl-S-S-C1-10 alkyl). In one embodiment, in vivo delivery enhancing moiety is conjugated to the 5’-end of one of the 5 sense and antisense strands and is of the formula
, or a salt thereof, wherein X is O or S (e.g., S). In these embodiments, Rligand is selected from the groups listed in Table R-1. Table R-1. An exemplary list of groups for Rligand
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In one embodiment, in vivo delivery enhancing moiety is bonded to the 5’-oxygen of the 5’- terminal nucleotide, and is of the formula 5
, In one embodiment, in vivo delivery enhancing moiety is bonded to the 5’-oxygen of the 5’- terminal nucleotide, and is of the formula -P(Y)(OH)-R5, wherein Y is O or S and R5 is:
. 10 In one embodiment, in vivo delivery enhancing moiety is bonded to the 3’-oxygen of the 3’- terminal nucleotide, and is of the formula -P(Y)(OH)-R3, wherein Y is O or S and R3 is:
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Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In some embodiments, in vivo delivery enhancing moiety is conjugated to the 3’-end or 5’- end of one of the sense and antisense strands via a carrier or linker, and the carrier or linker is an inverted abasic nucleotide, such as an inverted abasic deoxyribonucleotide or an inverted abasic ribonucleotide, each connected to the remainder of the oligonucleotide via a phosphodiester (PO) or 5 phosphorothioate (PS) linkage. Examples include, but are not limited to,
Q2 is a bond, C(O), S(O)2, or -P(Y’)(OH)-O-, Y and Y’ are independently O or S; and RL is as defined above. In some embodiments, in vivo delivery enhancing moiety is bonded to the 5’-oxygen of the 5’-terminal nucleotide and is of the formula
salt thereof, wherein each10 X is independently O or S (e.g., each is S); Rligand is selected from the groups listed in Table R-1; and L is a divalent linking group (e.g., C1-20 alkyl or C1-10 alkyl-S-S-C1-10 alkyl). For example, in vivo delivery enhancing moiety is bonded to the 5’-oxygen of the 5’-terminal nucleotide, and is of the formula
salt thereof, wherein each X is independently O or S 15 (e.g., each is S) and Rligand is selected from the groups listed in Table R-1. In some embodiments, Rligand is selected from the groups listed in Table R-2.
In some embodiments, in vivo delivery enhancing moiety is bonded to the 5’-oxygen of the 5’-terminal nucleotide, and is of the formula 82 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
salt thereof, wherein each X is independently O or S (e.g., each is S) and Rligand is selected from the groups listed in Table R-1, and L is a divalent linking group (e.g., C1-20 alkyl or C1-10 alkyl-S-S-C1-10 alkyl. In one embodiment, in vivo delivery enhancing moiety is bonded to the 5’-oxygen of the 5’- 5 terminal nucleotide, and is of the formula
salt thereof, wherein each X is O or S (e.g., each is S) and Rligand is selected from the groups listed in Table R-1. In some embodiments, Rligand is selected from the groups listed in Table R-2. In another embodiment, RL, RL1, and RL2 are each a group containing at least one targeting 10 moiety, such as an αvβ6 integrin targeting ligand described herein. In one embodiment, the targeting moiety can be selected from:
In one embodiment, the broken bond is connected to a group of the formula, **-L-ZZ-L’- , wherein ** represents the bond to the targeting ligand. 83 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO ZZ is a bridging group that may be formed, for example, by reaction of two functional groups, and can be selected from the group consisting of, -C(H)=N-, -C(H)=N-N(H)-, -C(H)=N-N(H)C(O)-, - C(H)=N-N(R)-, -C(H)=N-N(R)C(O)-, -C(H)=N-O-, -C(O)N(H)-, -C(O)N(H)-N(H)-, -C(O)N(H)- N(R)-, -C(O)N(R)-, -C(O)O-, -C(O)S-, -C(O)N(H)-, -C(O)N(H)-N(H)-, -C(O)N(H)-N(R)-, - 5 C(O)N(R)-, -C(S)N(H)-, -C(S)N(R)-, -C(S)O-, -C(S)S-, -C(S)N(H)-, -C(S)N(R)-, -N(H)C(O)N(H)-, - N(H)C(O)N(R)-, -N(H)C(O)O-, -N(H)C(O)S-, -N(H)C(S)N(H)-, -N(H)C(S)N(R)-, -N(H)C(S)O-, - N(H)C(S)S-, -S-S-, -CH2-S-, -CH2-O-, -CH2-N(H)-, -CH=CH-, and a click adduct, for example, selected from the following structures:
, , , , , , , 10 butyl, or hexyl); and RLa is hydrogen, C1-10alkyl (e.g., methyl, ethyl, propyl, isopropyl, t-butyl, isobutyl, butyl, or hexyl), C3-8cycloalkyl, 3-8 membered heterocyclyl, aryl (e.g., phenyl), or heteroaryl (e.g., 2-pyridyl). The term “click adduct,” as used herein, include those adducts formed by a copper(I)- catalyzed azide-alkyne cycloaddition reaction, a strain-promoted azide-alkyne cycloaddition, a strain- 15 promoted azide-trans-cycloalkene cycloaddition, and a thiol-maleimide Michael-addition reaction 84 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO including, for example, (i) an azide with a terminal alkyne or cycloalkyne (e.g. cyclooctyne, BCN, or DBCO); (ii) a tetrazine with a terminal alkyne or cycloalkyne (e.g. cyclooctyne); (iii) a thiol and maleimide (with or without hydrolysis of the product). In some embodiments, L and L’ are independently one of: 5 (a) -L1-[G-L2]q-G-L3-* wherein q is 0 or an integer selected from 1-10; (b) -L1-G-L2-G-L3-*; (c) -L1-G-L3-*; (d) -G-L3-*; (e) -L1-G-*; or 10 (f) -G-*. wherein in each of (a) -(f), * represent the bond to ZZ; L1 is selected from one of the following groups: (a) a bond, C(O), C(S), C(NRN), S(O)2, P(O)(OH), or P(S)(OH), wherein and RN is hydrogen or C1-6alkyl; 15 (b) a bond, C(O), P(O)(OH), or P(S)(OH); (c) a bond; (d) C(O); (e) P(O)(OH); or (f) P(S)(OH); 20 each L2 and L3 is independently selected from one of the following groups: (a) -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(RN)C(O)-, -OC(O)O-, -OC(O)N(RN)-, - N(RN)C(O)O-, -N(RN)C(O)N(RN)-, -OP(O)(OH)O- ,-OP(S)(OH)O-, -O-, and -N(RN)- , wherein each RN is independently hydrogen or C1-6alkyl; or (b) -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(RN)C(O)-, -OC(O)N(RN)-, -N(RN)C(O)O-,- 25 N(RN)C(O)N(RN)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; or (c) -C(O)N(RN)-, -N(RN)C(O)-, -OC(O)N(RN)-, -N(RN)C(O)O-, -N(RN)C(O)N(RN)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; or (d) -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(RN)C(O)-, -O-, and -N(RN)-, wherein each RN is 30 independently hydrogen or C1-6alkyl; or (e) -C(O)N(RN)-, -N(RN)C(O)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; and each G is independently selected from one of the following groups: (a) C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, 35 aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups; or 85 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO (b) C1-10alkyl, optionally substituted with 1, 2, or 3 R groups (e.g., 1 or 2 R groups; or 1 R group); or wherein each R group is independently selected from the group consisting of R’, C1-6alkyl, C1- 6haloalkyl, C2-6alkenyl, C2-6alkynyl, C3-8cycloalkyl, heterocyclyl, aryl, heteroaryl, C3- 5 8cycloalkylC1-6alkyl, heterocyclylC1-6alkyl, aryl C1-6alkyl, and heteroarylC1-6alkyl, each of which, other than R’, is optionally substituted with 1, 2, or 3 R’ groups, wherein each R’ is independently halogen, cyano, azido, nitro, -N(Rb)2, -O(Ra), -S(R0), -C(O)OR0, C(O)R0, -C(O)N(R0)2, -C(NR0)OR0, -C(NR0)R0, -C(NR0)N(R0)2, -C(S)OR0, -C(S)R0, -C(S)N( R0)2, -S(O)2R0, -S(O)2OR0, -S(O)2N(R0)2, -N(R0)C(O)OR0, -N(R0)C(O)R0, -N(R0)C(O)N(R0)2,10 -N(R0)S(O)2R0, -N(R0)S(O)2OR0, -N(R0)S(O)2N(R0)2, -OC(O)OR0, -OC(O)R0, - OC(O)N(R0)2, -OS(O)2R0, -OS(O)2OR0, -OS(O)2N(R0)2, or -SC(O)R0, wherein each R0 is independently hydrogen or C1-6alkyl; each Ra is independently hydrogen, C1-6alkyl, or a hydroxyl protecting group; and each Rb is independently hydrogen, C1-6alkyl, or a nitrogen protecting group. 15 In one embodiment of L or L’, q is 0, 1, 2, 3, 4, or 5. In another embodiment of L or L’, q is 0, 1, 2, 3, or 4. In another embodiment of L or L’, q is 0, 1, 2, or 3. In another embodiment of L or L’, q is 0, 1, or 2. In another embodiment of L or L’, q is 1, 2, 3, 4, or 5, In another embodiment of L or L’, q is 1, 2, 3, or 4. In another embodiment of L or L’, q is 1, 2, or 3. In another embodiment of L or L’, q is 1 or 2. In another embodiment of L or L’, q is 4. In another embodiment of L or L’, q is 3. In 20 another embodiment of L or L’, q is 2. In some embodiments, L is one of: (a)
, wherein k is an integer from 1 to 10; L1 is bond, C(O), C(S), C(NRN), S(O)2, P(O)(OH), or P(S)(OH) (e.g., L1 is a bond, C(O), P(O)(OH), or P(S)(OH)); and RN is hydrogen or C1-6alkyl; 25 (b)
, wherein k is an integer from 1 to 10; or an integer from 2 to 10; or an integer from 3 to 10; or an integer from 4 to 10; or an integer from 5 to 10; or an integer from 5 to 9; or an integer from 5 to 8; or an integer from 5 to 7; (c)
, wherein t is an integer from 0 to 10 (e.g., an integer from 1 to 5; or 1; or 2; or 3); 30 (d)
, wherein t is an integer from 0 to 10 (e.g., an integer from 1 to 5 or 1; or 2; or 3); a is an integer from 1 to 3; and s and s’ are each independently an integer from 1 to 86 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 24 (e.g., an integer from 1 to 16; an integer from 1 to 10; an integer from 3 to 10; an integer from 3 to 7; or an integer from 4 to 6); (e)
wherein and s, s’, and s’’ are independently is an integer from 1 to 24 (e.g., an integer from 1 to 16, an integer from 1 to 10, 5 an integer from 3 to 10, an integer from 3 to 7, or an integer from 4 to 6);
independently is an integer from 1 to 20 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6); and w is an integer from 1 to 20 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an 10 integer from 3 to 7 or an integer from 4 to 6); or and wherein in each of the preceding embodiments of L, * represents the bond to ZZ. In some embodiments, L’ is one of: (a)*-G-L1-, wherein L1 is a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); and G is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, each of which is optionally substituted with 1, 2, 3, or 4 R groups; 15 or L1 is a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); and G is C1-10alkyl; (b)*-G-[L2-G]q-L1-, wherein L1 is a bond, CH2, C(O), S(O)2, P(O)(OH), or P(S)(OH); each L2 is independently -A-B-A-; each A is independently a bond, -O-, -S-, or -N(RN)-, wherein RN is hydrogen or C1-6alkyl each B is independently a bond, CH2, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); each G is independently C1-10alkyl; 20 (c) -[G-L2]q-G-L3-*, wherein each L2 is independently a bond, C(O)O, OC(O), C(O)(NRN), N(RN)C(O), OP(O)(OH)O, or OP(S)(OH)O, wherein each RN is independently hydrogen or C1-6alkyl; each G is independently C1-10alkyl or C2-10alkenyl, each of which is optionally substituted with 1 or 2 R groups; or each L2 is independently C(O)(NRN), N(RN)C(O), OP(O)(OH)O, or OP(S)(OH)O wherein each RN is independently hydrogen or C1-6alkyl; 25 each G is independently C1-10alkyl, each of which is optionally substituted with 1 or 2 R groups; (d) *-L3-G-L1-, wherein L3 is -C(O)O- or C(O)N(RN)-, wherein RN is hydrogen or C1-6alkyl; L1 is - OP(O)(OH)O- or -OP(S)(OH)O-; and G is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3- 10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally 30 substituted with 1, 2, or 3 R groups (e.g., 1 or no R groups); (e) -L1-[G-L2]q-G-*, wherein L1 is a bond or -B-A-; each L2 is independently a bond, C(O)O, OC(O), C(O)(NRN), N(RN)C(O), OP(O)(OH)O, or OP(S)(OH)O, wherein each RN is 87 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO independently hydrogen or C1-6alkyl; and each G is independently C1-10alkyl or C2-10alkenyl, each of which is optionally substituted with 1 or 2 R groups; (f) -[G-L2]q-G-*, wherein each L2 is independently C(O)(NRN) , N(RN)C(O), OP(O)(OH)O, or OP(S)(OH)O wherein each RN is independently hydrogen or C1-6alkyl; and each G is 5 independently C1-10alkyl, each of which is optionally substituted with 1 or 2 R groups; (g) -C2-30alkyl-*, such as -C5-20alkyl-* or -C10-20alkyl-*; (h) -C1-10alkyl-*, optionally substituted with 1 or 2 R groups; (i) -C(O)-C2-30alkyl-*, such as -C(O)-C5-20alkyl-* or -C(O)-C10-20alkyl-*; wherein in each of (a) - (i), * is the bond to ZZ, and q, when present, is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 10 (e.g., an integer from 1 to 8, an integer from 1 to 5, or an integer from 1 to 3; or 0, 1, 2, or 3; or 0, 1, or 2; or 0 or 1; or 0; or 1; or 2). Examples of RL and RL1 that comprise a targeting ligand include, but are not limited to the following structures:
15 Additional examples of RL and RL1 that comprise a targeting ligand include, but are not limited to the following structures:
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Examples of RL2 that comprise a targeting ligand include, but are not limited to the following structures:
Additional examples of RL2 that comprise a targeting ligand include, but are not limited to the 5 following structures:
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In one embodiment of any of the preceding structures comprising a targeting moiety, each RX 5
, . In some embodiments, targeting moiety is bonded to the 3’-oxygen of the 3’-terminal nucleotide, and is of the formula -P(Y)(OH)-R3, wherein Y is O or S and R3 is:
. 10 In some embodiments, targeting moiety is bonded to the 5’-oxygen of the 5’-terminal nucleotide, and is of the formula -P(Y)(OH)-R5, wherein Y is O or S and R5 is: 90 ME1\53453057.v1
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. In another embodiment, multiple targeting ligands may be connected to a branched multivalent linker In certain embodiments, RL, RL1, and RL2 can comprise a branched linking group (Δ) capable 5 of supporting multiple targeting ligands (e.g., at least 2; or 2-8; or 2-6; or 2-4; or 2; or 3). For example, in one embodiment, the mutiple targeting moieties can be connected through an RL, RL1, and RL2 of the form, (RX-L-ZZ-)z-Δ-T- , wherein each RX is a targeting moiety; z is at least 2; or 2-8; or 2-6; or 2-4; or 2; or 3, 10 T is -L’-T’-**, wherein ** is the bond to Δ, and T’ is O, S, N(H), C(O), S(O)2, C(O)N(H), N(H)C(O), OC(O), OC(O), -P(O)(OH)-, -P(S)(OH)-, -OP(O)(OH)-, -OP(S)(OH)-, -P(O)(OH)O-, - P(S)(OH)O-, -OP(O)(OH)O-, or -OP(S)(OH)O-; and L , L’, and ZZ are each as described above, and each * represents the bond to the targeting ligand. 15 In some embodiments, T is selected from the following, wherein ** is the bond to Δ: (a) -C(O)-X1-L5-X2-C(O)-**, wherein X1 and X2 are each independently C1-10alkyl; or C2-10alkyl; or C4-10alkyl; or C6-10alkyl; or C2-8alkyl; or C2-6alkyl; or C2-4alkyl; (b) -C(O)-C2-20alkyl-C(O)-**, such as -C(O)-C2-12alkyl-C(O)-**, (c) -C(O)-C6-20alkyl-C(O)-**, such as -C(O)-C6-12alkyl-C(O)-**, 20 (d) -C(O)-C10alkyl-C(O)-** and (e) -C(O)-CH2CH2-C(O)-**, wherein each L5 is a bond, ZZ, or - A1-B1-A1- (e.g., a bond, -B1-A1- or -A1-B1-; or a bond; or ZZ), wherein each A1 is independently a bond, -O-, -S-, or -N(RN1)-, wherein RN1 is independently hydrogen or C1-6alkyl; each B1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); 25 and ZZ is as described above (such as -C(O)N(H)-, N(H)C(O)-, -OP(O)(OH)O-, -OP(S)(OH)O-, or a click adduct). In some embodiments, T is selected from the following, ** is the bond to Δ: (f) -N(H)C(O)-C2-20alkyl-C(O)-**, (g) - N(H)C(O)-C6-20alkyl-C(O)-**, such as - N(H)C(O)-C6-12alkyl-C(O)-**, 30 (h) - N(H)C(O)-C10alkyl-C(O)-**, (i) -C(O)-C2-20alkyl-C(O)N(H)-**, 91 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO (j) -C(O)-C6-20alkyl-C(O)N(H)-**, (k) -C(O)-C6-12alkyl-C(O)N(H)-**, (l) -C(O)-C10alkyl-C(O)N(H)-**, (m) -N(H)C(O)-C2-20alkyl-C(O)N(H)-**, 5 (n) - N(H)C(O)-C6-20alkyl-C(O)N(H)-**, (o) - N(H)C(O)-C6-12alkyl-C(O)N(H)-**, and (p) - N(H)C(O)-C10alkyl-C(O)N(H)-**. In some embodiments, T is selected from the following, ** is the bond to Δ: (a) -N(H)C(O)-X3-ZZ-X4-C(O)-**, 10 (b) -C(O)-X3-ZZ-X4-C(O)N(H)-**, (c) N(H)C(O)-X3-ZZ- X4-C(O)N(H)-**, wherein X3 and X4 are independently C2-12alkyl; or C4-10alkyl; or C6-10alkyl; or C4-8alkyl; and ZZ is as described above (such as -C(O)N(H)-, N(H)C(O)-, -OP(O)(OH)O-, -OP(S)(OH)O-, or a click adduct). In some embodiments, , T is selected from the following 15 (w) -L6-[G5-O]q5-G5-L4-**, wherein L4 and L6 are independently -A1-B1-A1-, wherein each A1 is independently a bond, -O-, -S-, or -N(RN1)-, wherein RN1 is hydrogen or C1-6alkyl; each B1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); each G5 is independently C1-10alkyl; (x) -C(O)-[CH2CH2-O]q5-G5-L4-**, L4 is -A1-B1-A1-, wherein each A1 is independently a 20 bond, -O-, -S-, or -N(RN1)-, wherein RN1 is hydrogen or C1-6alkyl; each B1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); G5 is C1-10alkyl. (y) -C(O)-[CH2CH2-O]q5-G5-L4-**, L4 is -A1-B1 or -B1-A1-, wherein each A1 is independently -O- or -N(H)-, and each B1 is independently C(O), G5 is C1-10alkyl (e.g., C2- 10alkyl or C2-6alkyl); and 25 (z) -C(O)-[CH2CH2-O]q5- C2-10alkyl-C(O)N(H)-**; wherein in each of the preceding ** is the bond to Δ, and q5, when present, is an integer selected from 1 to 20 (e.g., 1 to 10, or 2 to 10; or 2 – 8; or 1; or 2; or 3; or 4.) Examples of branched linking group (Δ) include, but are not limited to,
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wherein the broken bond is the bond to L’. Examples of -T1-Δ- include, but are not limited to,
,
5 Examples of RL and RL1 that comprise a branched linker to a targeting ligand include, but are not limited to the following structures:
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Examples of branched RL and RL1 include, but are not limited to, the following structures: 5
94 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO Examples of branched RL2 include, but are not limited to, the following structures: 5
. In some embodiments, targeting moiety is bonded to the 3’-oxygen of the 3’-terminal nucleotide, and is of the formula -P(Y)(OH)-R3, wherein Y is O or S and R3 is:
, wherein , r is an integer 10 selected from 1 - 10 (e.g., r is 7); and each R is:
. In some embodiments, targeting moiety is bonded to the 3’-oxygen of the 3’-terminal nucleotide, and is of the formula -P(Y)(OH)-R3, wherein Y is O or S and R3 is: 95 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
. In some embodiments, targeting moiety is bonded to the 3’-oxygen of the 3’-terminal nucleotide, and is of the formula -P(Y)(OH)-R3, wherein Y is O or S and R3 is:
. 5 In some embodiments, targeting moiety is bonded to the 5’-oxygen of the 5’-terminal nucleotide, and is of the formula -P(Y)(OH)-R5, wherein Y is O or S and R5 is:
selected from 1 - 10 (e.g., r is 7); and each R is:
, wherein RX is a targeting ligand. 10 In some embodiments, targeting moiety is bonded to the 5’-oxygen of the 5’-terminal nucleotide, and is of the formula -P(Y)(OH)-R5, wherein Y is O or S and R5 is:
ligand. 96 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In one embodiment of any of the preceding structures comprising a targeting moiety, each RX is an integrin-receptor targeting ligand such as,
. In some embodiments, the dsRNA agent comprises a double-stranded region formed between the sense and antisense strands and optionally one or two single-stranded non-loop overhang, and 5 wherein the one or more lipophilic moieties are conjugated to either the double-stranded region or the non-loop overhang. In some embodiments, the dsRNA agent does not contain a loop (e.g., stem loop) region. In some embodiments, the dsRNA agent contains a loop (e.g., stem loop) region, and the one or more lipophilic moieties are not conjugated to the loop (e.g., stem loop) region. In some embodiments, the dsRNA agent comprises a sense strand of 10 to 53 nucleotides in 10 length, in which the sense strand forms a duplex region with the antisense strand. For instance, the sense strand may be 10 to 49, 12 to 49, 12 to 45, 12 to 42, 12 to 40, 15 to 49, 15 to 45, 15 to 42, 15 to 40, 15 to 38, or 15 to 36 nucleotides in length. In some embodiments, the duplex region is at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21 nucleotides in length. In some embodiments, the region of complementarity to the target sequence is at least 19 contiguous 15 nucleotides in length. In some embodiments, the sense strand comprises at its 3′-end a stem-loop set forth as: S1-L- S2, in which S1 is complementary to S2, and in which L forms a loop between S1 and S2. In some embodiments, the first 17 to 25 nucleotides counting from 5’ end of the sense strand forms a duplex region with the antisense strand, and the last 11 to 28 counting from 5’ end of the 20 sense strand forms a 3′-end a stem-loop set forth as: S1-L-S2. In some embodiments, the length of the stem loop S1-L-S2 is 11 to 28, 13 to 26, or 15 to 24 nucleotides in length. In one embodiment, the stem loop S1-L-S2 is 16 nucleotides in length. In some embodiments, the stem loop S1-L-S2 comprises a sequence of 5’-GCAGCCGAAAGGCUGC-3’ (SEQ ID NO: 47). 25 In some embodiments, L is at least 3, 4, or 5 nucleotides in length. In some embodiments, L comprises a sequence of GAAA. In some embodiments, the sense strand is 36 nucleotides in length, the first 20 nucleotide counting from 5’ end of the sense strand forms a duplex region with the antisense strand, and the last 16 nucleotides forms a stem loop S1-L-S2. In one embodiment, the 16-nucleotide stem loop S1-L-S2 30 has the sequence of 5’-GCAGCCGAAAGGCUGC-3’ (SEQ ID NO: 161), wherein L is GAAA. 97 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In some embodiments, the one or more lipophilic moieties are conjugated to a non-terminal position of the sense strand. In some embodiments, the one or more lipophilic moieties are conjugated to one or more nucleotides of the stem loop S1-L-S2. In some embodiments, the one or more lipophilic moieties are 5 conjugated to one or more nucleotides of the loop L. In some embodiments, S1 and S2 are complementary and contain 4-10 nucleotides, e.g., S1 and S2 each contain 6 complementary nucleotides. In some embodiments, S1 and S2 are complementary and contain 4-10 nucleotides and L is GAAA, e.g., S1 and S2 each contain 6 complementary nucleotides and L is GAAA. 10 In some embodiments, the one or more lipophilic moieties containing one or more saturated or unsaturated C22 hydrocarbon chains are conjugated to one or more internal positions on at least one strand of the dsRNA agent. Dual Conjugation 15 In another embodiment, in vivo delivery enhancing moiety is connected in series with a targeting moiety, e.g., αvβ6 integrin targeting ligand, as described herein. For example, a sense or antisense strand can contain a series modification at the 3’-end or 5’-end of the oligonucleotide, 20
. such that one of L1 and L2 comprises the in vivo delivery enhancing moiety and the other comprises the targeting moiety, e.g., αvβ6 integrin targeting ligand as described herein. In one embodiment, the series modification is of the form, , wherein Q is selected from
wherein RL2 is according to any preceding 25 embodiment, wherein one of the broken bonds connects to a 5’-oxygen of a nucleoside or a 3’-oxygen of a nucleoside and the other connects to a 5’-terminal or 3’-terminal modification as described herein. 98 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In another example, a sense or antisense strand can contain a series modification of the form,
wherein RL2 is according to any preceding embodiment, each Y is independently O or S; one of the broken bonds connects to a 5’-oxygen of a nucleoside or a 3’-oxygen of a nucleoside and the other connects any of 5 the 5’-terminal modifications described above or 3’-terminal modifications described above. In one embodiment, a sense or antisense strand can contain a series modification of the form,
the broken bond connects to the 5’-oxygen of a 5’-terminal nucleoside; each Y is independently O or S; 10 one of R51 and R52 comprises a lipophilic group (e.g., an in vivo delivery enhancing moiety) and the other comprises a second ligand moiety (e.g., a targeting moiety, such as a αvβ6 integrin targeting ligand as described herein). In another embodiment, a sense or antisense strand can contain a series modification of the
15 the broken bond connects to the 5’-oxygen of a 5’-terminal nucleoside; each Y is independently O or S; one of R51 and R52 comprises a lipophilic group (e.g., an in vivo delivery enhancing moiety, such as any of RL or RL2 above) and the other comprises a second ligand moiety (e.g., a targeting moiety). 20 For example, an oligonucleotide may have a series modification at the 5’-end of the formula: 99 ME1\53453057.v1
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, wherein each Y is independently O or S. In another embodiment, a sense or antisense strand can contain a series modification of the 5 form,
, wherein the broken bond connects to the 3’-oxygen of a 3’-terminal nucleoside; each Y is independently O or S; one of R31 and R32 comprises a lipophilic group (e.g., an in vivo delivery enhancing moiety, such as any of RL2 above) and the other comprises a second ligand moiety (e.g., a targeting ligand). 10 For example an oligonucleotide may have a series modification at the 3’-end of the formula: 100 ME1\53453057.v1
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, wherein each Y is independently O or S. 5 In another embodiment, a sense or antisense strand can contain two different ligand modifications, one at the 3'-end of the strand and the other at the 5'-end of the strand:
such that one of L1 and L2 comprises the in vivo delivery enhancing moiety and the other comprises the targeting moiety, such as a αvβ6 integrin targeting ligand as described herein. 10 In another embodiment, a sense or antisense strand can contain two different ligand modifications, one is an internal modified nuceloside or modified internucleotide linkage of the strand and the other at the 3’-end or 5'-end of the strand: 15
such that one of L1 and L2 comprises the in vivo delivery enhancing moiety and the other comprises the targeting moiety, such as a αvβ6 integrin targeting ligand as described herein. The modified 101 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO nucleoside represented by L1 can be located at a position in the strand selected from positions 2 to n- 1, where the strand contains n nucleotides (e.g., n-1 is 20 when n is 21). For example, when L1 is at position 6, then segment (1) of the strand contains 5 nucleotides and segment (2) contains the remainder of the nucleotides within the strand. “Position” herein, when referring to a modified 5 nucleotide, nucleoside, or internucleotide linkage is counted from the 5’-end of the strand, for example, position 6 includes the 6th nucleotide from the 5’-end of the strand and the 6th internucleotide linkage counting from the 5’-end of the strand. In one embodiment, L1 comprises the in vivo delivery enhancing moiety and a sense or antisense strand can be represented by one of:
10 wherein B is an optionally modified nucleobase (e.g., A, C, G, U, or T); RL or RL1 comprises the in vivo delivery enhancing moiety, L2 comprises the targeting moiety. In one embodiment, RL is selected from the group consisting of:
In one embodiment, RL1 is selected from the group consisting of:
and 15
. 1. Linkers/Tethers Linkers/Tethers are connected to the at least one in vivo delivery enhancing moiety at a “tethering attachment point (TAP).” Linkers/Tethers may include any C1-C100 carbon-containing 20 moiety, (e.g. C1-C75, C1-C50, C1-C20, C1-C10; C1, C2, C3, C4, C5, C6, C7, C8, C9, or C10), and may have at 102 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO least one nitrogen atom. In certain embodiments, the nitrogen atom forms part of a terminal amino or amido (NHC(O)-) group on the linker/tether, which may serve as a connection point for the lipophilic moiety. Non-limited examples of linkers/tethers (underlined) include TAP-(CH2)nNH-; TAP- C(O)(CH2)nNH-; TAP-NR’’’’(CH2)nNH-, TAP-C(O)-(CH2)n-C(O)-; TAP-C(O)-(CH2)n-C(O)O-; TAP- 5 C(O)-O-; TAP-C(O)-(CH2)n-NH-C(O)-; T TAP-C(O)-NH-; TAP-C(O)-; TAP- (CH2)n-C(O)-; TAP-(CH2)n-C(O)O-; TAP- CH2)n-NH-C(O)-; in which n is 1-20
(e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20) and R’’’’ is C1-C6 alkyl. Preferably, n is 5, 6, or 11. In other embodiments, the nitrogen may form part of a terminal oxyamino group, e.g., -ONH2, or hydrazino group, -NHNH2. The linker/tether may optionally be substituted, 10 e.g., with hydroxy, alkoxy, perhaloalkyl, and/or optionally inserted with one or more additional heteroatoms, e.g., N, O, or S. Preferred tethered ligands may include, e.g., TAP- (CH2)nNH(LIGAND); TAP-C(O)(CH2)nNH(LIGAND); TAP-NR’’’’(CH2)nNH(LIGAND); TAP- (CH2)nONH(LIGAND); TAP-C(O)(CH2)nONH(LIGAND); TAP-NR’’’’(CH2)nONH(LIGAND); TAP-(CH2)nNHNH2(LIGAND), TAP-C(O)(CH2)nNHNH2(LIGAND); TAP-15 NR’’’’(CH2)nNHNH2(LIGAND); TAP-C(O)-(CH2)n-C(O)(LIGAND); TAP-C(O)-(CH2)n- C(O)O(LIGAND); TAP-C(O)-O(LIGAND); TAP-C(O)-(CH2)n-NH-C(O)(LIGAND); TAP-C(O)- (CH2)n(LIGAND); TAP-C(O)-NH(LIGAND); TAP-C(O)(LIGAND); TAP-(CH2)n-C(O) (LIGAND); TAP-(CH2)n-C(O)O(LIGAND); TAP-(CH2)n(LIGAND); or TAP-(CH2)n-NH-C(O)(LIGAND). In some embodiments, amino terminated linkers/tethers (e.g., NH2, ONH2, NH2NH2) can form an imino 20 bond (i.e., C=N) with the ligand. In some embodiments, amino terminated linkers/tethers (e.g., NH2, ONH2, NH2NH2) can acylated, e.g., with C(O)CF3. In some embodiments, the linker/ tether can terminate with a mercapto group (i.e., SH) or an olefin (e.g., CH=CH2). For example, the tether can be TAP-(CH2)n-SH, TAP-C(O)(CH2)nSH, TAP- (CH2)n-(CH=CH2), or TAP-C(O)(CH2)n(CH=CH2), in which n can be as described elsewhere. The 25 tether may optionally be substituted, e.g., with hydroxy, alkoxy, perhaloalkyl, and/or optionally inserted with one or more additional heteroatoms, e.g., N, O, or S. The double bond can be cis or trans or E or Z. In other embodiments, the linker/tether may include an electrophilic moiety, preferably at the terminal position of the linker/tether. Exemplary electrophilic moieties include, e.g., an aldehyde, 30 alkyl halide, mesylate, tosylate, nosylate, or brosylate, or an activated carboxylic acid ester, e.g. an NHS ester, or a pentafluorophenyl ester. Preferred linkers/tethers (underlined) include TAP- (CH2)nCHO; TAP-C(O)(CH2)nCHO; or TAP-NR’’’’(CH2)nCHO, in which n is 1-6 and R’’’’ is C1-C6 alkyl; or TAP-(CH2)nC(O)ONHS; TAP-C(O)(CH2) nC(O)ONHS; or TAP-NR’’’’(CH2) nC(O)ONHS, in which n is 1-6 and R’’’’ is C1-C6 alkyl; TAP-(CH2)nC(O)OC6F5; TAP-C(O)(CH2) nC(O) OC6F5; or35 TAP-NR’’’’(CH2) nC(O) OC6F5, in which n is 1-11 and R’’’’ is C1-C6 alkyl; or -(CH2)nCH2LG; TAP- C(O)(CH2)nCH2LG; or TAP-NR’’’’(CH2)nCH2LG, in which n can be as described elsewhere and R’’’’ is C1-C6 alkyl (LG can be a leaving group, e.g., halide, mesylate, tosylate, nosylate, brosylate). 103 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO Tethering can be carried out by coupling a nucleophilic group of a ligand, e.g., a thiol or amino group with an electrophilic group on the tether. In other embodiments, it can be desirable for the monomer to include a phthalimido group (K) at the terminal position of the l
. 5 In other embodiments, other protected amino groups can be at the terminal position of the linker/tether, e.g., alloc, monomethoxy trityl (MMT), trifluoroacetyl, Fmoc, or aryl sulfonyl (e.g., the aryl portion can be ortho-nitrophenyl or ortho, para-dinitrophenyl). Any of the linkers/tethers described herein may further include one or more additional linking groups, e.g., -O-(CH2)n-, -(CH2)n-SS-, -(CH2)n-, or -(CH=CH)-. 10 2. Cleavable linkers/tethers In some embodiments, at least one of the linkers/tethers can be a redox cleavable linker, an acid cleavable linker, an esterase cleavable linker, a phosphatase cleavable linker, or a peptidase cleavable linker. 15 In one embodiment, at least one of the linkers/tethers can be a reductively cleavable linker (e.g., a disulfide group). In one embodiment, at least one of the linkers/tethers can be an acid cleavable linker (e.g., a hydrazone group, an ester group, an acetal group, or a ketal group). In one embodiment, at least one of the linkers/tethers can be an esterase cleavable linker (e.g., 20 an ester group). In one embodiment, at least one of the linkers/tethers can be a phosphatase cleavable linker (e.g., a phosphate group). In one embodiment, at least one of the linkers/tethers can be a peptidase cleavable linker (e.g., a peptide bond). 25 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 substrates or which have no substrate specificity, including, e.g., oxidative or reductive enzymes or reductive agents such as mercaptans, present in 30 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 35 human serum is 7.4, while the average intracellular pH is slightly lower, ranging from about 7.1-7.3. 104 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 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 tethers will have a linkage group that is cleaved at a preferred pH, thereby releasing the iRNA agent from a ligand (e.g., a targeting or cell-permeable ligand, such as cholesterol) inside the cell, or into the desired compartment of the cell. 5 A chemical junction (e.g., a linking group) that links a ligand to an iRNA agent can include a disulfide bond. When the iRNA agent/ligand complex is taken up into the cell by endocytosis, the acidic environment of the endosome will cause the disulfide bond to be cleaved, thereby releasing the iRNA agent from the ligand (Quintana et al., Pharm Res.19:1310-1316, 2002; Patri et al., Curr. Opin. Curr. Biol.6:466-471, 2002). The ligand can be a targeting ligand or a second therapeutic agent that 10 may complement the therapeutic effects of the iRNA agent. A tether can include a linking group that is cleavable by a particular enzyme. The type of linking group incorporated into a tether can depend on the cell to be targeted by the iRNA agent. Tethers that contain peptide bonds can be conjugated to iRNA agents target to cell types rich in peptidases. 15 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, e.g., tissue the iRNA agent would be exposed to when administered to a subject. Thus one can determine the relative susceptibility to cleavage 20 between a first and a second condition, where the first is selected to be indicative of cleavage in a target cell and the second is selected to be indicative of cleavage in other tissues 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 animals. It may be useful to make initial evaluations in cell-free or culture conditions and to confirm by further evaluations in whole animals. In preferred 25 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). 3. Redox Cleavable Linking Groups 30 One class of cleavable linking groups are redox cleavable linking groups that are cleaved upon reduction or oxidation. An example of reductively cleavable linking group is a disulphide linking group (—S—S—). To determine if a candidate cleavable linking group is a suitable “reductively cleavable linking group,” or for example is suitable for use with a particular iRNA moiety and particular in vivo delivery enhancing moiety, one can look to methods described herein. 35 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 evaluated under conditions which are selected to mimic blood or serum conditions. In a preferred embodiment, candidate compounds are cleaved by at 105 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO most 10% 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 determined using standard enzyme 5 kinetics assays under conditions chosen to mimic intracellular media and compared to conditions chosen to mimic extracellular media. 4. Phosphate-Based Cleavable Linking Groups Phosphate-based linking groups are cleaved by agents that degrade or hydrolyze the 10 phosphate group. An example of an agent that cleaves phosphate groups in cells are enzymes such as phosphatases in cells. Examples of phosphate-based linking groups are —O—P(O)(ORk)-O—, — O—P(S)(ORk)-O—, —O—P(S)(SRk)-O—, —S—P(O)(ORk)-O—, —O—P(O)(ORk)-S—, —S— P(O)(ORk)-S—, —O—P(S)(ORk)-S—, —S—P(S)(ORk)-O—, —O—P(O)(Rk)-O—, —O— P(S)(Rk)-O—, —S—P(O)(Rk)-O—, —S—P(S)(Rk)-O—, —S—P(O)(Rk)-S—, —O—P(S)(Rk)-S—. 15 Preferred embodiments are —O—P(O)(OH)—O—, —O—P(S)(OH)—O—, —O—P(S)(SH)—O—, —S—P(O)(OH)—O—, —O—P(O)(OH)—S—, —S—P(O)(OH)—S—, —O—P(S)(OH)—S—, — S—P(S)(OH)—O—, —O—P(O)(H)—O—, —O—P(S)(H)—O—, —S—P(O)(H)—O—, —S— P(S)(H)—O—, —S—P(O)(H)—S—, —O—P(S)(H)—S—. A preferred embodiment is —O— P(O)(OH)—O—. These candidates can be evaluated using methods analogous to those described 20 above. 5. 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 environment with a pH 25 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 include but are not limited to hydrazones, ketals, acetals, esters, and esters of amino acids. Acid cleavable groups can have the general formula —C═NN—, C(O)O, or —OC(O). A preferred 30 embodiment is when the carbon attached to the oxygen of the ester (the alkoxy group) is an aryl group, substituted 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. 6. Ester-Based Linking Groups 35 Ester-based linking groups are cleaved by enzymes 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 linking groups have the general formula — 106 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO C(O)O—, or —OC(O)—. These candidates can be evaluated using methods analogous to those described above. 7. Peptide-Based Cleaving Groups 5 Peptide-based 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., dipeptides, 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 10 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 peptides and proteins and does not include the entire amide functional group. Peptide cleavable linking groups have the general formula —NHCHR1C(O)NHCHR2C(O)—, where R1 and R2 are the R groups of the two adjacent amino acids. These candidates can be evaluated using methods analogous to those described above. 15 8. Biocleavable linkers/tethers The linkers can also include biocleavable linkers that are nucleotide and non-nucleotide linkers or combinations thereof that connect two parts of a molecule. The non-nucleotide linkers include tethers or linkers derived from monosaccharides, disaccharides, oligosaccharides, and 20 derivatives thereof, aliphatic, alicyclic, hetercyclic, and combinations thereof. In some embodiments, at least one of the linkers (tethers) is a bio-clevable linker selected from the group consisting of DNA, RNA, disulfide, amide, functionalized monosaccharides or oligosaccharides of galactosamine, glucosamine, glucose, galactose, and mannose, and combinations thereof. 25 In one embodiment, the bio-cleavable carbohydrate linker may have 1 to 10 saccharide units, which have at least one anomeric linkage capable of connecting two siRNA units. When two or more saccharides are present, these units can be linked via 1-3, 1-4, or 1-6 sugar linkages, or via alkyl chains. Exemplary bio-cleavable linkers include: 107 ME1\53453057.v1
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5 108 ME1\53453057.v1
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109 ME1\53453057.v1
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. 5 More discussion about the biocleavable linkers may be found in WO2018136620, entitled “Endosomal Cleavable Linkers,” the entire contents of which are incorporated herein by reference. 9. Carriers In certain embodiments, the at least one in vivo delivery enhancing moiety is conjugated to 10 the dsRNA agent via a carrier that replaces one or more nucleotide(s). The carrier can be a cyclic group or an acyclic group. In one embodiment, the cyclic group is selected from the group consisting of pyrrolidinyl, pyrazolinyl, pyrazolidinyl, imidazolinyl, imidazolidinyl, piperidinyl, piperazinyl, [1,3]dioxolane, oxazolidinyl, isoxazolidinyl, morpholinyl, thiazolidinyl, isothiazolidinyl, quinoxalinyl, pyridazinonyl, tetrahydrofuryl, and decalin. In one 15 embodiment, the acyclic group is a moiety based on a serinol backbone or a diethanolamine backbone. In some embodiments, the carrier replaces one or more nucleotide(s) in the internal position(s) of the dsRNA agent. In other embodiments, the carrier replaces the nucleotides at the terminal end of the sense 20 strand or antisense strand. In one embodiment, the carrier replaces the terminal nucleotide on the 3’ end of the sense strand, thereby functioning as an end cap protecting the 3’ end of the sense strand. In one embodiment, the carrier is a cyclic group having an amine, for instance, the carrier may be 110 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO pyrrolidinyl, pyrazolinyl, pyrazolidinyl, imidazolinyl, imidazolidinyl, piperidinyl, piperazinyl, [1,3]dioxolanyl, oxazolidinyl, isoxazolidinyl, morpholinyl, thiazolidinyl, isothiazolidinyl, quinoxalinyl, pyridazinonyl, tetrahydrofuranyl, or decalinyl. A ribonucleotide subunit in which the ribose sugar of the subunit has been so replaced is 5 referred to herein as a ribose replacement modification subunit (RRMS). The carrier can be a cyclic or acyclic moiety and include two “backbone attachment points” (e.g., hydroxyl groups) and a ligand (e.g., the lipophilic moiety). The one or more C22 hydrocarbon chains can be directly attached to the carrier or indirectly attached to the carrier by an intervening linker/tether, as described above.
10 The ligand-conjugated monomer subunit may be the 5’ or 3’ terminal subunit of the iRNA molecule, i.e., one of the two “W” groups may be a hydroxyl group, and the other “W” group may be a chain of two or more unmodified or modified ribonucleotides. Alternatively, the ligand-conjugated monomer subunit may occupy an internal position, and both “W” groups may be one or more unmodified or modified ribonucleotides. More than one ligand-conjugated monomer subunit may be 15 present in an iRNA agent. (i) Sugar Replacement-Based Monomers, e.g., Ligand-Conjugated Monomers (Cyclic) Cyclic sugar replacement-based monomers, e.g., sugar replacement-based ligand-conjugated monomers, are also referred to herein as RRMS monomer compounds. The carriers may have the 20 general formula (LCM-2) provided below (in that structure preferred backbone attachment points can be chosen from R1 or R2; R3 or R4; or R9 and R10 if Y is CR9R10 (two positions are chosen to give two backbone attachment points, e.g., R1 and R4, or R4 and R9)). Preferred tethering attachment points include R7; R5 or R6 when X is CH2. The carriers are described below as an entity, which can be incorporated into a strand. Thus, it is understood that the structures also encompass the situations 25 wherein one (in the case of a terminal position) or two (in the case of an internal position) of the attachment points, e.g., R1 or R2; R3 or R4; or R9 or R10 (when Y is CR9R10), is connected to the phosphate, or modified phosphate, e.g., sulfur containing, backbone. E.g., one of the above-named R groups can be -CH2-, wherein one bond is connected to the carrier and one to a backbone atom, e.g., a linking oxygen or a central phosphorus atom. 111 ME1\53453057.v1
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(LCM-2) wherein: X is N(CO)R7, NR7 or CH2; 5 Y is NR8, O, S, CR9R10; Z is CR11R12 or absent; Each of R1, R2, R3, R4, R9, and R10 is, independently, H, ORa, or (CH2)nORb, provided that at least two of R1, R2, R3, R4, R9, and R10 are ORa and/or (CH2)nORb; Each of R5, R6, R11, and R12 is, independently, a ligand, H, C1-C6 alkyl optionally substituted 10 with 1-3 R13, or C(O)NHR7; or R5 and R11 together are C3-C8 cycloalkyl optionally substituted with R14; R7 can be a ligand, e.g., R7 can be Rd , or R7 can be a ligand tethered indirectly to the carrier, e.g., through a tethering moiety, e.g., C1-C20 alkyl substituted with NRcRd; or C1-C20 alkyl substituted with NHC(O)Rd; 15 R8 is H or C1-C6 alkyl; R13 is hydroxy, C1-C4 alkoxy, or halo; R14 is NRcR7; R15 is C1-C6 alkyl optionally substituted with cyano, or C2-C6 alkenyl; R16 is C1-C10 alkyl; 20 R17 is a liquid or solid phase support reagent; L is -C(O)(CH2)qC(O)-, or -C(O)(CH2)qS-; Ra is a protecting group, e.g., CAr3; (e.g., a dimethoxytrityl group) or Si(X5’)(X5”)(X5”’) in which (X5’),(X5”), and (X5”’) are as described elsewhere. Rb is P(O)(O-)H, P(OR15)N(R16)2 or L-R17; 25 Rc is H or C1-C6 alkyl; Rd is H or a ligand; Each Ar is, independently, C6-C10 aryl optionally substituted with C1-C4 alkoxy; n is 1-4; and q is 0-4. Exemplary carriers include those in which, e.g., X is N(CO)R7 or NR7, Y is CR9R10, and Z is 30 absent; or X is N(CO)R7 or NR7, Y is CR9R10, and Z is CR11R12; or X is N(CO)R7 or NR7, Y is NR8, and Z is CR11R12; or X is N(CO)R7 or NR7, Y is O, and Z is CR11R12; or X is CH2; Y is CR9R10; Z is CR11R12, and R5 and R11 together form C6 cycloalkyl (H, z = 2), or the indane ring system, e.g., X is CH2; Y is CR9R10; Z is CR11R12, and R5 and R11 together form C5 cycloalkyl (H, z = 1). In certain embodiments, the carrier may be based on the pyrroline ring system or the 4- 35 hydroxyproline ring system, e.g., X is N(CO)R7 or NR7, Y is CR9R10, and Z is absent (D). 112 ME1\53453057.v1
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. OFG1 is preferably attached to a primary carbon, e.g., an exocyclic alkylene group, e.g., a methylene group, connected to one of the carbons in the five-membered ring (- CH2OFG1 in D). OFG2 is preferably attached directly to one of the carbons in the five-membered ring (-OFG2 in D). For the pyrroline-based carriers, -CH2OFG1 may be attached to C-2 and OFG2 may be 5 attached to C-3; or -CH2OFG1 may be attached to C-3 and OFG2 may be attached to C-4. In certain embodiments, CH2OFG1 and OFG2 may be geminally substituted to one of the above-referenced carbons. For the 3-hydroxyproline-based carriers, -CH2OFG1 may be attached to C-2 and OFG2 may be attached to C-4. The pyrroline- and 4-hydroxyproline-based monomers may therefore contain linkages (e.g., carbon-carbon bonds) wherein bond rotation is restricted about that particular linkage,10 e.g. restriction resulting from the presence of a ring. Thus, CH2OFG1 and OFG2 may be cis or trans with respect to one another in any of the pairings delineated above Accordingly, all cis/trans isomers are expressly included. The monomers may also contain one or more asymmetric centers and thus occur as racemates and racemic mixtures, single enantiomers, individual diastereomers and diastereomeric mixtures. All such isomeric forms of the monomers are expressly included (e.g., the 15 centers bearing CH2OFG1 and OFG2 can both have the R configuration; or both have the S configuration; or one center can have the R configuration and the other center can have the S configuration and vice versa). The tethering attachment point is preferably nitrogen. Preferred examples of carrier D include the following: 20
. 113 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In certain embodiments, the carrier may be based on the piperidine ring system (E), e.g., X is
. OFG1 is preferably attached to a primary carbon, e.g., an exocyclic alkylene group, e.g., a 5 methylene group (n=1) or ethylene group (n=2), connected to one of the carbons in the six-membered ring [-(CH2)nOFG1 in E]. OFG2 is preferably attached directly to one of the carbons in the six- membered ring (-OFG2 in E). -(CH2)nOFG1 and OFG2 may be disposed in a geminal manner on the ring, i.e., both groups may be attached to the same carbon, e.g., at C-2, C-3, or C-4. Alternatively, - (CH2)nOFG1 and OFG2 may be disposed in a vicinal manner on the ring, i.e., both groups may be 10 attached to adjacent ring carbon atoms, e.g., -(CH2)nOFG1 may be attached to C-2 and OFG2 may be attached to C-3; -(CH2)nOFG1 may be attached to C-3 and OFG2 may be attached to C-2; - (CH2)nOFG1 may be attached to C-3 and OFG2 may be attached to C-4; or -(CH2)nOFG1 may be attached to C-4 and OFG2 may be attached to C-3. The piperidine-based monomers may therefore contain linkages (e.g., carbon-carbon bonds) wherein bond rotation is restricted about that particular 15 linkage, e.g. restriction resulting from the presence of a ring. Thus, -(CH2)nOFG1 and OFG2 may be cis or trans with respect to one another in any of the pairings delineated above. Accordingly, all cis/trans isomers are expressly included. The monomers may also contain one or more asymmetric centers and thus occur as racemates and racemic mixtures, single enantiomers, individual diastereomers and diastereomeric mixtures. All such isomeric forms of the monomers are expressly 20 included (e.g., the centers bearing CH2OFG1 and OFG2 can both have the R configuration; or both have the S configuration; or one center can have the R configuration and the other center can have the S configuration and vice versa). The tethering attachment point is preferably nitrogen. In certain embodiments, the carrier may be based on the piperazine ring system (F), e.g., X is r the morpholine ring system (G), e.g., X is N(CO)R7 25
. OFG1 is preferably attached to a primary carbon, e.g., an exocyclic alkylene group, e.g., a methylene group, connected to one of the carbons in the six-membered ring (-CH2OFG1 in F or G). OFG2 is preferably attached directly to one of the carbons in the six-membered rings (-OFG2 in F or 114 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO G). For both F and G, -CH2OFG1 may be attached to C-2 and OFG2 may be attached to C-3; or vice versa. In certain embodiments, CH2OFG1 and OFG2 may be geminally substituted to one of the above-referenced carbons.The piperazine- and morpholine-based monomers may therefore contain linkages (e.g., carbon-carbon bonds) wherein bond rotation is restricted about that particular linkage, 5 e.g. restriction resulting from the presence of a ring. Thus, CH2OFG1 and OFG2 may be cis or trans with respect to one another in any of the pairings delineated above. Accordingly, all cis/trans isomers are expressly included. The monomers may also contain one or more asymmetric centers and thus occur as racemates and racemic mixtures, single enantiomers, individual diastereomers and diastereomeric mixtures. All such isomeric forms of the monomers are expressly included (e.g., the 10 centers bearing CH2OFG1 and OFG2 can both have the R configuration; or both have the S configuration; or one center can have the R configuration and the other center can have the S configuration and vice versa). R’’’ can be, e.g., C1-C6 alkyl, preferably CH3. The tethering attachment point is preferably nitrogen in both F and G. In certain embodiments, the carrier may be based on the decalin ring system, e.g., X is CH2; Y 15 is CR9R10; Z is CR11R12, and R5 and R11 together form C6 cycloalkyl (H, z = 2), or the indane ring system, e.g., X is CH2; Y is CR9R10; Z is CR11R12, and R5 and R11 together form C5 cycloalkyl (H, z = 1).
. OFG1 is preferably attached to a primary carbon, e.g., an exocyclic methylene group (n=1) or 20 ethylene group (n=2) connected to one of C-2, C-3, C-4, or C-5 [-(CH2)nOFG1 in H]. OFG2 is preferably attached directly to one of C-2, C-3, C-4, or C-5 (-OFG2 in H). -(CH2)nOFG1 and OFG2 may be disposed in a geminal manner on the ring, i.e., both groups may be attached to the same carbon, e.g., at C-2, C-3, C-4, or C-5. Alternatively, -(CH2)nOFG1 and OFG2 may be disposed in a vicinal manner on the ring, i.e., both groups may be attached to adjacent ring carbon atoms, e.g., - 25 (CH2)nOFG1 may be attached to C-2 and OFG2 may be attached to C-3; -(CH2)nOFG1 may be attached to C-3 and OFG2 may be attached to C-2; -(CH2)nOFG1 may be attached to C-3 and OFG2 may be attached to C-4; or -(CH2)nOFG1 may be attached to C-4 and OFG2 may be attached to C-3; - (CH2)nOFG1 may be attached to C-4 and OFG2 may be attached to C-5; or -(CH2)nOFG1 may be attached to C-5 and OFG2 may be attached to C-4. The decalin or indane-based monomers may 30 therefore contain linkages (e.g., carbon-carbon bonds) wherein bond rotation is restricted about that particular linkage, e.g. restriction resulting from the presence of a ring. Thus, -(CH2)nOFG1 and OFG2 may be cis or trans with respect to one another in any of the pairings delineated above. Accordingly, all cis/trans isomers are expressly included. The monomers may also contain one or more asymmetric centers and thus occur as racemates and racemic mixtures, single enantiomers, individual 35 diastereomers and diastereomeric mixtures. All such isomeric forms of the monomers are expressly 115 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO included (e.g., the centers bearing CH2OFG1 and OFG2 can both have the R configuration; or both have the S configuration; or one center can have the R configuration and the other center can have the S configuration and vice versa). In a preferred embodiment, the substituents at C-1 and C-6 are trans with respect to one another. The tethering attachment point is preferably C-6 or C-7. 5 Other carriers may include those based on 3-hydroxyproline (J).
. Thus, -(CH2)nOFG1 and OFG2 may be cis or trans with respect to one another. Accordingly, all cis/trans isomers are expressly included. The monomers may also contain one or more asymmetric centers and thus occur as racemates and racemic mixtures, single enantiomers, individual 10 diastereomers and diastereomeric mixtures. All such isomeric forms of the monomers are expressly included (e.g., the centers bearing CH2OFG1 and OFG2 can both have the R configuration; or both have the S configuration; or one center can have the R configuration and the other center can have the S configuration and vice versa). The tethering attachment point is preferably nitrogen. Details about more representative cyclic, sugar replacement-based carriers can be found in 15 U.S. Patent Nos.7,745,608 and 8,017,762, which are herein incorporated by reference in their entireties. (ii) Sugar Replacement-Based Monomers (Acyclic) Acyclic sugar replacement-based monomers, e.g., sugar replacement-based ligand-conjugated 20 monomers, are also referred to herein as ribose replacement monomer subunit (RRMS) monomer compounds. Preferred acyclic carriers can have formula LCM-3 or LCM-4:
. In some embodiments, each of x, y, and z can be, independently of one another, 0, 1, 2, or 3. In formula LCM-3, when y and z are different, then the tertiary carbon can have either the R or S 25 configuration. In preferred embodiments, x is zero and y and z are each 1 in formula LCM-3 (e.g., based on serinol), and y and z are each 1 in formula LCM-3. Each of formula LCM-3 or LCM-4 below can optionally be substituted, e.g., with hydroxy, alkoxy, perhaloalkyl. Details about more representative acyclic, sugar replacement-based carriers can be found in U.S. Patent Nos.7,745,608 and 8,017,762, which are herein incorporated by reference in their 30 entireties. 116 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO The at least one in vivo delivery enhancing moiety may be conjugated to one or more internal positions on at least one strand, e.g., a sense strand or an antisense strand. Internal positions of a strand refers to the nucleotide on any position of the strand, except the terminal position from the 3’ end and 5’ end of the strand (e.g., excluding 2 positions: position 1 counting from the 3’ end and 5 position 1 counting from the 5’ end). In one embodiment, the at least one in vivo delivery enhancing moiety may be conjugated to one or more internal positions on at least one strand, which include all positions except the terminal two positions from each end of the strand (e.g., excluding 4 positions: positions 1 and 2 counting from the 3’ end and positions 1 and 2 counting from the 5’ end). In one embodiment, the at least one in 10 vivo delivery enhancing moiety is conjugated to one or more internal positions on at least one strand, which include all positions except the terminal three positions from each end of the strand (e.g., excluding 6 positions: positions 1, 2, and 3 counting from the 3’ end and positions 1, 2, and 3 counting from the 5’ end). In one embodiment, the at least one in vivo delivery enhancing moiety may be conjugated to 15 one or more internal positions on at least one strand, except the cleavage site region of the sense strand, for instance, the at least one in vivo delivery enhancing moiety is not conjugated to positions 9- 12 counting from the 5’-end of the sense strand, for example, the at least one in vivo delivery enhancing moiety is not conjugated to positions 9-11 counting from the 5’-end of the sense strand. Alternatively, the internal positions exclude positions 11-13 counting from the 3’-end of the sense 20 strand. In one embodiment, the at least one in vivo delivery enhancing moiety may be conjugated to one or more internal positions on at least one strand, which exclude the cleavage site region of the antisense strand. For instance, the internal positions exclude positions 12-14 counting from the 5’-end of the antisense strand. 25 In one embodiment, the at least one in vivo delivery enhancing moiety may be conjugated to one or more internal positions on at least one strand, which exclude positions 11-13 on the sense strand, counting from the 3’-end, and positions 12-14 on the antisense strand, counting from the 5’- end. In one embodiment, the at least one in vivo delivery enhancing moiety may be conjugated to 30 one or more of the following internal positions: positions 4-8 and 13-18 on the sense strand, and positions 6-10 and 15-18 on the antisense strand, counting from the 5’end of each strand. In one embodiment, the at least one in vivo delivery enhancing moiety may be conjugated to one or more of the following internal positions: positions 5, 6, 7, 15, and 17 on the sense strand, and positions 15 and 17 on the antisense strand, counting from the 5’end of each strand. 35 In one embodiment, the at least one in vivo delivery enhancing moiety may be conjugated to position 6 on the sense strand, counting from the 5’end of each strand. In some embodiments, the at least one in vivo delivery enhancing moiety may be conjugated to a nucleobase, sugar moiety, or internucleosidic phosphate linkage of the dsRNA agent. In one 117 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO embodiment, the at least one in vivo delivery enhancing moiety is conjugated to a sugar moiety of the dsRNA agent. In a further embodiment, the at least one in vivo delivery enhancing moiety is conjugated to the 2’ position of a ribose sugar of the dsRNA agent. 5 V. Alpha-v-Beta-6 (αvβ6) Integrin Targeting Ligands The present disclosure provides dual conjugated dsRNA agents for inhibiting expression of a target gene, i.e., a DMPK gene. In some embodiments, a dsRNA agent comprises an antisense strand and a sense strand; at least one αvβ6 integrin targeting ligand that mediates delivery to muscle tissue conjugated to at least one strand; and at least one in vivo delivery enhancing moiety conjugated to at 10 least one strand. Suitable αvβ6 integrin targeting ligands for use in the present disclosure are described in U.S. Patent Nos 10,023,568, 10,450,312, 10,144,733, 10,487,080, 105,13,517, and 10,000,489, as well as in International Application No. PCT/US2023/083947, filed on December 14, 2023, and in U.S. Provisional Application No.63/659,097, entitled “Dual Conjugate Compounds for Extrahepatic 15 Delivery,” filed on June 12, 2024, and in International Application No. PCT/US2025/XXXXXX, filed on June 11, 2025, entitled “Dual Conjugate Compounds for Extrahepatic Delivery”. The entire contents of each of the foregoing applications are incorporated herein by reference. Integrins are cell surface receptors that, upon ligand binding, activate signal transduction pathways including signaling pathways involved in cytoskeleton organization and cell cycle 20 regulation. Integrins are also involved in cell attachment to the extracellular matrix and the integrin ligands comprise common extracellular matrix components, including fibronectin, collagen, laminin, fibrinogen, thrombospondin, and glycoproteins (e.g., tenascin C, osteopontin, and nefronectin). In humans there are at least twenty-four known integrin heterodimers composed of an alpha and a beta subunit, e.g., αvβ6. It is the combination of the alpha and beta subunits which determines the ligand 25 specificity and function of the integrin. Nearly all cells express at least one integrin and the expression and/or activity of integrins can be influenced by other signal inducing molecules, such as cytokines or steroids. The main function of αvβ6 is the activation of cytokine transforming growth factor-b1 (TGF- β1). Latent-TGF-β1 is bound to the extracellular matrix, covered by its pro-peptide latency associated 30 peptide (LAP). αvβ6 binds LAP, and through cytoskeletal force releases TGF-β1. TGF-β1 regulates multiple processes including cell proliferation, differentiation, angiogenesis, epithelial-mesenchymal- transition (EMT) and immune suppression. These processes combine to heal wounds but when uncontrolled can promote tissue pathologies. The present disclosure provides dual conjugated dsRNA agents for inhibiting expression of a 35 DMPK gene that comprise an antisense strand and a sense strand; at least one αvβ6 integrin targeting ligand that mediates delivery to muscle tissue conjugated to at least one strand; and at least one in vivo delivery enhancing moiety conjugated to at least one strand. 118 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO A. Alpha-v-Beta-6 (αvβ6) Integrin Targeting Ligands Conjugated to dsRNA agents In one aspect, the dsRNA agent of the present disclosure is conjugated to at least one αvβ6 integrin targeting ligand. The at least one αvβ6 integrin targeting ligand may be conjugated to the dsRNA agent via a direct attachment to the dsRNA agent, e.g., a ribosugar of the dsRNA agent. 5 Alternatively, the at least one αvβ6 integrin targeting ligand may be conjugated to the dsRNA agent via a linker or a carrier as described herein. Exemplary αvβ6 integrin targeting ligands that can conjugated to the dsRNA agents of the disclosure can be found, e.g., in U.S. Patent Nos 10,023,568, 10,450,312, 10,144,733, 10,487,080, 105,13,517, and 10,000,489, as well as in International Patent Application No. PCT/US2023/083947, 10 filed on December 14, 2023, the entire contents of each of which are incorporated herein by reference. Exemplary αvβ6 integrin targeting ligands are also described in WO2024/086633, incorporated herein by reference. In one embodiment, the αvβ6 integrin targeting ligand may be conjugated to the dsRNA agent via a linker comprising a compound of the structure 15
L333 N-(aminocaproyl-DBCO)-4-hydroxyprolinol, wherein * represents the bond to the remainder of the dsRNA agent. In one embodiment, the αvβ6 integrin targeting ligand comprises the structure: 20
119 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 5
bond from RLig to the nitrogen, # is the bond to the integrin ligand, and * represents the bond to the remainder of the dsRNA agent. In one embodiment, the αvβ6 integrin targeting ligand comprises the structure: 10
wherein RLig is 120 ME1\53453057.v1
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bond to the remainder of the dsRNA agent. In one embodiment, the αvβ6 integrin targeting ligand comprises the structure: 1
121 ME1\53453057.v1
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bond from RLig to the nitrogen, # is the bond to the integrin ligand, and * represents the bond to the 5 remainder of the dsRNA agent. In one embodiment, the αvβ6 integrin targeting ligand comprises the structure: 10
122 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 5
bond from RLig to the nitrogen, # is the bond to the integrin ligand, and * represents the bond to the remainder of the dsRNA agent. In one embodiment, the αvβ6 integrin targeting ligand comprises the structure: 10
wherein RLig is 123 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
bond to the remainder of the dsRNA agent. In one embodiment, the αvβ6 integrin targeting ligand comprises the structure:
, 5 wherein * represents the bond to the remainder of the dsRNA agent. In one embodiment, the αvβ6 integrin targeting ligand comprises the structure:
, wherein * represents the bond to the remainder of the dsRNA agent. 10 In one embodiment, the αvβ6 integrin targeting ligand comprises the structure:
, wherein * represents the bond to the remainder of the dsRNA agent. In one embodiment, the αvβ6 integrin targeting ligand comprises the structure: 124 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
, wherein * represents the bond to the remainder of the dsRNA agent. In one embodiment, the αvβ6 integrin targeting ligand comprises the structure: 5
, wherein * represents the bond to the remainder of the dsRNA agent. In one embodiment, the αvβ6 integrin targeting ligand comprises the structure:
, wherein * represents the bond to the remainder of the dsRNA agent. 10 In some embodiments, the αvβ6 integrin targeting ligand or the αvβ6 integrin targeting ligand to the dsRNA agent of the present disclosure comprises a structure selected from the table below: 125 ME1\53453057.v1
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126 ME1\53453057.v1
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wherein Z1 is a linker linking the αvβ6 integrin targeting ligand to the remainder of the dsRNA agent and wherein * represents the bond to the remainder of the dsRNA agent. 127 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO B. Alpha-v-Beta-6 (αvβ6) Integrin Targeting Ligands Conjugated to a Carrier Group In some embodiments, the alpha-v-beta-6 (αvβ6) integrin targeting ligand may be conjugated to the dsRNA agent of the disclosure, e.g., to at least one strand of the dsRNA agent of the disclosure, 5 via a carrier group. In some embodiments, the alpha-v-beta-6 (αvβ6) integrin targeting ligand conjugated to the dsRNA agent of the disclosure, e.g., to at least one strand of the dsRNA agent of the disclosure, is represented by a compound of the Formula (X):
or a salt thereof, wherein: 10 r CH2; (e.g., O or CH2)
, wherein m is 0, 1, 2, 3, or 4; and each R2 is independently R, or two R2 groups on adjacent carbon atoms taken together with the atoms to which they are bound form a fused 4 – 8 membered ring (e.g,. cycloalkyl or 15 heterocyclyl ring) that is optionally substituted by 1, 2, 3 or 4 groups independently selected from group consisting of R and a nitrogen protecting group; A is an 5-membered heteroaryl optionally substituted with 1 or 2 substituents independently selected from methyl, ethyl, fluoro, hydroxymethyl, 2-hydroxypropan-2-yl, trifluoromethyl, difluoromethyl, and fluoromethyl; 20 Q is -COOR1 or tetrazolyl (e.g., 1,2,3,4-tetrazol-5-yl), wherein R1 is hydrogen or C1-6alkyl (e.g., methyl) ; and RL is -N(R3)(R4), -O(R5), -S(R5), or -R5, wherein R3 and R4 are either 25 (i) R3 is hydrogen or C1-6alkyl and R4 is R5; or (ii) R3 and R4 taken together with the nitrogen atom to which they are attached form a 4 – 8 membered monocyclic heterocyclyl group that is substituted with R5; and R5 is -L-ZZ-L’-RT wherein 30 L and L’ are independently -L1-[G-L2]q-G-L3-*, wherein * is the bond to ZZ; 128 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO q is 0 or an integer selected from 1 – 25; (e.g., 1-20, or 1-15); L1 is a bond or -B-A-; each L2 is independently -A-B-A-; L3 is a bond or -A-B-A-; 5 each G is independently -D-E-F-, wherein D, E, and F are independently a bond, C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups; each A is independently a bond, -O-, -S-, or -N(RN)-; each B is independently a bond, CH2, C(O), C(S), C(NRN), S(O), S(O)2, P(O)(OH), 10 P(S)(OH), or P(S)(SH); each RN is independently hydrogen or C1-6alkyl, or two RN within an -A-B-A- group taken together with the atoms to which they are connected from a 4-8 membered heterocyclyl; and ZZ is -A’-B’-A’- or a linking group formed by a reactive pair, wherein 15 each A’ is independently a bond, -O-, -S-, or -N(RN3)-; each B’ is independently a bond, CH2, C(O), C(S), C(NRN3), -C=N-, S(O), S(O)2, P(O)(OH), P(S)(OH), or P(S)(SH); and each RN3 is independently hydrogen or C1-6alkyl, or two RN3 within the -A’-B’-A’- group taken together with the atoms to which they are connected from a 4-8 membered heterocyclyl; 20 RT is -G0-ORT1, wherein G0 is absent or -D0-E0-F0-, wherein D0, E0, and F0 are independently a bond, C1-10alkyl, C2- 10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups; and 25 RT1 is LL-oligonucleotide, wherein LL is an oligonucleotide linking group connecting the αvβ6 integrin targeting ligand to oligonucleotide comprised in the dsRNA agent; and each R group is independently selected from the group consisting of R’, C1-6alkyl, C1- 6haloalkyl, C2-6alkenyl, C2-6alkynyl, C3-8cycloalkyl, heterocyclyl, aryl, heteroaryl, C3-8cycloalkylC1- 6alkyl, heterocyclylC1-6alkyl, aryl C1-6alkyl, heteroarylC1-6alkyl, each of which, other than R’, is 30 optionally substituted with 1, 2, or 3 R’ groups, wherein each R’ is independently halogen, cyano, azido, nitro, -N(Rb)2, -O(Ra), -S(R0), -C(O)OR0, C(O)R0, -C(O)N(R0)2, -C(NR0)OR0, -C(NR0)R0, -C(NR0)N(R0)2, -C(S)OR0, -C(S)R0, -C(S)N(R0)2, -S( O)2R0, -S(O)2OR0, -S(O)2N(R0)2, -N(R0)C(O)OR0, -N(R0)C(O)R0, -N(R0)C(O)N(R0)2, -N(R0)S(O)2R0, -N(R0)S(O)2OR0, -N(R0)S(O)2N(R0)2, -OC(O)OR0, -OC(O)R0, -OC(O)N(R0)2, -OS(O)2R0, - 35 OS(O)2OR0, -OS(O)2N(R0)2, or -SC(O)R0, wherein each R0 is independently hydrogen or C1-6alkyl; each Ra is independently hydrogen or C1- 6alkyl; and each Rb is independently hydrogen, C1-6alkyl, or a nitrogen protecting group. 129 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In some embodiments, in each -D-E-F- group, at least one of D, E, and F is not a bond; and RL is not N-morpholinyl. In some embodiments of Formula (X), in -N(R3)(R4), R3 and R4 do not form a morpholino ring. 5 In some embodiments of Formula (X), in each -A-B-A- group, B is only a bond when one of the A groups is not a bond. In some embodiments, each R group is independently selected from the group consisting of R’, C1-6alkyl, C1-6haloalkyl, C2-6alkenyl, C2-6alkynyl, C3-8cycloalkyl, heterocyclyl, aryl, heteroaryl, C3- 8cycloalkylC1-6alkyl, heterocyclylC1-6alkyl, aryl C1-6alkyl and heteroaryl1-6alkyl, each of which, other 10 than R’, is optionally substituted with 1, 2, or 3 R’ groups, wherein each R’ is independently halogen, cyano, azido, nitro, -N(Rb)2, -O(Ra), -S(R0), -C(O)OR0, -C(O)R0, -C(O)N(R0)2, -N(R0)C(O)R0, - OC(O)OR0, or -OC(O)R0, wherein each R0 is independently hydrogen or C1-6alkyl; each Ra is independently hydrogen or C1-6alkyl; and each Rb is independently hydrogen, C1-6alkyl, or a nitrogen protecting group. 15 In some embodiments, each R group is independently selected from the group consisting of R’, C1-6alkyl, C1-6haloalkyl, C2-6alkenyl, C2-6alkynyl, C3-6cycloalkyl, 5-6 membered heterocyclyl, phenyl, 5-6 membered heteroaryl, and benzyl, each of which, other than R’, is optionally substituted with 1, 2, or 3 R’ groups, wherein each R’ is independently halogen, cyano, azido, nitro, -N(Rb)2, - O(Ra), -S(R0), -C(O)OR0, -C(O)R0, -C(O)N(R0)2, -N(R0)C(O)R0, -OC(O)OR0, or -OC(O)R0,20 wherein each R0 is independently hydrogen or C1-6alkyl; each Ra is independently hydrogen or C1- 6alkyl; and each Rb is independently hydrogen, C1-6alkyl, or a nitrogen protecting group. In some embodiments, each R group is independently selected from the group consisting of R’, C1-6alkyl, C3-6cycloalkyl, 5-6 membered heterocyclyl, phenyl, 5-6 membered heteroaryl, and benzyl, each of which, other than R’, is optionally substituted with 1, 2, or 3 R’ groups, wherein each25 R’ is independently halogen, cyano, azido, nitro, -N(Rb)2, -O(Ra), -S(R0), -C(O)OR0, - C(O)R0, -C(O)N(R0)2, -N(R0)C(O)R0, -OC(O)OR0, or -OC(O)R0, wherein each R0 is independently hydrogen or C1-6alkyl; each Ra is independently hydrogen or C1-6alkyl; and each Rb is independently hydrogen, C1-6alkyl, or a nitrogen protecting group. In certain embodiments, the compound of formula (
30 In certain embodiments, the compound of formula (
130 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In certain embodiments, the compound of formula (
In certain embodiments, the compound of formula (
5 A. Embodiments, Formula (X) In some embodiments Formula (X), A is selected from an optionally substituted N- or a C- linked pyrazole, an optionally substituted N- or a C-linked triazole, and an optionally substituted N- or C-linked imidazole, wherein the optionally substituted N- or a C-linked pyrazole, the optionally substituted N- or a C-linked triazole, and the optionally substituted N- or C-linked imidazole is 10 optionally substituted by 1 or 2 substituents independently selected from methyl, ethyl, fluoro, hydroxymethyl, 2-hydroxypropan-2-yl, trifluoromethyl, difluoromethyl, and fluoromethyl. In some embodiments
, wherein R1 is hydrogen, methyl, or ethyl; R2 is hydrogen or fluoro; and R3 is hydrogen, methyl, or ethyl. 15
131 ME1\53453057.v1
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RY Embodiments, Formulae (X) In some embodiments of any one of Formula (X), in RY , each R2 is independently R as defined in Formula (X). 5
In some embodiments, RY is
(or its tautomer, ). In some embodiments,
. In some embodiments, in RY , two R2 groups on adjacent carbon atoms taken together with the atoms 10 to which they are bound form a fused 4 – 8 membered ring that is optionally substituted with 1, 2, 3 or 4 groups independently selected from group consisting of R and a nitrogen protecting group, wherein R is as defined in Formula (IV). In some embodiments,
15 4; and each R21 is independently selected from group consisting of R and a nitrogen protecting group, wherein R is as defined in Formula (IV). In some embodiments, RY is
, wherein p is 0, 1, 2, 3 or 4; and each R21 is independently selected from the group consisting of R and a nitrogen protecting group, wherein R is as defined in Formula (IV). 132 ME1\53453057.v1
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5 group. In some embodiments,
, wherein RP is a nitrogen protecting group. In some embodiments,
, wherein RP is a nitrogen protecting group. 10 In some embodiments,
. In some embodiments,
, wherein RP is a nitrogen protecting group. 133 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In some embodiments of any embodiment of RY wherein RP is present, then , RP is
, wherein r is 0, 1, 2, or 3; each RP2 is independently halogen, nitro, cyano, C1- 4alkoxy, C1-4alkyl, C1-4haloalkyl; and each RP3 is independently hydrogen, methyl, or ethyl. In some embodiments, when present, RP is methoxyacetyl (mac), phenoxyacetyl (pac), 2- 5 chlorophenoxyacetyl, 3-chlorophenoxyacetyl, 4-chlorophenoxyacetyl, 2,4-dichlorophenoxyacetyl, 2- methylphenoxyacetyl, 3-methylphenoxyacetyl, 4-methylphenoxyacetyl, 4-chloro-2- methylphenoxyacetyl, 2-nitrophenoxyacetyl, 3-nitrophenoxyacetyl, 4-nitrophenoxyacetyl, 2- isopropylphenoxyacetyl, 3-isopropylphenoxyacetyl, 4-isopropylphenoxyacetyl, 2-(t- butyl)phenoxyacetyl, 3-(t-butyl)phenoxyacetyl, 4-(t-butyl)phenoxyacetyl, 2-fluorophenoxyacetyl, 3-10 fluorophenoxyacetyl, 4-fluorophenoxyacetyl, 2,4-difluorophenoxyacetyl, 4- (trifluoromethoxy)phenoxyacetyl, 2-phenoxypropanoyl, 2-(4-chloro-2-methylphenoxy)propanoyl, or 2-(4-chlorophenoxy)propanoyl. In some embodiments, when present, RP is methoxyacetyl (mac), phenoxyacetyl (pac), 2- chlorophenoxyacetyl, 4-chlorophenoxyacetyl, 2-methylphenoxyacetyl, 4-methylphenoxyacetyl, or 4- 15 isopropylphenoxyacetyl. In some embodiments, when present, RP is methoxyacetyl (mac). In some embodiments, when present, RP is phenoxyacetyl (pac). In some embodiments, when present, R1 is C1-6alkyl
, wherein 20 r is 0, 1, 2, or 3; each RP2 is independently halogen, nitro, cyano, C1-4alkoxy, C1-4alkyl, C1-4haloalkyl; and each RP3 is independently hydrogen, methyl, or ethyl. In some embodiments or Formula (X), when present, R1 is C1-6alkyl and RP is methoxyacetyl (mac), phenoxyacetyl (pac), 2-chlorophenoxyacetyl, 3-chlorophenoxyacetyl, 4-chlorophenoxyacetyl, 2,4-dichlorophenoxyacetyl, 2-methylphenoxyacetyl, 3-methylphenoxyacetyl, 4-methylphenoxyacetyl, 25 4-chloro-2-methylphenoxyacetyl, 2-nitrophenoxyacetyl, 3-nitrophenoxyacetyl, 4-nitrophenoxyacetyl, 2-isopropylphenoxyacetyl, 3-isopropylphenoxyacetyl, 4-isopropylphenoxyacetyl, 2-(t- butyl)phenoxyacetyl, 3-(t-butyl)phenoxyacetyl, 4-(t-butyl)phenoxyacetyl, 2-fluorophenoxyacetyl, 3- fluorophenoxyacetyl, 4-fluorophenoxyacetyl, 2,4-difluorophenoxyacetyl, 4- (trifluoromethoxy)phenoxyacetyl, 2-phenoxypropanoyl, 2-(4-chloro-2-methylphenoxy)propanoyl, or 30 2-(4-chlorophenoxy)propanoyl. 134 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In some embodiments, when present, R1 is C1-6alkyl and RP is methoxyacetyl (mac), phenoxyacetyl (pac), 2-chlorophenoxyacetyl, 4-chlorophenoxyacetyl, 2-methylphenoxyacetyl, 4- methylphenoxyacetyl, or 4-isopropylphenoxyacetyl. In some embodiments, when present, R1 is C1-6alkyl and RP is methoxyacetyl (mac). 5 In some embodiments, when present, R1 is C1-6alkyl and RP is phenoxyacetyl (pac). In some embodiments, when present, R1 is methyl
, wherein r is 0, 1, 2, or 3; each RP2 is independently halogen, nitro, cyano, C1-4alkoxy, C1-4alkyl, C1-4haloalkyl; and each RP3 is independently hydrogen, methyl, or ethyl. In some embodiments, when present, R1 is methyl and RP is methoxyacetyl (mac),10 phenoxyacetyl (pac), 2-chlorophenoxyacetyl, 3-chlorophenoxyacetyl, 4-chlorophenoxyacetyl, 2,4- dichlorophenoxyacetyl, 2-methylphenoxyacetyl, 3-methylphenoxyacetyl, 4-methylphenoxyacetyl, 4- chloro-2-methylphenoxyacetyl, 2-nitrophenoxyacetyl, 3-nitrophenoxyacetyl, 4-nitrophenoxyacetyl, 2- isopropylphenoxyacetyl, 3-isopropylphenoxyacetyl, 4-isopropylphenoxyacetyl, 2-(t- butyl)phenoxyacetyl, 3-(t-butyl)phenoxyacetyl, 4-(t-butyl)phenoxyacetyl, 2-fluorophenoxyacetyl, 3-15 fluorophenoxyacetyl, 4-fluorophenoxyacetyl, 2,4-difluorophenoxyacetyl, 4- (trifluoromethoxy)phenoxyacetyl, 2-phenoxypropanoyl, 2-(4-chloro-2-methylphenoxy)propanoyl, or 2-(4-chlorophenoxy)propanoyl. In some embodiments, when present, R1 is methyl and RP is methoxyacetyl (mac), phenoxyacetyl (pac), 2-chlorophenoxyacetyl, 4-chlorophenoxyacetyl, 2-methylphenoxyacetyl, 4- 20 methylphenoxyacetyl, or 4-isopropylphenoxyacetyl. In some embodiments, when present, R1 is methyl and RP is methoxyacetyl (mac). In some embodiments, when present, R1 is methyl and RP is phenoxyacetyl (pac). In some embodiments, when present, R1 is hydrogen
, wherein r is 0, 1, 2, or 3; each RP2 is independently halogen, nitro, cyano, C1-4alkoxy, C1-4alkyl, C1-4haloalkyl; and 25 each RP3 is independently hydrogen, methyl, or ethyl. In some embodiments, when present, R1 is hydrogen and RP is methoxyacetyl (mac), phenoxyacetyl (pac), 2-chlorophenoxyacetyl, 3-chlorophenoxyacetyl, 4-chlorophenoxyacetyl, 2,4- dichlorophenoxyacetyl, 2-methylphenoxyacetyl, 3-methylphenoxyacetyl, 4-methylphenoxyacetyl, 4- chloro-2-methylphenoxyacetyl, 2-nitrophenoxyacetyl, 3-nitrophenoxyacetyl, 4-nitrophenoxyacetyl, 2-30 isopropylphenoxyacetyl, 3-isopropylphenoxyacetyl, 4-isopropylphenoxyacetyl, 2-(t- butyl)phenoxyacetyl, 3-(t-butyl)phenoxyacetyl, 4-(t-butyl)phenoxyacetyl, 2-fluorophenoxyacetyl, 3- 135 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO fluorophenoxyacetyl, 4-fluorophenoxyacetyl, 2,4-difluorophenoxyacetyl, 4- (trifluoromethoxy)phenoxyacetyl, 2-phenoxypropanoyl, 2-(4-chloro-2-methylphenoxy)propanoyl, or 2-(4-chlorophenoxy)propanoyl. In some embodiments, when present, R1 is hydrogen and RP is methoxyacetyl (mac), 5 phenoxyacetyl (pac), 2-chlorophenoxyacetyl, 4-chlorophenoxyacetyl, 2-methylphenoxyacetyl, 4- methylphenoxyacetyl, or 4-isopropylphenoxyacetyl. In some embodiments, when present, R1 is hydrogen and RP is methoxyacetyl (mac). In some embodiments, when present, R1 is hydrogen and RP is phenoxyacetyl (pac). 10 RT Embodiments, Formula (X) In some embodiments of Formula (X), RT is RT1. In some embodiments of Formula (X), RT is -G0-ORT1, wherein RT1 is as defined for Formula (X) and G0 is selected from: (a) G0 is absent or -D0-E0-F0-, wherein D0, E0, and F0 are independently a bond, C1- 15 10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups; (b) G0 is -D0-E0-F0-, wherein D0 and F0 are independently a bond or C1-10alkyl optionally substituted with 1, 2, 3, or 4 R groups; and 20 E0 is C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups; (c) G0 is -D0-E0-F0-, wherein D0 and F0 are independently a bond or C1-10alkyl optionally substituted with 1, 2, 3, or 4 R groups; and 25 E0 is 3-10 membered heterocyclyl optionally substituted with 1, 2, 3, or 4 R groups; and (d) G0 is 3-10 membered heterocyclyl optionally substituted with 1 or 2 R groups; examples include
, s tetrahydrofuranyl, pyrrolidinyl, piperidinyl, piperazinyl, or morpholinyl, each optionally substituted with 1 or 2 R groups; examples include: 30
(e) G0 is 3-10 membered-heterocyclyl-C1-10alkyl, optionally substituted with 1, 2, 3, or 4 R groups; examples include, 136 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
5 with 1, 2, 3, or 4 R groups (e.g., 1 or 2 R groups); (g) G0 is C1-10alkyl or C2-10alkenyl, each of which is optionally substituted with 1 or 2 R groups; (h) G0 is C1-10alkyl optionally substituted with 1 or 2 R groups; 10 (i) G0 is C1-10alkyl, optionally substituted with -O(Ra), wherein Ra is independently hydrogen or C1-6alkyl;
(j) G0 is C1-10alkyl, and (k) G0 is absent (a bond); wherein * represents the bond to L’, the broken bond represents the bond to ORT1, and R is - 15 C1-6alkyl-ORa or -ORa, wherein Ra is independently hydrogen or C1-6alkyl. -L’- Embodiments, Formula (X) In some embodiments of Formula (X), -L’- is *-G-L1-, wherein * is the bond to ZZ; and (a) L1 is a bond or -B-A-, wherein 20 A is a bond, -O-, -S-, or -N(RN)-; B is a bond, CH2, C(O), C(S), C(NRN), S(O), S(O)2, P(O)(OH), P(S)(OH), or P(S)(SH); each RN is independently hydrogen or C1-6alkyl; and G is -D-E-F-, wherein D, E, and F are independently a bond, C1-10alkyl, C2-10alkenyl, C2- 10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is 25 optionally substituted with 1, 2, 3, or 4 R groups; (b) L1 is a bond or -B-A-, wherein A is a bond, -O-, -S-, or -N(RN)-; B is a bond, CH2, C(O), C(S), C(NRN), S(O), S(O)2, P(O)(OH), P(S)(OH), or P(S)(SH); each RN is independently hydrogen or C1-6alkyl; and 137 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO G is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups; (c) L1 is a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); and G is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, each of which is optionally substituted with 1, 2, 3, 5 or 4 R groups; (d) L1 is a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); and G is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, each of which is optionally substituted with 1, 2, 3, or 4 R groups; or 10 (e) L1 is a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); and G is C1-10alkyl. In some embodiments of Formula (X), -L’- is *-G-[L2-G]q-L1-, wherein * is the bond to ZZ; q, is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 (e.g., an integer selected from 1 to 8, an integer selected from 1 to 5, or an integer from 1 to 3); and (a) L1 is a bond or -B-A-; 15 each L2 is independently -A-B-A-; each A is independently a bond, -O-, -S-, or -N(RN)-; each B is independently a bond, CH2, C(O), C(S), C(NRN), S(O), S(O)2, P(O)(OH), P(S)(OH), or P(S)(SH); each RN is independently hydrogen or C1-6alkyl; 20 each G is independently -D-E-F-, wherein D, E, and F are independently a bond, C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups; (b) L1 is a bond, CH2, C(O), C(S), C(NRN), S(O), S(O)2, P(O)(OH), P(S)(OH), or P(S)(SH); 25 each L2 is independently -A-B-A-; each A is independently a bond, -O-, -S-, or -N(RN)-; each B is independently a bond, CH2, C(O), C(S), C(NRN), S(O), S(O)2, P(O)(OH), P(S)(OH), or P(S)(SH); each RN is independently hydrogen or C1-6alkyl, and 30 each G is independently a bond, C1-10alkyl, optionally substituted with 1, 2, 3, or 4 R groups. (c) L1 is a bond, CH2, C(O), C(S), C(NRN), S(O), S(O)2, P(O)(OH), P(S)(OH), or P(S)(SH); each L2 is independently -A-B-A-; each A is independently a bond, -O-, -S-, or -N(RN)-, wherein RN is hydrogen or C1-6alkyl 35 each B is independently a bond, CH2, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); each G is independently C1-10alkyl, optionally substituted with 1, 2, 3, or 4 R groups (d) L1 is a bond, CH2, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH) each L2 is independently -A-B-A-; 138 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO each A is independently a bond, -O-, -S-, or -N(RN)-, wherein RN is hydrogen or C1-6alkyl each B is independently a bond, CH2, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); each G is independently C1-10alkyl, optionally substituted with 1, 2, 3, or 4 R groups; or 5 (e) L1 is a bond, CH2, C(O), S(O)2, P(O)(OH), or P(S)(OH); each L2 is independently -A-B-A-; each A is independently a bond, -O-, -S-, or -N(RN)-, wherein RN is hydrogen or C1-6alkyl each B is independently a bond, CH2, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); each G is independently C1-10alkyl; 10 In some embodiments of Formula (X), -L’- is -[G-L2]q-G-L3-*, wherein * is the bond to ZZ; and (i) q is 0, 1, 2, 3, 4, or 5; each L2 is independently -A-B-A-; L3 is a bond or -A-B-A-; 15 each A is independently a bond, -O-, -S-, or -N(RN)-; each B is independently a bond, CH2, C(O), C(S), C(NRN), S(O), S(O)2, P(O)(OH), P(S)(OH), or P(S)(SH); each RN is independently hydrogen or C1-6alkyl; each G is independently C1-10alkyl, C2-10alkenyl, C2-10alkynyl, each of which is optionally 20 substituted with 1, 2, 3, or 4 R groups; (ii) q is 0, 1, 2, or 3; each L2 is independently a bond, C(O)O, OC(O), C(O)(NRN), N(RN)C(O), SO2N(RN), N(RN)SO2, OP(O)(OH), OP(S)(OH), P(O)(OH)O, P(S)(OH)O, OP(O)(OH)O, or OP(S)(OH)O, wherein each RN is independently hydrogen or C1-6alkyl; 25 each G is independently C1-10alkyl, C2-10alkenyl, C2-10alkynyl, each of which is optionally substituted with 1 or 2 R groups; (iii) q is 0, 1, 2, or 3; each L2 is independently a bond, C(O)O, OC(O), C(O)(NRN), N(RN)C(O), OP(O)(OH)O, or OP(S)(OH)O, wherein each RN is independently hydrogen or C1-6alkyl; 30 each G is independently C1-10alkyl or C2-10alkenyl, each of which is optionally substituted with 1 or 2 R groups; (iv) q is 0, 1, 2, or 3 (e.g., q is 0, 1, or 2; or 0 or 1; or 0; or 1; or 2); each L2 is independently C(O)O or OC(O); each G is independently C1-10alkyl, each of which is optionally substituted with 1 or 2 R groups; 35 (v) q is 0, 1, 2, or 3 (e.g., q is 0, 1, or 2; or 0 or 1; or 0; or 1; or 2); each L2 is independently C(O)(NRN) or N(RN)C(O), wherein each RN is independently hydrogen or C1-6alkyl; each G is independently C1-10alkyl, each of which is optionally substituted with 1 or 2 R groups; 139 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO (vi) q is 0, 1, 2, or 3 (e.g., q is 0, 1, or 2; or 0 or 1; or 0; or 1; or 2); each L2 is independently OP(O)(OH)O, or OP(S)(OH)O (e.g., each is OP(O)(OH)O); each G is independently C1-10alkyl, each of which is optionally substituted with 1 or 2 R groups; or 5 (vii) q is 0, 1, 2, or 3 (e.g., q is 0, 1, or 2; or 0 or 1; or 0; or 1; or 2); each L2 is a bond; each G is independently C1-10alkyl, each of which is optionally substituted with 1 or 2 R groups. In some embodiments, -L’- is *-L3-G-L1-, wherein * is the bond to ZZ; and (a) L1 and L3 are independently -A-B-A-; 10 each G is independently C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, or 3 R groups; each A is independently a bond, -O-, -S-, or -N(RN)-, wherein RN is hydrogen or C1-6alkyl; and each B is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); 15 (b) L3 is -C(O)O- or C(O)N(RN)-, wherein RN is hydrogen or C1-6alkyl; L1 is -OP(O)(OH)O- or -OP(S)(OH)O-; and each G is independently C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, or 3 R groups; (c) L3 is -C(O)O- or C(O)N(RN)-, wherein RN is hydrogen or C1-6alkyl; 20 L1 is -OP(O)(OH)O- or -OP(S)(OH)O-; and each G is independently C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with one R group; (d) L3 is -C(O)O- or C(O)N(RN)-, wherein RN is hydrogen or C1-6alkyl; L1 is -OP(O)(OH)O- or -OP(S)(OH)O-; and 25 each G is independently C3-10cycloalkyl or 3-10 membered heterocyclyl; (e) L3 is -C(O)O- or C(O)N(RN)-, wherein RN is hydrogen or C1-6alkyl; L1 is -OP(O)(OH)O- or -OP(S)(OH)O-; and each G1 is independently C3-10cycloalkyl or 3-10 membered heterocyclyl; and In some embodiments, -
wherein X is O or S (e.g., S). 30 In some embodiments, -L’- is *-G-, wherein * is the bond to ZZ; and G is C1-10alkyl is optionally substituted with 1 or 2 R groups. In embodiments of Formula (X), including embodiments of Formulae (x-a) through (x-x), -L’- is --L1-[G-L2]q-G-L3-*, wherein * is the bond to ZZ; In some embodiments, -L’- is -L1-G-L3-*, wherein * is the bond to ZZ; 35 In some embodiments, -L’- is -L1-[G-L2]q-G-L3-*, wherein * is the bond to ZZ; q is 0, 1, 2, 3, 4, or 5; 140 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO L1 is a bond or -B-A-; each L2 is independently -A-B-A-; L3 is a bond or -A-B-A-; each A is independently a bond, -O-, -S-, or -N(RN)-; 5 each B is independently a bond, CH2, C(O), C(S), C(NRN), S(O), S(O)2, P(O)(OH), P(S)(OH), or P(S)(SH); each RN is independently hydrogen or C1-6alkyl; and each G is independently C1-10alkyl, C2-10alkenyl, C2-10alkynyl, each of which is optionally substituted with 1, 2, 3, or 4 R groups. 10 In some embodiments, -L’- is -L1-[G-L2]q-G-*, wherein * is the bond to ZZ; q is 0, 1, 2, or 3; L1 is a bond or -B-A-; each L2 is independently a bond, C(O)O, OC(O), C(O)(NRN), N(RN)C(O), SO2N(RN), N(RN)SO2, OP(O)(OH), OP(S)(OH), P(O)(OH)O, P(S)(OH)O, OP(O)(OH)O, or OP(S)(OH)O, wherein 15 each RN is independently hydrogen or C1-6alkyl; and each G is independently C1-10alkyl, C2-10alkenyl, C2-10alkynyl, each of which is optionally substituted with 1 or 2 R groups. In some embodiments, -L’- is -L1-[G-L2]q-G-*, wherein * is the bond to ZZ; q is 0, 1, 2, or 3; 20 L1 is a bond or -B-A-; each L2 is independently a bond, C(O)O, OC(O), C(O)(NRN), N(RN)C(O), OP(O)(OH)O, or OP(S)(OH)O, wherein each RN is independently hydrogen or C1-6alkyl; each G is independently C1-10alkyl or C2-10alkenyl, each of which is optionally substituted with 1 or 2 R groups. 25 In some embodiments, -L’- is -[G-L2]q-G-*, wherein * is the bond to ZZ; and (a) q is 0, 1, 2, or 3 (e.g., q is 0, 1, or 2; or 0 or 1; or 0; or 1; or 2); each L2 is independently C(O)O or OC(O); each G is independently C1-10alkyl, each of which is optionally substituted with 1 or 2 R groups; (b) q is 0, 1, 2, or 3 (e.g., q is 0, 1, or 2; or 0 or 1; or 0; or 1; or 2); 30 each L2 is independently C(O)(NRN) or N(RN)C(O), wherein each RN is independently hydrogen or C1-6alkyl; and each G is independently C1-10alkyl, each of which is optionally substituted with 1 or 2 R groups; (c) q is 0, 1, 2, or 3 (e.g., q is 0, 1, or 2; or 0 or 1; or 0; or 1; or 2); each L2 is independently OP(O)(OH)O, or OP(S)(OH)O (e.g., each is OP(O)(OH)O); and each 35 G is independently C1-10alkyl, each of which is optionally substituted with 1 or 2 R groups; or (d) q is 0, 1, 2, or 3 (e.g., q is 0, 1, or 2; or 0 or 1; or 0; or 1; or 2); 141 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO each L2 is a bond; and each G is independently C1-10alkyl, each of which is optionally substituted with 1 or 2 R groups. In some embodiments, -L’- is -C2-30alkyl-*, wherein * is the bond to ZZ, such as -C5- 20alkyl-* or -C10-20alkyl-*. 5 In some embodiments, -L’- is -C(O)-C2-30alkyl-*, wherein * is the bond to ZZ, such as -C(O)- C5-20alkyl-* or -C(O)-C10-20alkyl-*. L’-RT Embodiments In some embodiments, -
, wherein 10 * is the bond to ZZ; L1 is a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); and RT1 is as defined for Formula (X). In some embod
15 wherein * is the bond to ZZ; L1 is a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); and RT1 is as defined for Formula (X). In some embodiments, 20
wherein * is the bond to ZZ; L1 is a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); R is -OH or -C1-6alkyl-OH; and RT1 is as defined for Formula (X). 25 In som
wherein * is the bond to ZZ; L1 is a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); 142 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO R is -OH or -C1-6alkyl-OH; and RT1 is as defined for Formula (X). I
5 wherein* is the bond to ZZ; L1 is a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); R is -OH or -C1-6alkyl-OH; and RT1 is as defined for Formula (X). In some embodim 10
wherein * is the bond to ZZ; q is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 (e.g., an integer from 1 to 8, an integer from 1 to 5, or an integer from 1 to 3); 15 each L2 is (i) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(RN)C(O)-, -OC(O)O-, -OC(O)N(RN)-, -N(RN)C(O)O-, -N(RN)C(O)N(RN)-, -OP(O)(OH)O- ,- OP(S)(OH)O-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; or (ii) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-,20 -N(RN)C(O)-, -OC(O)N(RN)-, -N(RN)C(O)O-,-N(RN)C(O)N(RN)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; or (iii) is independently selected from the group consisting of -C(O)N(RN)-, -N(RN)C(O)-, - OC(O)N(RN)-, -N(RN)C(O)O-, -N(RN)C(O)N(RN)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; or 25 (iv) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)- , -N(RN)C(O)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; or (v) independently selected from the group consisting of -C(O)N(RN)-, -N(RN)C(O)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; (vi) independently selected from the group consisting of -C(O)N(RN)- and -N(RN)C(O), 30 wherein each RN is independently hydrogen or C1-6alkyl; L1 is a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); and RT1 is as defined for Formula (X). In some embodiments, -L’-RT is 143 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
wherein * is the bond to ZZ; 5 q is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 (e.g., an integer from 1 to 8, an integer from 1 to 5, or an integer from 1 to 3); each L2 is (i) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(RN)C(O)-, -OC(O)O-, -OC(O)N(RN)-, -N(RN)C(O)O-, -N(RN)C(O)N(RN)-, -OP(O)(OH)O- ,- 10 OP(S)(OH)O-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; or (ii) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(RN)C(O)-, -OC(O)N(RN)-, -N(RN)C(O)O-,-N(RN)C(O)N(RN)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; or (iii) is independently selected from the group consisting of -C(O)N(RN)-, -N(RN)C(O)-, - 15 OC(O)N(RN)-, -N(RN)C(O)O-, -N(RN)C(O)N(RN)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; or (iv) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)- , -N(RN)C(O)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; or (v) independently selected from the group consisting of -C(O)N(RN)-, -N(RN)C(O)-, -O-, 20 and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; (vi) independently selected from the group consisting of -C(O)N(RN)- and -N(RN)C(O), wherein each RN is independently hydrogen or C1-6alkyl; L1 is a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); and RT1 is as defined for Formula (X). 25 In some embodiments, -L’-RT is , , or , wherein * is the bond to ZZ; 30 q is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 (e.g., an integer from 1 to 8, an integer from 1 to 5, or an integer from 1 to 3); each L2 is 144 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO (i) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(RN)C(O)-, -OC(O)O-, -OC(O)N(RN)-, -N(RN)C(O)O-, -N(RN)C(O)N(RN)-, -OP(O)(OH)O- ,- OP(S)(OH)O-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; or (ii) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, 5 -N(RN)C(O)-, -OC(O)N(RN)-, -N(RN)C(O)O-,-N(RN)C(O)N(RN)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; or (iii) is independently selected from the group consisting of -C(O)N(RN)-, -N(RN)C(O)-, - OC(O)N(RN)-, -N(RN)C(O)O-, -N(RN)C(O)N(RN)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; or 10 (iv) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)- , -N(RN)C(O)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; or (v) independently selected from the group consisting of -C(O)N(RN)-, -N(RN)C(O)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; (vi) independently selected from the group consisting of -C(O)N(RN)- and -N(RN)C(O), 15 wherein each RN is independently hydrogen or C1-6alkyl; L1 is a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); and RT1 is as defined for Formula (X). In some embodim
20 wherein * is the bond to ZZ; q is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 (e.g., 1-8; or 1-5; or 1-3); each L2 is (i) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(RN)C(O)-, -OC(O)O-, -OC(O)N(RN)-, -N(RN)C(O)O-, -N(RN)C(O)N(RN)-, -OP(O)(OH)O- ,- 25 OP(S)(OH)O-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; or (ii) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(RN)C(O)-, -OC(O)N(RN)-, -N(RN)C(O)O-,-N(RN)C(O)N(RN)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; or (iii) is independently selected from the group consisting of -C(O)N(RN)-, -N(RN)C(O)-, - 30 OC(O)N(RN)-, -N(RN)C(O)O-, -N(RN)C(O)N(RN)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; or (iv) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)- , -N(RN)C(O)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; or (v) independently selected from the group consisting of -C(O)N(RN)-, -N(RN)C(O)-, -O-, 35 and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; 145 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO (vi) independently selected from the group consisting of -C(O)N(RN)- and -N(RN)C(O), wherein each RN is independently hydrogen or C1-6alkyl; L1 is a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); R is -OH or -C1-6alkyl-OH; and RT1 is as defined for Formula (X). 5 In some embodime ’
wherein * is the bond to ZZ; q is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 (e.g., an integer from 1 to 8, an integer from 1 to 5, or an 10 integer from 1 to 3); each L2 is (i) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(RN)C(O)-, -OC(O)O-, -OC(O)N(RN)-, -N(RN)C(O)O-, -N(RN)C(O)N(RN)-, -OP(O)(OH)O- ,- OP(S)(OH)O-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; or 15 (ii) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(RN)C(O)-, -OC(O)N(RN)-, -N(RN)C(O)O-,-N(RN)C(O)N(RN)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; or (iii) is independently selected from the group consisting of -C(O)N(RN)-, -N(RN)C(O)-, - OC(O)N(RN)-, -N(RN)C(O)O-, -N(RN)C(O)N(RN)-, -O-, and -N(RN)-, wherein each RN is 20 independently hydrogen or C1-6alkyl; or (iv) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)- , -N(RN)C(O)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; or (v) independently selected from the group consisting of -C(O)N(RN)-, -N(RN)C(O)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; 25 (vi) independently selected from the group consisting of -C(O)N(RN)- and -N(RN)C(O), wherein each RN is independently hydrogen or C1-6alkyl; L1 is a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); R is -OH or -C1-6alkyl-OH; and RT1 is as defined for Formula (X). 30 In some embodiments, -L’-RT is 146 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
wherein* is the bond to ZZ; q is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 (e.g., an integer from 1 to 8, an integer from 1 to 5, or an integer from 1 to 3); 5 each L2 is (i) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(RN)C(O)-, -OC(O)O-, -OC(O)N(RN)-, -N(RN)C(O)O-, -N(RN)C(O)N(RN)-, -OP(O)(OH)O- ,- OP(S)(OH)O-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; or (ii) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, 10 -N(RN)C(O)-, -OC(O)N(RN)-, -N(RN)C(O)O-,-N(RN)C(O)N(RN)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; or (iii) is independently selected from the group consisting of -C(O)N(RN)-, -N(RN)C(O)-, - OC(O)N(RN)-, -N(RN)C(O)O-, -N(RN)C(O)N(RN)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; or 15 (iv) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)- , -N(RN)C(O)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; or (v) independently selected from the group consisting of -C(O)N(RN)-, -N(RN)C(O)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; (vi) independently selected from the group consisting of -C(O)N(RN)- and -N(RN)C(O), 20 wherein each RN is independently hydrogen or C1-6alkyl; L1 is a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); R is -O(Ra) or -C1-6alkyl-O(Ra), wherein Ra is hydrogen or a hydroxyl protecting group; and RT1 is as defined for Formula (X). In some embodim 25
wherein* is the bond to ZZ; q is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 (e.g., an integer from 1 to 8, an integer from 1 to 5, or an integer from 1 to 3); 147 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO each L2 is (i) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(RN)C(O)-, -OC(O)O-, -OC(O)N(RN)-, -N(RN)C(O)O-, -N(RN)C(O)N(RN)-, -OP(O)(OH)O- ,- OP(S)(OH)O-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; or 5 (ii) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(RN)C(O)-, -OC(O)N(RN)-, -N(RN)C(O)O-,-N(RN)C(O)N(RN)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; or (iii) is independently selected from the group consisting of -C(O)N(RN)-, -N(RN)C(O)-, - OC(O)N(RN)-, -N(RN)C(O)O-, -N(RN)C(O)N(RN)-, -O-, and -N(RN)-, wherein each RN is 10 independently hydrogen or C1-6alkyl; or (iv) independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)- , -N(RN)C(O)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; or (v) independently selected from the group consisting of -C(O)N(RN)-, -N(RN)C(O)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; 15 (vi) independently selected from the group consisting of -C(O)N(RN)- and -N(RN)C(O), wherein each RN is independently hydrogen or C1-6alkyl; L1 is a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); R is -OH or -C1-6alkyl-OH; and RT1 is as defined for Formula (X). 20 In some em
wherein* is the bond to ZZ; L1 is a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); R is -O(Ra) or -C1-6alkyl-O(Ra), wherein Ra is hydrogen; and 25 RT1 is as defined for Formula (X). RL Embodiments, Formula (X) In one embodiment the Formula (X), or a salt thereof, RL is -N(R3)(R4), -O(R5), -S(R5), or -R5, wherein R5 is according to one Formulae (x-a) through (x-ab):
(x-a) (x-b) 148 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
149 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
(x-ab) wherein RP3 is hydrogen and L, ZZ, L’ and RT1 are as defined for Formula (X) or any embodiment herein. In another embodiment, RL is according to one of Formulae (xi-a) through (xi-m): 150 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
(xi-k) (xi-l) 151 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
wherein RP3 is hydrogen, and L, ZZ, L’ and RT1 are as defined for Formula (X) or any embodiment herein. In another embodiment, RL is according to one of Formulae (xi-n) through (xi-z):
(xi-w) (xi-x) (xi-y) 152 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
(xi-z) wherein RP3 is hydrogen, and L, ZZ, L’ and RT1 are as defined for Formula (X) or any embodiment herein. In some embodiments, RL is -N(R3)(R4), wherein R3 is hydrogen or C1-6alkyl and R4 is R5. In some embodiments, RL is -N(R3)(R4), wherein R3 is hydrogen and R4 is R5. 5 In some embodiments, RL is -N(R3)(R4), wherein R3 is C1-3alkyl and R4 is R5. In some embodiments, RL is -N(R3)(R4), wherein R3 is methyl and R4 is R5. In some embodiments, RL is --N(R3)(R4), wherein R3 and R4 taken together with the nitrogen atom to which they are attached form a 4 – 8 membered monocyclic heterocyclyl group that is substituted with R5. 10 In some embodiments, RL is --N(R3)(R4), wherein R3 and R4 taken together with the nitrogen atom to which they are attached form a 4 – 8 membered monocyclic heterocyclyl group that is substituted with R5, provided that R3 and R4 taken together with the nitrogen atom to which they are attached do not form a morpholino group. In some embodiments, RL is --N(R3)(R4), wherein R3 and R4 taken together with the nitrogen 15 atom to which they are attached form a group that is piperidinyl, piperazinyl, pyrrolidinyl, imidazolidinyl, pyrazolidinyl, oxazolidinyl, thiazolidinyl, azetidinyl, pyrrolinyl, imidazolinyl, or pyrazolinyl, each substituted with R5. In some embodiments,
. In one embodiment the Formula (X), or a salt thereof, RL is -N(R3)(R4). 20 In one embodiment the Formula (X), or a salt thereof, RL is -N(R3)(R4), wherein R3 and R4 taken together with the nitrogen atom to which they are attached form a 4 – 8 membered monocyclic heterocyclyl group that is substituted with R5. In some embodiments, RL is -O(R5). In some embodiments, RL is -R5. 25 In some embodiments,
24 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6). 153 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In some embodiments, RL is
, wherein * is a bond to a ZZ group; t is 0 to 10 (e.g., 1-5; or 1-3; or 1; or 2; or 3). L Embodiments, Formula (X) In some embodiments of any one of Formula (X) and any embodiments thereof, L is -L1-[G- 5 L2]q-G-L3-*, wherein * is the bond to ZZ. In another embodiment, wherein L is -L1-[G-L2]q-G-L3-*, wherein q is 0, 1, 2, 3, 4, or 5. In another embodiment , L is -L1-[G-L2]q-G-L3-*, wherein q is 0, 1, 2, 3, or 4 In another embodiment , L is -L1-[G-L2]q-G-L3-*, wherein q is 0, 1, 2, or 3. In another embodiment , L is -L1-[G-L2]q-G-L3-*, wherein q is 0, 1, or 2. 10 In another embodiment , L is -L1-[G-L2]q-G-L3-*, wherein q is 1, 2, 3, 4, or 5. In another embodiment , L is -L1-[G-L2]q-G-L3-*, wherein q is 1, 2, 3, or 4. In another embodiment , L is -L1-[G-L2]q-G-L3-*, wherein q is 1, 2, or 3. In another embodiment , L is -L1-[G-L2]q-G-L3-*, wherein q is 1 or 2. In another embodiment, L is -L1-[G-L2]q-G-L3-*, wherein q is 4. In another embodiment , L 15 is -L1-[G-L2]q-G-L3-*, wherein q is 3. In another embodiment, L is -L1-[G-L2]q-G-L3-*, wherein q is 2. In another embodiment, L is -L1-G-L2-G-L3-*. In another embodiment, L is -L1-G-L3-*. In another embodiment, L is -G-L3-*. In another embodiment , L is -L1-G-*. In another embodiment, L is -G-*. In another embodiment, wherein L is -[G-L2]q-G-*, wherein q is 1, 2, 3, 4, or 5 (e.g., q is 2; or 20 q is 3; or q is 4; or q is 5). In some embodiments, each instance of A-B-A- is independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(RN)C(O)-, -OC(O)O-, -OC(O)N(RN)-, - N(RN)C(O)O-, -N(RN)C(O)N(RN)-, -OP(O)(OH)O- ,-OP(S)(OH)O-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl. 25 In some embodiments, each instance of A-B-A- is independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(RN)C(O)-, -OC(O)N(RN)-, -N(RN)C(O)O-,- N(RN)C(O)N(RN)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl. In some embodiments, each instance of A-B-A- is independently selected from the group consisting of -C(O)N(RN)-, -N(RN)C(O)-, -OC(O)N(RN)-, -N(RN)C(O)O-, -N(RN)C(O)N(RN)-, -O-, 30 and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl. In some embodiments, each instance of A-B-A- is independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(RN)C(O)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl. In some embodiments, each instance of A-B-A- is independently selected from the group 35 consisting of -C(O)N(RN)-, -N(RN)C(O)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl. In some embodiments, 154 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO D and F are each independently a bond, C1-10alkyl, C2-10alkenyl, or C2-10alkynyl, each optionally substituted with 1, 2, 3, or 4 R groups; and E is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups. 5 In some embodiments, D and F are each independently a bond or C1-10alkyl optionally substituted with 1, 2, 3, or 4 R groups; and E is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups. 10 In some embodiments, each G is independently C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3- 10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups. In some embodiments, each G is independently C1-10alkyl, optionally substituted with 1, 2, or 3 R groups. In some embodiments, each G is independently C1-10alkyl. 15 In some embodiments, each G is independently C1-10alkyl, optionally substituted with 1 or 2 R groups. In some embodiments, each G is independently C1-10alkyl, optionally substituted with one R group.. In some embodiments, L is -L1-G-L3-*, wherein * is the bond to ZZ ; 20 G is -D-E-F-, wherein D, E, and F are independently a bond, C1-10alkyl, C2-10alkenyl, C2- 10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups; L1 is -B-A-; L3 is a bond or -A-B-A-; 25 each A is independently a bond, -O-, -S-, or -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl. each B is independently a bond, CH2, C(O), S(O)2, P(O)(OH), or P(S)(OH); and In some embodiments, L is -L1-G-L3-*, wherein * is the bond to ZZ; G is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, 30 or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups; L1 is -B-; L3 is a bond or -A-B-A-; each A is independently a bond, -O-, -S-, or -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; and 35 each B is independently a bond, CH2, C(O), S(O)2, P(O)(OH), or P(S)(OH; and In some embodiments, L is -L1-G-*, wherein * is the bond to ZZ; G is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups; 155 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO L1 is -B-A-, wherein, A is a bond, -O-, -S-, or -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; and B is a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH). 5 In some embodiments, L is -L1-G-*, wherein * is the bond to ZZ; G is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, each of which is optionally substituted with 1 or 2 R groups; L1 is -B-A-, wherein A is a bond, -O-, -S-, or -N(RN)-, each RN is independently hydrogen or C1-6alkyl; and 10 B is a bond, C(O), S(O)2, P(O)(OH), or P(S)(OH). In some embodiments L is -L1-G-*, wherein * is the bond to ZZ; G is C1-10alkyl or C2-10alkenyl, each of which is optionally substituted with 1 or 2 R groups; L1 is bond, C(O), S(O)2, P(O)(OH), or P(S)(OH); and RN is hydrogen or C1-6alkyl. 15 In some embodiments, L is
wherein * is the bond to ZZ; k is an integer from 1 to 10; L1 is bond, C(O), C(S), C(NRN), S(O)2, P(O)(OH), or P(S)(OH); and RN is hydrogen or C1- 6alkyl. In some embodiments, L is
wherein * is the bond to ZZ; k is an integer from 1 to 10; L1 is bond, C(O), P(O) 20 In some embodiments,
, wherein * is the bond to ZZ; k is an integer from 1 to 10; or an integer from 2 to 10; or an integer from 3 to 10; or an integer from 4 to 10; or an integer from 5 to 10; or an integer from 5 to 9; or an integer from 5 to 8; or an integer from 5 to 7. In another embodiment, wherein L is -[G-L2]q-G-*, wherein q is 1, 2, 3, 4, or 5 (e.g., q is 2; or q is 3; or q is 4; or q is 5), each G is independently C1-10alkyl and L2 is O, S, or N(H). 25 In another embodiment, wherein L is -[G-L2]q-G-*, wherein q is 1, 2, 3, 4, or 5 (e.g., q is 2; or q is 3; or q is 4; or q is 5), each G is independently C1-10alkyl and L2 is O. In another embodiment, wherein L is -[CH2CH2O]q-G-*, wherein q is 1, 2, 3, 4, or 5 (e.g., q is 2; or q is 3; or q is 4; or q is 5), G is independently C1-10alkyl. 30 In some embodiments, L is
, wherein * is the bond to ZZ; t is an integer from 0 to 10 (e.g., an integer from 1 to 5; or 1; or 2; or 3). In some embodiments, L is
, wherein * is the bond to ZZ. 156 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In some embodiments, L is
, wherein * is the bond to ZZ; t is 1 to 10 (e.g., 1-5; or 1-3; or 1; or 2; or 3); and z is 1-10 (e.g., 1-6; or 1-4; or 1; or 2; or 3 or 4 or 5 or 6). In some embodiments, L is
, wherein * is the bond to ZZ, and t is an integer from 1 to 5 (e.g., 1; or 2; or 3). 5
, wherein * is the bond to ZZ, t is an integer from 0 to 10 (e.g., an integer from 1 to 5 or 1; or 2; or 3); a is an integer from 1 to 3; and s and s’ are each independently an integer from 1 to 24 (e.g., an integer from 1 to 16; an integer from 1 to 10; an integer from 3 to 10; an integer from 3 to 7; or an 10 integer from 4 to 6). In some embodiments,
wherein * is the bond to ZZ; a is 1, 2 or 3; and each s, s’, and s” independently is an integer from 1 to 24 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7, or an integer from 4 to 6). In some embodiments, L is
wherein * is the bond to ZZ; and s, s’, 15 and s’’ are independently is an integer from 1 to 24 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7, or an integer from 4 to 6). In some embodiments,
wherein * is the bond to ZZ and each s, s’, and s” independently is an integer from 1 to 24(e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7, or an integer from 4 to 6) 20 In some embodiments, L is
wherein * is the bond to ZZ; s and k are independently is an integer from 1 to 20 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6); and w is an integer from 1 to 10 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6). 157 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In some embodiments, L is
wherein * is the bond to ZZ and w is an integer from 1 to 20 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6). In some embodiments, L is C1-20 alkyl. In some embodiments, L is C2-20 alkyl. In some 5 embodiments, L is C6-20 alkyl. In some embodiments, L is C8-12 alkyl. In some embodiments, L is C10 alkyl. In embodiments of Formula (X), including embodiments of Formulae (x-a) through (x-s) and (xi-a) through (xi-z), RP3, when present, is hydrogen. In another embodiment, the compound of Formula (X) is according to one of Formulae (X-b) 10 through (X-e) and (X-x) through (X-y):
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Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
or a salt thereof, wherein RP is hydrogen or a nitrogen protecting group (e.g., a nitrogen protecting group), wherein R and the remaining variables are as defined in Formula (X). In one embodiment of Formulae (X-b) through (X-e) and (X-x) through (X-y), R1 is hydrogen. In another embodiment of Formulae (X-b) through (X-e) and (X-x) through (X-y), R1 is C1-6alkyl (e.g., methyl or 5 t-butyl). In another embodiment of Formulae (X-b) through (X-e) and (X-x) through (X-y), R1 is hydrogen and RP is hydrogen. In another embodiment of Formulae (X-b) through (X-e) and (X-x) through (X-y), R1 is hydrogen and a nitrogen protecting group. In another embodiment of Formulae (X- b) through (X-e) and (X-x) through (X-y), R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In another embodiment of Formulae (X-b) through (X-e) and (X-x) through (X-y), R1 is C1-6alkyl (e.g., 10 methyl or t-butyl) and a nitrogen protecting group. -L-ZZ-L’-RT Embodiments In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) through (X-y), -L-ZZ-L’-RT is
159 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO (x-a). In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) through (X-y), -L-ZZ-L’-RT is
(x-b). In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) through (X-y), -L-ZZ-L’-RT is
(x-c). 5 In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) through (X-y), -L-ZZ-L’-RT is
In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) through (X-y), -L-ZZ-L’-RT is
In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) 10 through (X-y), -L-ZZ-L’-RT is
In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) through (X-y), -L-ZZ-L’-RT is 160 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) through (X-y), -L-ZZ-L’-RT is
(x-h). In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) through (X-y), -L-ZZ-L’-RT is
(x-i). 5 In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) through (X-y), -L-ZZ-L’-RT is
(x-j). In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) through (X-y), -L-ZZ-L’-RT is
(x-k). In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) 10 through (X-y), -L-ZZ-L’-RT is
(x-l). 161 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) through (X-y), -L-ZZ-L’-RT is
(x-m). In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) through (X-y), -L-ZZ-L’-RT is
(x-n). 5 In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) through (X-y), -L-ZZ-L’-RT is
(x-o). In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) through (X-y), -L-ZZ-L’-RT is
In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) 10 through (X-y), -L-ZZ-L’-RT is
(x-q). In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) through (X-y), -L-ZZ-L’-RT is 162 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
(x-r) In an embodiment, of any one of Formula (X) and Formulae (X-a) through (X-e) and (X-x) through (X-y), -L-ZZ-L’-RT is
5 RT1 Embodiments, Formula (X) Nucleotide Conjugates In embodiments of any embodiments of RL of Formula (X), Formula (X-a) through (X-e) and (X-x) through (X-y), Formula (x-a) through (x-s), and Formula (xi-a) through (xi-z), RT1 is -LL-oligonucleotide, wherein LL is a divalent linker that connects to the 3’-end of the 10 oligonucleotide, the 5’-end of the oligonucleotide, or an internal 2’- or 3’ position on an internal nucleotide (i.e., a nucleotide that is not the 5’-terminal or 3’-terminal nucleoside). In some embodiments. LL is a bond. In some embodiments, RT1 is -LL-oligonucleotide, wherein LL is a divalent linker that connects to the 3’-end of the oligonucleotide, such as one of: 15 directly to the 3’-carbon of the 3’-terminal nucleoside; directly to the 3’-O of the 3’-terminal nucleoside; directly to the 4’-carbon of the 3’-terminal nucleoside; directly to the 2’-carbon of the 3’-terminal nucleoside; or directly to the 2’-O of the 3’-terminal nucleoside. 20 In some embodiments, RT1 is -LL-oligonucleotide, wherein LL is a divalent linker that connects to the 5'-end of the oligonucleotide, such as one of: directly to the 5’-carbon of the 5’-terminal nucleoside; directly to the 5’-O of the 5’-terminal nucleoside; directly to the 4’-carbon of the 5’-terminal nucleoside; 25 directly to the 2’-carbon of the 5’-terminal nucleoside; or directly to the 2’-O of the 5’-terminal nucleoside. In some embodiments, RT1 is -LL-oligonucleotide, wherein LL is a divalent linker that connects to an internal 2’- or 3’ position on an internal nucleotide. 163 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In some embodiments, RT1 is -LL-oligonucleotide, wherein LL is a divalent linker that connects to an internal 2’- position on a internal nucleotide. In some embodiments, RT is RT1 , wherein RT1 is -LL-oligonucleotide, wherein LL is a divalent linker that connects to an internucleotide linkage (i.e., to an oxygen atom in a phosphodiester linkage 5 to form a phosphotriester; or to a nitrogen when the internucleotide linkage is a phosphoroamidate). In another embodiment of any of the preceding embodiments of RT1, when LL connects to a carbon atom on a nucleoside, then LL is -B3-A3-, wherein B3 is -P(O)(OH)-, -P(S)(OH)-, or -P(S)(SH)-; and A3 is -O-, -S-, or -N(H)- . 10 In another embodiment, when LL connects to a carbon atom on a nucleoside, then LL is -B3- A3-, wherein B3 is -P(O)(OH)- or-P(S)(OH)-; and A3 is -O-. In another embodiment, when LL connects to a oxygen atom on a nucleoside, then LL is - 15 P(O)(OH)-, -P(S)(OH)-, or -P(S)(SH). In another embodiment, when LL connects to a oxygen atom on a nucleoside, then LL is - P(O)(OH)- or -P(S)(OH)-. In another embodiment, when LL connects to a oxygen atom on a nucleoside, then LL is - P(O)(OH)-. 20 In another embodiment, when LL connects to a oxygen atom on a nucleoside, then LL is - P(S)(OH)-. In another embodiment, when LL connects to a oxygen atom on a nucleoside, then LL is -B3-A3-LL1-A3-B3-, wherein B3 is a bond, -C(O)-, C(S)-, C(NH), S(O), S(O)2, -P(O)(OH)-, -P(S)(OH)-, or -P(S)(SH); 25 A3 is a bond, -O-, -S-, or -N(H)- ; and LL1 is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl. In another embodiment, when LL connects to a oxygen atom on a nucleoside, then LL is -B3- LL1-B3-, wherein B3 is -C(O)-; and LL1 is C1-10alkyl. 30 In another embodiment, when LL connects to a oxygen atom on a nucleoside, then LL is-a bond. In certain embodiments, RT is RT1 wherein RT1 is is -LL-oligonucleotide, when LL connects to a oxygen atom on a nucleoside, and LL is a bond, the nucleoside is of Formula (X-f),
164 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein B is an optionally modified nucleobase (e.g., adenine, cytosine, uracil, guanine, 5- methylcytosine, or-5-methyluracil); L’ is according any of the preceding embodiments; and * represent the bond to ZZ. In some embodiments of Formula (X-f), -L’- is -L1-G-L3-*, wherein * is the bond to ZZ. 5 In some embodiments, -L’- is -C2-30alkyl-*, wherein the alkyl is optionally substituted with one or two R groups, and * is the bond to ZZ. In some embodiments, -L’- is -C2-30alkyl-*, wherein the alkyl is optionally substituted with one or two groups selected from the group consisting of halogen, hydroxy, C1-6alkoxy, amino, Cl-6alkylamino, di(C1-6alkylamino), cyano, carboxy , and * is the bond to ZZ. In some embodiments, -L’- is -C2-30alkyl-*, wherein the alkyl is optionally substituted with one group10 selected from the group consisting of halogen, hydroxy, C1-6alkoxy, amino, Cl-6alkylamino, di(C1- 6alkylamino), cyano, carboxy , and * is the bond to ZZ. In some embodiments, -L’- is -C2-30alkyl-*, wherein the alkyl is optionally substituted with one group selected from the group consisting of hydroxy, amino, and carboxy , and * is the bond to ZZ. In some embodiments, -L’- is -C2-30alkyl-*, wherein the alkyl is optionally substituted with hydroxy, and * is the bond to ZZ. 15 In some embodiments, -L’- is -C2-30alkyl-*, wherein * is the bond to ZZ. In some embodiments, -L’- is -C2-16alkyl-*, wherein * is the bond to ZZ. In some embodiments, -L’- is -C4-12alkyl-*, wherein * is the bond to ZZ. In some embodiments, -L’- is -C4-10alkyl-*, wherein * is the bond to ZZ. In some embodiments, -L’- is -C5-10alkyl-*, wherein * is the bond to ZZ. In some embodiments, -L’- is -C6alkyl- *, wherein * is the bond to ZZ. In some embodiments, -L’- is -C8alkyl-*, wherein * is the bond to ZZ. 20 In some embodiments, -L’- is -C10alkyl-*, wherein * is the bond to ZZ. In some embodiments of Formula (X-f), -L’- is -L1-[G-L2]q-G-L3-*, wherein * is the bond to ZZ; q is 0, 1, 2, 3, 4, or 5; L1 is a bond or -B-A-; 25 each L2 is independently -A-B-A-; L3 is a bond or -A-B-A-; each A is independently a bond, -O-, -S-, or -N(RN)-; each B is independently a bond, CH2, C(O), C(S), C(NRN), S(O)2, P(O)(OH), or P(S)(OH); each RN is independently hydrogen or C1-6alkyl; and 30 each G is independently C1-10alkyl, C2-10alkenyl, C2-10alkynyl, each of which is optionally substituted with 1, 2, 3, or 4 R groups. In some embodiments, -L’- is -L1-[G-L2]q-G-*, wherein * is the bond to ZZ, q is 0, 1, 2, or 3; L1 is a bond or -B-A-; and (a) each L2 is independently a bond, C(O)O, OC(O), C(O)(NRN), N(RN)C(O), SO2N(RN), 35 N(RN)SO2, OP(O)(OH), OP(S)(OH), P(O)(OH)O, P(S)(OH)O, OP(O)(OH)O, or OP(S)(OH)O, wherein each RN is independently hydrogen or C1-6alkyl; each G is independently C1-10alkyl, C2-10alkenyl, C2- 10alkynyl, each of which is optionally substituted with 1 or 2 R groups; or 165 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO (b) each L2 is independently a bond, C(O)O, OC(O), C(O)(NRN), N(RN)C(O), OP(O)(OH)O, or OP(S)(OH)O, wherein each RN is independently hydrogen or C1-6alkyl; and each G is independently C1-10alkyl or C2-10alkenyl, each of which is optionally substituted with 1 or 2 R groups. In some embodiments, -L’- is -[G-L2]q-G-*, wherein * is the bond to ZZ, q is 0, 1, 2, or 3 (e.g., 5 q is 0, 1, or 2; or 0 or 1; or 0; or 1; or 2); each G is independently C1-10alkyl, each of which is optionally substituted with 1 or 2 R groups, and one of: (a) each L2 is independently C(O)O or OC(O); (b) each L2 is independently C(O)(NRN) or N(RN)C(O), wherein each RN is independently hydrogen or C1-6alkyl 10 (c) each L2 is independently OP(O)(OH)O, or OP(S)(OH)O (e.g., each is OP(O)(OH)O); or (d) each L2 is a bond. In some embodiments, the compound of Formula (X) is according to one of Formulae (X-g) through (X-q):
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B is an optionally modified nucleobase (e.g., adenine, cytosine, uracil, guanine, 5- methylcytosine, or-5-methyluracil); each n is independently 0 or an integer selected from 1-10; (e.g., 1-5, or 1-3, or 3, or 2, or 1); 5 each m is independently integer selected from 1-20 (e.g., 2-12, or 2-10; or 2-6; or 2; or 3; or 4; or 5; or 6). In some embodiments, the compound of Formula (X) is according to one of Formulae (X-r) through (X-w):
167 ME1\53453057.v1
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L and ZZ are as defined in Formula (X) or in any embodiment preceding or below; B is an optionally modified nucleobase (e.g., adenine, cytosine, uracil, guanine, 5- methylcytosine, or-5-methyluracil); 10 each m is independently integer selected from 1-20 (e.g., 2-12, or 2-10; or 2-6; or 2; or 3; or 4; or 5; or 6); each n is independently 0 or an integer selected from 1-10; (e.g., 1-5, or 1-3, or 3, or 2, or 1); RP is hydrogen or a nitrogen protecting group (e.g., a nitrogen protecting group); and R1 is hydrogen or C1-6alkyl (e.g., methyl or t-butyl). 15 In one embodiment of Formulae (X-r) through (X-w), R1 is hydrogen. In another embodiment of Formulae (X-r) through (X-w), R1 is C1-6alkyl (e.g., methyl or t-butyl). In another embodiment of Formulae (X-r) through (X-w), R1 is hydrogen and RP is hydrogen. In another embodiment of Formulae (X-r) through (X-w), R1 is hydrogen and a nitrogen protecting group. In another embodiment of Formulae (X-r) through (X-w), R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP 168 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO is hydrogen. In another embodiment of Formulae (X-r) through (X-w), R1 is C1-6alkyl (e.g., methyl or t-butyl) and a nitrogen protecting group. In some embodiments, two adjacent nucleosides in the oligonucleotide have one of the 5
oligonucleotide, L’ is according any of the preceding embodiments; and B is an optionally modified nucleobase. Therein, each nucleoside of the two adjacent nucleosides is independently according to 10 any one of Formula (X-f) through (X-q). In certain embodiments, each nucleoside is according to the same Formula. In some embodiments, three adjacent nucleosides in the oligonucleotide have the formula
169 ME1\53453057.v1
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wherein each Y is independently O or S (or O; or S; or O then S or S then O, 5’ followed by 3’);
represents the remainder for the oligonucleotide, L’ is according any of the preceding 5 embodiments; and B is an optionally modified nucleobase; e.g., each Y is O. Therein, each nucleoside of the three adjacent nucleosides is independently according to any one of Formula (X-f) through (X- q). In certain embodiments, each nucleoside is according to the same Formula. In some embodiments, four adjacent nucleosides in the oligonucleotide have the formula, 10
oligonucleotide, L’ is according any of the preceding embodiments; and B is an optionally modified 170 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO nucleobase; e.g., each Y is O. Therein, each nucleoside of the four adjacent nucleosides is independently according to any one of Formula (X-f) through (X-q). In certain embodiments, each nucleoside is according to the same Formula. In certain embodiments, each nucleoside is according to the same Formula (X-u) or (X-w). 5 In certain embodiments, where RT is RT1, wherein RT1 is -LL-oligonucleotide, and when LL connects to an oxygen atom or nitrogen atom in an internucleotide linkage, the internucleotide linkage can be of the formula, including the 3’ and 5’ oxygen atoms of the preceding and following nucelosides, respectively,
(X-pa) (X-pb) (X-pc) wherein L’ can be, for example a bond, -S(O)2- or, in for Formula (X-pc), a 5 -8 membered 10 heterocyclyl ring optionally substituted with 1 or 2 R groups, as defined herein; and * represent the bond to ZZ. For example, the preceding includes,
(X-pd) (X-pe) (X-pf) wherein * represent the bond to ZZ; and RN5 is hydrogen or C1-10 alkyl. For example, the preceding includes,
(X-pg) (X-ph) (X-pi) 15 wherein * represent the bond to ZZ; m is an integer selected from 1 – 20 (e.g., 1-10, or 2-20, or 2-10, or 4-10, or 4-8; or 6-12; or 5; or 6; or 7; or 8; or 9; or 10), and RN5 is hydrogen or C1-10 alkyl. In another embodiment, the compound of Formula (X-pd) is 171 ME1\53453057.v1
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wherein Y’ is O or S, and RY, Y, R1, L, L’, and ZZ are as defined for Formula (X). In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t-butyl). In another embodiment, the compound is 5
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wherein Y’ is O or S, and RP, R1, L, L’, and ZZ are as defined for Formula (X). In another embodiment, the compound is 5
173 ME1\53453057.v1
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wherein each m is an integer selected from 1 – 20 (e.g., 2-20, 2-10, 1-10, 2-16, 4-16, 4-8, or 6-12), each n is independently 0 or an integer selected from 1-10; (e.g., 1-5, or 1-3, or 3, or 2, or 1); Y’ is O or S, and R1, L, L’, and ZZ are as defined for Formula (X). 10 In another embodiment, the compound of Formula (X-pe) is 174 ME1\53453057.v1
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wherein Y’ is O or S, and RY, Y, R1, L, L’, and ZZ are as defined for Formula (X). In one embodiment, Y’ is O. In another embodiment, Y’ is S. In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t- 5 butyl). In one embodiment, RP is hydrogen. In another embodiment, RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1- 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R1 is hydrogen. In one embodiment, 10 Y’ is S and R1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and RP is hydrogen. In one embodiment, Y’ is O and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and RP is hydrogen . In one embodiment, Y’ is S and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl 15 (pac)). In one embodiment, Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl 20 (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen . In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a 25 nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In another embodiment, the compound is 175 ME1\53453057.v1
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5 176 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein Y’ is O or S, and RP, R1, L, L’, and ZZ are as defined for Formula (X). In one embodiment, Y’ is O. In another embodiment, Y’ is S. In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t- butyl). 5 In one embodiment, RP is hydrogen. In another embodiment, RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1- 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R1 is hydrogen. In one embodiment Y’ is S and R1 is C1-6alkyl (e.g., methyl or t-butyl). 10 In one embodiment, Y’ is O and RP is hydrogen. In one embodiment, Y’ is O and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and RP is hydrogen . In one embodiment, Y’ is S and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). 15 In one embodiment, Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is C1-6alkyl 20 (e.g., methyl or t-butyl) and RP is hydrogen . In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen . In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl 25 (pac)).
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Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
5 wherein each m is an integer selected from 1 – 20 (e.g., 2-20, 2-10, 1-10, 2-16, 4-16, 4-8, or 6-12), Y’ is O or S, and RP, R1, L, L’, and ZZ are as defined for Formula (X). 178 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In one embodiment, Y’ is O. In another embodiment, Y’ is S. In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t- butyl). In one embodiment, RP is hydrogen. In another embodiment, RP is a nitrogen protecting group 5 (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R1 is hydrogen. In one embodiment, Y’ is S and R1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and RP is hydrogen. In one embodiment, Y’ is O and RP is a 10 nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and RP is hydrogen . In one embodiment, Y’ is S and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, 15 R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen . In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl 20 or t-butyl) and RP is hydrogen . In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). 25 For Formula (X), when RT1 is -LL-oligonucleotide and is conjugated at the 5’-end of the oligonucleotide, in one embodiment, RT1 can be represented as Formula (X-5’)
wherein LL is -P(Y)(OH)-, wherein Y is O or S (e.g., S); and * represents the bond to remainder of the compound of Formula (X). 30 In another embodiment of Formula (X), when RT1 is -LL-oligonucleotide and is conjugated at the 5’-end of the oligonucleotide, in one embodiment, RT1 can be represented as Formula (X-5’o) or Formula (X-5’s),
wherein * represents the bond to remainder of the compound of Formula (X). 179 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In an embodiment of Formula (X-5’), (X-5’o), and Formula (X-5’s), -L-ZZ-L’-RT represents any one of Formulae (x-a) through (x-s) . In representative embodiments, -L-ZZ-L’-RT represents Formula (
In other embodiments-L-ZZ-L’-RT represents one of the following formulae:
(x-n) (x-o) (x-s) 5 In other embodiments of Formula (X-5’), (X-5’o), and Formula (X-5’s), L-ZZ-L’-RT represents,
(x-m) In other embodiments of Formula (X-5’), (X-5’o), and Formula (X-5’s), L-ZZ-L’-RT 10 represents,
(x-s). In another embodiment, the compound of Formula (X) is 180 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
wherein Y’ is O or S, and RY, Y, R1, L, L’, and ZZ are as defined for formula (X) or any embodiment thereof. For Formula (X), when RT1 is -LL-oligonucleotide and is conjugated at the 3’-end of the 5 oligonucleotide, in one embodiment, RT1 can be represented as Formula (X-3’)
wherein LL is -P(Y)(OH)-, wherein Y is O or S (e.g., S); and * represents the bond to remainder of the compound of Formula (X). In another embodiment of Formula (X), when RT1 is -LL-oligonucleotide and is conjugated at 10 the 3’-end of the oligonucleotide, in one embodiment, RT1 can be represented as Formula (X-3’o) or Formula (X-3’s),
wherein * represents the bond to remainder of the compound of Formula (X). In an embodiment of Formula (X-3’), (X-3’o), and Formula (X-3’s), -L-ZZ-L’-RT represents 15 any one of Formulae (x-a) through (x-ab). In representative embodiments, -L-ZZ-L’-RT represents Formula (x-e),
. In other embodiments-L-ZZ-L’-RT represents one of the following formulae:
(x-a) (x-b) (x-c) 181 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
(x-aa) (x-ab) In other embodiments of Formula (X-3’), (X-3’o), and Formula (X-3’s), L-ZZ-L’-RT represents,
In other embodiments of Formula (X-3’), (X-3’o), and Formula (X-3’s), L-ZZ-L’-RT 5 represents,
182 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In other embodiments of Formula (X-3’), (X-3’o), and Formula (X-3’s), L-ZZ-L’-RT represents,
(x-p). In other embodiments of Formula (X-3’), (X-3’o), and Formula (X-3’s), L-ZZ-L’-RT 5 represents,
(x-ab). In other embodiments of Formula (X-3’), (X-3’o), and Formula (X-3’s), L-ZZ-L’-RT represents,
(x-r). In another embodiment of Formula (X), RL is 10
In another embodiment, the compound of Formula (X) is 183 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
wherein Y' is O or S, and RY, R1, Y, L’, ZZ, and L are as defined for Formula (X) or any embodiment thereof. In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., 5 methyl or t-butyl). In another embodiment, the compound of Formula (X) is
184 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein Y’ is O or S, and RY, Y, R1, L’, ZZ, and L are as defined for Formula (X) or any embodiment thereof. In another embodiment, the compound of Formula (X) is 5
wherein Y’ is O or S, and RP, R1, L’, ZZ, and L are as defined for Formula (X) or any embodiment thereof. In one embodiment, Y’ is O. In another embodiment, Y’ is S. In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t- 10 butyl). In another embodiment, -COOR1 is replaced with a carboxylic acid mimic, such as a tetrazolyl group (e.g., 1,2,3,4-tetrazol-5-yl). In one embodiment, RP is hydrogen. In another embodiment, RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1- 15 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R1 is hydrogen. In one embodiment, Y’ is S and R1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and RP is hydrogen . In one embodiment, Y’ is O and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and RP is hydrogen . In one embodiment, Y’ is S and RP is a 20 nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). 185 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In one embodiment, Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl 5 (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a 10 nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In another embodiment, the compound of Formula (X) is
15 wherein Y’ is O or S, and RP, R1, L’, ZZ, and L are as defined for Formula (X) or any embodiment thereof. In one embodiment, Y’ is O. In another embodiment, Y’ is S. In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t- butyl). 20 In one embodiment, RP is hydrogen. In another embodiment, RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). 186 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In one embodiment, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1- 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R1 is hydrogen. In one embodiment, Y’ is S and R1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and RP is hydrogen. In one embodiment, Y’ is O and RP is a 5 nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and RP is hydrogen. In one embodiment, Y’ is S and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, 10 R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen . In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl 15 or t-butyl) and RP is hydrogen. In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). 20 In another embodiment, the compound of Formula (X) is
187 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
, wherein Y’ is O or S, and RP, R1, L’, and L are as defined for Formula (X) or any embodiment thereof. In one embodiment, Y’ is O. In another embodiment, Y’ is S. 5 In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t- butyl). In one embodiment, RP is hydrogen. In another embodiment, RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1- 10 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R1 is hydrogen. In one embodiment, Y’ is S and R1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and RP is hydrogen. In one embodiment, Y’ is O and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and RP is hydrogen. In one embodiment, Y’ is S and RP is a 15 nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In 20 one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen . In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen . In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or 25 phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In another embodiment, the compound of Formula (X) is 188 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
wherein each m is independently an integer selected from 1-10; each n is independently 0 or an integer selected from 1-10; (e.g., 1-5, or 1-3, or 3, or 2, or 1); Y’ is O or S, and RP and R1 are 5 as defined for Formula (X) or any embodiment thereof. In one embodiment, each m is independently an integer selected from 2-10; or 2-8, or 2-6. In one embodiment, Y’ is O. In another embodiment, Y’ is S. In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t- butyl). 10 In one embodiment, RP is hydrogen. In another embodiment, RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1- 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R1 is hydrogen. In one embodiment, Y’ is S and R1 is C1-6alkyl (e.g., methyl or t-butyl). 15 In one embodiment, Y’ is O and RP is hydrogen. In one embodiment, Y’ is O and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and RP is hydrogen . In one embodiment, Y’ is S and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). 189 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In one embodiment, Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl 5 (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a 10 nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In another embodiment, the compound of Formula (X) is
15 wherein Y’ is O or S, and RP and R1 are as defined for Formula (X) or any embodiment thereof. In one embodiment, Y’ is O. In another embodiment, Y’ is S. In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t- butyl). In one embodiment, RP is hydrogen. In another embodiment, RP is a nitrogen protecting group 20 (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1- 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R1 is hydrogen. In one embodiment, Y’ is S and R1 is C1-6alkyl (e.g., methyl or t-butyl). 190 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In one embodiment, Y’ is O and RP is hydrogen. In one embodiment, Y’ is O and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and RP is hydrogen. In one embodiment, Y’ is S and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl 5 (pac)). In one embodiment, Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl10 (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is C1- 6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t- butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is 15 a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In another embodiment, the compound of Formula (X) is
191 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein Y’ is O or S, and RP, R1, L’, ZZ, and L are as defined for Formula (X) or any embodiment thereof. In one embodiment, Y’ is O. In another embodiment, Y’ is S. In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t- 5 butyl). In one embodiment, RP is hydrogen. In another embodiment, RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1- 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R1 is hydrogen. In one embodiment, 10 Y’ is S and R1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and RP is hydrogen. In one embodiment, Y’ is O and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and RP is hydrogen . In one embodiment, Y’ is S and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl 15 (pac)). In one embodiment, Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl 20 (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a 25 nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In another embodiment, the compound of Formula (X) is 192 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
wherein Y’ is O or S, and RP, R1, L’, and L are as defined for Formula (X) or any embodiment thereof. 5 In one embodiment, Y’ is O. In another embodiment, Y’ is S. In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t- butyl). In one embodiment, RP is hydrogen. In another embodiment, RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). 10 In one embodiment, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1- 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R1 is hydrogen. In one embodiment, Y’ is S and R1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and RP is hydrogen. In one embodiment, Y’ is O and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl 15 (pac)). In one embodiment, Y’ is S and RP is hydrogen. In one embodiment, Y’ is S and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen 20 protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl 193 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is C1- 6alkyl (e.g., methyl or t-butyl) and RP is hydrogen . In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen . In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t- butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) 5 or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In another embodiment, the compound of Formula (X) is 10
, wherein each m is independently an integer selected from 1-10; each n is independently 0 or an integer selected from 1-10; (e.g., 1-5, or 1-3, or 3, or 2, or 1); Y’ is O or S, and RP and R1 are as defined for Formula (X) or any embodiment thereof. In one embodiment, each m is independently an integer selected from 2-10; or 2-8, or 2-6. 15 In one embodiment, Y’ is O. In another embodiment, Y’ is S. In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t- butyl). In one embodiment, RP is hydrogen. In another embodiment, RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). 20 In one embodiment, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1- 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R1 is hydrogen. In one embodiment, Y’ is S and R1 is C1-6alkyl (e.g., methyl or t-butyl). 194 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In one embodiment, Y’ is O and RP is hydrogen . In one embodiment, Y’ is O and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and RP is hydrogen. In one embodiment, Y’ is S and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl 5 (pac)). In one embodiment, Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl10 (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is C1- 6alkyl (e.g., methyl or t-butyl) and RP is hydrogen . In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t- butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP 15 is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In another embodiment, the compound of Formula (X) is
20 wherein Y’ is O or S, and RP and R1 are as defined for Formula (X) or any embodiment thereof. In one embodiment, Y’ is O. In another embodiment, Y’ is S. 195 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t- butyl). In one embodiment, RP is hydrogen. In another embodiment, RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). 5 In one embodiment, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1- 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R1 is hydrogen. In one embodiment, Y’ is S and R1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and RP is hydrogen . In one embodiment, Y’ is O and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl 10 (pac)). In one embodiment, Y’ is S and RP is hydrogen. In one embodiment, Y’ is S and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen 15 protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) 20 and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In another embodiment, the compound of Formula (X) is 25
, wherein Y’ is O or S, and RP, R1, L’, ZZ, and L are as defined for Formula (X) or any embodiment thereof. In one embodiment, Y’ is O. In another embodiment, Y’ is S. 196 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t- butyl). In one embodiment, RP is hydrogen. In another embodiment, RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). 5 In one embodiment, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1- 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R1 is hydrogen. In one embodiment, Y’ is S and R1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and RP is hydrogen. In one embodiment, Y’ is O and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl 10 (pac)). In one embodiment, Y’ is S and RP is hydrogen. In one embodiment, Y’ is S and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen 15 protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is C1- 6alkyl (e.g., methyl or t-butyl) and RP is hydrogen . In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t- 20 butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In another embodiment, the compound of Formula (X) is 25
wherein Y’ is O or S, and RP, R1, L’, and L are as defined for Formula (X) or any embodiment thereof. In one embodiment, Y’ is O. In another embodiment, Y’ is S. 197 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t- butyl). In one embodiment, RP is hydrogen. In another embodiment, RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). 5 In one embodiment, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1- 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R1 is hydrogen. In one embodiment, Y’ is S and R1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and RP is hydrogen . In one embodiment, Y’ is O and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl 10 (pac)). In one embodiment, Y’ is S and RP is hydrogen. In one embodiment, Y’ is S and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen 15 protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) 20 and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In another embodiment, the compound of Formula (X) is 25
198 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein each m is independently an integer selected from 1-10; Y’ is O or S, and RP and R1, are as defined for Formula (X) or any embodiment thereof. In one embodiment, each m is independently an integer selected from 2-10; or 2-8, or 2-6. In one embodiment, Y’ is O. In another embodiment, Y’ is S. 5 In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t- butyl). In one embodiment, RP is hydrogen. In another embodiment, RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1- 10 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R1 is hydrogen. In one embodiment, Y’ is S and R1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and RP is hydrogen . In one embodiment, Y’ is O and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and RP is hydrogen. In one embodiment, Y’ is S and RP is a 15 nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In 20 one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is C1- 6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen . In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t- butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) 25 or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In another embodiment, the compound of Formula (X) is 199 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
wherein Y’ is O or S, and RP and R1 are as defined for Formula (X) or any embodiment thereof. In one embodiment, Y’ is O. In another embodiment, Y’ is S. In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t- 5 butyl). In one embodiment, RP is hydrogen. In another embodiment, RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1- 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R1 is hydrogen. In one embodiment, 10 Y’ is S and R1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and RP is hydrogen . In one embodiment, Y’ is O and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and RP is hydrogen. In one embodiment, Y’ is S and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl 15 (pac)). In one embodiment, Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl20 (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is C1- 6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen . In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t- butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is 25 a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In another embodiment, the compound of Formula (X) is 200 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
, wherein Y’ is O or S, and RP, R1, L’, ZZ, and L are as defined for Formula (X) or any embodiment thereof. In one embodiment, Y’ is O. In another embodiment, Y’ is S. 5 In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t- butyl). In one embodiment, RP is hydrogen. In another embodiment, RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1- 10 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R1 is hydrogen. In one embodiment, Y’ is S and R1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and RP is hydrogen . In one embodiment, Y’ is O and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and RP is hydrogen. In one embodiment, Y’ is S and RP is a 15 nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In 20 one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is C1- 6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen . In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t- butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) 25 or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In another embodiment, the compound of Formula (X) is 201 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
wherein Y’ is O or S, and RP, R1, L’, and L are as defined for Formula (X) or any embodiment thereof. In one embodiment, Y’ is O. In another embodiment, Y’ is S. 5 In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t- butyl). In one embodiment, RP is hydrogen. In another embodiment, RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1- 10 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R1 is hydrogen. In one embodiment, Y’ is S and R1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and RP is hydrogen. In one embodiment, Y’ is O and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and RP is hydrogen. In one embodiment, Y’ is S and RP is a 15 nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In 20 one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or 25 phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In another embodiment, the compound of Formula (X) is 202 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
wherein each m is independently an integer selected from 1-10; Y’ is O or S, and RP and R1, are as defined for Formula (X) or any embodiment thereof. In one embodiment, each m is independently an integer selected from 2-10; or 2-8, or 2-6. 5 In one embodiment, Y’ is O. In another embodiment, Y’ is S. In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t- butyl). In one embodiment, RP is hydrogen. In another embodiment, RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). 10 In one embodiment, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1- 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R1 is hydrogen. In one embodiment, Y’ is S and R1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and RP is hydrogen. In one embodiment, Y’ is O and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl 15 (pac)). In one embodiment, Y’ is S and RP is hydrogen. In one embodiment, Y’ is S and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen 20 protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is C1- 6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t- 25 butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP 203 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In another embodiment, the compound of Formula (X) is
5 wherein Y’ is O or S, and RP and R1 are as defined for Formula (X) or any embodiment thereof. In one embodiment, Y’ is O. In another embodiment, Y’ is S. In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t- butyl). In one embodiment, RP is hydrogen. In another embodiment, RP is a nitrogen protecting group 10 (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1- 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R1 is hydrogen. In one embodiment, Y’ is S and R1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and RP is hydrogen. In one embodiment, Y’ is O and RP is a 15 nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and RP is hydrogen. In one embodiment, Y’ is S and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, 20 R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl 25 or t-butyl) and RP is hydrogen. In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a 204 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In another embodiment, the compound of Formula (X) is
, 5 wherein Y’ is O or S, and RP, R1, L’, ZZ, and L are as defined for Formula (X) or any embodiment thereof. In one embodiment, Y’ is O. In another embodiment, Y’ is S. In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t- butyl). 10 In one embodiment, RP is hydrogen. In another embodiment, RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1- 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R1 is hydrogen. In one embodiment, Y’ is S and R1 is C1-6alkyl (e.g., methyl or t-butyl). 15 In one embodiment, Y’ is O and RP is hydrogen. In one embodiment, Y’ is O and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and RP is hydrogen. In one embodiment, Y’ is S and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). 20 In one embodiment, Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is C1-6alkyl 25 (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a 205 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In another embodiment, the compound of Formula (X) is
, 5 wherein Y’ is O or S, and RP, R1, L’, and L are as defined for Formula (X) or any embodiment thereof. In one embodiment, Y’ is O. In another embodiment, Y’ is S. In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t- butyl). 10 In one embodiment, RP is hydrogen. In another embodiment, RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1- 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R1 is hydrogen. In one embodiment, Y’ is S and R1 is C1-6alkyl (e.g., methyl or t-butyl). 15 In one embodiment, Y’ is O and RP is hydrogen. In one embodiment, Y’ is O and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and RP is hydrogen. In one embodiment, Y’ is S and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). 20 In one embodiment, Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is C1- 25 6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t- butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP 206 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In another embodiment, the compound of Formula (X) is
, 5 wherein each m is independently an integer selected from 1-10; Y’ is O or S, and RP and R1 are as defined for Formula (X) or any embodiment thereof. In one embodiment, each m is independently an integer selected from 2-10; or 2-8, or 2-6. In one embodiment, Y’ is O. In another embodiment, Y’ is S. In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t- 10 butyl). In one embodiment, RP is hydrogen. In another embodiment, RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R1 is hydrogen. In one 15 embodiment, Y’ is S and R1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and RP is hydrogen. In one embodiment, Y’ is O and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and RP is hydrogen. In one embodiment, Y’ is S and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl 20 (pac)). In one embodiment, Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl25 (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is C1- 6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t- butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) 207 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In another embodiment, the compound of Formula (X) is 5
, wherein Y’ is O or S, and RP and R1 are as defined for Formula (X) or any embodiment thereof. In one embodiment, Y’ is O. In another embodiment, Y’ is S. In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t- butyl). 10 In one embodiment, RP is hydrogen. In another embodiment, RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1- 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R1 is hydrogen. In one embodiment, Y’ is S and R1 is C1-6alkyl (e.g., methyl or t-butyl). 15 In one embodiment, Y’ is O and RP is hydrogen. In one embodiment, Y’ is O and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and RP is hydrogen. In one embodiment, Y’ is S and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). 20 In one embodiment, Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is C1- 25 6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t- butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is 208 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). ZZ Embodiments, Formula (X) 5 In embodiments of Formula (X), Formula (X-a) through (X-w), including embodiments of Formulae (x-a) through (x-s) and (xi-a) through (xi-z) ZZ is a linking group formed by a reactive
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wherein RLa is hydrogen, C1-10alkyl (e.g., methyl, ethyl, propyl, isopropyl, t-butyl, isobutyl, butyl, or hexyl), C3-8cycloalkyl, 3-8 membered heterocyclyl, aryl (e.g., phenyl), or heteroaryl (e.g., 2- pyridyl). In some embodiments, ZZ comprises Group(1). In some embodiments, ZZ comprises 5 Group(2). In some embodiments, ZZ comprises Group(3). In some embodiments, ZZ comprises Group(4). In some embodiments, ZZ comprises Group(5). In some embodiments, ZZ comprises Group(6). In some embodiments, ZZ comprises Group(7). In some embodiments, ZZ comprises Group(8). In some embodiments, ZZ comprises Group(9). In some embodiments, ZZ comprises Group(10). In some embodiments, ZZ comprises Group(11). In some embodiments, ZZ comprises 10 Group(12). In some embodiments, wherein ZZ is -A’-B’-A’-. In some embodiments, ZZ is -A’-B’-A’-, wherein each A’ is independently a bond, -O-, -S-, or -N(RN3)-, wherein RN3 is independently hydrogen or C1-6alkyl and 15 each B’ is independently CH2, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH). In some embodiments, ZZ is CH2, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH). In some embodiments, ZZ is C(O), C(S), or S(O)2. In some embodiments, ZZ is P(O)(OH), or P(S)(OH). In some embodiments, ZZ is –C(O)-. 20 In some embodiments, ZZ is -A’-B’- or -B’-A’- wherein each A’ is independently -O-, -S-, or -N(RN3)-; each B’ is independently CH2, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); and each RN3 is independently hydrogen or C1-6alkyl. In some embodiments, ZZ is -A’-B’- or -B’-A’- wherein 25 each A’ is independently -O- or -N(RN3)-, wherein RN3 is independently hydrogen or C1- 6alkyl. each B’ is independently CH2, C(O), S(O)2, P(O)(OH), or P(S)(OH); and 210 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO each RN3 is independently hydrogen or C1-6alkyl. In some embodiments, ZZ is -CH2O-, -OCH2-, -S-S-, -C=N-, -C=N-O-, -C=N-N(RN3)-, - N=C-, -O-N=C-, -N(RN3)-N=C-, -C(O)N(RN3)-, -N(RN3)C(O)-, -C(O)O-, -OC(O)-, -OC(O)N(RN3)-, - N(RN3)C(O)O-, -N(RN3)C(O)N(RN3)-, -S(O)2N(RN3)-, -N(RN3)S(O)2-, -OP(O)(OH)O-, -OP(S)(OH)O-, 5 -OP(O)(OH)-, -OP(S)(OH)-, -P(O)(OH)O-, or -P(S)(OH)O-. wherein RN3 is independently hydrogen or C1-6alkyl. In some embodiments, ZZ is -CH2O- or -OCH2-. In some embodiments, ZZ is -S-S-. In some embodiments, ZZ is -C=N-, -C=N-O-, -C=N-N(RN3)-, -N=C-, -O-N=C-, or -N(RN3)- 10 N=C-, wherein RN3 is independently hydrogen or C1-6alkyl. In some embodiments, ZZ is -C(O)N(RN3)-, -N(RN3)C(O)-, -C(O)O-, -OC(O)-, - OC(O)N(RN3)-, -N(RN3)C(O)O-, -N(RN3)C(O)N(RN3)-, -S(O)2N(RN3)-, or -N(RN3)S(O)2-, wherein RN3 is independently hydrogen or C1-6alkyl. In some embodiments, ZZ is -C(O)N(RN3)- or -N(RN3)C(O)-, wherein RN3 is independently 15 hydrogen or C1-6alkyl. In some embodiments, ZZ is -C(O)O- or -OC(O)-. In some embodiments, ZZ is -OC(O)N(RN3)-, -N(RN3)C(O)O-, or -N(RN3)C(O)N(RN3)-, wherein RN3 is independently hydrogen or C1-6alkyl. In some embodiments, ZZ is -N(RN3)C(O)N(RN3)-, wherein RN3 is independently hydrogen 20 or C1-6alkyl. In some embodiments, ZZ is -OC(O)N(RN3)- or -N(RN3)C(O)O-, wherein RN3 is independently hydrogen or C1-6alkyl. In some embodiments, ZZ is -OP(O)(OH)O-, -OP(S)(OH)O-, -OP(O)(OH)-, -OP(S)(OH)-, - P(O)(OH)O-, or -P(S)(OH)O-. 25 In some embodiments, ZZ is -OP(O)(OH)O- or -OP(S)(OH)O-. In some embodiments, ZZ is -OP(S)(OH)O-. In some embodiments, ZZ is -OP(O)(OH)O-. In some embodiments, ZZ is -OP(O)(OH)-, -OP(S)(OH)-, -P(O)(OH)O-, or -P(S)(OH)O-. In some embodiments, ZZ is -OP(S)(OH)- or -P(S)(OH)O-. 30 In some embodiments, ZZ is -OP(O)(OH)- or -P(O)(OH)O-. 211 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
. Species of Formula (X) 5 In another embodiment, the compound of Formula (X) is selected from the group consisting of: (X-a) (X-b) (X-c) (X-d) (X-e) (X-f) 212 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO (X-g) (X-h)
In another embodiment, the compound of Formula (X) is selected from the group consisting of:
213 ME1\53453057.v1
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214 ME1\53453057.v1
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215 ME1\53453057.v1
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216 ME1\53453057.v1
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wherein * or the broken bond represents the bond to the remainder of the dsRNA agent. In another embodiment, the compound of Formula (X) is selected from the group consisting of: 217 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
wherein * represents the bond to the remainder of the dsRNA agent. In another embodiment, the compound of Formula (X) is selected from the group
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219 ME1\53453057.v1
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wherein * represents the bond to the remainder of the dsRNA agent. C. Alpha-v-Beta-6 (αvβ6) Integrin Targeting Ligands Conjugated to a Branched Carrier Group 5 In some embodiments, the alpha-v-beta-6 (αvβ6) integrin targeting ligand may be conjugated to the dsRNA agent of the disclosure, e.g., to at least one strand of the dsRNA agent of the disclosure, via a branched carrier group, e.g., a b. In some embodiments, the alpha-v-beta-6 (αvβ6) integrin targeting ligand conjugated to the dsRNA agent of the disclosure, e.g., to at least one strand of the dsRNA agent of the disclosure, is represented by a compound of Formula (XV): 10 (Φ-ZZ-)xΔ-T-RT (XV) or a salt thereof, wherein x is 2, 3, 4, 5, 6, 7, or 8; T is a divalent linking group; Δ is a branching group; 15 each ZZ is independently -A’-B’-A’- or a linking group formed by a first reactive pair, wherein 220 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO each A’ is independently a bond, -O-, -S-, or -N(RN3)-; each B’ is independently a bond, CH2, C(O), C(S), C(NRN3), -C=N-, S(O), S(O)2, P(O)(OH), P(S)(OH), or P(S)(SH); and each RN3 is independently hydrogen or C1-6alkyl, or two RN3 within the -A’-B’-A’- group 5 taken together with the atoms to which they are connected from a 4-8 membered heterocyclyl; and RT is -RT1 or -G0-ORT1, wherein G0 is -D0-E0-F0-, wherein D0, E0, and F0 are independently a bond, C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, 10 or 4 R groups; and RT1 is -LL-oligonucleotide, wherein LL is an oligonucleotide linking group connecting the αvβ6 integrin targeting ligand to the oligonucleotide comprised in the dsRNA agent; and each Φ is a compound of the Formula (XII),
wherein: 15 Y is O, N(H), S, or CH2; R1 is hydrogen, or C1-6alkyl (e.g., methyl), or a carboxylic acid mimic ;
, wherein m is 0, 1, 2, 3, or 4; and each R2 is independently R, or two R2 groups on adjacent carbon atoms taken together with 20 the atoms to which they are bound form a fused 4 – 8 membered ring that is optionally substituted by 1, 2, 3 or 4 groups independently selected from group consisting of R and a nitrogen protecting group; A is an 5-membered heteroaryl optionally substituted with 1 or 2 substituents independently selected from methyl, ethyl, fluoro, hydroxymethyl, 2-hydroxypropan-2-yl, trifluoromethyl, difluoromethyl, and fluoromethyl; 25 Q is -COOR1 or tetrazolyl (e.g., 1,2,3,4-tetrazol-5-yl); and RL is -N(R3)(R4), -O(R5), -S(R5), or -R5, wherein R3 and R4 are either (viii) R3 is hydrogen or C1-6alkyl and R4 is R5; or 30 (ix) R3 and R4 taken together with the nitrogen atom to which they are attached form a 4 – 8 membered monocyclic heterocyclyl group that is substituted with R5; 221 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO and R5 is -L-* wherein L is -L1-[G-L2]q-G-L3-*, * is the bond to a ZZ; and q is 0 or an integer selected from 1 – 25; (e.g., 1-20, or 1-15); 5 L1 is a bond or -B-A-; each L2 is independently -A-B-A-; L3 is a bond or -A-B-A-; each G is independently -D-E-F-, wherein D, E, and F are independently a bond, C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3- 10 10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups; each A is independently a bond, -O-, -S-, or -N(RN)-; each B is independently a bond, CH2, C(O), C(S), C(NRN), S(O), S(O)2, P(O)(OH), P(S)(OH), or P(S)(SH); 15 each RN is independently hydrogen or C1-6alkyl, or two RN within an -A-B-A- group taken together with the atoms to which they are connected from a 4-8 membered heterocyclyl. Embodiment for the variables of Formula (XII), and (XV) that are the same as Formula (X) are as described above for Formula (X). For example, embodiments for the variable ZZ are each as described above for Formula (X); embodiments for the variable RT and L are each as described above 20 for Formula (X). In certain embodiments, the compound of formula (
25 T Embodiments, Formula (XV) In some embodiments, T is a bond or **-L6-G1-[L5-G1]q1-L4-, wherein ** is the bond to RT; q1 is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10; each L4, L5, and L6 are independently a bond, -A1-B1-A1- or ZZ1; 222 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO ZZ1 is a group formed by reaction of a reactive pair (e.g., a reaction between an azide and an alkyne or a cycloalkyne); each G1 is independently -D1-E1-F1-, wherein D1, E1, and F1 are independently a bond, C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, 5 each of which is optionally substituted with 1, 2, or 3 R groups; each A1 is independently a bond, -O-, -S-, or -N(RN1)-; each B1 is independently a bond, C(O), C(S), C(NRN1), S(O), S(O)2, P(O)(OH), P(S)(OH), or P(S)(SH); each RN1 is independently hydrogen or C1-6alkyl, or two RN1 within an -A1-B1-A1- 10 group taken together with the atoms to which they are connected from a 4-8 membered heterocyclyl. In some embodiments, T is **-L6-G1-L5-G1-L4-, wherein ** is the bond to RT; L4 and L6 are independently -A1-B1-A1-; each L5 is a bond or - A1-B1-A1- (e.g., a bond, -B1-A1- or -A1-B1-; or a bond); each G1 is independently C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 15 membered heterocyclyl, aryl, or heteroaryl (e.g., C1-10alkyl or C2-10alkenyl); each A1 is independently a bond, -O-, -S-, or -N(RN1)-, wherein RN1 is independently hydrogen or C1-6alkyl; and each B1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH). 20 In some embodiments, T is **-L6-G1-[L5-G1]q1-L4-, wherein ** is the bond to RT; q1 is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10; each L4, L5, and L6 are independently a bond or -A1-B1-A1-, or ZZ1; ZZ1 is a group formed by reaction of an azide and alkyne or cycloalkyne; 25 each G1 is independently C1-10alkyl, each A1 is independently a bond, -O-, -S-, or -N(RN1)-; each B1 is independently a bond, C(O), C(S), C(NRN1), S(O), S(O)2, P(O)(OH), P(S)(OH), or P(S)(SH); and each RN1 is independently hydrogen or C1-6alkyl. 30 In a further embodiment, one L5 is ZZ1. In a further embodiment, ZZ1 comprises:
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. In some embodiments, T is **-L6-G1-L5-G1-L4-, wherein ** is the bond to RT; L4 and L6 are independently -A1-B1- or -B1-A1-; 5 each L5 is a bond or - A1-B1-A1- (e.g., a bond, -B1-A1- or -A1-B1-; or a bond); each G1 is independently C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl (e.g., C1-10alkyl or C2-10alkenyl); each A1 is independently a bond, -O-, -S-, or -N(RN1)-, wherein RN1 is independently hydrogen or C1-6alkyl;and 10 each B1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH). In some embodiments, T is **-B1-G1-L5-G1-B1-, wherein ** is the bond to RT; each L5 is a bond or - A1-B1-A1- (e.g., a bond, -B1-A1- or -A1-B1-; or a bond); each G1 is independently C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl (e.g., C1-10alkyl or C2-10alkenyl); 15 each A1 is independently a bond, -O-, -S-, or -N(RN1)-, wherein RN1 is independently hydrogen or C1-6alkyl; and each B1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH). In some embodiments, T is **-L6-G1-L5-G1-L4-, wherein ** is the bond to RT; L4 and L6 are independently -A1-B1-A1-; 20 each L5 is a bond or - A1-B1-A1- (e.g., a bond, -B1-A1- or -A1-B1-; or a bond); each G1 is independently C1-10alkyl or C2-10alkenyl; each A1 is independently a bond, -O-, -S-, or -N(RN1)-, wherein RN1 is independently hydrogen or C1-6alkyl; and each B1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH). 25 In some embodiments, T is **-L6-G1-L5-G1-L4-, wherein ** is the bond to RT; L4 and L6 are independently -B1-A1- or -A1-B1-; each L5 is a bond or - A1-B1-A1- (e.g., a bond, -B1-A1- or -A1-B1-; or a bond); each G1 is independently C1-10alkyl or C2-10alkenyl; each A1 is independently a bond, -O-, -S-, or -N(RN1)-, wherein RN1 is independently 30 hydrogen or C1-6alkyl; and each B1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH). In some embodiments, T is **-B1-G1-L5-G1-B1-, wherein ** is the bond to RT; each L5 is a bond or - A1-B1-A1- (e.g., a bond, -B1-A1- or -A1-B1-; or a bond); each G1 is independently C1-10alkyl or C2-10alkenyl; 224 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO each A1 is independently a bond, -O-, -S-, or -N(RN1)-, wherein RN1 is independently hydrogen or C1-6alkyl; and each B1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH). In some embodiments, T is **-B1-C1-10alkyl-L5-C1-10alkyl-B1-, wherein 5 ** is the bond to RT; each L5 is a bond or - A1-B1-A1- (e.g., a bond, -B1-A1- or -A1-B1-; or a bond); each A1 is independently a bond, -O-, -S-, or -N(RN1)-, wherein RN1 is independently hydrogen or C1-6alkyl; and each B1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH). 10 In some embodiments, T is -L4-G1-L6-**, wherein ** is the bond to RT; L4 and L6 are independently -A1-B1-A1-; each G1 is independently C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, or 3 R groups; 15 each A1 is independently a bond, -O-, -S-, or -N(RN1)-, wherein RN1 is hydrogen or C1- 6alkyl; and each B1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH). In some embodiments, T is -L4-G1-L6-**, wherein ** is the bond to RT; 20 L4 is -C(O)O- or C(O)N(RN1)-, wherein RN1 is hydrogen or C1-6alkyl; L6 is -OP(O)(OH)O- or -OP(S)(OH)O-; and each G1 is independently C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, or 3 R groups. 25 In some embodiments, T is one of:
(d) **-L6-G1-ZZ1-L5-G1-L4-, 30 (e) **-L6-G1-L5-G1-ZZ1-G1-L4-; or (f) **-L6-G1-ZZ1-G1-L4-, wherein the sum of q2 and q3 is less than q1 In certain embodiments, q2 and q3 are independently 0, 1, 2, 3 or 4. In certain embodiments, each G1 is independently C1-20 alkyl (e.g., C2-15alkyl; or C2- 12alkyl; or C2-10alkyl; or C2-8alkyl; or C2-6alkyl). 35 In certain embodiments, each L5 is independently -C(O)O-, -OC(O)-, -C(O)N(H)-, - N(H)C(O)-, -OC(O)O-, -OC(O)N(H)-, -N(H)C(O)O-, -N(H)C(O)N(H)-, -P(O)(OH)O-, -OP(S)(OH)-, -OP(O)(OH)O, -OP(S)(OH)O, -P(O)(OH)O-, or -P(S)(OH)O-. In certain embodiments, each L5 is 225 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO independently -C(O)O-, -OC(O)-, -C(O)N(H)- or -N(H)C(O)-. In certain embodiments, each L5 is independently -C(O)N(H)- or -N(H)C(O)-. In certain embodiments, each G1 is independently C1-20 alkyl (e.g., C2-15alkyl; or C2-12alkyl; or C2-10alkyl); and each L5 is independently -C(O)O-, -OC(O)-, -C(O)N(H)-, -N(H)C(O)-, -OC(O)O-, - 5 OC(O)N(H)-, -N(H)C(O)O-, -N(H)C(O)N(H)-, -P(O)(OH)O-, -OP(S)(OH)-, -OP(O)(OH)O, - OP(S)(OH)O, -P(O)(OH)O-, or -P(S)(OH)O-. In certain embodiments, each G1 is independently C1-20 alkyl (e.g., C2-15alkyl; or C2-12alkyl; or C2-10alkyl); and each L5 is independently -C(O)O-, -OC(O)-, -C(O)N(H)- or -N(H)C(O)-. In certain embodiments, L6 is a bond. In certain embodiments, L6 is -C(O)-, -S(O)2-, - 10 P(O)(OH)-, or -P(S)(OH)-. In certain embodiments, L6 is -P(O)(OH)- or -P(S)(OH)-. In certain embodiments, L6 is -P(O)(OH)-. In certain embodiments, L6 is -P(S)(OH)-. In certain embodiments, L6 is -C(O)-. In certain embodiments, L4 is -C(O)O-, -OC(O)-, -C(O)N(H)-, -N(H)C(O)-, -OC(O)O-, - OC(O)N(H)-, -N(H)C(O)O-, -N(H)C(O)N(H)-, -P(O)(OH)O-, -OP(S)(OH)-, -OP(O)(OH)O, -15 OP(S)(OH)O, -P(O)(OH)O-, or -P(S)(OH)O-. In certain embodiments, L4 is -P(O)(OH)O-, - OP(S)(OH)-, -OP(O)(OH)O, -OP(S)(OH)O, -P(O)(OH)O-, or -P(S)(OH)O-. In certain embodiments, L4 is -C(O)O-, -OC(O)-, -C(O)N(H)-, or -N(H)C(O)-. In some embodiments, T is one of: 20
(d) **-L6-G1-ZZ1-L5-G1-L4-, (e) **-L6-G1-L5-G1-ZZ1-G1-L4-; or (f) **-L6-G1-ZZ1-G1-L4-, wherein the sum of q2 and q3 is less than q1; and ZZ1 is selected from the group consisting of:
226 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
hexyl), C3-8cycloalkyl, 3-8 membered heterocyclyl, aryl (e.g., phenyl), or heteroaryl (e.g., 2-pyridyl); and the sum of q2 and q3 is less than q1 In certain embodiments, q2 and q3 are independently 0, 1, 2, 3 or 4. In certain embodiments, 5 each G1 is independently C1-20 alkyl (e.g., C2-15alkyl; or C2-12alkyl; or C2-10alkyl; or C2-8alkyl; or C2- 6alkyl). In certain embodiments, each L5 is independently -C(O)O-, -OC(O)-, -C(O)N(H)-, - N(H)C(O)-, -OC(O)O-, -OC(O)N(H)-, -N(H)C(O)O-, -N(H)C(O)N(H)-, -P(O)(OH)O-, -OP(S)(OH)-, -OP(O)(OH)O, -OP(S)(OH)O, -P(O)(OH)O-, or -P(S)(OH)O-. In certain embodiments, each L5 is 10 independently -C(O)O-, -OC(O)-, -C(O)N(H)- or -N(H)C(O)-. In certain embodiments, each L5 is independently -C(O)N(H)- or -N(H)C(O)-. In certain embodiments, each G1 is independently C1-20 alkyl (e.g., C2-15alkyl; or C2-12alkyl; or C2-10alkyl); and each L5 is independently -C(O)O-, -OC(O)-, -C(O)N(H)-, -N(H)C(O)-, -OC(O)O-, - OC(O)N(H)-, -N(H)C(O)O-, -N(H)C(O)N(H)-, -P(O)(OH)O-, -OP(S)(OH)-, -OP(O)(OH)O, - 15 OP(S)(OH)O, -P(O)(OH)O-, or -P(S)(OH)O-. In certain embodiments, each G1 is independently C1-20 alkyl (e.g., C2-15alkyl; or C2-12alkyl; or C2-10alkyl); and each L5 is independently -C(O)O-, -OC(O)-, -C(O)N(H)- or -N(H)C(O)-. In certain embodiments, L6 is a bond. In certain embodiments, L6 is -C(O)-, -S(O)2-, - P(O)(OH)-, or -P(S)(OH)-. In certain embodiments, L6 is -P(O)(OH)- or -P(S)(OH)-. In certain 20 embodiments, L6 is -P(O)(OH)-. In certain embodiments, L6 is -P(S)(OH)-. In certain embodiments, L6 is -C(O)-. In certain embodiments, L4 is -C(O)O-, -OC(O)-, -C(O)N(H)-, -N(H)C(O)-, -OC(O)O-, - OC(O)N(H)-, -N(H)C(O)O-, -N(H)C(O)N(H)-, -P(O)(OH)O-, -OP(S)(OH)-, -OP(O)(OH)O, - OP(S)(OH)O, -P(O)(OH)O-, or -P(S)(OH)O-. In certain embodiments, L4 is -P(O)(OH)O-, - 25 OP(S)(OH)-, -OP(O)(OH)O, -OP(S)(OH)O, -P(O)(OH)O-, or -P(S)(OH)O-. In certain embodiments, L4 is -C(O)O-, -OC(O)-, -C(O)N(H)-, or -N(H)C(O)-. In some embodiments, T is one of: (a) **-L6-C2-12alkyl-[L5-C2-12alkyl]q2-ZZ1-[L5-C2-12alkyl]q3-L4-; (c) **-L6- C2-12alkyl-L5-C2-12alkyl-ZZ1-L5-C2-12alkyl-L4-; 30 (d) **-L6-C2-12alkyl-ZZ1-L5-C2-12alkyl-L4-, (e) **-L6-C2-12alkyl-L5-C2-12alkyl-ZZ1-C2-12alkyl-L4-; or (f) **-L6-C2-12alkyl-ZZ1-C2-12alkyl-L4-, 227 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein the sum of q2 and q3 is less than q1 In certain embodiments, q2 and q3 are independently 0, 1, 2, 3 or 4. In certain embodiments, each L5 is independently -C(O)O-, -OC(O)-, -C(O)N(H)-, - N(H)C(O)-, -OC(O)O-, -OC(O)N(H)-, -N(H)C(O)O-, -N(H)C(O)N(H)-, -P(O)(OH)O-, -OP(S)(OH)-, 5 -OP(O)(OH)O, -OP(S)(OH)O, -P(O)(OH)O-, or -P(S)(OH)O-. In certain embodiments, each L5 is independently -C(O)O-, -OC(O)-, -C(O)N(H)- or -N(H)C(O)-. In certain embodiments, each L5 is independently -C(O)N(H)- or -N(H)C(O)-. In certain embodiments, L6 is a bond. In certain embodiments, L6 is -C(O)-, -S(O)2-, - P(O)(OH)-, or -P(S)(OH)-. In certain embodiments, L6 is -P(O)(OH)- or -P(S)(OH)-. In certain 10 embodiments, L6 is -P(O)(OH)-. In certain embodiments, L6 is -P(S)(OH)-. In certain embodiments, L6 is -C(O)-. In certain embodiments, L4 is -C(O)O-, -OC(O)-, -C(O)N(H)-, -N(H)C(O)-, -OC(O)O-, - OC(O)N(H)-, -N(H)C(O)O-, -N(H)C(O)N(H)-, -P(O)(OH)O-, -OP(S)(OH)-, -OP(O)(OH)O, - OP(S)(OH)O, -P(O)(OH)O-, or -P(S)(OH)O-. In certain embodiments, L4 is -P(O)(OH)O-, - 15 OP(S)(OH)-, -OP(O)(OH)O, -OP(S)(OH)O, -P(O)(OH)O-, or -P(S)(OH)O-. In certain embodiments, L4 is -C(O)O-, -OC(O)-, -C(O)N(H)-, or -N(H)C(O)-. In some embodiments, T is selected from the following, wherein ** is the bond to RT: (q) **-C(O)-C1-10alkyl-L5-C1-10alkylC(O)-, (r) **-C(O)-C2-10alkyl-L5-C2-10alkyl-C(O)-, 20 (s) **-C(O)-C4-10alkyl-L5-C4-10alkyl-C(O)-, (t) **-C(O)-C6-10alkyl-L5-C6-10alkyl-C(O)-, (u) **-C(O)-C2-8alkyl-L5-C2-8alkyl-C(O)-, (v) **-C(O)-C2-6alkyl-L5-C2-6alkyl-C(O)-, (w) **-C(O)-C2-4alkyl-L5-C2-4alkyl-C(O)- 25 (x) **-C(O)-C2-20alkyl-C(O)-, (y) **-C(O)-C2-12alkyl-C(O)-, (z) **-C(O)-C6-20alkyl-C(O)-, (aa) **-C(O)-C6-12alkyl-C(O)-, (bb) **-C(O)-C10alkyl-C(O)- and 30 (cc) **-C(O)-CH2CH2-C(O)-, wherein each L5 is a bond or - A1-B1-A1- (e.g., a bond, -B1-A1- or -A1-B1-; or a bond), wherein each A1 is independently a bond, -O-, -S-, or -N(RN1)-, wherein RN1 is independently hydrogen or C1-6alkyl; and each B1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH). 35 In some embodiments, T is selected from the following, wherein ** is the bond to RT:
228 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO (ff) **- N(H)C(O)-C6-12alkyl-C(O)-, (gg) **- N(H)C(O)-C10alkyl-C(O)-, (hh) **-C(O)-C2-20alkyl-C(O)N(H)-, (ii) **-C(O)-C6-20alkyl-C(O)N(H)-, 5 (jj) **-C(O)-C6-12alkyl-C(O)N(H)-, (kk) **-C(O)-C10alkyl-C(O)N(H)-, (ll) **-N(H)C(O)-C2-20alkyl-C(O)N(H)-, (mm) **- N(H)C(O)-C6-20alkyl-C(O)N(H)-, (nn) **- N(H)C(O)-C6-12alkyl-C(O)N(H)-, 10 and (oo) **- N(H)C(O)-C10alkyl-C(O)N(H). In some embodiments, T is -L4-G1-L6-**, wherein ** is the bond to RT; L4 is -C(O)O- or C(O)N(RN1)-, wherein RN1 is hydrogen or C1-6alkyl; L6 is -OP(O)(OH)O- or -OP(S)(OH)O-; and 15 each G1 is independently C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with one R group. In some embodiments, T is -L4-G1-L6-**, wherein ** is the bond to RT; L4 is -C(O)O- or C(O)N(RN1)-, wherein RN1 is hydrogen or C1-6alkyl; L6 is -OP(O)(OH)O- or -OP(S)(OH)O-; and 20 each G1 is independently C3-10cycloalkyl or 3-10 membered heterocyclyl. In some embodiments, T is -L4-G1-L6-**, wherein ** is the bond to RT; L4 is -C(O)O- or C(O)N(RN1)-, wherein RN1 is hydrogen or C1-6alkyl; L6 is -OP(O)(OH)O- or -OP(S)(OH)O-; and each G1 is independently C3-10cycloalkyl or 3-10 membered heterocyclyl. 25 In some embodiments,
wherein ** is the bond to RT; and X is O or S (e.g., S). In some embodiments, T is **-L6-[G5-O]q5-G5-L4-, wherein ** is the bond to RT; q5 is an integer selected from 1 to 20; L4 and L6 are independently -A1-B1-A1-, wherein 30 each A1 is independently a bond, -O-, -S-, or -N(RN1)-, wherein RN1 is hydrogen or C1-6alkyl; each B1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); each G5 is independently C1-10alkyl; and each L10 is -O-. In some embodiments, T is **-C(O)-[CH2CH2-O]q5-G5-L4-, wherein ** is the bond to RT; 35 q5 is an integer selected from 1 to 20; L4 is -A1-B1-A1-, wherein 229 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO each A1 is independently a bond, -O-, -S-, or -N(RN1)-, wherein RN1 is hydrogen or C1-6alkyl; each B1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); G5 is C1-10alkyl. In some embodiments, T is **-C(O)-[CH2CH2-O]q5-G5-L4-, wherein ** is the bond to RT; 5 q5 is an integer selected from 1 to 20; L4 is -A1-B1 or -B1-A1-, wherein each A1 is independently -O- or -N(H)-, each B1 is independently C(O), G5 is C1-10alkyl (e.g., C2-10alkyl or C2-6alkyl). 10 In some embodiments, T is **-C(O)-[CH2CH2-O]q5- C2-10alkyl-C(O)N(H)-, wherein ** is the bond to RT, wherein q5 is an integer selected from 1 to 20 (e.g., 1 to 10, or 2 to 10; or 2 – 8; or 1; or 2; or 3; or 4.) In some embodiments, Formula (XV) is according to one of Formulae (XVa) through (XVc), respectively:
(XVc). 15 Δ Embodiments, Formula (XV) In some embodiments, Δ is #–[G2-L7]q2-* or #–G3-([L7-G4]q3-*)y, wherein 20 # is the bond to T; y is 1, 2, 3, 4, or 5; q2 is 1, 2, 3, 4, 5, 6, 7, or 8; q3 is 0, 1, 2, 3, 4, 5, 6, 7, or 8; each G2, G3, and G4 is independently -D2-E2-F2-, wherein 25 D2, E2, and F2 are independently a bond, C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, 4, or 5 RB groups, and wherein each G2 and G4 optionally contains at least one bond to a ZZ (e.g., one bond to a ZZ); or G3 is N and y is 2; 230 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO each L7 is independently -A2-B2-A2-; wherein each A2 is independently a bond, -O-, -S-, or -N(RN2)-; each B2 is independently a bond, C(O), C(S), C(NRN2), S(O), S(O)2, P(O)(OH), P(S)(OH), or P(S)(SH); and 5 each RN2 is independently hydrogen, C1-6alkyl, a bond to a ZZ, or two RN2 within an -A2-B2- A2- group taken together with the atoms to which they are connected from a 4-8 membered heterocyclyl; and each RB is independently halogen, cyano, azido, nitro, -N(R10)2, -O(R10), -S(R10), -C(O)OR10,10 -C(O)R10, -C(O)N(R10)2, -C(NR10)OR10, -C(NR10)R10, -C(NR10)N(R10)2, -C(S)OR10, - C(S)R10, -C(S)N(R10)2, -S(O)2R10, -S(O)2OR10, -S(O)2N(R10)2, -N(R10)C(O)OR10, -N(R10)C(O)R10, -N( R10)C(O)N(R10)2, -N(R10)S(O)2R10, -N(R10)S(O)2OR10, -N(R10)S(O)2N(R10)2, -OC(O)OR10, - OC(O)R10, -OC(O)N(R10)2, -OS(O)2R10, -OS(O)2OR10, -OS(O)2N(R10)2, or -SC(O)R10, wherein each R10 is independently hydrogen, C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered 15 heterocyclyl, aryl, or heteroaryl.provided that Δ contains x bonds to ZZ. In some embodiments, Δ is #–[G2-L7]q2-* wherein # is the bond to T; q2 is 1, 2, 3, 4, 5, 6, 7, or 8; q3 is 0, 1, 2, 3, 4, 5, 6, 7, or 8; 20 each G2, G3, and G4 is independently -D2-E2-F2-, wherein D2, E2, and F2 are independently a bond, C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, 4, or 5 RB groups, and wherein each G2 optionally contains at least one bond to ZZ; 25 each L7 is independently -A2-B2-A2-; each A2 is independently a bond, -O-, -S-, or -N(RN2)-; each B2 is independently a bond, C(O), C(S), C(NRN2), S(O), S(O)2, P(O)(OH), P(S)(OH), or P(S)(SH); each RN2 is independently hydrogen, C1-6alkyl, a bond to a ZZ, or two RN2 within an -A2-B2- 30 A2- group taken together with the atoms to which they are connected from a 4-8 membered heterocyclyl; each RB is independently halogen, cyano, azido, nitro, -N(R10)2, -O(R10), -S(R10), -C(O)OR10, -C(O)R10, -C(O)N(R10)2, -C(NR10)OR10, -C(NR10)R10, -C(NR10)N(R10)2, -C(S)OR10, - C(S)R10, -C(S)N(R10)2, -S(O)2R10, -S(O)2OR10, -S(O)2N(R10)2, -N(R10)C(O)OR10, -N(R10)C(O)R10, -N(35 R10)C(O)N(R10)2, -N(R10)S(O)2R10, -N(R10)S(O)2OR10, -N(R10)S(O)2N(R10)2, -OC(O)OR10, - OC(O)R10, -OC(O)N(R10)2, -OS(O)2R10, -OS(O)2OR10, -OS(O)2N(R10)2, or -SC(O)R10, wherein each R10 is independently hydrogen, C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3- 10 membered heterocyclyl, aryl, or heteroaryl. 231 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In one embodiment, -Δ- is #–[G2-L7]q2-*, where # is the bond to T and * is a bond to a ZZ group. For example, such embodiments include the following,
wherein each * is a bond to a ZZ; # is the bond to T, each G2 is independently C1-10alkyl, C2-10alkenyl, C3-10cycloalkyl, 3-10 membered 5 heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, 4, or 5 RB groups; and each L7 is independently -A2-B2-A2-, wherein each A2 is independently a bond, -O-, -S-, or - N(RN2)-; each B2 is independently a bond, C(O), S(O)2, P(O)(OH), or P(S)(OH). In one embodiment, each G2 is independently C1-10alkyl, each optionally substituted with 1 or 2 RB groups. In one embodiment, each G2 is independently C1-10alkyl. 10 In one embodiment, each L7 is independently -A2-B2-A2-, wherein each A2 is independently a bond, -O-, -S-, or -N(RN2)-; and each B2 is independently a bond, C(O) or S(O)2, provided that at least one A2 is not a bond. In one embodiment, each L7 is independently -A2-B2- or - B2-A2-, wherein each A2 is independently, -O-, -S-, or -N(RN2)-; and each B2 is independently a bond, C(O) or S(O)2. 15 For example, such embodiments include each of the following,
wherein # is the bond to T and each * is a bond to a ZZ group. ; and each G2 is independently C1-10alkyl. For example, such embodiments include each of the following, wherein # is the bond to T and each * is a bond to a ZZ;
232 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
wherein # is the bond to T and each * is a bond to a ZZ group. In one embodiment, -#–G3-([L7-G4]q3-*)y,where # is the bond to T and * is a bond to a ZZ group. For example, such embodiments include each of the following,
5 wherein # is the bond to T, each * is a bond to a ZZ group, and each L7 is selected from the group consisting of -O-, -S-, -N(H)-, -C(O)O-, -OC(O)-, - C(O)N(H)-, -OC(O)O-, -N(H)C(O)O-, -OC(O)N(H)-, -OP(O)(OH)O-, or -OP(S)(OH)O-; and each G4 is independently -D2-E2-F2-, wherein each D2 and F2 are independently a bond or C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3- 10 10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, 4, or 5 RB groups, and each E2 is independently bond, C1-10alkyl, C2-10alkenyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, 4, or 5 RB groups, provided that E2 is not a bond with D2 and F2 are each bonds. 15 In one embodiment of -#–G3-([L7-G4]q3-*)y, each L7 is selected from the group consisting of -O-, -S-, -N(H)-, -N(H)C(O)-, -C(O)N(H)-, - OP(O)(OH)O-, and -OP(S)(OH)O-; and each G4 is independently -D2-E2-F2-, wherein each D2 and F2 are independently a bond or C1-10alkyl; 233 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO each E2 is independently C1-10alkyl, C2-10alkenyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, 4, or 5 RB groups. In one embodiment of -#–G3-([L7-G4]q3-*)y, each L7 is selected from the group consisting of -O-, -S-, -N(H)-, -N(H)C(O)-,-C(O)N(H)-, - 5 OP(O)(OH)O-, and -OP(S)(OH)O-; and each G4 is independently C1-10alkyl, C2-10alkenyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, 4, or 5 RB . In one embodiment of -#–G3-([L7-G4]q3-*)y, each L7 is selected from the group consisting of -O-, -S-, -N(H)-, -N(H)C(O)-, -C(O)N(H)-, - 10 OP(O)(OH)O-, and -OP(S)(OH)O-; and each G4 is independently C1-10alkyl which is optionally substituted with 1 or, 2 5 RB groups. In one embodiment of -#–G3-([L7-G4]q3-*)y each L7 is selected from the group consisting of -O-, -S-, -N(H)-, --N(H)C(O)-, C(O)N(H)-, - 15 OP(O)(OH)O-, and -OP(S)(OH)O-; and each G4 is independently C1-10alkyl. In one embodiment of -#–G3-([L7-G4]q3-*)y, each L7 is selected from the group consisting of --N(H)C(O)- and C(O)N(H)-; and each G4 is independently C1-10alkyl. 20 For example, such embodiments include each of the following, wherein each * is a bond to a
wherein # is the bond to T and each * is a bond to a ZZ group. 234 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO ZZ Embodiments, Formulae (XV) and (XVa) through (XVc) In embodiments of Formulae (XV) and (XVa) through (XVc), ZZ is a linking group formed by a reactive pair. 5 In some embodiments, ZZ comprises a group selected from the group consisting of
235 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
In some embodiments, ZZ comprises Group(1). In some embodiments, ZZ comprises Group(2). In some embodiments, ZZ comprises Group(3). In some embodiments, ZZ comprises Group(4). In some embodiments, ZZ comprises Group(5). In some embodiments, ZZ comprises Group(6). In some embodiments, ZZ comprises Group(7). In some embodiments, ZZ comprises 5 Group(8). In some embodiments, ZZ comprises Group(9). In some embodiments, ZZ comprises Group(10). In some embodiments, ZZ comprises Group(11). In some embodiments, ZZ comprises Group(12). In some embodiments, wherein ZZ is -A’-B’-A’-. In some embodiments, ZZ is -A’-B’-A’-, wherein 10 each A’ is independently a bond, -O-, -S-, or -N(RN3)-, wherein RN3 is independently hydrogen or C1-6alkyl and each B’ is independently CH2, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH). In some embodiments, ZZ is CH2, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH). In some embodiments, ZZ is C(O), C(S), or S(O)2. 15 In some embodiments, ZZ is P(O)(OH), or P(S)(OH). In some embodiments, ZZ is –C(O)-. In some embodiments, ZZ is -A’-B’- or -B’-A’- wherein each A’ is independently -O-, -S-, or -N(RN3)-; each B’ is independently CH2, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); and 20 each RN3 is independently hydrogen or C1-6alkyl. In some embodiments, ZZ is -A’-B’- or -B’-A’- wherein each A’ is independently -O- or -N(RN3)-, wherein RN3 is independently hydrogen or C1- 6alkyl. each B’ is independently CH2, C(O), S(O)2, P(O)(OH), or P(S)(OH); and 25 each RN3 is independently hydrogen or C1-6alkyl. In some embodiments, ZZ is -CH2O-, -OCH2-, -S-S-, -C=N-, -C=N-O-, -C=N-N(RN3)-, - N=C-, -O-N=C-, -N(RN3)-N=C-, -C(O)N(RN3)-, -N(RN3)C(O)-, -C(O)O-, -OC(O)-, -OC(O)N(RN3)-, - 236 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO N(RN3)C(O)O-, -N(RN3)C(O)N(RN3)-, -S(O)2N(RN3)-, -N(RN3)S(O)2-, -OP(O)(OH)O-, -OP(S)(OH)O-, -OP(O)(OH)-, -OP(S)(OH)-, -P(O)(OH)O-, or -P(S)(OH)O-. wherein RN3 is independently hydrogen or C1-6alkyl. In some embodiments, ZZ is -CH2O- or -OCH2-. 5 In some embodiments, ZZ is -S-S-. In some embodiments, ZZ is -C=N-, -C=N-O-, -C=N-N(RN3)-, -N=C-, -O-N=C-, or -N(RN3)- N=C-, wherein RN3 is independently hydrogen or C1-6alkyl. In some embodiments, ZZ is -C(O)N(RN3)-, -N(RN3)C(O)-, -C(O)O-, -OC(O)-, - OC(O)N(RN3)-, -N(RN3)C(O)O-, -N(RN3)C(O)N(RN3)-, -S(O)2N(RN3)-, or -N(RN3)S(O)2-, wherein RN3 10 is independently hydrogen or C1-6alkyl. In some embodiments, ZZ is -C(O)N(RN3)- or -N(RN3)C(O)-, wherein RN3 is independently hydrogen or C1-6alkyl. In some embodiments, ZZ is -C(O)O- or -OC(O)-. In some embodiments, ZZ is -OC(O)N(RN3)-, -N(RN3)C(O)O-, or -N(RN3)C(O)N(RN3)-, 15 wherein RN3 is independently hydrogen or C1-6alkyl. In some embodiments, ZZ is -N(RN3)C(O)N(RN3)-, wherein RN3 is independently hydrogen or C1-6alkyl. In some embodiments, ZZ is -OC(O)N(RN3)- or -N(RN3)C(O)O-, wherein RN3 is independently hydrogen or C1-6alkyl. 20 In some embodiments, ZZ is -OP(O)(OH)O-, -OP(S)(OH)O-, -OP(O)(OH)-, -OP(S)(OH)-, - P(O)(OH)O-, or -P(S)(OH)O-. 25
and
. 30 237 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO RT Embodiments, Formulae (XV) and (XVa) through (XVc) In some embodiments of Formula (XV), RT is RT1 and is as defined for Formula (X). In some embodiments of Formula (XV), RT is -G0-ORT1, wherein RT1 is as defined for Formula (X) and G0 is selected from: 5 (c) G0 is -D0-E0-F0-, wherein D0 and F0 are independently a bond or C1-10alkyl optionally substituted with 1, 2, 3, or 4 R groups; and E0 is C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups; 10 (d) G0 is -D0-E0-F0-, wherein D0 and F0 are independently a bond or C1-10alkyl optionally substituted with 1, 2, 3, or 4 R groups; and E0 is 3-10 membered heterocyclyl optionally substituted with 1, 2, 3, or 4 R groups; and (e) G0 is 3-10 membered heterocyclyl optionally substituted with 1 or 2 R groups; 15
(f) G0 is pyrrolidinyl, piperidinyl, piperazinyl, or morpholinyl, each optionally substituted with 1 or 2 R groups; examples include:
(g) G0 is 3-10 membered-heterocyclyl-C1-10alkyl, optionally substituted with 1, 2, 3, or 4 20 R groups; examples include,
(h) G0 is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, each of which is optionally substituted 25 with 1, 2, 3, or 4 R groups (e.g., 1 or 2 R groups); 238 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO (i) G0 is C1-10alkyl or C2-10alkenyl, each of which is optionally substituted with 1 or 2 R groups; (j) G0 is C1-10alkyl optionally substituted with 1 or 2 R groups; 5 (k) G0 is C1-10alkyl, optionally substituted with -O(Ra), wherein Ra is independently hydrogen, C1-6alkyl, or a hydroxyl protecting group; e.g.,
, (l) G0 is C1-10alkyl, and (m) G0 is absent (a bond); 10 wherein * represents the bond to T, the broken bond represents the bond to ORT1, and R is - C1-6alkyl-ORa or -ORa, wherein Ra is independently hydrogen or C1-6alkyl. Φ Embodiments In one embodiment, RY is defined in the structure of Formula (XII) according to any one of 15 the RY Embodiments of Formula (IV). In another embodiment, Formula (XII) has the structure described above for any embodiment of Formula (IV), where the variable Z is replaced by a bond to a ZZ group. In another embodiment, Formula (XII) has the structure of any one of Formula (XII-a) through (XII-h) and (XII-t): 20
(XII-e) (XII-f) 239 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
(XII-t) wherein p is0, 1, 2 or 3; each R21 is independently selected from group consisting of R and a nitrogen protecting 5 group, and RP is a nitrogen protecting group, and R, R1, and RL are as defined above for Formula (XII). L Embodiments Formula and (XII-a) through (XII-h) and (XII-r)
In some embodiments of any one of Formula (XII) and Formulae (XII-a) through (XII-h) and 10 (XII-r), L is -L1-[G-L2]q-G-L3-*, wherein * is the bond to a ZZ group. In another embodiment, wherein L is -L1-[G-L2]q-G-L3-*, wherein q is 0, 1, 2, 3, 4, or 5. In another embodiment , L is -L1-[G-L2]q-G-L3-*, wherein q is 0, 1, 2, 3, or 4 In another embodiment , L is -L1-[G-L2]q-G-L3-*, wherein q is 0, 1, 2, or 3. In another embodiment , L is -L1-[G-L2]q-G-L3-*, wherein q is 0, 1, or 2. 15 In another embodiment , L is -L1-[G-L2]q-G-L3-*, wherein q is 1, 2, 3, 4, or 5. In another embodiment , L is -L1-[G-L2]q-G-L3-*, wherein q is 1, 2, 3, or 4. In another embodiment , L is -L1-[G-L2]q-G-L3-*, wherein q is 1, 2, or 3. In another embodiment , L is -L1-[G-L2]q-G-L3-*, wherein q is 1 or 2. In another embodiment, L is -L1-[G-L2]q-G-L3-*, wherein q is 4. In another embodiment , L 20 is -L1-[G-L2]q-G-L3-*, wherein q is 3. In another embodiment, L is -L1-[G-L2]q-G-L3-*, wherein q is 2. 240 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In another embodiment, L is -L1-G-L2-G-L3-*. In another embodiment nts, L is -L1-G-L3-*. In another embodiment, L is -G-L3-*. In another embodiment , L is -L1-G-*. In another embodiment, L is -G-*. In another embodiment, wherein L is -[G-L2]q-G-*, wherein q is 1, 2, 3, 4, or 5 (e.g., q 5 is 2; or q is 3; or q is 4; or q is 5). In some embodiments, each instance of A-B-A- is independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(RN)C(O)-, -OC(O)O-, -OC(O)N(RN)-, - N(RN)C(O)O-, -N(RN)C(O)N(RN)-, -OP(O)(OH)O- ,-OP(S)(OH)O-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl. 10 In some embodiments, each instance of A-B-A- is independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(RN)C(O)-, -OC(O)N(RN)-, -N(RN)C(O)O-,- N(RN)C(O)N(RN)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl. In some embodiments, each instance of A-B-A- is independently selected from the group consisting of -C(O)N(RN)-, -N(RN)C(O)-, -OC(O)N(RN)-, -N(RN)C(O)O-, -N(RN)C(O)N(RN)-, -O-, 15 and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl. In some embodiments, each instance of A-B-A- is independently selected from the group consisting of -C(O)O-, -OC(O)-, -C(O)N(RN)-, -N(RN)C(O)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl. In some embodiments, each instance of A-B-A- is independently selected from the group 20 consisting of -C(O)N(RN)-, -N(RN)C(O)-, -O-, and -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl. In some embodiments, D and F are each independently a bond, C1-10alkyl, C2-10alkenyl, or C2-10alkynyl, each optionally substituted with 1, 2, 3, or 4 R groups; and 25 E is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups. In some embodiments, D and F are each independently a bond or C1-10alkyl optionally substituted with 1, 2, 3, or 4 R groups; and 30 E is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups. In some embodiments, each G is independently C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3- 10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups. 35 In some embodiments, each G is independently C1-10alkyl, optionally substituted with 1, 2, or 3 R groups. In some embodiments, each G is independently C1-10alkyl, optionally substituted with 1 or 2 R groups. 241 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In some embodiments, each G is independently C1-10alkyl, optionally substituted with one R group In some embodiments, L is -L1-G-L3-*, wherein * is the bond to a ZZ group ; G is -D-E-F-, wherein D, E, and F are independently a bond, C1-10alkyl, C2-10alkenyl, C2- 5 10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups; L1 is -B-A-; L3 is a bond or -A-B-A-; each A is independently a bond, -O-, -S-, or -N(RN)-, wherein each RN is independently 10 hydrogen or C1-6alkyl. each B is independently a bond, CH2, C(O), S(O)2, P(O)(OH), or P(S)(OH); and In some embodiments, L is -L1-G-L3-*, wherein * is the bond to a ZZ group; G is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups; 15 L1 is -B-; L3 is a bond or -A-B-A-; each A is independently a bond, -O-, -S-, or -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; and each B is independently a bond, CH2, C(O), S(O)2, P(O)(OH), or P(S)(OH; and 20 In some embodiments, L is -L1-G-*, wherein * is the bond to a ZZ group; G is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups; L1 is -B-A-, wherein, A is a bond, -O-, -S-, or -N(RN)-, wherein each RN is independently hydrogen or C1-6alkyl; 25 and B is a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH). In some embodiments, L is -L1-G-*, wherein * is the bond to a ZZ group; G is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, each of which is optionally substituted with 1 or 2 R groups; 30 L1 is -B-A-, wherein A is a bond, -O-, -S-, or -N(RN)-, each RN is independently hydrogen or C1-6alkyl; and B is a bond, C(O), S(O)2, P(O)(OH), or P(S)(OH). In some embodiments L is -L1-G-*, wherein * is the bond to a ZZ group; G is C1-10alkyl or C2-10alkenyl, each of which is optionally substituted with 1 or 2 R groups; 35 L1 is bond, C(O), S(O)2, P(O)(OH), or P(S)(OH); and RN is hydrogen or C1-6alkyl. 242 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In some embodiments, L is
wherein * is the bond to a ZZ group; k is an integer from 1 to 10; L1 is bond, C(O), C(S), C(NRN), S(O)2, P(O)(OH), or P(S)(OH); and RN is hydrogen or C1-6alkyl. In some embodiments, L is
wherein * is the bond to a ZZ group; k is an 5 integer from 1 to 10; L1 is bond, C(O), P(O)(OH), or P(S)(OH). In some embodiments, L is
, wherein * is the bond to a ZZ group; k is an integer from 1 to 10; or an integer from 2 to 10; or an integer from 3 to 10; or an integer from 4 to 10; or an integer from 5 to 10; or an integer from 5 to 9; or an integer from 5 to 8; or an integer from 5 to 7. 10 In some embodiments, L is
, wherein * is the bond to a ZZ group; t is an integer from 0 to 10 (e.g., an integer from 1 to 5; or 1; or 2; or 3). In some embodiments,
wherein * is the bond to a ZZ group; t is an integer from 0 to 10 (e.g., an integer from 1 to 5 or 1; or 2; or 3); a is an integer from 1 to 3; and s and s’ are each independently an integer from 1 to 15 24 (e.g., an integer from 1 to 16; an integer from 1 to 10; an integer from 3 to 10; an integer from 3 to 7; or an integer from 4 to 6). In some embodiments,
wherein * is the bond to a ZZ group; a is 1, 2 or 3; and each s, s’, and s” independently is an integer from 1 to 24 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7, or an integer20 from 4 to 6). In some embodiments, L is
wherein * is the bond to a ZZ group; and s, s’, and s’’ are independently is an integer from 1 to 24 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7, or an integer from 4 to 6). 243 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In some embodiments,
wherein * is the bond to a ZZ group; and each s, s’, and s” independently is an integer from 1 to 24(e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7, or an integer from 4 to 6). In some embodiments, L is
wherein * is the bond to ZZ; s and 5 k are independently is an integer from 1 to 20 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6); and w is an integer from 1 to 10 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6). In some embodiments, L is
wherein * is the bond to ZZ 10 and w is an integer from 1 to 20 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6). In some embodiments, L is C1-20 alkyl. In some embodiments, L is C2-20 alkyl. In some embodiments, L is C6-20 alkyl. In some embodiments, L is C8-12 alkyl. In some embodiments, L is C10 alkyl. 15 In another embodiment, wherein L is -[G-L2]q-G-*, wherein q is 1, 2, 3, 4, or 5 (e.g., q is 2; or q is 3; or q is 4; or q is 5), each G is indepdently C1-10alkyl and L2 is O, S, or N(H). In another embodiment, wherein L is -[G-L2]q-G-*, wherein q is 1, 2, 3, 4, or 5 (e.g., q is 2; or q is 3; or q is 4; or q is 5), each G is indepdently C1-10alkyl and L2 is O. In another embodiment, wherein L is -[CH2CH2O]q-G-*, wherein q is 1, 2, 3, 4, or 520 (e.g., q is 2; or q is 3; or q is 4; or q is 5), G is indepdently C1-10alkyl. In some embodiments, L is
, wherein * is the bond to ZZ; t is an integer from 0 to 10 (e.g., an integer from 1 to 5; or 1; or 2; or 3). In some embodiments, L is
, wherein * is the bond to ZZ. In some embodiments, L is
, wherein * is the bond to ZZ; t is 1 to 10 25 (e.g., 1-5; or 1-3; or 1; or 2; or 3); and z is 1-10 (e.g., 1-6; or 1-4; or 1; or 2; or 3 or 4 or 5 or 6). 244 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In some embodiments, L is
, wherein * is the bond to ZZ, and t is an integer from 1 to 5 (e.g., 1; or 2; or 3). In some embodiments,
, wherein * is the bond to ZZ. RL Embodiments, Formulae (XII) and (XII-a) through (XII-h) and (XII-r) 5 In some embodiments of any one of Formula (XII) and Formulae (XII-a) through (XII-h) and (XII-r), RL is -N(R3)(R4), wherein R3 is hydrogen or C1-6alkyl and R4 is R5. In some embodiments, RL is -N(R3)(R4), wherein R3 is hydrogen and R4 is R5. In some embodiments, RL is -N(R3)(R4), wherein R3 is C1-3alkyl and R4 is R5. In some embodiments, RL is -N(R3)(R4), wherein R3 is methyl and R4 is R5. 10 In some embodiments, RL is --N(R3)(R4), wherein R3 and R4 taken together with the nitrogen atom to which they are attached form a 4 – 8 membered monocyclic heterocyclyl group that is substituted with R5. In some embodiments, RL is --N(R3)(R4), wherein R3 and R4 taken together with the nitrogen atom to which they are attached form a 4 – 8 membered monocyclic heterocyclyl group that 15 is substituted with R5, provided that R3 and R4 taken together with the nitrogen atom to which they are attached do not form a morpholino group. In some embodiments, RL is --N(R3)(R4), wherein R3 and R4 taken together with the nitrogen atom to which they are attached form a group that is piperidinyl, piperazinyl, pyrrolidinyl, imidazolidinyl, pyrazolidinyl, oxazolidinyl, thiazolidinyl, azetidinyl, pyrrolinyl, imidazolinyl, or 20 pyrazolinyl, each substituted wi In some embodiments,
. In some embodiments, RL is 25
2, 3, 4, 5, 6, 7, 8, 9 or 10); a is an integer from 1 to 3 and s and s’ are each independently an integer from 1 to 24 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6). 245 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In some embodiments,
wherein * is a bond to a ZZ group; a is an integer from 1 to 3; and s, s’, and s’’ are each independently an integer from 1 to 24 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6). 5 In some embodiments,
wherein * is a bond to a ZZ group; and s, s’, and s’’ are independently is an integer from 1 to 24 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6. In some embodiments, RL is 10
wherein * is a bond to a ZZ group; s, s’, and s’’ are independently an integer from 1 to 24 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6); and t is an integer from 1 to 10 (e.g., an integer from 1 to 8, an integer from 1 to 5, an integer from 1 to 3, or 1, or 2, or 3). 15 In some embodiments, RL is
, , wherein * is a bond to a ZZ group; s is an integer from 1 to 24 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 t 20
, wherein * is a bond to a ZZ group; s is an integer from 1 to 24 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6); and t is an integer from 0 to 10 (e.g., an integer from 1 to 8, an integer from 1 to 5, an integer from 1 to 3, or 1, or 2, or 3). 25 In some embodiments, RL is -R5. 246 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In some embodiments,
24 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6). In some embodiments, RL is
, wherein * is a bond to a ZZ group; t 5 is 0 to 10 (e.g., 1-5; or 1-3; or 1 In some embodiments,
wherein * is a bond to a ZZ group; s and k are independently is an integer from 1 to 20 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6); and w is an integer from 1 to 10 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to10 10, an integer from 3 to 7 or an integer from 4 to 6). In some embodiments, RL is
wherein * is a bond to a ZZ group. In some embodiments, RL is 247 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
wherein * is a bond to a ZZ group and w is an integer selected from 1-10 (e.g., 2-10, 2-8, 4-8).
. 5 In some embodiments, the compound of Formula (XII) is according to one of Formulae (XII-i) through
(XII-j) 248 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
(XII-s) wherein * is a bond to a ZZ group, p is 0, 1, 2, or 3 (e.g., 0); each R21 is independently selected from group consisting of R and a nitrogen protecting group, 5 and L is defined according to Formula (XII), or according to any of the preceding embodiments of L. In one embodiment of Formulae (XII-i) through (XII-l) and (XII-s), R1 is hydrogen. In another embodiment of Formulae (XII-i) through (XII-l) and (XII-s), R1 is C1-6alkyl (e.g., methyl or t- butyl). 10 In some embodiments, the compound of Formula (XII) is according to one of Formulae (XII- m) through (XII-q) and (XII-t):
249 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
or a salt thereof, wherein * is a bond to a ZZ group, p is 0, 1 or 2; each R21 is independently selected from group consisting of R; RP is hydrogen or a nitrogen protecting group (e.g., a nitrogen protecting group), 5 and L is defined according to Formula (XII), or according to any of the preceding embodiments of L, wherein R and the remaining variables are as defined in Formula (XII). In some embodiments, the compound of Formula (XII) is according to one of Formulae (XII-u) through (XII-z):
(XII-u) (XII-v) 250 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
or a salt thereof, wherein * is a bond to a ZZ group, p is 0, 1 or 2; each R21 is independently selected from group consisting of R; RP is hydrogen or a nitrogen protecting group (e.g., a nitrogen protecting group), and L is defined according to Formula (XII), or according to any of the preceding 5 embodiments of L, wheren R and the remaining variables are as defined in Formula (XII). In one embodiment of Formulae (XII-m) through (XII-q) and (XII-t) through (XII-z), R1 is hydrogen. In another embodiment of Formulae (XII-m) through (XII-q) and (XII-t) through (XII-z), R1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment of the compound of Formula (XV), 10 Φ is selected from Formula (XII) and any one of Formula (XII-a) through (XII-q) and (XII-t) through (XII-z); ZZ is -CH2O-, -OCH2-, -S-S-, -C=N-, -C=N-O-, -C=N-N(RN3)-, -N=C-, -O-N=C-, -N(RN3)- N=C-, -C(O)N(RN3)-, -N(RN3)C(O)-, -C(O)O-, -OC(O)-, -OC(O)N(RN3)-, -N(RN3)C(O)O-, - N(RN3)C(O)N(RN3)-, -S(O)2N(RN3)-, -N(RN3)S(O)2-, -OP(O)(OH)O-, -OP(S)(OH)O-, -OP(O)(OH)-, - 15 OP(S)(OH)-, -P(O)(OH)O-, or -P(S)(OH)O-. wherein RN3 is independently hydrogen or C1-6alkyl; Δ is selected from,
251 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
wherein # is the bond to T and each * is a bond to a ZZ group; and
wherein ** represents the bond to T, and the remaining variables are as defined in Formula (XV), and any embodiment thereof. 5 In one embodiment of the compound of Formula (XV), Φ is selected from Formula (XII) and any one of Formula (XII-a) through (XII-q) and (XII-t) through (XII-z); ZZ is - C(O)N(RN3)-, -N(RN3)C(O)-, -C(O)O-, -OC(O)-, wherein RN3 is independently hydrogen or C1-6alkyl; 10 Δ is selected from,
wherein # is the bond to T and each * is a bond to a ZZ group.
15 and the remaining variables are as defined in Formula (XV), and any embodiment thereof. In one embodiment of the compound of Formula (XV), 252 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO Φ is selected from Formula (XII) and any one of Formula (XII-a) through (XII-q) and (XII-t) through (XII-z); ZZ is -CH2O-, -OCH2-, -S-S-, -C=N-, -C=N-O-, -C=N-N(RN3)-, -N=C-, -O-N=C-, -N(RN3)- N=C-, -C(O)N(RN3)-, -N(RN3)C(O)-, -C(O)O-, -OC(O)-, -OC(O)N(RN3)-, -N(RN3)C(O)O-, - 5 N(RN3)C(O)N(RN3)-, -S(O)2N(RN3)-, -N(RN3)S(O)2-, -OP(O)(OH)O-, -OP(S)(OH)O-, -OP(O)(OH)-, - OP(S)(OH)-, -P(O)(OH)O-, or -P(S)(OH)O-. wherein RN3 is independently hydrogen or C1-6alkyl; Δ is selected from, \
wherein # is the bond to T and each * is a bond to a ZZ group, G3 is C1-10alkyl; 10 each G4 is independently C1-10alkyl; and
, , wherein ** represents the bond to T, and the remaining variables are as defined in Formula (XV), and any embodiment thereof. In one embodiment of the compound of Formula (XV), 15 Φ is selected from Formula (XII) and any one of Formula (XII-a) through (XII-q) and (XII-t) through (XII-z); ZZ is -C(O)-, -C(O)N(RN3)-, -N(RN3)C(O)-, -C(O)O-, -OC(O)-, wherein RN3 is independently hydrogen or C1-6alkyl; Δ is selected from,
, , , 253 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
, bond
and the remaining variables are as defined in Formula (XV), and any embodiment thereof. 5 In one embodiment of the compound of Formula (XV), Φ is selected from Formula (XII) and any one of Formula (XII-i) through (XII-q) and (XII-t) through (XII-z); ZZ is -OP(O)(OH)O-, -OP(S)(OH)O-, -C(O)N(RN3)-, -N(RN3)C(O)-, -C(O)O-, -OC(O)-, wherein RN3 is independently hydrogen or C1-6alkyl; 10
T is **-L6-G1-L5-G1-L4-, wherein ** is the bond to RT; L4 and L6 are independently -B1-A1- or -A1-B1-; 254 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO each L5 is a bond or - A1-B1-A1- (e.g., a bond, -B1-A1- or -A1-B1-; or a bond); each G1 is independently C1-10alkyl or C2-10alkenyl; each A1 is independently a bond, -O-, -S-, or -N(RN1)-, wherein RN1 is independently hydrogen or C1-6alkyl; and 5 each B1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); and
wherein ** represents the bond to T, and the remaining variables are as defined in Formula (XV), and any embodiment thereof. In one embodiment of the compound of Formula (XV), 10 Φ is selected from Formula (XII) and any one of Formula (XII-m) through (XII-q) and (XII-t) through (XII-z); ZZ is -OP(O)(OH)O-, -OP(S)(OH)O-, -C(O)N(RN3)-, -N(RN3)C(O)-, -C(O)O-, -OC(O)-, wherein RN3 is independently hydrogen or C1-6alkyl; 15
T is **-L6-G1-L5-G1-L4-, wherein ** is the bond to RT; L4 and L6 are independently -B1-A1- or -A1-B1-; each L5 is a bond or - A1-B1-A1- (e.g., a bond, -B1-A1- or -A1-B1-; or a bond); each G1 is independently C1-10alkyl or C2-10alkenyl; 20 each A1 is independently a bond, -O-, -S-, or -N(RN1)-, wherein RN1 is independently hydrogen or C1-6alkyl; and each B1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); and
wherein ** represents the bond to T, 25 and the remaining variables are as defined in Formula (XV), and any embodiment thereof. 255 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In one embodiment of the compound of Formula (XV), Φ is selected from Formula (XII) and any one of Formula (XII-m) through (XII-q) and (XII-t) through (XII-z); ZZ is -C(O)N(H)- or -N(H)C(O)-; 5 Δ is T is **-L6-G1-L5-G1-L4-, wherein ** is the bond to RT; L4 is -A1-B1-; L6 is -B1-; L5 is a bond, -B1-A1-, or -A1-B1-; 10 each G1 is independently C1-10alkyl; each A1 is independently a bond, -O- or -N(H); bond t
, 15 and the remaining variables are as defined in Formula (XV), and any embodiment thereof. In one embodiment of the compound of Formula (XV) is according to the structure,
wherein RP3 is hydrogen; 256 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO Φ is selected from Formula (XII) and any one of Formula (XII-m) through (XII-q) and (XII- t); ZZ is -C(O)N(H)- or -N(H)C(O)-; and T is **-L6-G1-L5-G1-L4-, wherein ** is the bond to RT; L4 is -A1-B1-; 5 L6 is -B1-; L5 is a bond, -B1-A1-, or -A1-B1-; each G1 is independently C1-10alkyl; each A1 is independently a bond, -O- or -N(H); each B1 is C(O); 10 and the remaining variables are as defined in Formula (XV), and any embodiment thereof. In one embodiment of the compound of Formula (XV), Φ is selected from Formula (XII) and any one of Formula (XII-m) through (XII-q) and (XII-t) through (XII-z); ZZ is -OP(O)(OH)O-, -OP(S)(OH)O-, -C(O)N(RN3)-, -N(RN3)C(O)-, -C(O)O-, -OC(O)-, 15 wherein RN3 is independently hydrogen or C1-6alkyl;
T is ***-L6-[G5-O]q5-G5-L4-, wherein q5 is an integer selected from 1 to 20; L4 and L6 are independently -A1-B1-A1-, wherein 20 each A1 is independently a bond, -O-, -S-, or -N(RN1)-, wherein RN1 is hydrogen or C1-6alkyl; each B1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); each G5 is independently C1-10alkyl; and
wherein ** represents the bond to T, 25 and the remaining variables are as defined in Formula (XV), and any embodiment thereof. 257 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In one embodiment of the compound of formula (XV),is of the structure,
wherein Φ is selected from Formula (XII) and any one of Formula (XII-m) through (XII-q) and (XII-t) 5 through (XII-z), wherein L is
wherein * is the bond to ZZ; s and k are independently is an integer from 1 to 20 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6); and w is an integer from 1 to 10 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6); ; 10 ZZ is -C(O)N(H)-, -N(H)C(O)-; T is ***-L6-[G5-O]q5-G5-L4-, wherein q5 is an integer selected from 1 to 20; L4 and L6 are independently -A1-B1-A1-, wherein each A1 is independently a bond, -O-, -S-, or -N(RN1)-, wherein RN1 is hydrogen or C1-6alkyl; 15 and each B1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH); each G5 is independently C1-10alkyl; and the remaining variables are as defined in Formula (XV), and any embodiment thereof. In one embodiment of the compound of formula (XV),is of the structure,
20 wherein Φ is selected from Formula (XII) and any one of Formula (XII-m) through (XII-q) and (XII-t) through (XII-z), wherein L is
wherein * is the bond to ZZ and w is an integer from 1 to 20 (e.g., an integer from 1 to 16, an integer from 1 to 10, an integer from 3 to 10, an integer from 3 to 7 or an integer from 4 to 6; 258 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO ZZ is -C(O)N(H)-, -N(H)C(O)-; T is **-C(O)-[CH2CH2-O]q5- C2-10alkyl-C(O)N(H)-, wherein ** is the bond to the pyrrolidine ring and q5 is an integer selected from 1 to 20 (e.g., 1 to 10, or 2 to 10; or 2 – 8; or 1; or 2; or 3; or 4); and the remaining variables are as defined in Formula (XV), and any embodiment thereof. 5 RT1 Embodiments, Formula (XV) In embodiments of any embodiments of RL of Formula (XV), Formula (XV-a) through (XV- k), RT1 is -LL-oligonucleotide, wherein LL is a divalent linker that connects to the 3’-end of the 10 oligonucleotide, the 5’-end of the oligonucleotide, or an internal 2’- or 3’ position on a internal nucleotide (i.e., a nucleotide that is not the 5’-terminal or 3’-terminal nucleoside). In some embodiments, RT1 is -LL-oligonucleotide, wherein LL is a divalent linker that connects to the 3’-end of the oligonucleotide, such as one of : directly to the 3’-carbon of the 3’-terminal nucleoside; 15 directly to the 3’-O of the 3’-terminal nucleoside; directly to the 4’-carbon of the 3’-terminal nucleoside; directly to the 2’-carbon of the 3’-terminal nucleoside; or directly to the 2’-O of the 3’-terminal nucleoside. In some embodiments, RT1 is -LL-oligonucleotide, wherein LL is a divalent linker that 20 connects to the 5'-end of the oligonucleotide, such as one of: directly to the 5’-carbon of the 5’-terminal nucleoside; directly to the 5’-O of the 5’-terminal nucleoside; directly to the 4’-carbon of the 5’-terminal nucleoside; directly to the 2’-carbon of the 5’-terminal nucleoside; or 25 directly to the 2’-O of the 5’-terminal nucleoside. In some embodiments, RT1 is -LL-oligonucleotide, wherein LL is a divalent linker that connects to an internal 2’- or 3’ position on an internal nucleotide. In some embodiments, RT1 is -LL-oligonucleotide, wherein LL is a divalent linker that connects to an internal 2’- position on a internal nucleotide. 30 In another embodiment of any of the preceding embodiments of RT1, when LL connects to a carbon aton on a nucleoside, then LL is -B3-A3-, wherein B3 is -P(O)(OH)-, -P(S)(OH)-, or -P(S)(SH)-; and A3 is -O-, -S-, or -N(H)- . In another embodiment, when LL connects to a carbon atom on a nucleoside, then LL is -B3- 35 A3-, wherein B3 is -P(O)(OH)- or-P(S)(OH)-; and A3 is -O-. 259 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In another embodiment, when LL connects to a oxygen atom on a nucleoside, then LL is - P(O)(OH)-, -P(S)(OH)-, or -P(S)(SH). In another embodiment, when LL connects to a oxygen atom on a nucleoside, then LL is - P(O)(OH)- or -P(S)(OH)-. 5 In another embodiment, when LL connects to a oxygen atom on a nucleoside, then LL is - P(O)(OH)-. In another embodiment, when LL connects to a oxygen atom on a nucleoside, then LL is - P(S)(OH)-. In another embodiment, when LL connects to a oxygen atom on a nucleoside, then 10 LL is -B3-A3-LL1-A3-B3-, wherein B3 is a bond, -C(O)-, C(S)-, C(NH), S(O), S(O)2, -P(O)(OH)-, -P(S)(OH)-, or -P(S)(SH); A3 is a bond, -O-, -S-, or -N(H)- ; and LL1 is C1-10alkyl, C2-10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl. 15 In another embodiment, when LL connects to a oxygen atom on a nucleoside, then LL is -B3- LL1-B3-, wherein B3 is -C(O)-; and LL1 is C1-10alkyl. In certain embodiments, where RT is RT1,wherein RT1 is -LL-oligonucleotide, when LL connects to a oxygen atom on a nucleoside, and LL is a bond, the nucleoside is of Formula (XV-f),
(XV-f) wherein B is an optionally modified nucleobase (e.g., adenine, cytosine, uracil, guanine, 5- 20 methylcytosine, or-5-methyluracil); Tis according any of the preceding embodiments; and * represent the bond to ZZ. In some embodiments of Formula (XV-f), -T- is -L1-G-L3-*, wherein * is the bond to ZZ. In some embodiments, -T- is -C2-30alkyl-*, wherein the alkyl is optionally substituted with one or two R groups, and * is the bond to ZZ. In some embodiments, -T- is -C2-30alkyl-*, wherein the alkyl 25 is optionally substituted with one or two groups selected from the group consisting of halogen, hydroxy, C1-6alkoxy, amino, Cl-6alkylamino, di(C1-6alkylamino), cyano, carboxy , and * is the bond to ZZ. In some embodiments, -T- is -C2-30alkyl-*, wherein the alkyl is optionally substituted with one group selected from the group consisting of halogen, hydroxy, C1-6alkoxy, amino, Cl-6alkylamino, di(C1- 6alkylamino), cyano, carboxy , and * is the bond to ZZ. In some embodiments, -T- is -C2-30alkyl-*, 30 wherein the alkyl is optionally substituted with one group selected from the group consisting of hydroxy, amino, and carboxy , and * is the bond to ZZ. In some embodiments, -T- is -C2-30alkyl-*, wherein the alkyl is optionally substituted with hydroxy, and * is the bond to ZZ. 260 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In some embodiments, -T- is -C2-30alkyl-*, wherein * is the bond to ZZ. In some embodiments, -T- is -C2-16alkyl-*, wherein * is the bond to ZZ. In some embodiments, -T- is -C4-12alkyl-*, wherein * is the bond to ZZ. In some embodiments, -T- is -C4-10alkyl-*, wherein * is the bond to ZZ. In some embodiments, -T- is -C5-10alkyl-*, wherein * is the bond to ZZ. In some embodiments, -T- is -C6alkyl- 5 *, wherein * is the bond to ZZ. In some embodiments, -T- is -C8alkyl-*, wherein * is the bond to ZZ. In some embodiments, -T- is -C10alkyl-*, wherein * is the bond to ZZ. In some embodiments of Formula (XV-f), -T- is -L1-[G-L2]q-G-L3-*, wherein * is the bond to ZZ; q is 0, 1, 2, 3, 4, or 5; 10 L1 is a bond or -B-A-; each L2 is independently -A-B-A-; L3 is a bond or -A-B-A-; each A is independently a bond, -O-, -S-, or -N(RN)-; each B is independently a bond, CH2, C(O), C(S), C(NRN), S(O)2, P(O)(OH), or P(S)(OH); 15 each RN is independently hydrogen or C1-6alkyl; and each G is independently C1-10alkyl, C2-10alkenyl, C2-10alkynyl, each of which is optionally substituted with 1, 2, 3, or 4 R groups. In some embodiments, -T- is -L1-[G-L2]q-G-*, wherein * is the bond to ZZ, q is 0, 1, 2, or 3; L1 is a bond or -B-A-; and 20 (a) each L2 is independently a bond, C(O)O, OC(O), C(O)(NRN), N(RN)C(O), SO2N(RN), N(RN)SO2, OP(O)(OH), OP(S)(OH), P(O)(OH)O, P(S)(OH)O, OP(O)(OH)O, or OP(S)(OH)O, wherein each RN is independently hydrogen or C1-6alkyl; each G is independently C1-10alkyl, C2-10alkenyl, C2- 10alkynyl, each of which is optionally substituted with 1 or 2 R groups; or 25 (b) each L2 is independently a bond, C(O)O, OC(O), C(O)(NRN), N(RN)C(O), OP(O)(OH)O, or OP(S)(OH)O, wherein each RN is independently hydrogen or C1-6alkyl; and each G is independently C1-10alkyl or C2-10alkenyl, each of which is optionally substituted with 1 or 2 R groups. In some embodiments, -T- is -[G-L2]q-G-*, wherein * is the bond to ZZ, q is 0, 1, 2, or 3 (e.g., q is 0, 1, or 2; or 0 or 1; or 0; or 1; or 2); each G is independently C1-10alkyl, each of which is optionally 30 substituted with 1 or 2 R groups.and (c) each L2 is independently C(O)O or OC(O); (d) each L2 is independently C(O)(NRN) or N(RN)C(O), wherein each RN is independently hydrogen or C1-6alkyl (e) each L2 is independently OP(O)(OH)O, or OP(S)(OH)O (e.g., each is OP(O)(OH)O); 35 or (f) each L2 is a bond. In some embodiments, the compound of Formula (XV) is according to one of Formulae (XV- g) through (XV-q): 261 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
B is an optionally modified nucleobase (e.g., adenine, cytosine, uracil, guanine, 5- methylcytosine, or-5-methyluracil); each n is independently 0 or an integer selected from 1-10; (e.g., 1-5, or 1-3, or 3, or 2, or 1); 5 each m is independently integer selected from 1-20 (e.g., 2-12, or 2-10; or 2-6; or 2; or 3; or 4; or 5; or 6). 262 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In some embodiments, the compound of Formula (XV) is according to one of Formulae (XV- r) through (XV-w):
263 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
or a salt thereof, wherein L and ZZ are as defined in Formula (XV) or in any embodiment preceding or below; B is an optionally modified nucleobase (e.g., adenine, cytosine, uracil, guanine, 5- 5 methylcytosine, or-5-methyluracil); each m is independently integer selected from 1-20 (e.g., 2-12, or 2-10; or 2-6; or 2; or 3; or 4; or 5; or 6); 264 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO RP is hydrogen or a nitrogen protecting group (e.g., a nitrogen protecting group); and R1 is hydrogen or C1-6alkyl (e.g., methyl or t-butyl). In one embodiment of Formulae (XV-r) through (XV-w), R1 is hydrogen. In another embodiment of Formulae (XV-r) through (XV-w), R1 is C1-6alkyl (e.g., methyl or t-butyl). In another 5 embodiment of Formulae (XV-r) through (XV-w), R1 is hydrogen and RP is hydrogen. In another embodiment of Formulae (XV-r) through (XV-w), R1 is hydrogen and a nitrogen protecting group. In another embodiment of Formulae (XV-r) through (XV-w), R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In another embodiment of Formulae (XV-r) through (XV-w), R1 is C1-6alkyl (e.g., methyl or t-butyl) and a nitrogen protecting group. 10 In certain embodiments, where RT is RT1 , wherein RT1 is -LL-oligonucleotide, when LL connects to a oxygen atom or nitrogen atom in an internucleotide linkage, the internucleotide linkage can be of the formula, including the 3’ and 5’ oxygen atoms of the preceding and following nucelosides, respectively,
(XV-pa) (XV-pb) (XV-pc) wherein T can be, for example a bond, -S(O)2- or, in for Formula (XV-i), a 5 -8 membered 15 heterocyclyl ring optionally substituted with 1 or 2 R groups, as defined herein ; and * represent the bond to Δ. For example, the preceding includes,
(XV-pd) (XV-pe) (XV-pf) wherein * represent the bond to Δ; and RN5 is hydrogen or C1-10 alkyl. For example, the preceding includes,
(XV-pg) (XV-ph) (XV-pi) 20 wherein * represent the bond to Δ; m is an integer selected from 1 – 20 (e.g., 1-10, or 2-20, or 2-10, or 4-10, or 4-8; or 6-12; or 5; or 6; or 7; or 8; or 9; or 10), and RN5 is hydrogen or C1-10 alkyl. In another embodiment, the compound of Formula (XV-pd) is 265 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
wherein Y’ is O or S, and RY, Y, R1, L, T, Δ, and ZZ are as defined for Formula (XV). In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t-butyl). 5
266 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
wherein Y’ is O or S, and R1, T, Δ, RP, L, and ZZ are as defined for Formula (XV). In another embodiment, the compound is
267 ME1\53453057.v1
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wherein each m is an integer selected from 1 – 20 (e.g., 2-20, 2-10, 1-10, 2-16, 4-16, 4-8, or 6-12), Y’ is O or S, and R1, Δ, RP and ZZ are as defined for Formula (XV). 5 In another embodiment, the compound of Formula (XV-pe) is 268 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
wherein Y’ is O or S, and RY, Y, R1, L, T , Δ, and ZZ are as defined for Formula (XV). In one embodiment, Y’ is O. In another embodiment, Y’ is S. In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t- 5 butyl). In one embodiment, RP is hydrogen. In another embodiment, RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1- 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R1 is hydrogen. In one embodiment, 10 Y’ is S and R1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and RP is hydrogen . In one embodiment, Y’ is O and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and RP is hydrogen . In one embodiment, Y’ is S and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl 15 (pac)). In one embodiment, Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl 20 (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen . In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen . In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a 25 nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In another embodiment, the compound is 269 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
270 ME1\53453057.v1
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271 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
wherein Y’ is O or S, and R1, L, T, Δ, RP, and ZZ are as defined for Formula (XV). In one embodiment, Y’ is O. In another embodiment, Y’ is S. 5 In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t- butyl). In one embodiment, RP is hydrogen. In another embodiment, RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1- 10 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R1 is hydrogen. In one embodiment, Y’ is S and R1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and RP is hydrogen . In one embodiment, Y’ is O and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and RP is hydrogen . In one embodiment, Y’ is S and RP is a 15 nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In 272 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen . In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen . In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) 5 and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In another embodiment, the compound is 10
273 ME1\53453057.v1
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5 wherein each m is an integer selected from 1 – 20 (e.g., 2-20, 2-10, 1-10, 2-16, 4-16, 4-8, or 6-12), Y’ is O or S, and R1, Δ, RP, and ZZ are as defined for Formula (XV). In one embodiment, Y’ is O. In another embodiment, Y’ is S. 274 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t- butyl). In one embodiment, RP is hydrogen. In another embodiment, RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). 5 In one embodiment, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1- 6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R1 is hydrogen. In one embodiment, Y’ is S and R1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is O and RP is hydrogen . In one embodiment, Y’ is O and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl 10 (pac)). In one embodiment, Y’ is S and RP is hydrogen . In one embodiment, Y’ is S and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen 15 protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen . In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen . In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t-butyl) 20 and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In another embodiment, when LL connects to a oxygen atom on a nucleoside, then LL is-a 25 bond. For Formula (XV), when RT1 is -LL-oligonucleotide and is conjugated at the 5’-end of the oligonucleotide, in one embodiment, RT1 can be represented as Formula (XV-5’) (XV-5’) wherein LL is -P(Y)(OH)-, wherein Y is O or S (e.g., S); and * represents the bond to 30 remainder of the compound of Formula (XV). In another embodiment of Formula (XV), when RT1 is -LL-oligonucleotide and is conjugated at the 5’-end of the oligonucleotide, in one embodiment, RT1 can be represented as Formula (XV-5’o) or Formula (
35 wherein * represents the bond to remainder of the compound of Formula (XV). In another embodiment, a compound of Formula (XV) can be represented by, 275 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
wherein Y’ is O or S, x is an integer selected from 2 to 8, and Δ, RY, Y, R1, L, T, and ZZ are as defined for Formula (XV) or any embodiment thereof. For Formula (XV), when RT1 is -LL-oligonucleotide and is conjugated at the 3’-end of the 5 oligonucleotide, in one embodiment, RT1 can be represented as Formula (XV-3’)
wherein LL is -P(Y)(OH)-, wherein Y is O or S (e.g., S); and * represents the bond to remainder of the compound of Formula (XV). In another embodiment of Formula (XV), when RT1 is -LL-oligonucleotide and is conjugated 10 at the 3’-end of the oligonucleotide, in one embodiment, RT1 can be represented as Formula (XV-3’o) or Formula (
wherein * represents the bond to remainder of the compound of Formula (XV). In another embodiment, a compound of Formula (XV) can be represented by, 15
, wherein Y’ is O or S, x is an integer selected from 2 to 8, and Δ, RY, Y, R1, L, T, and ZZ are as defined for Formula (XV) or any embodiment thereof. In one embodiment, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t-butyl). In another embodiment, the compound of Formula (XV) is 276 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
5 wherein m is an integer selected from 1 – 10; n in an integer selected from 1 – 6; L4 and L6 are independently -B1-A1- or -A1-B1-; each L5 is a bond or - A1-B1-A1- (e.g., a bond, -B1-A1- or -A1-B1-; or a bond); each G1 is independently C1-10alkyl or C2-10alkenyl; each A1 is independently a bond, -O-, -S-, or -N(RN1)-, wherein RN1 is independently 10 hydrogen or C1-6alkyl; and each B1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH). In another embodiment of Formula (XV-x), each Φ is
, wherein m is an integer selected from 1 – 10. 277 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In another embodiment of Formula (XV-x), each Φ is
, wherein m is an integer selected from 1 – 10; In another embodiment of Formula (XV-x), each
5 , wherein m is an integer selected from 1 – 10; In another embodiment of Formula (XV-x), each
, wherein m is an integer selected from 1 – 10. In another embodiment of Formula (XV-x), each Φ is 10
, wherein m is an integer selected from 1 – 10; 278 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
wherein m is an integer selected from 1 – 10; and n is an integer selected from 1 – 6.
5 wherein m is an integer selected from 1 – 10; and n is an integer selected from 1 – 6. In another embodiment of Formula (XV-x), each
. In another embodiment of Formula (XV-x), each
. 10 In another embodiment of Formula (XV-x) and each of the preceding embodiments thereof, L4 and L6 are independently -B1-A1- or -A1-B1-; 279 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO L5 is a bond, -B1-A1- or -A1-B1-; each G1 is independently C1-10alkyl; each A1 is independently a bond, -O-, -S-, or -N(RN1)-, wherein RN1 is independently hydrogen or C1-6alkyl; and 5 each B1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH). In another embodiment of Formula (XV-x) and each of the preceding embodiments thereof, L4 is -B1-A1- or -A1-B1-; L6 is B1; L5 is a bond, -B1-A1- or -A1-B1-; 10 each G1 is independently C1-10alkyl; each A1 is independently -O- or -N(H)-, and each B1 is independently C(O), S(O)2, P(O)(OH), or P(S)(OH). In another embodiment of Formula (XV-x) and each of the preceding embodiments thereof, -L4-G1-L5-G1-L4- is -B1-C1-10alkyl-L5-C1-10alkyl-B1-A1- 15 L5 is a bond, -B1-A1- or -A1-B1-; each A1 is independently -O- or -N(H)-, and each B1 is independently C(O), S(O)2, P(O)(OH), or P(S)(OH). In another embodiment of Formula (XV-x) and each of the preceding embodiments thereof, -L4-G1-L5-G1-L4- is -C(O)-C1-10alkyl-L5-C1-10alkyl-C(O)N(H)-, wherein L5 is a bond, -B1-A1-20 or -A1-B1-, wherein A1 is -O- or -N(H)-, and B1 is C(O), S(O)2, P(O)(OH), or P(S)(OH). In another embodiment of Formula (XV-x) and each of the preceding embodiments thereof,
In another embodiment, the compound of Formula (XV) is 25
wherein Y’ is O or S; each ZZ is N(H)C(O) or C(O)N(H); 280 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO each
wherein m is an integer selected from 1 – 10; n in an integer selected from 1 – 6; L5 is a bond or - A1-B1-A1- (e.g., a bond, -B1-A1- or -A1-B1-; or a bond); each G1 is independently C1-10alkyl; 5 each A1 is independently a bond, -O-, -S-, or -N(RN1)-, wherein RN1 is independently hydrogen or C1-6alkyl; and
wherein m is an integer selected from 1 – 10 R1 is hydrogen or C1-6alkyl (e.g., hydrogen); and RP is 10 hydrogen or a nitrogen protecting group (e.g., hydrogen). . In another embodiment of Formula (XV-x1), each Φ is
, wherein m is an integer selected from 1 – 10 ; R1 is hydrogen or C1-6alkyl (e.g., hydrogen); and RP is hydrogen or a nitrogen protecting group (e.g., 15 hydrogen). ; 281 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In another embodiment of Formula (XV-x1), each
wherein m is an integer selected from 1 – 10; ; R1 is hydrogen or C1-6alkyl (e.g., hydrogen); and RP is hydrogen or a nitrogen protecting group (e.g., hydrogen).. 5 In another embodiment of Formula (XV-x1), each
wherein m is an integer selected from 1 – 10 ; R1 is hydrogen or C1-6alkyl (e.g., hydrogen); and RP is hydrogen or a nitrogen protecting group (e.g., hydrogen).. 10
hydrogen or a nitrogen protecting group (e.g., hydrogen).. ; 282 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
, wherein m is an integer selected from 1 – 10; and n is an integer selected from 1 – 6.
, 5 wherein m is an integer selected from 1 – 10; and n is an integer selected from 1 – 6.
, wherein R1 is hydrogen or C1-6alkyl (e.g., hydrogen); and RP is hydrogen or a nitrogen protecting group (e.g., hydrogen). 283 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
, wherein R1 is hydrogen or C1-6alkyl (e.g., hydrogen); and RP is hydrogen or a nitrogen protecting group (e.g., hydrogen). 5 In another embodiment, the compound of Formula (XV) is
wherein Y’ is O or S; e
10 wherein m is an integer selected from 1 – 10; n is an integer selected from 1-6; L5 is a bond or - A1-B1-A1- (e.g., a bond, -B1-A1- or -A1-B1-; or a bond); each G1 is independently C1-10alkyl; each A1 is independently a bond, -O-, -S-, or -N(RN1)-, wherein RN1 is independently hydrogen or C1-6alkyl; and 15 each B1 is independently a bond, C(O), C(S), S(O)2, P(O)(OH), or P(S)(OH). 284 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In another embodiment of Formula (XV-x2), each Φ is
hydrogen). 5 In another embodiment of Formula (XV-x2), each Φ is
, wherein m is an integer selected from 1 – 10; ; R1 is hydrogen or C1-6alkyl (e.g., hydrogen); and RP is hydrogen or a nitrogen protecting group (e.g., hydrogen). 10 In another embodiment of Formula (XV-x2), each Φ is
, wherein m is an integer selected from 1 – 10; R1 is hydrogen or C1-6alkyl (e.g., hydrogen); and RP is hydrogen or a nitrogen protecting group (e.g.,15 hydrogen). 285 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In another embodiment of Formula (XV-x2), each Φ is
, wherein m is an integer selected from 1 – 10 R1 is hydrogen or C1-6alkyl (e.g., hydrogen); and RP is hydrogen or a nitrogen protecting group (e.g., hydrogen). In another embodiment of Formula (XV-x2), each Φ is 5
hydrogen). In another embodiment of Formula (XV-x2), each
, wherein m is an integer selected from 1 – 10; and n is an integer selected from 1 – 6; R1 is hydrogen or10 C1-6alkyl (e.g., hydrogen); and RP is hydrogen or a nitrogen protecting group (e.g., hydrogen). 286 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In another embodiment of Formula (XV-x2), each
, wherein m is an integer selected from 1 – 10; and n is an integer selected from 1 – 6; R1 is hydrogen or C1-6alkyl (e.g., hydrogen); and RP is hydrogen or a nitrogen protecting group (e.g., hydrogen). 5 In another embodiment of Formula (XV-x2), each
, wherein R1 is hydrogen or C1-6alkyl (e.g., hydrogen); and RP is hydrogen or a nitrogen protecting group (e.g., hydrogen). In another embodiment of Formula (XV-x2), each Φ is 10
, wherein R1 is hydrogen or C1-6alkyl (e.g., hydrogen); and RP is hydrogen or a nitrogen protecting group (e.g., hydrogen).In one embodiment of Formula (XV- x), (XV-x1), and (XV-x2), and each of the preceding embodiments thereof, Y’ is O. In another embodiment, Y’ is S. In one embodiment of Formula (XV-x), (XV-x1), and (XV-x2), and each of the preceding 15 embodiments thereof, R1 is hydrogen. In another embodiment, R1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment of Formula (XV-x), (XV-x1), and (XV-x2), and each of the preceding embodiments thereof, RP is hydrogen. In another embodiment, RP is a nitrogen protecting group (e.g., t- butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). 287 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In one embodiment of Formula (XV-x), (XV-x1), and (XV-x2), and each of the preceding embodiments thereof, Y’ is O and R1 is hydrogen. In one embodiment, Y’ is O and R1 is C1-6alkyl (e.g., methyl or t-butyl). In one embodiment, Y’ is S and R1 is hydrogen. In one embodiment, Y’ is S and R1 is C1-6alkyl (e.g., methyl or t-butyl). 5 In one embodiment of Formula (XV-x), (XV-x1), and (XV-x2), and each of the preceding embodiments thereof, Y’ is O and RP is hydrogen . In one embodiment, Y’ is O and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S and RP is hydrogen. In one embodiment, Y’ is S and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). 10 In one embodiment of Formula (XV-x), (XV-x1), and (XV-x2), and each of the preceding embodiments thereof ,Y’ is O, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is S, R1 is hydrogen and RP is hydrogen. In one embodiment, Y’ is O, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl15 (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is O, R1 is C1- 6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is hydrogen. In one embodiment, Y’ is O, R1 is C1-6alkyl (e.g., methyl or t- butyl) and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In one embodiment, Y’ is S, R1 is C1-6alkyl (e.g., methyl or t-butyl) and RP is 20 a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). In other embodiments of Formula (XV), the compound is of the structure:
wherein each
25 1-10; 2-10; 2-6; 4; 3; 2; or 1) ; and 288 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
In other embodiments of Formula (XV), the compound is of the structure: 5
10 In other embodiments of Formula (XV), the compound is of the structure: 289 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 5
. In some embodiments of Formula (XV), the compound is of the structure: 290 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO ,
, wherein * represents the bond to the remainder of the dsRNA agent. In another embodiment, the compound of Formula (XV) is 5
291 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
wherein * represents the bond to the remainder of the dsRNA agent. In another embodiment, the compound of Formula (XV) is, 5
wherein * represents the bond to the remainder of the dsRNA agent. In another embodiment, the compound of Formula (XV) is, 10
292 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
wherein * represents the bond to the remainder of the dsRNA agent. In another embodiment, the compound of Formula (XV) is, 5
wherein * represents the bond to the remainder of the dsRNA agent. 293 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In another embodiment, the compound of Formula (XV) is,
wherein B is an optionally modified nucleobase (e.g., cytosine, uracil, 5-methylcytosine, 5- 5
wherein * represents the bond to the remainder of the dsRNA agent. 10 VI. Delivery of an RNAi Agent of the Disclosure The delivery of a RNAi agent of the disclosure to a cell e.g., a cell within a subject, such as a human subject (e.g., a subject in need thereof, such as a subject having a target gene-associated (i.e., DMPK-associated) disorder, can be achieved in a number of different ways. For example, delivery 15 may be performed by contacting a cell with an RNAi agent of the disclosure either in vitro or in vivo. In vivo delivery may also be performed directly by administering a composition comprising an RNAi agent, e.g., a dsRNA, to a subject. Alternatively, in vivo delivery may be performed indirectly by administering one or more vectors that encode and direct the expression of the RNAi agent. These alternatives are discussed further below. 20 In general, any method of delivering a nucleic acid molecule (in vitro or in vivo) can be adapted for use with a RNAi agent of the disclosure. For in vivo delivery, factors to consider in order to deliver an RNAi agent include, for example, biological stability of the delivered agent, prevention of non-specific effects, and accumulation of the delivered agent in the target tissue. For administering a RNAi agent systemically for the treatment of a disease, the RNA can be modified or alternatively 25 delivered using a drug delivery system; both methods act to prevent the rapid degradation of the 294 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO dsRNA by endo- and exo-nucleases in vivo. Modification of the RNA or the pharmaceutical carrier can also permit targeting of the RNAi agent to the target tissue and avoid undesirable off-target effects (e.g., without wishing to be bound by theory, use of GNAs as described herein has been identified to destabilize the seed region of a dsRNA, resulting in enhanced preference of such 5 dsRNAs for on-target effectiveness, relative to off-target effects, as such off-target effects are significantly weakened by such seed region destabilization). RNAi agents can be modified by chemical conjugation to lipophilic groups such as cholesterol to enhance cellular uptake and prevent degradation. In an alternative embodiment, the RNAi agent can be delivered using drug delivery systems such as a nanoparticle, a dendrimer, a polymer, liposomes, or a cationic delivery system. In 10 some embodiments, a RNAi agent forms a complex with cyclodextrin for systemic administration. Certain aspects of the instant disclosure relate to a method of reducing the expression of a target gene, i.e., DMPK, in a cell, comprising contacting said cell with the double-stranded RNAi agent of the disclosure. In one embodiment, the cell is a skeletal muscle. In one embodiment, the cell is a cardiac muscle cell. In one embodiment, the cell is an adipocyte. 15 In certain embodiments, the RNAi agent is taken up on one or more tissue or cell types present in organs, e.g., liver, skeletal muscle, cardiac muscle, adipose tissue. Another aspect of the disclosure relates to a method of reducing the expression and/or activity of a target gene in a subject, comprising administering to the subject the double-stranded RNAi agent of the disclosure. 20 Another aspect of the disclosure relates to a method of treating a subject having a target gene- associated disorder or at risk of having or at risk of developing a target gene-associated disorder, comprising administering to the subject a therapeutically effective amount of the double-stranded RNAi agent of the disclosure, thereby treating the subject. In one embodiment, the double-stranded RNAi agent is administered subcutaneously. 25 In one embodiment, the double-stranded RNAi agent is administered intramuscularly. In one embodiment, the double-stranded RNAi agent is administered by intravenously. For ease of exposition the formulations, compositions and methods in this section are discussed largely with regard to modified siRNA compounds. It may be understood, however, that these formulations, compositions and methods can be practiced with other siRNA compounds, e.g., 30 unmodified siRNA compounds, and such practice is within the disclosure. A composition that includes a RNAi agent can be delivered to a subject by a variety of routes. Exemplary routes include pulmonary system, intravenous, subcutaneous, oral, topical, rectal, anal, vaginal, nasal, and ocular. The RNAi agents of the disclosure can be incorporated into pharmaceutical compositions suitable for administration. Such compositions typically include one or more species of RNAi agent 35 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 absorption delaying agents, and the like, compatible with pharmaceutical administration. The use of such media and agents for pharmaceutically active 295 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active compound, use thereof in the compositions is contemplated. Supplementary active compounds can also be incorporated into the compositions. The pharmaceutical compositions of the present disclosure may be administered in a number 5 of ways depending upon whether local or systemic treatment is desired and upon the area to be treated. Administration may be intratracheal, intranasal, topical (including ophthalmic, vaginal, rectal, intranasal, transdermal), oral, parenteral, or pulmonary, e.g., by inhalation or insufflation of powders or aerosols, including by nebulizer. Parenteral administration includes intravenous drip, subcutaneous, intraperitoneal, or intramuscular injection administration. 10 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 RNAi agent in powder or aerosol form. The vascular endothelial cells could be targeted by coating a balloon catheter with the RNAi agent and mechanically introducing the RNA. 15 Aqueous compositions may be sterile and may optionally contain buffers, diluents, absorption enhancers and other suitable additives. Such administration permits both systemic and local delivery of the double stranded RNAi agents of the disclosure. Formulations for topical administration may include transdermal patches, ointments, lotions, creams, gels, drops, suppositories, sprays, liquids, and powders. Conventional pharmaceutical 20 carriers, aqueous, powder or oily bases, thickeners and the like may be necessary or desirable. Coated condoms, gloves, and the like may also be useful. Compositions for oral administration include powders or granules, suspensions or solutions in water, syrups, elixirs or non-aqueous media, tablets, capsules, lozenges, or troches. In the case of tablets, carriers that can be used include lactose, sodium citrate and salts of phosphoric acid. Various 25 disintegrants such as starch, and lubricating agents such as magnesium stearate, sodium lauryl sulfate and talc, are commonly used in tablets. For oral administration in capsule form, useful diluents are lactose and high molecular weight polyethylene glycols. When aqueous suspensions are required for oral use, the nucleic acid compositions can be combined with emulsifying and suspending agents. If desired, certain sweetening or flavoring agents can be added. 30 Formulations for parenteral administration may include sterile aqueous solutions which may also contain buffers, diluents, and other suitable additives. For intravenous use, the total concentration of solutes may be controlled to render the preparation isotonic. In one embodiment, the administration of the siRNA compound, e.g., a double-stranded siRNA compound, is parenteral, e.g., intravenous (e.g., as a bolus or as a diffusible infusion), 35 intradermal, intraperitoneal, intramuscular, subcutaneous, transmucosal, buccal, sublingual, endoscopic, rectal, oral, vaginal, topical, pulmonary system, intranasal, urethral, or ocular. Administration can be provided by the subject or by another person, e.g., a health care provider. The 296 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO medication can be provided in measured doses or in a dispenser which delivers a metered dose. Selected modes of delivery are discussed in more detail below. A. Vector encoded RNAi agents of the Disclosure 5 RNAi agents targeting the target gene can be expressed from transcription units inserted into DNA or RNA vectors (see, e.g., Couture, A, et al., TIG. (1996), 12:5-10; WO 00/22113, WO 00/22114, and US 6,054,299). Expression can be sustained (months or longer), depending upon the specific construct used and the target tissue or cell type. These transgenes can be introduced as a linear construct, a circular plasmid, or a viral vector, which can be an integrating or non-integrating 10 vector. The transgene can also be constructed to permit it to be inherited as an extrachromosomal plasmid (Gassmann, et al., (1995) Proc. Natl. Acad. Sci. USA 92:1292). The individual strand or strands of a RNAi agent can be transcribed from a promoter on an expression vector. Where two separate strands are to be expressed to generate, for example, a dsRNA, two separate expression vectors can be co-introduced (e.g., by transfection or infection) into a target 15 cell. Alternatively, each individual strand of a dsRNA can be transcribed by promoters both of which are located on the same expression plasmid. In one embodiment, a dsRNA is expressed as inverted repeat polynucleotides joined by a linker polynucleotide sequence such that the dsRNA has a stem and loop structure. RNAi agent expression vectors are generally DNA plasmids or viral vectors. Expression 20 vectors compatible with eukaryotic cells, such as those compatible with vertebrate cells, can be used to produce recombinant constructs for the expression of a RNAi agent as described herein. Delivery of RNAi agent expressing vectors can be systemic, such as by intravenous or intramuscular administration, by administration to target cells ex-planted from the patient followed by reintroduction into the patient, or by any other means that allows for introduction into a desired target cell. 25 Viral vector systems which can be utilized with the methods and compositions described herein include, but are not limited to, (a) adenovirus vectors; (b) retrovirus vectors, including but not limited to lentiviral vectors, moloney murine leukemia virus, etc.; (c) adeno- associated virus vectors; (d) herpes simplex virus vectors; (e) SV 40 vectors; (f) polyoma virus vectors; (g) papilloma virus vectors; (h) picornavirus vectors; (i) pox virus vectors such as an orthopox, e.g., vaccinia virus vectors30 or avipox, e.g. canary pox or fowl pox; and (j) a helper-dependent or gutless adenovirus. Replication- defective viruses can also be advantageous. Different vectors will or will not become incorporated into the cells’ genome. The constructs can include viral sequences for transfection, if desired. Alternatively, the construct can be incorporated into vectors capable of episomal replication, e.g. EPV and EBV vectors. Constructs for the recombinant expression of a RNAi agent will generally require 35 regulatory elements, e.g., promoters, enhancers, etc., to ensure the expression of the RNAi agent in target cells. Other aspects to consider for vectors and constructs are known in the art. VII. Pharmaceutical Compositions 297 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO The present disclosure also includes pharmaceutical compositions and formulations which include the RNAi agents of the disclosure. In one embodiment, provided herein are pharmaceutical compositions containing an RNAi agent, as described herein, and a pharmaceutically acceptable carrier. The pharmaceutical compositions containing the RNAi agent are useful for treating a subject 5 who would benefit from inhibiting or reducing the expression of a target gene, e.g., a subject having a DMPK–associated disorder, e.g., DM1. Such pharmaceutical compositions are formulated based on the mode of delivery. One example is compositions that are formulated for systemic administration via parenteral delivery, e.g., by intravenous (IV), intramuscular (IM), or for subcutaneous (subQ) delivery. 10 In some embodiments, the pharmaceutical compositions of the disclosure are pyrogen free or non-pyrogenic. In one embodiment, the delivery vehicle can deliver an iRNA compound, e.g., a double- stranded iRNA compound, or ssiRNA compound, (e.g., a precursor thereof, e.g., a larger siRNA compound which can be processed into a ssiRNA compound, or a DNA which encodes an siRNA 15 compound, e.g., a double-stranded siRNA compound, or ssiRNA compound, or precursor thereof) to a cell by a topical route of administration. The delivery vehicle can be microscopic vesicles. In one example the microscopic vesicles are liposomes. In some embodiments the liposomes are cationic liposomes. In another example the microscopic vesicles are micelles.In one aspect, the disclosure features a pharmaceutical composition including an siRNA compound, e.g., a double-stranded siRNA 20 compound, or ssiRNA compound, (e.g., a precursor thereof, 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) in an injectable dosage form. In one embodiment, the injectable dosage form of the pharmaceutical composition includes sterile aqueous solutions or dispersions and sterile powders. In some embodiments the sterile 25 solution can include a diluent such as water; saline solution; fixed oils, polyethylene glycols, glycerin, or propylene glycol. In one aspect, the disclosure features a pharmaceutical composition including an siRNA compound, e.g., a double-stranded siRNA compound, or ssiRNA compound, (e.g., a precursor thereof, e.g., a larger siRNA compound which can be processed into a ssiRNA compound, or a DNA 30 which encodes an siRNA compound, e.g., a double-stranded siRNA compound, or ssiRNA compound, or precursor thereof) in oral dosage form. In one embodiment, the oral dosage form is selected from the group consisting of tablets, capsules and gel capsules. In another embodiment, the pharmaceutical composition includes an enteric material that substantially prevents dissolution of the tablets, capsules or gel capsules in a mammalian stomach. In some embodiments the enteric material 35 is a coating. The coating can be acetate phthalate, propylene glycol, sorbitan monoleate, cellulose acetate trimellitate, hydroxy propyl methyl cellulose phthalate or cellulose acetate phthalate. In one embodiment, the oral dosage form of the pharmaceutical composition includes a penetration enhancer, e.g., a penetration enhancer described herein. 298 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO In another embodiment, the oral dosage form of the pharmaceutical composition includes an excipient. In one example the excipient is polyethyleneglycol. In another example the excipient is precirol. In another embodiment, the oral dosage form of the pharmaceutical composition includes a 5 plasticizer. The plasticizer can be diethyl phthalate, triacetin dibutyl sebacate, dibutyl phthalate or triethyl citrate. VIII. Methods of the Disclosure Another aspect of the disclosure relates to a method of reducing the expression of a DMPK 10 gene in a cell, comprising contacting the cell with a dsRNA agent of the disclosure. The methods include contacting the cell with a dsRNA agent of the disclosure and maintaining the cell for a time sufficient to obtain degradation of the mRNA transcripts of a target gene, i.e., DMPK, thereby inhibiting expression of the target gene in the cell. Reduction in gene expression can be assessed by any methods known in the art. For example, 15 a reduction in the expression of a target may be determined by determining the mRNA expression level of the target gene using methods routine to one of ordinary skill in the art, e.g., northern blotting, qRT-PCR; by determining the protein level of a target protein using methods routine to one of ordinary skill in the art, such as western blotting, immunological techniques or histology based methods, such as IHC and ISH. 20 In the methods of the disclosure the cell may be contacted in vitro or in vivo, i.e., the cell may be within a subject. Contacting a cell in vivo with the RNAi agent includes contacting a cell or group of cells within a subject, e.g., a human subject, with the RNAi agent. Combinations of in vitro and in vivo methods of contacting a cell are also possible. The cell may be muscle cell, such as a skeletal muscle cell (e.g. myocytes, endothelial cells, 25 macrophages, and neutrophils), a cardiac muscle cell (e.g. cardiomyocytes, fibroblasts), or a smooth muscle cell. A cell suitable for treatment using the methods of the disclosure may be any cell that expresses a target gene. A cell suitable for use in the methods of the disclosure may be a mammalian cell, e.g., a primate cell (such as a human cell or a non-human primate cell, e.g., a monkey cell or a 30 chimpanzee cell), a non-primate cell (such as a rat cell, or a mouse cell. In one embodiment, the cell is a human cell, e.g., a human liver cell or a human kidney cell. Contacting a cell may be direct or indirect, as discussed above. Furthermore, contacting a cell may be accomplished via a targeting ligand, including any ligand described herein or known in the art. In some embodiments, the targeting ligand is a carbohydrate moiety, e.g., a GalNAc ligand, or any 35 other ligand that directs the RNAi agent to a site of interest. In certain embodiments, the RNAi agent does not include a targeting ligand. The term “inhibiting,” as used herein, is used interchangeably with “reducing,” “silencing,” “downregulating,” “suppressing” and other similar terms, and includes any level of inhibition. In 299 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO certain embodiments, a level of inhibition, e.g., for an RNAi agent of the instant disclosure, can be assessed in cell culture conditions, e.g., wherein cells in cell culture are transfected via LipofectamineTM-mediated transfection at a concentration in the vicinity of a cell of 10 nM or less, 1 nM or less, etc. Knockdown of a given RNAi agent can be determined via comparison of pre-treated 5 levels in cell culture versus post-treated levels in cell culture, optionally also comparing against cells treated in parallel with a scrambled or other form of control RNAi agent. Knockdown in cell culture of, e.g., 50% or more, can thereby be identified as indicative of “inhibiting” or “reducing”, “downregulating” or “suppressing”, etc. having occurred. It is expressly contemplated that assessment of targeted mRNA or encoded protein levels (and therefore an extent of “inhibiting”, etc. caused by a 10 RNAi agent of the disclosure) can also be assessed in in vivo systems for the RNAi agents of the instant disclosure, under properly controlled conditions as described in the art. The phrase “inhibiting expression of a target gene” or “inhibiting expression of a target,” as used herein, includes inhibition of expression of any target gene (such as, e.g., a mouse target gene, a rat target gene, a monkey target gene, or a human target gene) as well as variants or mutants of a 15 target gene that encode a target protein. Thus, the target gene may be a wild-type target gene, a mutant target gene , or a transgenic target gene in the context of a genetically manipulated cell, group of cells, or organism. “Inhibiting expression of a target gene” includes any level of inhibition of a target gene, e.g., at least partial suppression of the expression of a target gene, such as an inhibition by at least 20%. In 20 certain embodiments, inhibition is by at least 30%, at least 40%, at least 50%, at least about 60%, at least 70%, at least about 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%; or to below the level of detection of the assay method. In certain method, inhibition is measured at a 10 nM concentration of the siRNA using the luciferase assay provided in Example 1. 25 The expression of a target gene may be assessed based on the level of any variable associated with target gene expression, e.g., target mRNA level or target protein level. Inhibition may be assessed by a decrease in an absolute or relative level of one or more of these variables compared with a control level. The control level may be any type of control level that is utilized in the art, e.g., a pre-dose baseline level, or a level determined from a similar subject, cell, 30 or sample that is untreated or treated with a control (such as, e.g., buffer only control or inactive agent control). In some embodiments of the methods of the disclosure, expression of a target gene (i.e., a DMPK gene) is inhibited by at least 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, or 95%, or to below the level of detection of the assay. In certain embodiments, the methods include a clinically 35 relevant inhibition of expression of a target gene, e.g. as demonstrated by a clinically relevant outcome after treatment of a subject with an agent to reduce the expression of a target gene. Inhibition of the expression of a target gene may be manifested by a reduction of the amount of mRNA expressed by a first cell or group of cells (such cells may be present, for example, in a 300 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO sample derived from a subject) in which a target gene is transcribed and which has or have been treated (e.g., by contacting the cell or cells with a RNAi agent of the disclosure, or by administering a RNAi agent of the disclosure to a subject in which the cells are or were present) such that the expression of a target gene is inhibited, as compared to a second cell or group of cells substantially 5 identical to the first cell or group of cells but which has not or have not been so treated (control cell(s) not treated with a RNAi agent or not treated with a RNAi agent targeted to the genome of interest). The degree of inhibition may be expressed in terms of: (mRNAincontrolcells) - (mRNAin treated cells) ^100 % (mRNAincontrol cells) 10 In other embodiments, inhibition of the expression of a target gene may be assessed in terms of a reduction of a parameter that is functionally linked to a target gene expression, e.g., target protein expression. Target gene silencing may be determined in any cell expressing a target gene, either endogenous or heterologous from an expression construct, and by any assay known in the art. 15 Inhibition of the expression of a target protein may be manifested by a reduction in the level of the target protein that is expressed by a cell or group of cells (e.g., the level of protein expressed in a sample derived from a subject). As explained above, for the assessment of genome suppression, the inhibition of protein expression levels in a treated cell or group of cells may similarly be expressed as a percentage of the level of protein in a control cell or group of cells. 20 A control cell or group of cells that may be used to assess the inhibition of the expression of a target gene includes a cell or group of cells that has not yet been contacted with an RNAi agent of the disclosure. For example, the control cell or group of cells may be derived from an individual subject (e.g., a human or animal subject) prior to treatment of the subject with an RNAi agent. The level of target gene mRNA that is expressed by a cell or group of cells may be 25 determined using any method known in the art for assessing RNA expression. In one embodiment, the level of expression of target gene in a sample is determined by detecting a transcribed polynucleotide, or portion thereof, e.g., mRNA of the target gene. RNA may be extracted from cells using RNA extraction techniques including, for example, using acid phenol/guanidine isothiocyanate extraction (RNAzol B; Biogenesis), RNeasyTM RNA preparation kits (Qiagen®) or PAXgene (PreAnalytix, 30 Switzerland). Typical assay formats utilizing ribonucleic acid hybridization include nuclear run-on assays, RT-PCR, RNase protection assays, northern blotting, in situ hybridization, microarray analysis, and or histology based methods such as IHC and ISH. Circulating target mRNA may be detected using methods the described in WO2012/177906, the entire contents of which are hereby incorporated herein by reference. 35 In some embodiments, the level of expression of target gene is determined using a nucleic acid probe. The term “probe”, as used herein, refers to any molecule that is capable of selectively binding to a specific target nucleic acid or protein, or fragment thereof. Probes can be synthesized by 301 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO one of skill in the art, or derived from appropriate biological preparations. Probes may be specifically designed to be labeled. Examples of molecules that can be utilized as probes include, but are not limited to, RNA, DNA, proteins, antibodies, and organic molecules. Isolated mRNA can be used in hybridization or amplification assays that include, but are not 5 limited to, Southern or northern analyses, polymerase chain reaction (PCR) analyses and probe arrays. One method for the determination of RNA levels involves contacting the isolated RNA with a nucleic acid molecule (probe) that can hybridize to target RNA. In one embodiment, the RNA is immobilized on a solid surface and contacted with a probe, for example by running the isolated RNA on an agarose gel and transferring the RNA from the gel to a membrane, such as nitrocellulose. In an alternative 10 embodiment, the probe(s) are immobilized on a solid surface and the RNA is contacted with the probe(s), for example, in an Affymetrix® gene chip array. A skilled artisan can readily adapt known RNA detection methods for use in determining the level of target mRNA. An alternative method for determining the level of expression of target in a sample involves the process of nucleic acid amplification or reverse transcriptase (to prepare cDNA) of for example 15 mRNA in the sample, e.g., by RT-PCR (the experimental embodiment set forth in Mullis, 1987, US Patent No.4,683,202), ligase chain reaction (Barany (1991) Proc. Natl. Acad. Sci. USA 88:189-193), self sustained sequence replication (Guatelli et al. (1990) Proc. Natl. Acad. Sci. USA 87:1874-1878), transcriptional amplification system (Kwoh et al. (1989) Proc. Natl. Acad. Sci. USA 86:1173-1177), Q-Beta Replicase (Lizardi et al. (1988) Bio/Technology 6:1197), rolling circle replication (Lizardi et 20 al., US Patent No.5,854,033) or any other nucleic acid amplification method, followed by the detection of the amplified molecules using techniques well known to those of skill in the art. These detection schemes are especially useful for the detection of nucleic acid molecules if such molecules are present in very low numbers. In particular aspects of the disclosure, the level of expression of target is determined by quantitative fluorogenic RT-PCR (i.e., the TaqManTM System), by a Dual- 25 Glo® Luciferase assay, or by other art-recognized method for measurement of target expression or mRNA level. The expression level of target mRNA may be monitored using a membrane blot (such as used in hybridization analysis such as northern, Southern, dot, and the like), or microwells, sample tubes, gels, beads or fibers (or any solid support comprising bound nucleic acids). See US Patent Nos. 30 5,770,722, 5,874,219, 5,744,305, 5,677,195 and 5,445,934, which are incorporated herein by reference. The determination of target expression level may also comprise using nucleic acid probes in solution. In some embodiments, the level of RNA expression is assessed using branched DNA (bDNA) assays or real time PCR (qPCR). The use of this PCR method is described and exemplified in the 35 Examples presented herein. Such methods can also be used for the detection of target nucleic acids. The level of target protein expression may be determined using any method known in the art for the measurement of protein levels. Such methods include, for example, electrophoresis, capillary electrophoresis, high performance liquid chromatography (HPLC), thin layer chromatography (TLC), 302 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO hyperdiffusion chromatography, fluid or gel precipitin reactions, absorption spectroscopy, a colorimetric assays, spectrophotometric assays, flow cytometry, immunodiffusion (single or double), immunoelectrophoresis, western blotting, radioimmunoassay (RIA), enzyme-linked immunosorbent assays (ELISAs), immunofluorescent assays, electrochemiluminescence assays, and the like. Such 5 assays can also be used for the detection of proteins indicative of the presence or replication of target proteins. In some embodiments, the efficacy of the methods of the disclosure in the treatment of a target gene-related disease is assessed by a decrease in target mRNA level (e.g, by assessment of a blood target gene level, or otherwise). 10 In some embodiments, the efficacy of the methods of the disclosure in the treatment of a target gene-related disease is assessed by a decrease in target mRNA level (e.g, by assessment of a liver or kidney sample for target level, by biopsy, or otherwise). In some embodiments of the methods of the disclosure, the RNAi agent is administered to a subject such that the RNAi agent is delivered to a specific site within the subject. The inhibition of 15 expression of target may be assessed using measurements of the level or change in the level of target mRNA or target protein in a sample derived from a specific site within the subject, e.g., liver or kidney cells. In certain embodiments, the methods include a clinically relevant inhibition of expression of target, e.g. as demonstrated by a clinically relevant outcome after treatment of a subject with an agent to reduce the expression of target gene. 20 As used herein, the terms detecting or determining a level of an analyte are understood to mean performing the steps to determine if a material, e.g., protein, RNA, is present. As used herein, methods of detecting or determining include detection or determination of an analyte level that is below the level of detection for the method used. The in vivo methods of the disclosure may include administering to a subject a composition 25 containing a RNAi agent, where the RNAi agent includes a nucleotide sequence that is complementary to at least a part of an RNA transcript of the target gene of the subject to be treated. When the organism to be treated is a mammal such as a human, the composition can be administered by any means known in the art including, but not limited to oral, intraperitoneal, or parenteral routes, including intravenous, intramuscular, subcutaneous, transdermal, airway (aerosol), nasal, rectal, and 30 topical (including buccal and sublingual) administration. In certain embodiments, the compositions are administered by intravenous infusion or injection. In certain embodiments, the compositions are administered by subcutaneous injection. In certain embodiments, the compositions are administered orally. In certain embodiments, the compositions are administered by pulmonary delivery, e.g., oral inhalation or intranasal delivery. 35 In some embodiments, the administration is via a depot injection. A depot injection may release the RNAi agent in a consistent way over a prolonged time period. Thus, a depot injection may reduce the frequency of dosing needed to obtain a desired effect, e.g., a desired inhibition of the target gene, or a therapeutic or prophylactic effect. A depot injection may also provide more consistent 303 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO serum concentrations. Depot injections may include subcutaneous injections or intramuscular injections. In certain embodiments, the depot injection is a subcutaneous injection. In one embodiment, the double-stranded RNAi agent is administered by pulmonary system administration, e.g., intranasal administration or oral inhalative administration. Pulmonary system 5 administration may be via a syringe, a dropper, atomization, or use of device, e.g., a passive breath driven or active power driven single/-multiple dose dry powder inhaler (DPI) device. The mode of administration may be chosen based upon whether local or systemic treatment is desired and based upon the area to be treated. The route and site of administration may be chosen to enhance targeting. 10 In one aspect, the present disclosure also provides methods for inhibiting the expression of a DMPK gene in a mammal. The methods include administering to the mammal a composition comprising a dsRNA that targets a target gene, i.e., DMPK, in a cell of the mammal and maintaining the mammal for a time sufficient to obtain degradation of the RNA transcript of the target gene, thereby inhibiting expression of the target gene in the cell. Reduction in genome expression can be 15 assessed by any methods known it the art and by methods, e.g. qRT-PCR, described herein. Reduction in protein production can be assessed by any methods known it the art and by methods, e.g. ELISA, described herein. The present disclosure further provides methods of treatment of a subject in need thereof. The treatment methods of the disclosure include administering an RNAi agent of the disclosure to a 20 subject, e.g., a subject that would benefit from inhibition of DMPK gene expression, such as a subject having myotonic dystrophy type 1 (DM1), in a therapeutically effective amount of a RNAi agent targeting a target gene or a pharmaceutical composition comprising a RNAi agent targeting a target gene. An RNAi agent of the disclosure may be administered as a “free RNAi agent.” A free RNAi 25 agent is administered in the absence of a pharmaceutical composition. The naked RNAi agent may be in a suitable buffer solution. The buffer solution may comprise acetate, citrate, prolamine, carbonate, or phosphate, or any combination thereof. In one embodiment, the buffer solution is phosphate buffered saline (PBS). The pH and osmolarity of the buffer solution containing the RNAi agent can be adjusted such that it is suitable for administering to a subject. In certain embodiments, the free RNAi 30 agent may be formulated in water or normal saline. Alternatively, an RNAi agent of the disclosure may be administered as a pharmaceutical composition, such as a dsRNA liposomal formulation. In one aspect, the present disclosure provides a method of treating a subject having a DMPK- associated disorder, such as myotonic dystrophy type 1 (DM1), comprising administering to the 35 subject a therapeutically effective amount of a dsRNA agent of the disclosure, thereby treating the subject. In another aspect, the present disclosure provides a method of preventing at least one symptom in a subject having a disorder that would benefit from reduction in dystrophy myotonic 304 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO protein kinase (DMPK) expression, e.g., DM1, comprising administering to the subject a prophylactically effective amount of a dsRNA agent or pharmaceutical composition of the disclosure. The treatment methods of the disclosure may ameliorate at least on sign or symptom of the disease and/or progression of the disease. 5 The dsRNA agent of the disclosure can be delivered to a subject by a variety of routes, depending on the type of genes targeted and the type of disorders to be treated. In some embodiments, the dsRNA agent is administered extra-hepatically, such as intravenous, intramuscular, or subcutaneous administration. The disclosure further provides methods for the use of a RNAi agent or a pharmaceutical 10 composition thereof, e.g., for treating a subject that would benefit from reduction or inhibition of DMPK gene expression, e.g., a subject having a DMPK-associated disorder, in combination with other pharmaceuticals or other therapeutic methods, e.g., with known pharmaceuticals or known therapeutic methods, such as, for example, those which are currently employed for treating these disorders. 15 Examples of the additional therapeutic agents which can be used with an RNAi agent of the disclosure include, but are not limited to, calcium channel blockers, sodium channel blockers such as procainamide, phenytoin and mexiletine, tricyclic antidepressant drugs such as clomipramine or imipramine, benzodiazepines, calcium antagonists, taurine and prednisone, neurostimulants such as methylphenidate for excessive daytime sleepiness, ataract surgery, treatment for diabetes, and/or 20 synthetic testosterone. The RNAi agent and additional therapeutic agents may be administered at the same time or in the same combination, or the additional therapeutic agent can be administered as part of a separate composition or at separate times or by another method known in the art or described herein. In one embodiment, the method includes administering a composition featured herein such 25 that expression of the target gene is decreased, for at least one month. In some embodiments, expression is decreased for at least 2 months, 3 months, or 6 months. In certain embodiments, administration includes a loading dose administered at a higher frequency, e.g., once per day, twice per week, once per week, for an initial dosing period, e.g., 2-4 doses. 30 In some embodiments, the RNAi agents useful for the methods and compositions featured herein specifically target RNAs (primary or processed) of the DMPK gene. Compositions and methods for inhibiting the expression of these genes using RNAi agents can be prepared and performed as described herein. Administration of the dsRNA according to the methods of the disclosure may result in a 35 reduction of the severity, signs, symptoms, or markers of such diseases or disorders in a patient with a target gene-associated disorder. By “reduction” in this context is meant a statistically significant or clinically significant decrease in such level. The reduction can be, for example, at least 5%, 10%, 305 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or about 100%. Efficacy of treatment or prevention of disease can be assessed, for example by measuring disease progression, disease remission, symptom severity, reduction in pain, quality of life, dose of a 5 medication required to sustain a treatment effect, level of a disease marker or any other measurable parameter appropriate for a given disease being treated or targeted for prevention. It is well within the ability of one skilled in the art to monitor efficacy of treatment or prevention by measuring any one of such parameters, or any combination of parameters. It is well within the ability of one skilled in the art to monitor efficacy of treatment or prevention by measuring any one of such parameters, or any 10 combination of parameters. In connection with the administration of a RNAi agent targeting a target DMPK gene of interest or pharmaceutical composition thereof, "effective against" a DMPK- associated disorder indicates that administration in a clinically appropriate manner results in a beneficial effect for at least a statistically significant fraction of patients, such as an improvement of symptoms, a cure, a reduction in disease, extension of life, improvement in quality of life, or other15 effect generally recognized as positive by medical doctors familiar with treating target gene- associated disorders and the related causes. A treatment or preventive effect is evident when there is a statistically significant improvement in one or more parameters of disease status, or by a failure to worsen or to develop symptoms where they would otherwise be anticipated. As an example, a favorable change of at least 20 10% in a measurable parameter of disease, and at least 20%, 30%, 40%, 50%, or more can be indicative of effective treatment. Efficacy for a given RNAi agent drug or formulation of that drug can also be judged using an experimental animal model for the given disease as known in the art. When using an experimental animal model, efficacy of treatment is evidenced when a statistically significant reduction in a marker or symptom is observed. 25 Alternatively, the efficacy can be measured by a reduction in the severity of disease as determined by one skilled in the art of diagnosis based on a clinically accepted disease severity grading scale. Any positive change resulting in e.g., lessening of severity of disease measured using the appropriate scale, represents adequate treatment using a RNAi agent or RNAi agent formulation as described herein. 30 The RNAi agent can be administered over a period of time, on a regular basis. In certain embodiments, after an initial treatment regimen, the treatments can be administered on a less frequent basis. Administration of the RNAi agent can reduce target gene levels, e.g., in a cell, tissue, blood sample or other compartment of the patient by at least 20%, 30%, 40%, 50%, 55%, 60%, 65%, 70,% 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or at least about 99% or more. In one embodiment, 35 administration of the RNAi agent can reduce target gene levels, e.g., in a cell, tissue, blood sample, or other compartment of the patient by at least 50%. Before administration of a full dose of the RNAi agent, patients can be administered a smaller dose, such as a 5% infusion reaction, and monitored for adverse effects, such as an allergic 306 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO reaction. In another example, the patient can be monitored for unwanted immunostimulatory effects, such as increased cytokine (e.g., TNF-alpha or INF-alpha) levels. Alternatively, the RNAi agent can be administered by oral administration, pulmonary administration, intravenously, i.e., by intravenous injection, or subcutaneously, i.e., by subcutaneous 5 injection. One or more injections may be used to deliver the desired, e.g., monthly dose of RNAi agent to a subject. The injections may be repeated over a period of time. The administration may be repeated on a regular basis. In certain embodiments, after an initial treatment regimen, the treatments can be administered on a less frequent basis. A repeat-dose regimine may include administration of a therapeutic amount of RNAi agent on a regular basis, such as monthly or extending to once a quarter, 10 twice per year, once per year. In certain embodiments, the RNAi agent is administered about once per month to about once per quarter (i.e., about once every three months). IX. Kits In certain aspects, the instant disclosure provides kits that include a suitable container containing a pharmaceutical formulation of a dsRNA agent of the disclosure. In certain embodiments, the 15 individual components of the pharmaceutical formulation may be provided in one container. Alternatively, it may be desirable to provide the components of the pharmaceutical formulation separately in two or more containers, e.g., one container for a dsRNA agent and at least another for a pharmaceutically acceptable carrier, e.g., PBS. The kit may be packaged in a number of different configurations such as one or more containers in a single box. The different components can be 20 combined, e.g., according to instructions provided with the kit. The components can be combined according to a method described herein, e.g., to prepare and administer a pharmaceutical composition. The kit can also include a delivery device. Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs. 25 Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the RNAi agents and methods featured in the disclosure, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are 30 illustrative only and not intended to be limiting. An informal Sequence Listing is filed herewith and forms part of the specification as filed. This disclosure is further illustrated by the following examples which should not be construed as limiting. The entire contents of all references, patents and published patent applications cited throughout this application, as well as the informal Sequence Listing and Figures, are hereby 35 incorporated herein by reference. 307 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO EXAMPLES Example 1. dsRNA Synthesis Source of reagents Where the source of a reagent is not specifically given herein, such reagent can be obtained 5 from any supplier of reagents for molecular biology at a quality/purity standard for application in molecular biology. siRNA Design siRNAs targeting the human myotonic dystrophy protein kinase (DMPK) gene (human: 10 GenBank NM_004409.5, NCBI GeneID: 1760) were designed using custom R and Python scripts. The human DMPK, transcript variant 2, REFSEQ NM_004409.5 mRNA, has a length of 2799 bases. A detailed list of the unmodified DMPK sense and antisense strand nucleotide sequences are provided in Table 2. A detailed list of the modified DMPK sense and antisense strand nucleotide sequences are 15 provided in Table 3. siRNA Synthesis siRNAs were designed, synthesized, and prepared using methods known in the art. Briefly, siRNA sequences were synthesized on a 1 µmol scale using a Mermade 192 20 synthesizer (BioAutomation) with phosphoramidite chemistry on solid supports. The solid support was controlled pore glass (500-1000 Å) loaded with a custom GalNAc ligand (3’-GalNAc conjugates), universal solid support (AM Chemicals), or the first nucleotide of interest. Ancillary synthesis reagents and standard 2-cyanoethyl phosphoramidite monomers (2’-deoxy-2’-fluoro, 2’-O- methyl, RNA, DNA) were obtained from Thermo-Fisher (Milwaukee, WI), Hongene (China), or 25 Chemgenes (Wilmington, MA, USA). Additional phosphoramidite monomers were procured from commercial suppliers, prepared in-house, or procured using custom synthesis from various CMOs. Phosphoramidites were prepared at a concentration of 100 mM in either acetonitrile or 9:1 acetonitrile:DMF and were coupled using 5-Ethylthio-1H-tetrazole (ETT, 0.25 M in acetonitrile) with a reaction time of 400 s. Phosphorothioate linkages were generated using a 100 mM solution of 3- 30 ((Dimethylamino-methylidene) amino)-3H-1,2,4-dithiazole-3-thione (DDTT, obtained from Chemgenes (Wilmington, MA, USA)) in anhydrous acetonitrile/pyridine (9:1 v/v). Oxidation time was 5 minutes. All sequences were synthesized with final removal of the DMT group (“DMT-Off”). Upon completion of the solid phase synthesis, solid-supported oligoribonucleotides were treated with 300 µL of Methylamine (40% aqueous) at room temperature in 96 well plates for 35 approximately 2 hours to afford cleavage from the solid support and subsequent removal of all additional base-labile protecting groups. For sequences containing any natural ribonucleotide linkages (2’-OH) protected with a tert-butyl dimethyl silyl (TBDMS) group, a second deprotection step was performed using TEA.3HF (triethylamine trihydrofluoride). To each oligonucleotide solution in 308 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO aqueous methylamine was added 200 µL of dimethyl sulfoxide (DMSO) and 300 µL TEA.3HF and the solution was incubated for approximately 30 mins at 60 °C. After incubation, the plate was allowed to come to room temperature and crude oligonucleotides were precipitated by the addition of 1 mL of 9:1 acetontrile:ethanol or 1:1 ethanol:isopropanol. The plates were then centrifuged at 4 °C 5 for 45 mins and the supernatant carefully decanted with the aid of a multichannel pipette. The oligonucleotide pellet was resuspended in 20 mM NaOAc and subsequently desalted using a HiTrap size exclusion column (5 mL, GE Healthcare) on an Agilent LC system equipped with an autosampler, UV detector, conductivity meter, and fraction collector. Desalted samples were collected in 96 well plates and then analyzed by LC-MS and UV spectrometry to confirm identity and quantify 10 the amount of material, respectively. Duplexing of single strands was performed on a Tecan liquid handling robot. Sense and antisense single strands were combined in an equimolar ratio to a final concentration of 10 µM in 1x PBS in 96 well plates, the plate sealed, incubated at 100 °C for 10 minutes, and subsequently allowed to return slowly to room temperature over a period of 2-3 hours. The concentration and identity of 15 each duplex was confirmed and then subsequently utilized for in vitro screening assays. siRNAs comprising an alpha-v-beta-6 (αvβ6) integrin targeting ligand and/or an in vivo delivery enhancing moiety were designed and synthesized as described in International Application Nos. PCT/US2022/046668, filed on October 14, 2022, and PCT/US2023/083947, filed on December 14, 2023, and in U.S. Provisional Application No.63/659,097, entitled “Dual Conjugate Compounds 20 for Extrahepatic Delivery,” filed on June 12, 2024, and in International Application No. PCT/US2025/XXXXXX, filed on June 11, 2025, entitled “Dual Conjugate Compounds for Extrahepatic Delivery”. The entire contents of each of the foregoing applications are incorporated herein by reference. 25 Example 2. In vitro Screening Methods Cell culture and 384-well transfections CCL-136 (rhabdomyosarcoma) cells were grown to near confluence at 37°C in an atmosphere of 5% CO2 in Eagle’s Minimum Essential Medium (Gibco) supplemented with 10% FBS (ATCC) before being released from the plate by trypsinization. Transfection was carried out by adding 7.5 ^l 30 of Opti-MEM plus 0.1 ^l of Lipofectamine RNAiMax per well (Invitrogen, Carlsbad CA. cat # 13778-150) to 2.5 ^l of each siRNA duplex to an individual well in a 384-well plate. The mixture was then incubated at room temperature for 15 minutes. Forty ^l of complete growth media without antibiotic containing ~1.5 x104 cells were then added to the siRNA mixture. Cells were incubated for 24 hours prior to RNA purification. Single dose experiments were performed at 10nM, 1.667nM, 35 0.278nM, 0.046nM, 0.0077nM, 0.0013nM, 0.00021nM, or 0.000036nM final duplex concentration. In vitro Dual-Luciferase Reporter Assay 309 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO To measure DMPK siRNA in vitro activity, Dual-Luc assay was performed using psiCHECK-2 vector. The psiCHECK-2 vector was obtained from Promega (Catalog No. C8021 [Madison, WI]). Cynomolgus (cyno) DMPK target were synthesized and incorporated into the psiCHECK-2 vector by Blue Heron Biotech [Bothell, WA]. Dual-Luc assay was performed by co- 5 transfection in Cos-7 cells. The assay was performed in a 384-well format (5,000 cells per well) with 10 ng of each Dual-luciferase construct and DMPK duplex at a range of concentrations of 10 nM, 1.667 nM, 0.278 nM, 0.046 nM, 0.0077 nM, 0.0013 nM, 0.00021 nM, or 0.000036 nM using Invitrogen Lipofectamine® 2000 (Thermo Fisher Scientific [Waltham, MA] Catalog No.11668019). Forty-eight hours after transfection, Firefly (transfection control) and Renilla (fused to target 10 sequence) luciferase were measured in a Molecular Devices M5 spectrophotometer (Molecular Devices, LLC [San Jose, CA]). siRNA activity was determined by normalizing the Renilla (DMPK) signal to the Firefly (control) signal within each well. The magnitude of siRNA activity was then assessed relative to cells that were transfected with the same vector but were not treated with siRNA or were treated with a non-targeting siRNA. 15 Total RNA isolation using DYNABEADS mRNA Isolation Kit (Invitrogen™, part #: 610-12) Cells were lysed in 75^l of Lysis/Binding Buffer containing 3 µL of beads per well and mixed for 10 minutes on an electrostatic shaker. The washing steps were automated on a Biotek EL406, using a magnetic plate support. Beads were washed (in 90^L) once in Buffer A, once in 20 Buffer B, and twice in Buffer E, with aspiration steps in between. Following a final aspiration, complete 10^L RT mixture was added to each well, as described below. cDNA synthesis using ABI High capacity cDNA reverse transcription kit (Applied Biosystems, Foster City, CA, Cat #4368813) 25 A master mix of 1µl 10X Buffer, 0.4^l 25X dNTPs, 1^l Random primers, 0.5^l Reverse Transcriptase, 0.5^l RNase inhibitor and 6.6^l of H2O per reaction were added per well. Plates were sealed, agitated for 10 minutes on an electrostatic shaker, and then incubated at 37 degrees C for 2 hours. Following this, the plates were agitated at 80 degrees C for 8 minutes. 30 Real time PCR Two microlitre (µl) of cDNA were added to a master mix containing 0.5µl of human GAPDH TaqMan Probe (4326317E), 0.5µl human DMPK, 2µl nuclease-free water and 5µl Lightcycler 480 probe master mix (Roche Cat # 04887301001) per well in a 384 well plates (Roche cat # 04887301001). Real time PCR was done in a LightCycler480 Real Time PCR system (Roche). 35 The results of the single dose screens in CCL-136 assays of the agents listed in Tables 2 and 3 are provided in Table 4. The average percent DMPK mRNA remaining is shown for each dose in Table 4. 310 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO The results of the single dose Dual-Luciferase assays of the agents listed in Tables 2 and 3 are provided in Table 5. The average percent DMPK mRNA remaining is shown for each dose in Table 5. It is to be understood that, throughout the application, a duplex name without a decimal is equivalent to a duplex name with a decimal, which merely references the batch number of the duplex. 5 Table 1. Abbreviations of nucleotide monomers used in nucleic acid sequence representation. It will be understood that these monomers, when present in an oligonucleotide, are mutually linked by 5'-3'- phosphodiester bonds; and it is understood that when the nucleotide contains a 2’-fluoro modification, then the fluoro replaces the hydroxy at that position in the parent nucleotide (i.e., it is a 2’-deoxy-2’- 10 fluoronucleotide). It is to be further understood that the nucleotide abbreviations in the table omit the 3’-phosphate (i.e., they are 3’-OH) when placed at the 3’-terminal position of an oligonucleotide.
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Table 3. Modified Sense and Antisense Strand Sequences of DMPK dsRNA Agents
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Table 4. Single Dose Screen for Human DMPK in CCL-136 Cells
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Table 5. Screen for DMPK KD in Cos-7 Cells
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Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO Example 3. In vivo Screening Methods DMPK-targeting siRNA duplexes with human/cynomolgus cross-reactivity were further investigated for their effectiveness in non-human primates. A single 1 mg/kg, 3 mg/kg, or 9 mg/kg dose of DMPK targeting 5 siRNAs was subcutaneously administered to cynomolgus monkeys on day 1. Study groups contained either 3 or 4 monkeys. Muscle tissue samples were collected post scheduled euthanasia on day 85. mRNA was extracted from muscle tissue and the DMPK mRNA % remaining was quantified using qPCR normalized to housekeeping genes (PPIB (HKG1) and/or AAD1 (HKG2)). The results are shown in Tables 6-8 and FIG.1. The results in Table 6 are from a separate study from the results in 10 Table 7 and Table 8. Table 6:
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Table 8
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Example 4. In vivo Screening Methods An siRNA duplex targeting DMPK with human/cynomolgus cross-reactivity (AD-3100656) and containing an in vivo delivery enhancing moiety conjugated to the sense strand and an αvβ6 5 integrin targeting ligand at the 3’end of the sense strand having the chemical structure of L493 (as shown herein) was further investigated for its effectiveness in non-human primates. A single 3 mg/kg dose was subcutaneously administered to cynomolgus monkeys on day 1. Muscle tissue samples were collected post scheduled euthanasia on day 32. mRNA was extracted from muscle tissue and the DMPK mRNA % remaining was quantified using qPCR normalized to housekeeping genes (PPIB10 (HKG1) and AAD1 (HKG2)). The results are shown in FIG.2. 335 ME1\53453057.v1
Claims
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO We claim: 1. A double stranded ribonucleic acid (dsRNA) agent for inhibiting expression of a dystrophy myotonic protein kinase (DMPK) gene in a cell, or a pharmaceutically acceptable salt thereof, 5 comprising a sense strand and an antisense strand forming a double stranded region, wherein the antisense strand comprises at least 15 contiguous nucleotides differing by no more than three nucleotides from any one of the antisense strand nucleotide sequences in any one of Tables 2-3. 10 2. A double stranded ribonucleic acid (dsRNA) agent for inhibiting expression of a dystrophy myotonic protein kinase (DMPK) gene, or a pharmaceutically acceptable salt thereof, comprising a sense strand and an antisense strand forming a double stranded region; wherein the antisense strand comprises at least 15 contiguous nucleotides differing by no 15 more than three nucleotides from any one of the antisense strand nucleotide sequences in any one of Tables 2-3; at least one alpha-v-beta-6 (αvβ6) integrin targeting ligand that mediates delivery to muscle tissue conjugated to at least one strand; and at least one in vivo delivery enhancing moiety conjugated to one or more internal positions 20 on at least one strand. 3. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 1 or 2, wherein the sense strand comprises at least 15 contiguous nucleotides differing by no more than three nucleotides from any one of the sense strand nucleotide sequences in any one of Tables 2-3. 25 4. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-3, wherein the sense strand comprises at least 15 contiguous nucleotides differing by no more than two nucleotides from any one of the sense strand nucleotide sequences in any one of Tables 2-3 and the antisense strand comprises at least 15 contiguous nucleotides differing by no more than two 30 nucleotides from any one of the antisense strand nucleotide sequences in any one of Tables 2-3. 5. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-4, wherein the sense strand comprises at least 15 contiguous nucleotides differing by no more than one nucleotide from any one of the sense strand nucleotide sequences in any one of Tables 2-3 and the 35 antisense strand comprises at least 15 contiguous nucleotides differing by no more than one nucleotide from any one of the antisense strand nucleotide sequences in any one of Tables 2-3. 336 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 6. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-5, wherein the sense strand comprises a nucleotide sequence selected from the group consisting of any one of the sense strand nucleotide sequences in any one of Tables 2-3 and the antisense strand 5 comprises a nucleotide sequence selected from the group consisting of any one of the antisense strand nucleotide sequences in any one of Tables 2-3. 7. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-6, wherein the dsRNA agent, or a pharmaceutically acceptable salt thereof, comprises at least one 10 nucleotide comprising a nucleotide modification. 8. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-7, wherein all of the nucleotides of the sense strand comprise a nucleotide modification; all of the nucleotides of the antisense strand comprise a nucleotide modification; or all of the nucleotides of the 15 sense strand and all of the nucleotides of the antisense strand comprise a nucleotide modification. 9. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 7 or 8, wherein at least one of the nucleotide modifications is selected from the group consisting of a deoxy-nucleotide modification, a 3’-terminal deoxythimidine (dT) nucleotide modification, a 2'-O-methyl nucleotide 20 modification, a 2'-fluoro nucleotide modification, a 2'-deoxy nucleotide modification, a locked nucleotide modification, an unlocked nucleotide modification, a conformationally restricted nucleotide modification, a constrained ethyl nucleotide modification, an abasic nucleotide modification, a 2’-amino nucleotide modification, a 2’-O-allyl nucleotide modification, 2’-C-alkyl nucleotide modification, 2’-hydroxly nucleotide modification, a 2’-methoxyethyl nucleotide 25 modification, a 2’-O-alkyl nucleotide modification, a morpholino nucleotide modification, a phosphoramidate modification, a non-natural base comprising nucleotide modification, a tetrahydropyran nucleotide modification, a 1,5-anhydrohexitol nucleotide modification, a cyclohexenyl nucleotide modification, a nucleotide comprising a phosphorothioate group modification, a nucleotide comprising a methylphosphonate group modification, a nucleotide 30 comprising a 5’-phosphate modification, a nucleotide comprising a 5’-phosphate mimic modification, a thermally destabilizing nucleotide modification, a glycol modified nucleotide (GNA) modification, a nucleotide comprising a 2’ phosphate, and a 2-O-(N-methylacetamide) nucleotide modification; and combinations thereof. 35 10. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 7-9, wherein at least one of the modified nucleotides is selected from the group consisting of LNA, HNA, 337 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO CeNA, 2’-methoxyethyl, 2’-O-alkyl, 2’-O-allyl, 2’-C- allyl, 2’-fluoro, 2’-deoxy, 2’-hydroxyl, and glycol; and combinations thereof. 11. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 7-10, 5 wherein at least one of the modified nucleotides is selected from the group consisting of a deoxy- nucleotide, a 2'-O-methyl modified nucleotide, a 2'-fluoro modified nucleotide, a 2'-deoxy-modified nucleotide, a glycol modified nucleotide (GNA), a nucleotide comprising a 2’ phosphate, a nucleotide comprising a phosphorothioate group, and a vinyl-phosphonate nucleotide; and combinations thereof. 10 12. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 7-11, wherein at least one of the nucleotide modifications is a thermally destabilizing nucleotide modification. 13. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 12, wherein the 15 thermally destabilizing nucleotide modification is selected from the group consisting of an abasic modification; a mismatch with the opposing nucleotide in the duplex; a destabilizing sugar modification, a 2’-deoxy modification, an acyclic nucleotide, an unlocked nucleic acid (UNA), and a glycerol nucleic acid (GNA). 20 14. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-13, further comprising a phosphate or phosphate mimic at the 5’-end of the antisense strand. 15. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 14, wherein the phosphate mimic is a 5’-vinyl phosphonate (VP). 25 16. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-15, wherein the 3’ end of the sense strand is protected via an end cap which is a cyclic group having an amine, said cyclic group being selected from the group consisting of pyrrolidinyl, pyrazolinyl, pyrazolidinyl, imidazolinyl, imidazolidinyl, piperidinyl, piperazinyl, [1,3]dioxolanyl, oxazolidinyl, 30 isoxazolidinyl, morpholinyl, thiazolidinyl, isothiazolidinyl, quinoxalinyl, pyridazinonyl, tetrahydrofuranyl, and decalinyl. 17. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-16, wherein the double stranded region is 19-30 nucleotide pairs in length. 35 338 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 18. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 17, wherein the double stranded region is 19-25 nucleotide pairs in length. 19. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 17, wherein the 5 double stranded region is 19-23 nucleotide pairs in length. 20. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 17, wherein the double stranded region is 23-27 nucleotide pairs in length. 10 21. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 17, wherein the double stranded region is 21-23 nucleotide pairs in length. 22. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-21, wherein each strand is independently no more than 30 nucleotides in length. 15 23. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-22, wherein the sense strand is 21 nucleotides in length and the antisense strand is 23 nucleotides in length. 20 24. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-23, wherein the dsRNA agent, or a pharmaceutically acceptable salt thereof, comprises at least one single- stranded overhang. 25. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 24, wherein the 25 single-stranded overhang is 1, 2 or 3 nucleotides in length. 26. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-25, wherein at least one end of the dsRNA agent, or a pharmaceutically acceptable salt thereof, is blunt- ended. 30 27. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-26, wherein the dsRNA agent, or a pharmaceutically acceptable salt thereof, further comprises at least one phosphorothioate or methylphosphonate internucleotide linkage. 35 28. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 27, wherein the phosphorothioate or methylphosphonate internucleotide linkage is at the 3’-terminus of one strand. 339 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 29. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 27, wherein the phosphorothioate or methylphosphonate internucleotide linkage is at the 5’-terminus of one strand. 5 30. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 27, wherein the phosphorothioate or methylphosphonate internucleotide linkage is at both the 5’- and 3’-terminus of one strand. 31. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 30, wherein the 10 dsRNA agent comprises 6-10 phosphorothioate or methylphosphonate internucleotide linkages. 32. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 31, wherein the dsRNA agent comprises 7 phosphorothioate or methylphosphonate internucleotide linkages. 15 33. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-32, wherein the αvβ6 integrin targeting ligand comprises a structure represented by Formula (X):
or a salt thereof, wherein: Y is O, N(H), S, or CH2;
, wherein 20 m is 0, 1, 2, 3, or 4; and each R2 is independently R, or two R2 groups on adjacent carbon atoms taken together with the atoms to which they are bound form a fused 4 – 8 membered ring that is optionally substituted by 1, 2, 3 or 4 groups independently selected from group consisting of R and a nitrogen protecting group; A is an 5-membered heteroaryl optionally substituted with 1 or 2 substituents independently selected 25 from methyl, ethyl, fluoro, hydroxymethyl, 2-hydroxypropan-2-yl, trifluoromethyl, difluoromethyl, and fluoromethyl; 340 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO Q is -COOR1 or tetrazolyl (e.g., 1,2,3,4-tetrazol-5-yl), wherein R1 is hydrogen or C1-6alkyl (e.g., methyl) ; and RL is -N(R3)(R4), -O(R5), -S(R5), or -R5, wherein 5 R3 and R4 are either (iii) R3 is hydrogen or C1-6alkyl and R4 is R5; or (iv) R3 and R4 taken together with the nitrogen atom to which they are attached form a 4 – 8 membered monocyclic heterocyclyl group that is substituted with R5; and 10 R5 is -L-ZZ-L’-RT wherein L and L’ are independently -L1-[G-L2]q-G-L3-*, wherein * is the bond to ZZ; q is 0 or an integer selected from 1 to 25; L1 is a bond or -B-A-; 15 each L2 is independently -A-B-A-; L3 is a bond or -A-B-A-; each G is independently -D-E-F-, wherein D, E, and F are independently a bond, C1-10alkyl, C2- 10alkenyl, C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups; 20 each A is independently a bond, -O-, -S-, or -N(RN)-; each B is independently a bond, CH2, C(O), C(S), C(NRN), S(O), S(O)2, P(O)(OH), P(S)(OH), or P(S)(SH); each RN is independently hydrogen or C1-6alkyl, or two RN within an -A-B-A- group taken together with the atoms to which they are connected from a 4-8 membered heterocyclyl; 25 and ZZ is -A’-B’-A’- or a linking group formed by a reactive pair, wherein each A’ is independently a bond, -O-, -S-, or -N(RN3)-; each B’ is independently a bond, CH2, C(O), C(S), C(NRN3), -C=N-, S(O), S(O)2, P(O)(OH), P(S)(OH), or P(S)(SH); and 341 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO each RN3 is independently hydrogen or C1-6alkyl, or two RN3 within the -A’-B’-A’- group taken together with the atoms to which they are connected from a 4-8 membered heterocyclyl; RT is RT1 or -G0-ORT1, wherein G0 is absent or -D0-E0-F0-, wherein D0, E0, and F0 are independently a bond, C1-10alkyl, C2-10alkenyl, 5 C2-10alkynyl, C3-10cycloalkyl, 3-10 membered heterocyclyl, aryl, or heteroaryl, each of which is optionally substituted with 1, 2, 3, or 4 R groups; RT1 is LL-oligonucleotide, wherein LL is an oligonucleotide linking group connecting the αvβ6 integrin targeting ligand to oligonucleotide comprised in the dsRNA agent; and each R group is independently selected from the group consisting of R’, C1-6alkyl, C1-6haloalkyl, C2- 10 6alkenyl, C2-6alkynyl, C3-8cycloalkyl, heterocyclyl, aryl, heteroaryl, C3-8cycloalkylC1-6alkyl, heterocyclylC1-6alkyl, aryl C1-6alkyl, heteroarylC1-6alkyl, each of which, other than R’, is optionally substituted with 1, 2, or 3 R’ groups, wherein each R’ is independently halogen, cyano, azido, nitro, -N(Rb)2, -O(Ra), -S(R0), -C(O)OR0, C(O)R0, -C(O)N(R0)2, -C(NR0)OR0, -C(NR0)R0, -C(NR0)N(R0)2, -C(S)OR0, -C(S)R0, -C(S)N(R0)2, -S( 15 O)2R0, -S(O)2OR0, -S(O)2N(R0)2, -N(R0)C(O)OR0, -N(R0)C(O)R0, -N(R0)C(O)N(R0)2, -N(R0)S(O)2R0, -N(R0)S(O)2OR0, -N(R0)S(O)2N(R0)2, -OC(O)OR0, -OC(O)R0, -OC(O)N(R0)2, -OS(O)2R0, - OS(O)2OR0, -OS(O)2N(R0)2, or -SC(O)R0, wherein each R0 is independently hydrogen or C1-6alkyl; each Ra is independently hydrogen or C1-6alkyl; and each Rb is independently hydrogen, C1-6alkyl, or a nitrogen protecting group 20 provided that in each -D-E-F- group, at least one of D, E, and F is not a bond; and RL is not N- morpholinyl. 34. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 33, wherein the αvβ6 integrin targeting ligand of Formula (X) is 342 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO
, wherein Y’ is O or S, and RP and R1 are as defined for Formula (X) or any embodiment thereof. 35. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 34, wherein Y’ is O. 5 36. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 34, wherein Y’ is S. 37. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 34-36, wherein R1 is hydrogen. 10 38. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 34-36, wherein R1 is C1-6alkyl (e.g., methyl or t-butyl). 39. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 34-38, 15 wherein RP is hydrogen. 40. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 34-38, wherein RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). 20 41. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 34-40, wherein Y’ is O and R1 is hydrogen. 42. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 34-40, 25 wherein Y’ is O and R1 is C1-6alkyl. 343 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 43. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 34-40, wherein Y’ is S and R1 is hydrogen. 44. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 34-40, 5 wherein Y’ is S and R1 is C1-6alkyl. 45. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 34-44, wherein Y’ is O and RP is hydrogen. 10 46. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 34-44, wherein Y’ is O and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). 47. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 34-44, 15 wherein Y’ is S and RP is hydrogen 48. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 34-44, wherein Y’ is S and RP is a nitrogen protecting group (e.g., t-butoxycarbonyl (Boc), benzyloxycarbonyl (Cbz) or phenoxyacetyl (pac)). 20 49. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 34-48, wherein Y’ is O, R1 is hydrogen and RP is hydrogen. 50. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 34-48, 25 wherein Y’ is S, R1 is hydrogen and RP is hydrogen. 51. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 34-48, wherein Y’ is O, R1 is hydrogen and RP is a nitrogen protecting group. 30 52. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 34-48, wherein Y’ is S, R1 is hydrogen and RP is a nitrogen protecting group. 53. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 34-48, wherein Y’ is O, R1 is C1-6alkyl and RP is hydrogen. 35 344 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 54. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 34-48, wherein Y’ is S, R1 is C1-6alkyl and RP is hydrogen. 55. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 34-48, 5 wherein Y’ is O, R1 is C1-6alkyl and RP is a nitrogen protecting group. 56. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 34-48, wherein Y’ is S, R1 is C1-6alkyl and RP is a nitrogen protecting group. 10 57. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-56, wherein the αvβ6 integrin targeting ligand is
wherein a broken bond represents a bond to the remainder of the dsRNA, or a pharmaceutically acceptable salt thereof. 15 58. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-57, wherein the in vivo delivery enhancing moiety comprises at least one C10-C26 hydrocarbon chain. 59. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 58, wherein the in 20 vivo delivery enhancing moiety comprises at least one C22 hydrocarbon chain. 2. 60. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 59, wherein the at least one C22 hydrocarbon chains is an aliphatic, alicyclic, or polyalicyclic compound. 345 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 61. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 60, wherein the at least one C22 hydrocarbon chains contains a functional group selected from the group consisting of hydroxyl, amine, carboxylic acid, sulfonate, phosphate, thiol, azide, and alkyne. 5 62. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 59-61, wherein the at least one C22 hydrocarbon chains is a C22 acid. 63. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 62, wherein the C22 10 acid is selected from the group consisting of docosanoic acid, 6-octyltetradecanoic acid, 10- hexylhexadecanoic acid, all-cis-7,10,13,16,19-docosapentaenoic acid, all-cis-4,7,10,13,16,19- docosahexaenoic acid, all-cis-13,16-docosadienoic acid, all-cis-7,10,13,16-docosatetraenoic acid, all- cis-4,7,10,13,16-docosapentaenoic acid, and cis-13-docosenoic acid. 3.15 64. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 59-61, wherein the at least one C22 hydrocarbon chains is a C22 alcohol. 65. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 64, wherein the C22 alcohol is selected from the group consisting of 1-docosanol, 6-octyltetradecan-1-ol, 10- 20 hexylhexadecan-1-ol, cis-13-docosen-1-ol, docosan-9-ol, docosan-2-ol, docosan-10-ol, docosan-11-ol, and cis-4,7,10,13,16,19-docosahexanol. 66. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 59-61, wherein the at least one C22 hydrocarbon chains is a C22 amide. 25 67. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 66, wherein the C22 amide is selected from the group consisting of (E)-Docos-4-enamide, (E)-Docos-5-enamide, (Z)- Docos-9-enamide, (E)-Docos-11-enamide,12-Docosenamide, (Z)-Docos-13-enamide, (Z)-N- Hydroxy-13-docoseneamide, (E)-Docos-14-enamide, 6-cis-Docosenamide, 14-Docosenamide Docos- 30 11-enamide, (4E,13E)-Docosa-4,13-dienamide, and (5E,13E)-Docosa-5,13-dienamide. 68. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 58 -67, wherein the at least one C10-C26 hydrocarbon chain is unsubstituted or substituted with at least one functional group selected from the group consisting of hydroxyl, amine, carboxylic acid, sulfonate, phosphate, 35 thiol, azide, and alkyne. 346 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 69. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 68, wherein the at least one C10-C26 hydrocarbon chain is substituted with a carboxylic acid group. 70. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-69, 5 wherein the in vivo delivery enhancing moiety is attached to the dsRNA agent, or a pharmaceutically acceptable salt thereof, via a linker or via a carrier or via an internucleotide phosphate linkage. 71. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 70, wherein the in vivo delivery enhancing moiety is attached to the dsRNA agent via a linker. 10 72. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 71, wherein the linker comprises an ether, a thioether, a urea, a carbonate, an amine, an amide, a maleimide-thioether, a disulfide, a phosphodiester, a sulfonamide linkage, a product of a click reaction, or carbamate. 15 73. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 71 or 72, wherein the linker is selected from the group consisting of -(CH2)nNH-; -C(O)(CH2)nNH-; -NR’’’’(CH2)nNH-, -C(O)-(CH2)n-C(O)-; -C(O)-(CH2)n-C(O)O-; -C(O)-O-; -C(O)-(CH2)n-NH-C(O)-; -C(O)-(CH2)n-; - C(O)-NH-; -C(O)-; -(CH2)n-C(O)-; -(CH2)n-C(O)O-; -(CH2)n-; and -(CH2)n-NH-C(O)-; wherein n is a number from 1 to 20; and R’’’’ is C1-C6 alkyl. 20 74. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 70-73, wherein the linker comprises –(CH2)n-NH-C(O)- or –(CH2)n-NH-C(O)-(CH2)2-C(COOH)-NH-C(O)-, wherein n is a number from 1 to 20. 25 75. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim any one of claims 70-74, wherein the linker comprises –(CH)2-O-(CH2CH2)-(O)-(CH2CH2)-NH-C(O)-. 76. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-75, wherein the in vivo delivery enhancing moiety is represented by the following structure: 30
, 347 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 5
10 wherein a broken bond represents a bond to the remainder of the dsRNA agent, or a pharmaceutically acceptable salt thereof. 77. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-76, 15 wherein the in vivo delivery enhancing moiety is represented by the following structure:
, 348 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO wherein a broken bond represents a bond to the remainder of the dsRNA, or a pharmaceutically acceptable salt thereof. 78. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-77, 5 wherein the at least one αvβ6 integrin targeting ligand is conjugated to the sense strand. 79. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 78, wherein the at least one αvβ6 integrin targeting ligand is conjugated to the 3’-end of the sense strand. 10 80. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 78, wherein the at least one αvβ6 integrin targeting ligand is conjugated to the 5’-end of the sense strand. 81. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 78, wherein the at least one αvβ6 integrin targeting ligand is conjugated to both the 5’-end and the 3’-end of the sense 15 strand. 82. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 78, wherein the at least one αvβ6 integrin targeting ligand is conjugated to an internal position of the sense strand. 20 83. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-77, wherein the at least one αvβ6 integrin targeting ligand is conjugated to the antisense strand. 84. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 83, wherein the at least one αvβ6 integrin targeting ligand is conjugated to the 3’ end antisense strand. 25 85. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 83, wherein the at least one αvβ6 integrin targeting ligand is conjugated to the 5’ end of the antisense strand. 86. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 83, wherein the at 30 least one αvβ6 integrin targeting ligand is conjugated to both the 5’-end and the 3’-end of the antisense strand. 87. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 83, wherein the at least one αvβ6 integrin targeting ligand is conjugated to an internal position of the antisense strand. 35 349 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 88. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-87, wherein the at least one in vivo delivery enhancing moiety is conjugated to an internal position of the sense strand. 5 89. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 88, wherein the at least one in vivo delivery enhancing moiety is conjugated to one or more of the following internal positions: positions 4-8 and 13-18 on the sense strand, counting from the 5’ end. 90. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 89, wherein the at 10 least one in vivo delivery enhancing moiety is conjugated to one or more of the following internal positions: positions 5, 6, 7, 15, 16 and 17 on the sense strand, counting from the 5’-end. 91. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 90, wherein the at least one in vivo delivery enhancing moiety is conjugated to position 6 on the sense strand, counting 15 from the 5’-end. 92. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-87, wherein the at least one in vivo delivery enhancing moiety is conjugated to an internal position of the antisense strand. 20 93. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 92, wherein the at least one in vivo delivery enhancing moiety is conjugated to one or more of the following internal positions: positions 6-10 and 15-18 on the antisense strand, counting from the 5’-end. 25 94. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of claim 93, wherein the at least one in vivo delivery enhancing moiety is conjugated to one or more of the following internal positions: positions 15, 16 and 17 on the antisense strand, counting from the 5’-end. 95. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-94, 30 wherein the at least one αvβ6 integrin targeting ligand and the at least one in vivo delivery enhancing moiety are both conjugated to the sense strand. 96. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-94, wherein the at least one αvβ6 integrin targeting ligand and the at least one in vivo delivery enhancing 35 moiety are both conjugated to the antisense strand. 350 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 97. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-94, wherein the at least one αvβ6 integrin targeting ligand is conjugated to the sense strand and the at least one in vivo delivery enhancing moiety is conjugated to the antisense strand. 5 98. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-94, wherein the at least one αvβ6 integrin targeting ligand is conjugated to the antisense strand and the at least one in vivo delivery enhancing moiety is conjugated to the sense strand. 99. The dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-98,10 wherein the dsRNA agent is selected from the group consisting of AD-2702386, AD-2702387, AD- 2814835, AD-2814836, AD-2814837, AD-2814838, AD-2814839, or AD-3100656. 100. A cell containing the dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-99. 15 101. A pharmaceutical composition for inhibiting expression of a dystrophy myotonic protein kinase (DMPK) gene, comprising the dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-99 and a pharmaceutically acceptable carrier. 20 102. The pharmaceutical composition of claim 101, wherein dsRNA agent, or a pharmaceutically acceptable salt thereof, is in an unbuffered solution. 103. The pharmaceutical composition of claim 102, wherein the unbuffered solution is saline or water. 25 104. The pharmaceutical composition of claim 101, wherein said dsRNA agent, or a pharmaceutically acceptable salt thereof, is in a buffer solution. 105. The pharmaceutical composition of claim 104, wherein the buffer solution comprises acetate, 30 citrate, prolamine, carbonate, or phosphate or any combination thereof. 106. The pharmaceutical composition of claim 105, wherein the buffer solution is phosphate buffered saline (PBS). 35 107. A method of inhibiting expression of a dystrophy myotonic protein kinase (DMPK) gene in a cell, the method comprising contacting the cell with the dsRNA agent, or a pharmaceutically 351 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO acceptable salt thereof, of any one of claims 1-99, or the pharmaceutical composition of any one of claims 101-106, thereby inhibiting expression of the DMPK gene in the cell. 108. The method of claim 107, wherein the cell is a muscle cell. 5 109. The method of claim 108, wherein the cell is a skeletal muscle cell, a cardiac muscle cell, and/or a smooth muscle cell. 110. The method of any one of claims 107-109, wherein the cell is within a subject. 10 111. The method of claim 110, wherein the subject is a human. 112. The method of claim 110 or 111, wherein the subject has an DMPK-associated disorder. 15 113. The method of claim 112, wherein the DMPK-associated disorder is myotonic dystrophy type 1 (DM1). 114. The method of any one of claims 107-113, wherein contacting the cell with the dsRNA agent inhibits the expression of the DMPK gene by at least 50%, 60%, 70%, 80%, 90%, or 95%. 20 115. The method of any one of claims 107-114, wherein inhibiting expression of the DMPK gene decreases DMPK protein level in serum of the subject by at least 50%, 60%, 70%, 80%, 90%, or 95%. 116. A method of treating a subject having a disorder that would benefit from reduction in 25 dystrophy myotonic protein kinase (DMPK) expression, comprising administering to the subject a therapeutically effective amount of the dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-98, or the pharmaceutical composition of any one of claims 101-106, thereby treating the subject having the disorder that would benefit from reduction in DMPK expression. 30 117. A method of preventing at least one symptom in a subject having a disorder that would benefit from reduction in dystrophy myotonic protein kinase (DMPK) expression, comprising administering to the subject a prophylactically effective amount of the dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-99, or the pharmaceutical composition of any one of claims 101-106, thereby preventing at least one symptom in the subject 35 having the disorder that would benefit from reduction in DMPK expression. 352 ME1\53453057.v1
Attorney Docket No.121301-24020 Alnylam Reference No. ALN-529-WO 118. The method of claim 116, wherein treating comprises amelioration of at least on sign or symptom of the disease. 119. The method of claim 116, where treating comprises prevention of progression of the disease. 5 120. The method of any one of claims 116-119, wherein the disorder is an DMPK-associated disorder. 121. The method of claim 120, wherein the DMPK-associated disorder is myotonic dystrophy type 10 1 (DM1). 122. The method of any one of claims 116-121, wherein the subject is a human. 123. The method of any one of claims 116-122, wherein the dsRNA agent, or a pharmaceutically 15 acceptable salt thereof, is administered to the subject subcutaneously. 124. The method of any one of claims 116-123, wherein the dsRNA agent, or a pharmaceutically acceptable salt thereof, is administered to the subject intramuscularly. 20 125. The method of any one of claims 116-124, further comprising administering to the subject an additional therapeutic agent for treatment of a DMPK-associated disorder. 126. A kit comprising the dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-99 or the pharmaceutical composition of any one of claims 101-106. 25 127. A vial comprising the dsRNA agent, or a pharmaceutically acceptable salt thereof, of any one of claims 1-99 or the pharmaceutical composition of any one of claims 101-106. 128. A syringe comprising the dsRNA agent, or a pharmaceutically acceptable salt thereof, of any 30 one of claims 1-99 or the pharmaceutical composition of any one of claims 101-106. 129. An RNA-induced silencing complex (RISC) comprising an antisense strand of any of the dsRNA agents, or a pharmaceutically acceptable salt thereof, of claims 1-99. 35 353 ME1\53453057.v1
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| PCT/US2025/033136 Pending WO2025259747A2 (en) | 2024-06-12 | 2025-06-11 | Dystrophy myotonic protein kinase (dmpk) irna compositions and methods of use thereof |
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