DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim(s) 1-14 are pending.
Election
Applicant’s election without traverse of sense strand SEQ ID NO: 67 and antisense strand SEQ ID NO: 68, in the reply filed on 02/10/2026, is acknowledged.
Claim(s) 1-4, 9, 11, and 13 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 02/10/2026.
Claim(s) 5-8, 10, 12, and 14 are under consideration.
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55 for application KR10-2020-0178838, filed 12/18/2020.
Information Disclosure Statement
Receipt of the information disclosure statement(s) on 06/16/2023, 07/09/2024, and 07/08/2025 are acknowledged. The signed and initialed PTO-1449 form(s) has/have been mailed with this action.
Specification
The use of the term(s):
Lipofectamine 2000 (Page 24, Line 8), (Page 39, Line 13), and (Page 40, Line 23);
Lipofectamine RNAiMAX (Page 28, Line(s) 7, 12, 17), (Page 32, Line(s) 6 and11), (Page 36, Line 17);
which is/are a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claim(s) 5-8 and 14 are rejected under 35 U.S.C. 103 as being unpatentable over
Hinkle et al (US 2017/0349900 A1; published December 7th, 2017).
Hinkle et al teaches, “… RNAi agents, e.g., double- stranded RNAi agents, targeting the hepatitis B virus (HBV) genome, and methods of using such RNAi agents to inhibit expression of one or more HBV genes and methods of treating subjects having an HBV infection and/or HBV-associated disorder, e.g., chronic hepatitis B infection.”, (Abstract).
Regarding claim(s) 5-7 Hinkle et al teaches, “Accordingly, in one aspect, the present invention provides double stranded RNAi agents for inhibiting expression of hepatitis B virus (HBV) in a cell. The double stranded RNAi agents include a sense strand and an antisense strand forming a double- stranded region, wherein said sense strand comprises at least 15 contiguous nucleotides differing by no more than 3 nucleotides from the nucleotide sequence of SEQ ID NO: l, and said antisense strand comprises at least 15 contiguous nucleotides differing by no more than 3 nucleotides from the nucleotide sequence of SEQ ID NO:2, wherein substantially all of the nucleotides of said sense strand and substantially all of the nucleotides of said antisense strand are modified nucleotides, wherein said sense strand is conjugated to a ligand attached at the 3 '-terminus, and wherein the ligand is one or more GalNAc derivatives attached through a bivalent or trivalent branched linker.”, (paragraph [0014]). Furthermore, Hinkle et al teaches, “Based on these assays, RNAi agents targeting five sites in the HBV X ORF (nucleotides 1551, 1577, 1580, 1806, and 1812 of GenBank Accession No. NC_003977.1 were selected for lead optimization and additional agents were designed and synthesized. These additional agents are evaluated in in vitro assays as described above. A detailed list of the additional unmodified sense and antisense strand sequences targeting the HBV X ORF is shown in Table 25. A detailed list of the additional modified sense and antisense strand sequences targeting the HBV X ORF is shown in
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Table 26.”, (Paragraph [0705] and Figure 2).
Hinkle et al teaches “AD-66808 and AD-66809”, which are double stranded RNAi agents with a sense strand and antisense strand. SEQ ID NO: 67 (sense) of the instant application is 100% identical to nucleotides 4-19 of SEQ ID NOs: 1207 and 1208. SEQ ID NO: 68 (antisense) of the instant application is 100% identical to nucleotides 1-19 of SEQ ID NOs: 1263 and 1264.
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Hinkle et al further teaches, “As used herein, the term “nucleotide overhang” refers to at least one unpaired nucleotide that protrudes from the duplex structure of an iRNA, e.g., a dsRNA. 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 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 present on the 5′-end, 3′-end or both ends of either an antisense or sense strand of a dsRNA.”, (paragraph [0234]). Further, “…The RNAi may also have a blunt end, located at the 5′-end of the antisense strand (or the 3′-end of the sense strand) or vice versa. Generally, the antisense strand of the RNAi has a nucleotide overhang at the 3′-end, and the 5′-end is blunt. While not wishing to be bound by theory, the asymmetric blunt end at the 5′-end of the antisense strand and 3′-end overhang of the antisense strand favor the guide strand loading into RISC process.”, (paragraph [0312]).
Regarding claim 8, Table 26 of Hinkle et al teaches various modifications to the sense and antisense strands, including 2’-Fluro, 2’-MOE, and phosphorothioate modifications. Table 27 and Figure 2 of Hinkle et al teaches in vivo screening of AD-66808 and AD-66809.
Moreover, “In certain aspects of the invention, the double-stranded RNAi agents of the invention include agents with chemical modifications as disclosed, for example, in WO 2013/075035, filed on Nov. 16, 2012, the entire contents of which are incorporated herein by reference. As shown herein and in PCT Publication No. WO 2013/075035, a superior result may be obtained by introducing one or more motifs of three identical modifications on three consecutive nucleotides into a sense strand and/or antisense strand of an RNAi agent, particularly at or near the cleavage site. In some embodiments, the sense strand and antisense strand of the RNAi agent may otherwise be completely modified. The introduction of these motifs interrupts the modification pattern, if present, of the sense and/or antisense strand. The RNAi agent may be optionally conjugated with a GalNAc derivative ligand, for instance on the sense strand. The resulting RNAi agents present superior gene silencing activity. More specifically, it has been surprisingly discovered that when the sense strand and antisense strand of the double-stranded RNAi agent are completely modified to have one or more motifs of three identical modifications on three consecutive nucleotides at or near the cleavage site of at least one strand of an RNAi agent, the gene silencing activity of the RNAi agent was superiorly enhanced.”, ([0305] to [0306]).
“In one embodiment, the RNAi agent comprises the pattern of the alternating motif of 2′-O-methyl modification and 2′-F modification on the sense strand initially has a shift relative to the pattern of the alternating motif of 2′-O-methyl modification and 2′-F modification on the antisense strand initially, i.e., the 2′-O-methyl modified nucleotide on the sense strand base pairs with a 2′-F modified nucleotide on the antisense strand and vice versa. The 1 position of the sense strand may start with the 2′-F modification, and the 1 position of the antisense strand may start with the 2′-O-methyl modification. The introduction of one or more motifs of three identical modifications on three consecutive nucleotides to the sense strand and/or antisense strand interrupts the initial modification pattern present in the sense strand and/or antisense strand. This interruption of the modification pattern of the sense and/or antisense strand by introducing one or more motifs of three identical modifications on three consecutive nucleotides to the sense and/or antisense strand surprisingly enhances the gene silencing activity to the target gene.”, (see paragraph [0338] to [0339]).
Regarding claim 14, Hinkle et al teaches, “In one aspect, the present invention provides methods of treating a subject having a Hepatitis B virus (HBV) infection. The methods include administering to the subject a therapeutically effective amount of the double stranded RNAi agent of the invention, or the composition of the invention, or the vector of the invention, or the pharmaceutical composition of the invention, thereby treating said subject. In another aspect, the present invention provides methods of treating a subject having a Hepatitis B virus (HBV)-associated disorder. The methods include administering to the subject a therapeutically effective amount of the double stranded RNAi agent of the invention, or the composition of the invention, or the vector of the invention, or the pharmaceutical composition of the invention, thereby treating said subject.”, (paragraphs [0078] to [0079]).
Despite, Hinkle et al teaching the claimed SEQ ID NOs: 67 and 68 (found in table 25 above), double stranded RNAi agents, modifications such as 2’-MOE, 2’-F, alternating 2’MOE/2’F, trivalent GalNac additions at the 3’ end of the sense strand, blunt ends, and overhangs, Hinkle et al does not explicitly teach that the sense strand is 15-17 nucleotides.
However, Hinkle et al does teach, “In one embodiment, the double-stranded region is 15-30 nucleotide pairs in length. In another embodiment, the double-stranded region is 17-23 nucleotide pairs in length. In yet another embodiment, the double-stranded region is 17-25 nucleotide pairs in length…. In one embodiment, each strand has 15-30 nucleotides”, (see paragraphs [0021] to [0022]). Furthermore, Hinkle et al teaches, “The skilled person is well aware that dsRNAs having a duplex structure of between about 20 and 23 base pairs, e.g., 21, base pairs have been hailed as particularly effective in inducing RNA interference (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 3, 4, 6, 7, 12, 13, 22, 23, 25, and 26, dsRNAs described herein can include at least one strand of a length of minimally 21 nucleotides. It can be reasonably expected that shorter duplexes having one of the sequences of any one of Tables 3, 4, 6, 7, 12, 13, 22, 23, 25, and 26 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 15, 16, 17, 18, 19, 20, or more contiguous nucleotides derived from one of the sequences of any one of Tables 3, 4, 6, 7, 12, 13, 22, 23, 25, and 26, and differing in their ability to inhibit the expression of a HBV 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 invention.”, (see paragraph [0277]).
Moreover, “While a target sequence is generally about 15-30 nucleotides in length, there is wide variation in the suitability of particular sequences in this range for directing cleavage of any given target RNA. Various software packages and the guidelines set out herein provide guidance for the identification of optimal target sequences for any given gene target, but an empirical approach can also be taken in which a “window” or “mask” of a given size (as a non-limiting example, 21 nucleotides) is literally or figuratively (including, e.g., in silico) placed on the target RNA sequence to identify sequences in the size range that can serve as target sequences. By moving the sequence “window” progressively one nucleotide upstream or downstream of an initial target sequence location, the next potential target sequence can be identified, until the complete set of possible sequences is identified for any given target size selected. This process, coupled with systematic synthesis and testing of the identified sequences (using assays as described herein or as known in the art) to identify those sequences that perform optimally can identify those RNA sequences that, when targeted with an iRNA agent, mediate the best inhibition of target gene expression. Thus, while the sequences identified, for example, in any one of Tables 3, 4, 6, 7, 12, 13, 22, 23, 25, and 26 represent effective target sequences, it is contemplated that further optimization of inhibition efficiency can be achieved by progressively “walking the window” one nucleotide upstream or downstream of the given sequences to identify sequences with equal or better inhibition characteristics. Further, it is contemplated that for any sequence identified, e.g., in any one of Tables 3, 4, 6, 7, 12, 13, 22, 23, 25, and 26, further optimization could be achieved by systematically either adding or removing nucleotides to generate longer or shorter sequences and testing those sequences generated by walking a window of the longer or shorter size up or down the target RNA from that point. Again, coupling this approach to generating new candidate targets with testing for effectiveness of iRNAs based on those target sequences in an inhibition assay as known in the art and/or as described herein can lead to further improvements in the efficiency of inhibition. Further still, such optimized sequences can be adjusted by, e.g., the introduction of modified nucleotides as described herein or as known in the art, addition or changes in overhang, or other modifications as known in the art and/or discussed herein to further optimize the molecule (e.g., increasing serum stability or circulating half-life, increasing thermal stability, enhancing transmembrane delivery, targeting to a particular location or cell type, increasing interaction with silencing pathway enzymes, increasing release from endosomes) as an expression inhibitor.”, (see paragraphs [0279] to [0280]).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify SEQ ID NOs: 1207 and 1208 of Hinkle et al to have 15, 16, or 17 nucleotides, as taught by Hinkle et al, to yield the predictable results of effective inhibition of expression of the HBV gene as taught by Hinkle et al. One would have been motivated to modify SEQ ID NOs: 1207 and 1208 to improve efficiency of inhibition.
Thus, claims 5-8 and 14 are unpatentable over Hinkle et al.
Claim(s) 10 and 12 are rejected under 35 U.S.C. 103 as being unpatentable over Hinkle et al (US 2017/0349900 A1; published December 7th, 2017) as applied to claim 5 above, and further in view of Khvorova and Watts (The chemical evolution of oligonucleotide therapies of clinical utility, Nature Biotechnology, Vol 35, Issue 3, Published February 27th, 2017).
All limitations taught in Hinkle et al from the above rejection, apply herein.
Hinkle et al further teaches, “In one embodiment, a double-stranded RNAi agent comprises 6-8 phosphorothioate internucleotide linkages.”, (paragraph [0341]).
Hinkle et al does not teach (1) a 5’-phosphate group linkage on the antisense strand, (2) the alternating modifications of 2’-MOE and 2’-Fluro with a stretch of three identical modifications in the middle of either the antisense or sense stand as claimed, and (3) phosphorothioate bond locations.
Khvorova and Watts teach multiple designs that enable effective targeting to the liver.
More specifically, Khvorova and Watts teach, (1) “The 5′-phosphate of a siRNA guide strand is essential for recognition by RISC. siRNAs with a 5′-hydroxyl are efficiently phosphorylated and loaded onto Ago2 inside cells. Blocking phosphorylation of the 5′-hydroxyl in siRNA prevents RISC loading and activity. Chemical modification (e.g., 2′-OMe or 2′-F) of the 5′-ribose of the guide strand can interfere with intracellular phosphorylation but the activity of these 5′-modified guide strands can be restored if a 5′-phosphate is introduced chemically...”, (Page 243, column 2, paragraph 3).
“Phosphatase-resistant analogs of the 5′-phosphate can improve in vivo efficacy. Ionis modified the 5′ end of single-stranded siRNA (ss-siRNA) with E-vinyl phosphonate (5′-E-VP), which substitutes the bridging oxygen with carbon in the context of a double bond (Fig. 2). The 5′-E-VP is in a suitable conformation for RISC binding, whereas the other stereoisomer (5′-Z-VP) shows reduced activity due to inappropriate positioning of the phosphonate. In this context, 5′ chemical stabilization was absolutely essential for the in vivo efficacy of ss-siRNAs”, (Page 243, column 2, paragraph 4).
“5′-E-VP has a major impact on the in vivo efficacy of GalNAc-conjugated siRNAs, discussed below. The effect is not specific to GalNAc: phosphate stabilization of hydrophobically modified siRNAs significantly enhances the distribution, accumulation, and retention of intact oligonucleotide in primary and secondary tissues, and extends the duration of effect beyond a month after injection (R. Haraszti, L. Roux, and A.K., unpublished data). In the absence of lipid formulation, therefore, metabolic stabilization of the 5′-phosphate is essential for stability, biodistribution, activity, and duration of effect of therapeutic siRNAs in vivo. Notably, phosphate stabilization also increases the accumulation of guide strand in tissues, probably because it provides additional protection from XRN1-mediated hydrolysis. XRN1 is the primary cellular nuclease that rapidly degrades 5′-phosphorylated RNA and DNA, but it does not recognize metabolically stable 5′-phosphate analogs (R. Haraszti, L. Roux, and A.K., unpublished data).”, (Page 244, column 1, paragraph 1).
“For best results, GalNAc conjugation requires a metabolically stable oligonucleotide scaffold; that is, modification of every nucleotide to remove all ribose moieties and metabolic stabilization of the 5′-phosphate. The resulting GalNAc-conjugated siRNA and ASO compounds show exceptional stability and duration of effect, allowing monthly or even semiannual subcutaneous injections.”, (Page 244, column 1, paragraph 5).
Further, Khvorva and Watts teach, (2) “The 2-F and 2-OMe modifications favor the C3′-endo ribose conformation and support the A-form helical structure of the guide strand, which positions the target mRNA into the cleavage center of RISC. But both modifications introduce slight structural distortions. 2′-F-RNA slightly overwinds the duplex (leading to more stacking and higher Tm), and 2′-OMe-RNA slightly underwinds the duplex (less stacking). Either modification is tolerated in any individual position of an siRNA, but a fully modified 2′-OMe guide strand is completely inactive, and a fully modified 2′-F guide strand often has substantially reduced activity. When 2′-OMe and 2′-F modifications are alternated, however, the combination creates a compound ideally suited for RISC assembly and function.”, (Page 243, column 1, paragraph 3).
“Thermodynamic or structural tuning may further enhance the efficacy of modified siRNAs. Many of the advanced clinical compounds carry additional stretches of 2′-OMe and 2′-F (for example, three of either modification in a row, or sometimes longer stretches of 2′-OMe) in the context of the alternating 2′-F–2′-OMe-RNA pattern (Fig. 3). The pattern was designed to chemically mimic the sinusoidal thermodynamic stability described for highly functional siRNAs.”, (Page 243, column 1, paragraph 4)).
Khvorva and Watts teach, (3), “Additional nuclease stability is conferred by backbone modifications. Limited phosphorothioates are tolerated by Ago2, and phosphorothioate modifications at both ends of both strands of an siRNA duplex are incorporated into many of the leading clinical candidates. This simple combination of backbone and sugar modification provides additional resistance to exonucleases—the primary effectors of RNA degradation—and an order-of-magnitude increase in oligonucleotide accumulation in vivo.”, (Page 243, column 2, paragraph 2).
Lastly, Figure 3 of Khvorva and Watts teach the evolution of RNAi technologies. Specifically teaching a double-stranded modified RNAi agent, with a blunt end, overhangs, alternating modifications of 2’-MOE and ‘2-F, a stretch of three identical modifications, phosphorothioate bonds, a trivalent GalNac, and a 5’ phosphate modification. See below.
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Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify either RNAi agent, AD-66808 or AD-66809 of Hinkle et al, specifically (1) SEQ ID NOs: 1207 and 1208 as taught by the combined teachings of Hinkle et al above and (2) SEQ ID NOs: 1263 and 1264, to add a 5’-phosphate group linkage on the antisense strand, alternate the 2’-MOE and 2’-F modifications with at least one stretch on either/or both strands of three identical modifications, and have between 6-8 phosphorothioate bonds in the RNAi agent (2 on the sense strand, and 6 on the antisense strand) to yield the predictive results of (1) enhanced stability and increased durations in vivo, (2) increased gene silencing activity, (3) thermodynamic stability, and (4) nuclease stability, as taught by both Hinkle et al, and Khvorova and Watts,
One would have been motivated to make such modifications because of the following: First, the GalNac moiety requires a metabolically stable oligonucleotide, and for proper
metabolic stabilization, the 5′-phosphate is essential for stability, biodistribution, activity, and duration of effect of therapeutic siRNAs in vivo (as taught by Khvorova and Watts).
Second, chemical modification (e.g., 2′-OMe or 2′-F) of the 5′-ribose of the guide strand
can interfere with intracellular phosphorylation but the activity of these 5′-modified guide strands can be restored if a 5′-phosphate is introduced chemically (as taught by Khvorova and Watts).
Third, when the sense strand and antisense strand of the double-stranded RNAi agent are completely modified to have one or more motifs of three identical modifications on three consecutive nucleotides at or near the cleavage site of at least one strand of an RNAi agent, the gene silencing activity of the RNAi agent was superiorly enhanced, which also chemically mimics sinusoidal thermodynamic stability described for highly functional siRNAs (as taught by both Hinkle et al and Khvorova and Watts).
Fourth, nuclease stability is conferred through backbone modifications, and limited phosphorothioates are tolerated by Ago2, thus, modifying the terminal ends of the siRNA duplex has been a going model for enhanced stability while maintaining Ago2 tolerance, and has already been a design incorporated into many of the leading clinical candidates (as taught by Khvorova and Watts).
Thus, claim(s) 10 and 12, are rejected as being unpatentable over Hinkle et al in view of Khvorova and Watts.
Conclusion
No claims allowed.
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/L.M.T./Examiner, Art Unit 1637
/Jennifer Dunston/Supervisory Patent Examiner, Art Unit 1637