DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claims 1, 10, 18 and 40 have been amended. Claims 1, 2, 4, 5, 10, 18, 40, and 52-54 are pending and under consideration.
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1, 2, 4, 18, 40 and 52-54 are rejected under 35 U.S.C. 103 as being unpatentable over of Li et al (WO2009/029688, cited in a prior action) in view of Xia et al (Pharmaceutical Research, 2007, Vol. 24, pp. 2309-2316, reference of the IDS filed 7/21/2021), Tororella and Karagiannis (Journal of Membrane Biology, 2014, Vol. 247, pp. 291-307, cited in a prior action), Cuellar et al (Nucleic Acids Research, 2015, Vol. 43, pp. 1189-1203, cited in a prior action), Tan et al (Analytical Biochemistry, 2012, Vol. 430, pp. 171-178), Chu and Orgel (DNA, 1985, Vol. 4, pp. 327-331), Acchione et al (mAbs, 2012, Vol. 4, pp. 362-372, cited in a prior action), Ward (WO97/34631, cited in a prior action) and Shen et al (Nature Biotechnology, 2012, Vol. 10, pp. 184-189, plus Supplemental, pages 1-26).
Li et al teach a conjugate comprising a duplex RNA molecule comprising a sense and antisense strand, wherein the duplex is capable of effecting selective gene silencing in a eukaryotic cell, wherein the duplex is conjugated to an antibody (claim 76). Li et al teach that each strand may be conjugated with one or more moieties, such as antibodies, to increase functionality (page 24, lines 7-10 of the 2nd full paragraph). Li et al teach that each strand may have modified nucleotides or nucleotide analogs (page 24, lines 4-6 of the 2nd full paragraph). Li et al teach that nucleotide analog is a back-bone modified ribonucleotide containing a phosphorothioate group (claim 87) which meets the same limitation in instant claim 4. Li et al teach that the modification includes replacement of the 2’OH group by R which is C1-C6 alkyl (claim 17 of ‘688) and specifically 2’-O-methyl (page 14, line 12) which meets the same the limitation of 2’ modified nucleotide in claims 1 and 40 and the limitation of 2’-O-methyl in claim 2. Li et al also teach that modifications can be introduced into the ribose portion of the RNA including locked nucleic acids and 2’fluoropyrimidines (page 34, 3rd paragraph under the heading “4.3.1 Modifications of the RNA molecules”) which also meet the limitations of claim 2. Li et al teach that chemical modifications introduced into the RNA molecules improve the half-life and reduce the risk of non-specific effects of gene targeting (page 34, lines 2-4 under the heading “4.3.1 Modifications of the RNA molecules”). Li et al teach that the first strand comprises a sequence being substantially complementary to an oncogene (lines 1-3 of claim 115 of ‘688) which meets the same limitation in instant claim 1. Li et al specifically teach that the first strand of the RNA duplex is substantially complimentary to the target mRNA sequence of erbB, which meets the limitation of a receptor tyrosine kinase in claim 52, and EGFR in claim 53; KRAS which meets the limitations of a regulatory GTPase in claim 52 and KRAS in claim 53, myc which meets the limitations of a transcription factor in claim 52 and myc in claim 54 and β-catenin which meets the limitation of instant claim 53 (claim 115, lines 8-10 and 18).
Li et al teach that for gene silencing in mammalian cells the current art teaches that the structure of siRNA is a symmetric double stranded RNA with a length of 19-21 nucleotides and 3' overhangs on both ends to be effective in mammalian cells and to avoid cellular innate ''anti-viral" responses, but it is now well established in the field that this 'Optimal" structure can still trigger interferon responses, and pose significant challenges to the development of RNAi-based research and RNAi-based therapeutics (page 2, first full paragraph).
Li et al teach that there is a need to develop novel approaches to effective RNAi in mammalian cells through a novel design of siRNAs having better efficacy and potency, rapid onset of action, better durability, and a shorter length of the RNA duplex to avoid non-specific interferon like response and to reduce the cost of synthesis for research and pharmaceutical development of RNAi therapeutics (page 2, second full paragraph).
Li et al teach a novel class of small duplex RNAs that can induce potent gene silencing in mammalian cells, which is termed herein asymmetrical interfering RNAs (aiRNA) which have length asymmetry between the two RNA strands (page 2, line 1-4, under the heading “Summary of the Invention”). Li et al teach that the novel structural design is not only functionally potent in effecting gene silencing, but offers several advantages over the current state-of-art siRNAs. including much shorter length than the current siRNA, which reduces the cost of synthesis and abrogates/reduces the length-dependent triggering of nonspecific interferon-like responses (page 2, line 4-8, under the heading “Summary of the Invention”). Li et al teach that the asymmetry of the aiRNA structure abrogates/reduces sense-strand mediated off-target effects (page 2, lines 8-10, under the heading “Summary of the Invention”). Li et al teach that aiRNA is more efficacious, potent, rapid-onset, and durable than siRNA in inducing gene silencing, and that aiRNA can be used in all areas that siRNA or shRNA are currently being applied including RNAi-based therapies (page 2, lines 10-13, under the heading “Summary of the Invention”).
Li et al teach that each strand of the duplex may be conjugated with one or more functionality-enhancing moieties including antibodies or antibody fragments (page 24, lines 7-9), and claim 76 of ‘688).
Li et al teach that the method of modulating gene expression by the aiRNAs of the invention (page 3, lines 1-5 of the bottom paragraph) include the modulation of malignant disease (page 4, lines 10-13, 15 and 19) which meets the limitation of instant claim 40.
Li et al teach that one or more of the nucleotides in the RNA molecule of the invention can be substituted with deoxynucleotides or modified nucleotides or nucleotide analogues and that the substitution can enhance a physical property of the RNA molecule such as strand affinity, solubility and resistance to RNase degradation or otherwise enhance stability(page 31, first paragraph under the heading “3.3 Nucleotide substitution”). Li et al teach that within the RNA molecules of the present invention, chemical modifications can be introduced to the phosphate backbone (e.g., phosphorothioate linkages), the ribose (e.g., locked nucleic acids, 2-deoxy-2'-fluorouridine, 2’- O-methyl), and/or the base (e.g., 2'-fluoropyrimidines) (page 34, third paragraph under “4.3.1. Modifications of the RNA molecules”) which meet the limitations of claim 2 for 2’-O-methyl, and locked nucleic acid and the limitations of claim 4 for phosphothioate linkages. Li et al teach the introduction of phosphorothioate (P=S) linkage into the RNA molecules, e.g., at the 3’-overhang, for providing protection against exonuclease (page 35, lines 6-8) which meets the same limitation in claim 4..
Li et al teach that chemical modifications at the 2' position of the ribose, such as 2'-O-mthylpurines and 2'-fluoropyrimidines, increase resistance to endonuclease activity in serum (page 34, lines 1-3 of the bottom paragraph) and that the 2'-O-methyl modifications can also eliminate or reduce the interferon induction (page 34, lines 4-5).
Li et al do not teach that the antibody of the conjugate is an anti-transferrin monoclonal antibody, or antigen binding fragment thereof, comprising a modification for modulating an interaction with Fc receptors. Li et al do not teach the nature of the linker, X, or the conjugation of X to a to a cysteine residue of the antibody, wherein A-X is conjugated to the 5’ end of the sense strand.
Xia et al teach siRNA conjugated to an anti-rat transferrin receptor antibody (page 2310, lines 11-12 under the heading “Materials”) at the 3’ terminus or 5’ terminus of the sense strand (Figure 1(A) and (B)). Xia et al teach that that there was a 79-86% inhibition of the targeted gene expression when either the 5’biotin or the 3’biotin was administered in a rat model system of in vivo Brain cancer (page 2313, second column, lines 7-10 and page 2311,under the heading “In vivo Brain Cancer Model”).
Tororella and Karagiannis teach that the expression of the transferrin receptor is significantly upregulated in cancer cells allowing for its use as a recognition structure for the active targeting of tumor cells (page 295, second column, lines 1-10 of the second full paragraph). Tororella and Karagiannis teach that transferrin-mediated endocytosis is highly efficient, leading to high turnover rates (page 295, second column, lines 11-15 of the second full paragraph). Tororella and Karagiannis teach that targeting the transferrin receptor through its endocytic mechanism for the delivery of anti-cancer compounds will allow for efficient and selective uptake, enhanced therapeutic cellular concentrations and increased efficacy against malignant cells.
Cuellar et al teach antibody -mediated siRNA delivery using ThioMab–siRNA conjugates (title). Cuellar et al teach that prior methods of RNAi silencing using antibody-siRNA complexes relied on non-specific electrostatic interactions resulting in heterogeneous aggregates (page 1190, first column, lines 5-13 of the first full paragraph). Cuellar et al teach heterogeneity of drug loading onto antibodies affects clearance, maximum tolerated dose and efficacy (page 1190, first column, lines 13-14 of the first full paragraph). Cuellar et al teach that in order to overcome this, antibody-stabilized siRNAs attached to discreet positions on the antibody backbone with defined antibody-siRNA stoichiometry (page 1190, first column, lines 1-9 of the second full paragraph). Cuellar et al teach that the antibody- RNA conjugates were made by the method of Tan et al (page 1190, lines 1-2 under the heading “siRNAs and antibody-siRNA conjugates”). Cuellar et al teach that the stabilized siRNA sequence 2’-O-methylated bases and 2’-fluorobases, and that the sense strand comprised a dye at the 5’ terminus and an N-6 modification at the 3’ terminus (page 1190, second column, lines 2-6 under the heading “siRNAs and antibody-siRNA conjugates”). Cuellar et al teach that the amine group on the 3’ terminus was conjugated to a cysteine residue previously introduced at A118C of the heavy chain thus providing wo discreet positions for siRNA coupling (page 1192, lines 5-10 under the heading “Synthesis and purification of well-defined antibody-siRNA conjugates (ARCs)”). Cuellar et al teach that the amine tagged siRNA was reacted with a NHS linker to form the thiol reactive siRNA-linker adduct, and that this adduct was covalently reacted with thiol groups on the antibody (page 1192, lines 18-22 under the heading “Synthesis and purification of well-defined antibody-siRNA conjugates (ARCs)”). This meets the limitation in claim 1 for when X is a heterobifunctional liker , X is conjugated to a cysteine residue of the antibody, A. .
Tan et al teach the same chemically stabilized RNA as used by Cuellar et al, wherein the sense strand had a fluorescent dye at the 5’end and an amino group at the 3’end wherein the amino group was attached to engineered thiol groups on the heavy chains of an antibody using the smack linker or a SPDB linker (page 172, first column, lines 1-14 under the heading “siRNA and antibody -siRNA conjugates”) which meets the limitation of a heterobifunctional linker in claim 1.
Chu and Orgel teach a derivative of the 5’ terminal phosphate of an oligonucleotide by displacement of a imidazole intermediate with a hexamethylene diamine at the terminal phosphate (Figure 1):
PNG
media_image1.png
63
658
media_image1.png
Greyscale
PNG
media_image2.png
67
466
media_image2.png
Greyscale
One of skill in the art would take as the derivative formed with the hexamethylene diamine of Chu and Orgel as being equivalent to the N-6 modification taught by Tan et al and Cuellar et al at the 3’ terminus.
It would have been prima facie obvious to modify the 5’ end of the siRNA of Li et al with the N-6 derivative of Chu et al and Orgel et al, and use the amino derivative to react with the linkers of Tan et al for attachment to engineered thiol groups of an anti-transferrin antibody. One of skill in the art would have been motivated to do so by the teachings of Cuellar et al regarding the need for more homogenous populations of antibody RNA conjugates to overcome the problems of clearance, maximum tolerated dose and efficacy. One of skill in the art would have been motivated to derivatize the 5’ terminus of the sense strand with the hexamethylene diamine of Chu and Orgel for reaction with the SMCC linker or the SPDB linker because although Tan et al and Cuellar et al teach the derivatization of the 3’ terminus of the sense strand modified by the N-6 derivative, Xia et al teach siRNA conjugated to an anti-rat transferrin receptor antibody (page 2310, lines 11-12 under the heading “Materials”) at the 3’ terminus or 5’ terminus of the sense strand. Thus, it would be obvious to conjugate the antibody to either end of the sense strand.
Regarding the requirement for an anti-transferring receptor antibody, Xia et al teach siRNA conjugated to an anti-rat transferrin receptor antibody at the 3’ terminus or 5’ terminus of the sense strand and the 79-86% inhibition of the targeted gene expression when either the 5’biotin or the 3’biotin was administered in a rat model system. Tororella and Karagiannis teach that the significant upregulation of the transferrin receptor in cancer cells allowing for its use as a recognition structure for the active targeting of tumor cells and the high efficiently of transferrin-mediated endocytosis, leading to high turnover rates. Tororella and Karagiannis teach that targeting the transferrin receptor through its endocytic mechanism for the delivery of anti-cancer compounds will allow for efficient and selective uptake, enhanced therapeutic cellular concentrations and increased efficacy against malignant cells. One of skill in the art would be motivated to select an anti-transferrin receptor antibody for the delivery of the siRNA targeting the oncogenes of Li et al.
Regarding the requirement for a modification for modulating an interaction with Fc receptors, Acchione et al teach that increased circulating half-life has often been associated with improved therapeutic efficiency for ADCs (page 367, second column, lines 1-2).
Ward teaches a method of making an antibody with increased serum half-life comprising identifying a first amino acid in the hinge region that is suspected of being involved in FcRn binding; identifying one or more second amio acids in the spatial region of the first amino acid, wherein the side chain of the second amino acid or acids is exposed to solvent in the native antibody; making an antibody with random mutations of one or more of the second amino acids to make a mutant antibody and identifying a mutant antibody having increased serum half-life (claim 16 of ‘631). Ward teaches that several mutations can be reliably engineered into an antibody conjugate including substitutions at Thr 252, Thr 254, Thr 256, Met 309, Glu 311 or Asp 315 (page 6, third full paragraph).
It would have been prima facie obvious at the time prior to the effective filing date to modify the anti-transferrin antibody by substitutions at Thr 252, Thr 254, Thr 256, Met 309, Glu 311 or Asp 315. One of skill in the art would have been motivated to modify the anti-transferrin antibody to increase the circulating half-life of the resulting conjugate because Acchione et al teach that increased circulating half-life has often been associated with improved therapeutic efficiency for ADCs.
Regarding the requirement that “X” is conjugated to a cysteine residue in the Fc region and the molecule of Formula I has a drug-to-antibody ratio of greater than 2, Shen et al supplemental teach that the selection of Fc-ThioMabs of trastuzumab based on the predicted highest fractional solvent accessibility and lack of interference with the effector function of the Fc (page 2, lines 1-6 under the heading “Supplementary Figures and Legends”). Shen et al supplemental teach that the V278C, S371C and S396C variants conjugated to Biotin-PEO-maleimide provided 100% biotinylation in the case of the V278C , S371C and S396C ThioMabs with two biotin linkers per antibody (page 2, lines 6-10 under the heading “Supplementary Figures and Legends”). Shen et al compared the in vivo activity of a conjugate made from Fc-S396C, LC-205C and HC-A114C and determined that the LC-205C conjugate had the greatest activity, followed by HC-A114C which had moderate activity and Fc-S396C which had little to no activity (page 185, first column, first full paragraph). Shen et al teach that in vivo activities of the conjugates were proportional to the circulating levels of the conjugates over 28 days, which reflected the differential stability of the linkers at the different positions in the Fc (page 185, first column, second full paragraph). Shen et al demonstrated by testing the stability of alternative Fc conjugates, Fc-V278C and Fc-S371C, that the Fc antibody domain, per se, was not responsible for the loss of drug (page 185, second column, lines 18-21). Shen et al teach that the conjugates made from Fc-V278C and Fc-S371C were more stable than a conjugate made from S396C and were comparable in stability to the conjugate made from HC-A114C (page 185, second column, lines 11-18). Shen et al teach that in addition to solvent accessibility, structural and chemical properties such as neighboring proton donors/acceptors and local protein conformation can contribute to the linker stability (page 188, first column, lines 12-17).
It would have been prima facie obvious to screen the anti-transferrin antibody for positions on the Fc which did not interference with Fc effector function, for ThioMab conjugation sites which exhibited stability, such as Fc-V278C. It would have been prima facie obvious to optimize the location of the conjugates for linker stability and overall number of conjugates, such that the number was greater than 2, on the anti-transferrin antibody. One of skill in the art would have been motivated to do so in order to maximize the desired effect of the antibody drug conjugates in the treatment of cancer.
Claims 1, 2, 4, 10, 18, 40 and 52-54 are rejected under 35 U.S.C. 103 as being unpatentable over Li et, Xia et al, Tororella and Karagiannis, Cuellar et al, Tan et al, Chu and Orgel, Acchione et al, Ward, and Dennis et al as applied to claims 1, 2, 4, 18, 40 and 52-54, above, and further in view of Bettencourt et al (WO2013/166004, cited in a previous action).
The combined teachings of Li et, Xia et al, Tororella and Karagiannis, Cuellar et al, Tan et al, Chu and Orgel, Acchione et al and Ward, render obvious the claims with respect to the oncogene being KRAS as specifically taught by Li et al.
Li et al does not specifically teach that the double stranded RNA for silencing KRAS comprises a sequence of SEQ ID NO: 16-75, 452-1955, 1956-1962, 1967-2002, 2013-2032, 2082-2109 or 2117 as required in claim 10. .
Betencourt et al teach that Ras genes are transforming oncogenes (paragraph [00150]). Bettencourt et al teach RNA interference agent to KRAS which are useful in the treatment of KRAS-related diseases such as cancers (paragraphs [0006]-[0007]). Betencourt et al teach anti-sense strands of siRNA for knocking down KRAS expression that which are identical to the instant SEQ ID NO: 43, 45, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39 and 41 (Table 1, pp. 6, 8, 9 and 10: SEQ ID NO: 1283, 1284, 1431, 1432, 1446, 1473, 1475, 1476, 1477, 1481, 1482, 1485, 1486, 1494, and 1515, respectively).
It would have been prima facie obvious at the time of the effective filing date to use the anti-sense strands of Betencourt et al wherein the complementary sense strands comprised the instant SEQ ID NO: 43, 45, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39 and 41, for the RNA duplex in the conjugate rendered obvious by the combined teachings of Li et al, Xia et al, Casi et al, Acchione et al, Tororella and Karagiannis and Ward.
One of skill in the art would have been motivated to do so because Li et al teach that KRAS is a target for silencing by the inventive aiRNA duplex conjugated to an antibody, and the teachings of Betencourt et al regarding the particular antisense sequences that silence KRAS.
Claims 1, 2, 4, 5, 18, 40 and 52-54 are rejected under 35 U.S.C. 103 as being unpatentable over Li et, Xia et al, Tororella and Karagiannis, Cuellar et al, Tan et al, Chu and Orgel, Acchione et al, Ward and Shen et al, as applied to claims 1, 2, 4, 18, 40 and 52-54, above, and further in view of Walker et al (Pharmaceutical Research, 1995, Vol. 12, pp. 1548-1553, cited in a prior action), Czauderna et al (Nucleic Acids Research, 2003, Vol. 31, pp. 2705-271, cited in a prior action) and Watts et al (Drug Discovery Today, 2008, Vol. 13, pp. 842-855, cited in a prior action).
Claim 5 requires that the molecule of claim 1 has at least one inverted abasic moiety at least one terminus.
Walker et al teach that it may be necessary to use oligonucleotides that are less sensitive to nuclease digestion such as phosphothioate and-protected oligos or methylphosphonate analogs, for stability in serum (page 1552, first column, 2nd paragraph, lines 25-29).
Czauderna et al teach that data on serum stability of RNA indicates that endonucleases are primarily responsible for the RNA degradation, with exonucleases contributing to a lesser extent (page 2715, first column, lines 22-24).
Watts et al teach that inverted abasic end caps, especially at the termini of the sense strand provides increased exonuclease stability to siRNA (page 846, lines 1-4 of the third paragraph under the heading “Modifications to the overhangs and termini”).
It would have been prima facie obvious at the time of the effective filing date to use inverted abasic end caps for at least one terminus of the RNA duplex of Li et al. One of skill in the art would have been motivated to do so by the suggestion of Walker et al to use oligonucleotides which are less sensitive to nuclease digestion; the teachings of Czaudena et al, that exonucleases are responsible in part for siRNA degradation and the teachings of Watts et al that abasic end caps at the termini of the sense strand provide increased stability to siRNA. One of skill in the art would understand that the abasic end caps would provide increased resistance of the RNA duplex of Li et al to exonucleases.
All claims are rejected. All other rejections as set forth in the prior Office action are withdrawn.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KAREN A CANELLA whose telephone number is (571)272-0828. The examiner can normally be reached M-F 10-6:30.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Julie Wu can be reached at 571-272-5205. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
KAREN A. CANELLA
Examiner
Art Unit 1643
/Karen A. Canella/Primary Examiner, Art Unit 1643
Prosecution Insights