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 .
Amendments
In the reply filed 8/21/2025, Applicant has amended Claims 1 and 6, and added new claims, Claims 22-24.
Claims 14-15, and 17-20 are pending but withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a non-elected invention, there being no allowable generic or linking claim.
Claims 1-2, 4-6 and 21-24 are under consideration.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 8/21/2025 was filed after the mailing date of the non-final Office action on 5/21/2025. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Withdrawn Claim Objections
The objection to Claim 1 has been withdrawn due to Applicant’s amendment.
Withdrawn 35 USC § 112(b)
The prior rejection of Claim 6 under 35 U.S.C. § 112(b) pre-AIA 2nd paragraph as being indefinite is withdrawn in light of Applicant’s amendments of instant claim to describe the targeting protein.
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 of this title, 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 set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied 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.
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, 4-6, and 21 stand rejected under 35 U.S.C. 103 as being unpatentable over Crews et al., (WO2013/106643, filed 1/11/2013, published 7/18/2013, see IDS filed 1/20/2022) in view of Crews et al., (WO2012/078559, filed 6/11/2011, published 6/14/2012, see IDS filed 1/20/2022), Schneekloth et al., (JACS, 2004, 126, 3748-3754, see IDS filed 1/20/2022), Wandless et al. (US 8,173,792, filed 2/08/2008, patented 5/08/2022, prior art of record), and Mali et al. (US Patent 9,023,649, filed 6/30/2014, patented 5/05/2015, see IDS filed 1/20/2022)
dFKBP-12 embodiment
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[AltContent: textbox ([img-media_image2.png])]Crews et al., (2013) teaches a composition comprising a cell and a heterobifunctional compound that induces degradation of an endogenous target protein of interest (Abstract, p. 7, last para., p. 8, 1st & 2nd para). Specifically, in regard to claims 1 and 21, Crews teaches a genus of heterobifunctional compounds that that can bind to a FKBP12 protein, and a subunit of the E3 ubiquitin ligase, wherein the protein is brought in proximity of the ubiquitin ligase, is ubiquitinated, and then degraded by the proteasome (p. 364, p. 395). Specifically in regard to the heterobifunctional compounds of claims 1 and 21, Crews teaches the moiety of the heterobifunctional compound that binds the ubiquitin ligase is identical to Applicant’s compound dFKBP-12 (p. 250-253, see excerpt on p. 268 adjacent).
[AltContent: textbox ([img-media_image3.png])]In regard to the linker of the heterobifunctional compound, Crews teaches the ubiquitin ligand binding moiety with a tetra-ethoxy linker attached to a targeting compound of interest such as the estrogen receptor (p. 292, see also Fig. 18, drawing page 101, below). Furthermore, Crews also teaches a tri-ethoxy linker in very similar ubiquitin ligand binding moieties in the adjacent structure in Fig. 18 (see also p. 293-298).
[AltContent: textbox ([img-media_image4.png])] Finally, in regard to the moiety that targets FKBP, Crews (2013) teaches the FK506 derivative of compound XI, wherein “R” represents the linker group (p. 80, p. 381, see below), which is identical to the FKBP targeting moiety of Applicant’s compound dFKBP-12
Accordingly, it would have been obvious to one of ordinary skill in the art at the time of filing to prepare the heterobifunctional compound comprising the above FKBP binding moiety and the above ubiquitin ligase binding moiety with a tri-ethoxy linker as suggested by Crews (2013) with a reasonable expectation of success. The ordinary skilled artisan would have been motivated to do so as taught by Crews (2013) because of the ease of synthesis with an available tri-ethoxy benzene initiator (see also p. 293-297).
However, although Crews (2013) teaches the heterobifunctional compound is to be in a cell, they are silent with respect to genetically modifying the cells to comprise a nucleic acid encoding a FKBP12 fusion protein of the endogenous target protein of interest.
Nevertheless, Crews (2013) discloses such a composition in their previous work of Crews (2012) that is incorporated by reference (p. 87, 2nd para. of Crews 2013).
In regard to claims 1 and 21, Crews (2012) teaches a genetically modified cell comprising a nucleic acid encoding a dTAG heterobifunctional compound targeting protein (i.e., a Halotag),
wherein said nucleic acid is in-frame in a 5’ orientation with the nucleic acid of a gene encoding an endogenous target protein of interest,
[AltContent: textbox ([img-media_image5.png])]wherein a fusion protein of the heterobifunctional compound targeting protein and the endogenous target protein of interest is expressed,
wherein a heterobifunctional compound (e.g., HyT13) is capable of binding to (a) the dTAG heterobifunctional compound targeting protein domain of the fusion protein and (b) a ubiquitin ligase,
wherein the fusion protein is ubiquitinated and then degraded by the proteasome (Abstract, p. 3, 2nd para. to p. 4, 1st para., p. 21, last para. to p. 22, 1st para., p. 35, 2nd para., p. 76, 3rd para., see Fig. 4, adjacent).
Accordingly, it would have been obvious to one of ordinary skill in the art at the time of filing to prepare a composition comprising a cell and a heterobifunctional compound of dFKBP12 as suggested by Crews (2013), and to modify the cell to comprise a donor nucleic acid encoding the binding region of the FKBP12 dTAG in-frame in a 5’ orientation with the nucleic acid of a gene encoding an endogenous target protein of interest as taught by Crews (2012) with a reasonable expectation of success. The ordinary skilled artisan would have been motivated to do so for several reasons. First, as stated supra, Crews (2013) incorporates Crews (2012) by reference, thus it would have been obvious to one of ordinary skill when to modify the teachings of Crews (2013) to incorporate the teachings of Crews (2012). Furthermore, Crews (2012) teaches that by creating a fusion protein between the dTAG and an endogenous protein confers the ability to regulate any protein of interest in living systems with small molecules (Abstract).
However, in regard to claims 1 and 21, Crews (2013) and Crews (2012) are silent to the amino acid sequence that the FKBP fusion protein.
[AltContent: textbox ([img-media_image6.png])]Schneekloth et al., (2004), who has Crews (2013) a co-author, teaches a cell comprising a nucleic acid encoding FKBP binding protein binding domain that binds a heterobifunctional compound comprising the FK506 derivative of compound XI of Crews (2013) and a peptide based domain for binding the E3 ubiquitin ligase (p. 3749, Fig. 1, see also Scheme 1 excerpt adjacent from p. 3750). In regard to claims 1 and 21, Schneekloth teaches that the FKBP binding protein is the FKBP12 F36V variant that allows compound XI binding without disrupting endogenous FKBP12 function (p. 3749, Results). Although Schneekloth indicates that the nucleic acid encoding the FKBP12 F36V is commercially available through ARIAD Pharmaceuticals, they do not provide an animo acid sequence. Nevertheless, the amino acid sequence for FKBP12 F36V was well known in the prior art, such as being taught as SEQ ID NO:1 from Wandless et al. (2012), which is 100% identical to the amino acid sequence of SEQ ID NO:2 (see SCORE search 5/16/2025, rai.file, result #1).
Accordingly, it would have been obvious to one of ordinary skill in the art at the time of filing to prepare a composition comprising a heterobifunctional compound of dFKBP12, and a modified the cell to comprise a FKBP12 dTAG in-frame in a 5’ orientation with an endogenous target protein of interest as suggested by Crews (2013) incorporating Crews (2012) and choose the FKBP12F36V sequence as taught by Schneekloth a reasonable expectation of success. The ordinary skilled artisan would have been motivated to do so for several reasons. First, as stated supra, Crews is a co-author of Schneekloth, thus it would have been obvious to one of ordinary skill when to modify the teachings of Crews to look to scientific publication of analogous art for enabling disclosures. Furthermore, Schneekloth demonstrates that the FKB12F36V sequence can be successfully used as a fusion protein in order to target degradation of a protein of interest using a heterobifunctional compound comprising the FK506 derivative of compound XI of Crews (2013). Finally, considering that Wandless et al. teaches the amino acid sequence for the FKBP12 F36V of SEQ ID NO:2, the successful cloning and sequencing of the cDNA encoding a known protein is obvious, and thus unpatentable, if (1) there was some suggestion or motivation in the prior art to clone the cDNA, and (2) there was a “reasonable expectation of success,” based on "detailed enabling methodology" in the prior art. Ex parte Kubin, 83 U.S.P.Q.2d (BNA) 1410 (B.P.A.I. 2007), aff'd, 561 F.3d 1351 (Fed. Cir. 2009).
However, in regard to claims 1 and 21, although Crews (2012) teaches the dTag is knocked in via homologous recombination using nucleases such that it is fused to the protein of interest (p. 35, 2nd para., p. 76, 3rd para.), they are silent with respect to the genetically modified cell comprising a nucleic acid encoding a CRISPR-Cas9 nuclease system for knocking in of the donor nucleic acid encoding the dTag domain of the fusion protein.
With respect to claims 1, 5 and 21, Mail et al., teaches a genetically modified cell comprising (i) a donor nucleic acid and (ii) a nucleic acid encoding a CRISPR-Cas9 nuclease system for the integration of the donor nucleic acid via homologous recombination at an endogenous target locus in human cells (col 3, last para., col 5, 3rd para., col 6 1st para., col 7, “Examples of multiplexing applications”, see also Figs. 4, 5A, and 7).
Accordingly, it would have been obvious to one of ordinary skill in the art at the time of filing to prepare the genetically modified cell comprising the donor nucleic acid encoding the heterobifunctional compound targeting domain (i.e., FKBP12 F36V dTAG) that is to be integrated by homologous recombination in-frame with the endogenous target protein to form the degradable dTAG fusion protein as suggested by Crews (2013) and Crews (2012), and substitute a CRISPR-Cas9 nuclease system for the integration of the donor DNA via homologous recombination at an endogenous target locus as taught by Mali with a reasonable expectation of success. The ordinary skilled artisan would have been motivated to do so as taught by Mali because the guide RNAs used for targeting the CRISPR-Cas9 nucleases can be synthesized easily in large numbers (col 14, Example VI; col 17, Example XVI) unlike ZFN and TALEN nucleases, yet the CRISPR system allows for homologous recombination of donor templates with high efficiency and specificity (col 14-col 15, Examples IX-XI).
In regard to claim 2, Crews (2013) teaches the composition is to be administered to a human (p. 3, Objects of the Invention), and Crews (2012) teaches the cell is a human cell (p. 20, 5th para.), which would have been obvious.
In regard to claim 4, Crews (2013) teaches the target protein can be associated with a disease caused by overexpression of the protein or a dysregulated protein such as in cancer (p. 8, 2nd para., p. 52, 2nd para. to p. 53, 1st para.), and Crews (2012) teaches that the endogenous protein of interest is associated with disease such a cancer characterized by a gain of function mutation such as RasG12V (p. 73, last para. Fig. 3).
In regard to claim 6, Schneekloth evidences that the FKBP12 binding moiety of Crews (2013) is specific to FKBP12 F36V and therefore should not interfere with the function of the endogenous protein of interest (p. 3749, last para.). Furthermore, Crews (2012) teaches that the protein of interest fused to the dTag is stable in the absence of the degradation signal and should function normally until the heterobifunctional compound is provided (p. 35, last para., p. 75, last para.).
Hence, the claimed invention as a whole was prima facie obvious in the absence of evidence to the contrary.
RESPONSE TO ARGUMENTS
Applicant's arguments filed on 8/21/2025 are acknowledged.
First, Applicant argues that although Crews 2013 teaches heterobifunctional compounds to recruit endogenous proteins to the E3 ubiquitin ligase for degradation, they are silent to a dTAG hybrid endogenous protein for doing so, and Applicant argues that Crews 2013 is silent to a FKBP(F36V) dTAG of SEQ ID NO:2. Furthermore, there is no rationale to modify Crews 2013 to make a dTAG comprising SEQ ID NO:2 fused to an endogenous protein. Furthermore, Applicant argues that although the secondary reference of Crews 2012, is incorporated by reference into Crews 2013, this incorporation by reference is limited to the specific context of haloalkane dehalogenase fusion proteins. Applicant argues the two Crews teach dissimilar methods of degrading target proteins, and that Crews 2012 would have led the artisan in a different direction than instant invention. Specifically, Crews 2012 is directed to the haloTAG system, which Crews 2012 viewed as an improvement with respect to the methods using FKBP system.
Second, Applicant argues that Crews 2013 has a fundamentally different objective, wherein the heterobifunctional compounds function irreversibly and the degradation of the target endogenous protein cannot be further controlled once the compound has been administered. Applicant argues that by contrast, instant method allows for targeted protein degradation of dTAG fused proteins using a heterobifunctional compound in a controlled, tunable fashion.
Third, Applicant argues that the Examiner conclusion of obviousness is hindsight-driven, and that none of the 5 cited publication teaches dFKBP-6 to dFKBP-13. Applicant argues that in order to construct dFKBP-12, the Examiner has pieced together disparate disclosures from Crews 2013, and does not provide a sound rationale for constructing dFKBP-12. Applicant argues that although the supporting reference of Schneekloth teaches the FKBP12 targeting moiety, it does not teach linker or E3 ligase binding moiety of dFKBP-12, and one would not have made dFKBP-12. Moreover, Applicant argues that although Wandless teaches the FKPB12(F36V) of SEQ ID NO:2, it does not remedy the deficiencies of the two Crews. Furthermore, Mali is silent to the dTAG systems.
Finally, Applicant argues there was no reasonable expectation of success in using the claimed composition. Applicant argues that at the time of filing the art concerning heterobifunctional compounds (i.e., PROTACs) was unpredictable and highly empirical, and the efficacy of moieties for binding the target protein so as to induce ubiquitin ligation could not be predicted. Specifically, Applicant cites the post-filing art of Tan 2018, who reviews PROTACs for targeting degradation of CDK9, and concludes that not all inhibitor compounds of CDK9 are well suited to be targeting ligands. Applicant cites the post-filing art of Li 2020, who summarizes that it is unreliable to predict the outcomes of PROTACs based on the POI inhibitor it contains. Applicant cites the post-filing art of Bondeson 2018, who reports that the extent of degradation does not necessarily correlate with the PROTACs affinity for the protein kinase target, and when the broad spectrum kinase inhibitor Foretinib was linked to the CRBN ligand thalidomide, the kinase inhibitor bound much fewer kinases. Applicant cites the post-filing art of Crews 2017, who teaches that despite the PROTAC binding its kinase target, it did not induce degradation, and that certain PROTACs comprising the tyrosine kinase inhibitor targeting moiety of imatinib could not induce degradation. Finally, Applicant cites the post-filing art of Nandave 2024, who teaches that design of the linker connecting the POI and E3 ligase binding moiety is crucial for efficacy, selectivity, and pharmacokinetics of the PROTACs.
Applicant's arguments and the post-filing art of Tan 2018, Li 2020, Bondeson 2020, Crews 2017, and Nandave 2024, have been fully considered but they are not persuasive.
In response to Applicant's first argument, a 35 U.S.C. § 103(a) based test for obviousness is not whether the features of a secondary reference may be bodily incorporated into the structure of the primary reference; nor is it that the claimed invention must be expressly suggested in any one or all of the references. Rather, the test is what the combined teachings of the references would have suggested to those of ordinary skill in the art. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981). In instant case, Crews (2013) is directed to the degradation of endogenous proteins using heterobifunctional compounds, which include a VHL ligand and FKBP12 ligand that are exactly the same as dFKBP-12 binding moieties of instant claims. In regard to the incorporation by reference of Crews (2012) into Crews (2013), as a first matter, it would have been understood that the incorporation by reference is an incorporation of Crews (2012) is in its entirety, not just sections dedicated to haloalkane dehydrogenase (Halo) fusion proteins. Nevertheless, it is this very concept of using Halo tagged fusion proteins as recruiting tools to bind a dedicated and specific ligand to recruit the Halo tagged fusion protein to the E3 ubiquitin ligase that is to be incorporated into Crews (2013). As stated supra, Crews (2012) teaches that by creating a fusion protein between the dTAG and the endogenous protein confers the ability to regulate any protein of interest in living systems with the heterobifunctional compound. Thus, contrary to Applicant’s assertion, the two Crews do rely on similar methods of using heterobifunctional compounds to degrade endogenous proteins, but Crews (2012) takes the method one step further by creating a fusion protein to do so, thereby allowing a single dedicated and specific heterobifunctional compound to be used. As far as Crews (2012) statements regarding the FKBP12 system, these concerns are cured by Crews (2013) who teaches a very specific and high affinity ligand of FKBP12 (Compound IX). Importantly, Schneekloth makes clear that Compound IX (alias AP21998) was developed by ARIAD Pharmaceuticals to bind to the F36V mutant FKBP12 protein, without disrupting endogenous FKBP12 function.
In response to Applicant’s second argument directed to the tunable and controlled fashion of degradation by instantly claimed system, MPEP 2144 (IV) states that the reason or motivation to modify a reference may often suggest what the inventor has done, but for a different purpose or to solve a different problem. It is not necessary that the prior art suggest the combination to achieve the same advantage or result discovered by Applicant. See, e.g., In re Kahn, 441 F.3d 977, 987, 78 USPQ2d 1329, 1336 (Fed. Cir. 2006). In instant case, the prior art of Crews (2012) teaches that by creating a fusion protein between the dTAG and the endogenous protein confers the ability to regulate any protein of interest in living systems with the heterobifunctional compound. The fact that Applicant has recognized another advantage which would flow naturally from following the suggestion of the prior art cannot be the basis for patentability when the differences would otherwise be obvious. See Ex parte Obiaya, 227 USPQ 58, 60 (Bd. Pat. App. & Inter. 1985).
In response to Applicant’s third argument directed to the improper hindsight construction of the dFKBP-12 heterobifunctional compound, it must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. See In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971). As stated supra, Crews (2013) teaches the VHL ligand for binding the E3 ubiquitin ligase that is exactly the same as the VHL ligand moiety of dFKBP-12, and Crews (2013) teaches the FK506 derivative of compound XI that is exactly the same as the FKBP12 binding moiety of dFKBP-12. Both of these ligands were well known and understood as being high affinity and specific for their targets (see Schneekloth et al.), and Crews (2013) presents them as embodiments for constructing the UTM-linker-PTM heterobifunctional compound, and a combination of these embodiments would have been predictably obvious to one of ordinary skill in the art under KSR. In regard to the linker of dFKBP-12, as stated supra, Crews (2013) teaches a triple ethoxy linker between a VHL ligand and the target moiety (albeit estrogen derivates) (see Fig. 18), and also teaches that the linker group is based on a polyethylene glycol “between about 2 and 4 ethylene glycole units” (p. 47, 3rd para.). Accordingly, one of ordinary skill in the art would have immediately envisaged the option of the 3 ethylene glycol units found in the linker of dFKBP-12.
[AltContent: textbox ([img-media_image7.png])]In response to Applicant’s final argument directed to the reasonable expectation of success of making and using the dFKBP-12 heterobifunctional compound to degrade a FKBP tagged fusion protein, as a first matter, Arguments of counsel cannot take the place of factually supported objective evidence in the record. See In re Schulze, 346 F.2d 500, 602, 145 USPQ 716, 718 (CCPA 1965), In re Huang, 100 F.3d 135, 139-40, 40 USPQ2d 1685, 1689 (Fed. Cir. 1996); In re De Blauwe, 736 F.2d 699, 705, 222 USPQ 191, 196 (Fed. Cir. 1984). In regard to the post-filing art supplied by the Applicant, it must be noted that the unpredictability in using PROTACs to degrade a protein as presented by Tan 2018, Li 2020, Benson 2018, and Crews 2017 arises from the POI targeting moiety used (e.g., kinase inhibitor). This problem is entirely circumvented by the teaches of Crews (2013) et al., who teach that Compound IX is to be used, which had already been established by Schneekloth as being effective and specific for FKBP12(F36V) tagged proteins. In regard to the post-filing art of Nandave (2024), although they make clear that design of the linker is important, they also indicate that the polyethylene glycol based linkers of Crews (2013) were known to impart the required length and flexibility to PROTACs (see adjacent excerpt from Fig. 2.5 of Nandave). Thus, the post-filing art establishes that the taught triple-ethoxy linkers of Crews (2013) were a predictably obvious choice.
Applicant is reminded that any conclusions of unpredictability have to be made in the context of this particular in vitro system. The targeting moieties and chemistries for making the heterobifunctional dFKBP-12 compound were well known, as was making and using FKBP12(F36V) fusion proteins, thus there was a reasonable expectation of success of causing some degradation of any endogenous protein of a cell in vitro. Furthermore, the Federal Circuit has established that absolute predictability is not a necessary prerequisite to a case of obviousness. Rather, a degree of predictability that one of ordinary skill would have found to be reasonable is sufficient. The Federal Circuit concluded that Applicant’s “[g]ood science and useful contributions do not necessarily result in patentability.” Id. at 1364, 83 USPQ2d at 1304.
New Claim Rejections - 35 USC § 103
as necessitated by amendment
Claims 1-2, 4-6, and 21-24 are rejected under 35 U.S.C. 103 as being unpatentable over Crews et al., (US2016/0058872, filed 7/06/2015, see IDS filed 1/20/2022) in view of Crews et al., (WO2012/078559, filed 6/11/2011, published 6/14/2012, see IDS filed 1/20/2022), Schneekloth et al., (JACS, 2004, 126, 3748-3754, see IDS filed 1/20/2022), Wandless et al. (US 8,173,792, filed 2/08/2008, patented 5/08/2022), and Mali et al. (US Patent 9,023,649, filed 6/30/2014, patented 5/05/2015, see IDS filed 1/20/2022)
dFKBP-7 embodiment
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[AltContent: textbox ([img-media_image9.png])]Crews et al., (2016) teaches a composition comprising a cell and a heterobifunctional compound that induces degradation of an endogenous target protein of interest (Abstract, [0002, 0012-0016]). Specifically, in regard to claims 1 and 21-24, Crews teaches a genus of heterobifunctional compounds that that can bind to a FKBP12 protein, and a cereblon (CRBN) subunit of the E3 ubiquitin ligase, wherein the protein is brought in proximity of the ubiquitin ligase, is ubiquitinated, and then degraded by the proteasome ([0012, 0017]). Specifically in regard to the heterobifunctional compounds of claims 1 and 21-24, Crews (2016) teaches the thalidomide moiety of the heterobifunctional compound that binds the CRBN of the ubiquitin ligase is identical to Applicant’s compound dFKBP-7 (p. 16, top right, see excerpt above).
[AltContent: textbox ([img-media_image10.png])]In regard to the linker of the heterobifunctional compound, Crews (2016) teaches the thalidomide ubiquitin ligand binding moiety it attached to propyloxy and ethyloxy based linkers attached to a targeting compound of interest (e.g., kinase inhibitor) (p. 34, 4th from top, p. 42, top, see excerpts adjacent). Furthermore, Crews teaches that the linker group is based on a polyethylene glycol “between about 2 and 4 ethylene glycole units” ([0125]), and provides a genus of linkers that comprise 3 ethylene glycol units, and linkers with a propylene adjacent to the amide attached to the PTM and/or ULM targeting groups (p. 19 table).
[AltContent: textbox ([img-media_image11.png])] Finally, in regard to the moiety that targets FKBP, Crews (2016) teaches the FK506 derivative of compound XI, wherein “R” represents the linker group (p. 44, [0253], see adjacent), which is identical to the FKBP targeting moiety of Applicant’s compound dFKBP-7.
Accordingly, it would have been obvious to one of ordinary skill in the art at the time of filing to prepare the heterobifunctional compound comprising the above FKBP binding moiety and the above ubiquitin ligase binding moiety comprising a triple-ethoxy linker with terminal propylene/amides as suggested by Crews (2016) with a reasonable expectation of success. The ordinary skilled artisan would have been motivated to do so as taught by Crews (2016) because of the ease of synthesis with the available triple-ethoxy benzene initiator ([0555-0567]).
However, although Crews (2016) teaches the heterobifunctional compound is to be in a cell, they are silent with respect to genetically modifying the cells to comprise a nucleic acid encoding a FKBP12 fusion protein of the endogenous target protein of interest.
Nevertheless, Crews (2016) discloses such a composition in their previous work of Crews (2012) that is incorporated by reference ([0145] of Crews 2016).
In regard to claims 1 and 21, Crews (2012) teaches a genetically modified cell comprising a nucleic acid encoding a dTAG heterobifunctional compound targeting protein (i.e., a Halotag),
wherein said nucleic acid is in-frame in a 5’ orientation with the nucleic acid of a gene encoding an endogenous target protein of interest,
[AltContent: textbox ([img-media_image5.png])]wherein a fusion protein of the heterobifunctional compound targeting protein and the endogenous target protein of interest is expressed,
wherein a heterobifunctional compound (e.g., HyT13) is capable of binding to (a) the dTAG heterobifunctional compound targeting protein domain of the fusion protein and (b) a ubiquitin ligase,
wherein the fusion protein is ubiquitinated and then degraded by the proteasome (Abstract, p. 3, 2nd para. to p. 4, 1st para., p. 21, last para. to p. 22, 1st para., p. 35, 2nd para., p. 76, 3rd para., see Fig. 4, adjacent).
Accordingly, it would have been obvious to one of ordinary skill in the art at the time of filing to prepare a composition comprising a cell and a heterobifunctional compound of dFKBP7 as suggested by Crews (2016), and to modify the cell to comprise a donor nucleic acid encoding the binding region of the FKBP dTAG in-frame in a 5’ orientation with the nucleic acid of a gene encoding an endogenous target protein of interest as taught by Crews (2012) with a reasonable expectation of success. The ordinary skilled artisan would have been motivated to do so for several reasons. First, as stated supra, Crews (2016) incorporates Crews (2012) by reference, thus it would have been obvious to one of ordinary skill when to modify the teachings of Crews (2016) to incorporate the teachings of Crews (2012). Furthermore, Crews (2012) teaches that by creating a fusion protein between the dTAG and an endogenous protein confers the ability to regulate any protein of interest in living systems with small molecules (Abstract).
However, in regard to claims 1 and 21, Crews (2016) and Crews (2012) are silent to the amino acid sequence that the FKBP fusion protein.
[AltContent: textbox ([img-media_image6.png])]Schneekloth et al., (2004), who has Crews (2016) a co-author, teaches a cell comprising a nucleic acid encoding FKBP binding protein binding domain that binds a heterobifunctional compound comprising the FK506 derivative of compound XI of Crews (2016) and a peptide based domain for binding the E3 ubiquitin ligase (p. 3749, Fig. 1, see also Scheme 1 excerpt adjacent from p. 3750). In regard to claims 1 and 21, Schneekloth teaches that the FKBP binding protein is the FKBP12 F36V variant that allows compound XI binding without disrupting endogenous FKBP12 function (p. 3749, Results). Although Schneekloth indicates that the nucleic acid encoding the FKBP12 F36V is commercially available through ARIAD Pharmaceuticals, they do not provide an animo acid sequence. Nevertheless, the amino acid sequence for FKBP12 F36V was well known in the prior art, such as being taught as SEQ ID NO:1 from Wandless et al. (2012), which is 100% identical to the amino acid sequence of SEQ ID NO:2 (see SCORE search 5/16/2025, rai.file, result #1).
Accordingly, it would have been obvious to one of ordinary skill in the art at the time of filing to prepare a composition comprising a heterobifunctional compound of dFKBP7, and a modified the cell to comprise a FKBP dTAG in-frame in a 5’ orientation with an endogenous target protein of interest as suggested by Crews (2016) incorporating Crews (2012) and choose the FKBP12F36V sequence as taught by Schneekloth a reasonable expectation of success. The ordinary skilled artisan would have been motivated to do so for several reasons. First, as stated supra, Crews is a co-author of Schneekloth, thus it would have been obvious to one of ordinary skill when to modify the teachings of Crews to look to scientific publication of analogous art for enabling disclosures. Furthermore, Schneekloth demonstrates that the FKB12F36V sequence can be successfully used as a fusion protein in order to target degradation of a protein of interest using a heterobifunctional compound comprising the FK506 derivative of compound XI of Crews (2013). Finally, considering that Wandless et al. teaches the amino acid sequence for the FKBP12 F36V of SEQ ID NO:2, the successful cloning and sequencing of the cDNA encoding a known protein is obvious, and thus unpatentable, if (1) there was some suggestion or motivation in the prior art to clone the cDNA, and (2) there was a “reasonable expectation of success,” based on "detailed enabling methodology" in the prior art. Ex parte Kubin, 83 U.S.P.Q.2d (BNA) 1410 (B.P.A.I. 2007), aff'd, 561 F.3d 1351 (Fed. Cir. 2009).
However, in regard to claims 1 and 21, although Crews (2012) teaches the dTag is knocked in via homologous recombination using nucleases such that it is fused to the protein of interest (p. 35, 2nd para., p. 76, 3rd para.), they are silent with respect to the genetically modified cell comprising a nucleic acid encoding a CRISPR-Cas9 nuclease system for knocking in of the donor nucleic acid encoding the dTag domain of the fusion protein.
With respect to claims 1, 5 and 21, Mail et al., teaches a genetically modified cell comprising (i) a donor nucleic acid and (ii) a nucleic acid encoding a CRISPR-Cas9 nuclease system for the integration of the donor nucleic acid via homologous recombination at an endogenous target locus in human cells (col 3, last para., col 5, 3rd para., col 6 1st para., col 7, “Examples of multiplexing applications”, see also Figs. 4, 5A, and 7).
Accordingly, it would have been obvious to one of ordinary skill in the art at the time of filing to prepare the genetically modified cell comprising the donor nucleic acid encoding the heterobifunctional compound targeting domain (i.e., FKBP12 F36V dTAG) that is to be integrated by homologous recombination in-frame with the endogenous target protein to form the degradable dTAG fusion protein as suggested by Crews (2016) and Crews (2012), and substitute a CRISPR-Cas9 nuclease system for the integration of the donor DNA via homologous recombination at an endogenous target locus as taught by Mali with a reasonable expectation of success. The ordinary skilled artisan would have been motivated to do so as taught by Mali because the guide RNAs used for targeting the CRISPR-Cas9 nucleases can be synthesized easily in large numbers (col 14, Example VI; col 17, Example XVI) unlike ZFN and TALEN nucleases, yet the CRISPR system allows for homologous recombination of donor templates with high efficiency and specificity (col 14-col 15, Examples IX-XI).
In regard to claim 2, Crews (2016) teaches the composition is to be administered to a human ([0019, 0021, 0047, 0139]), and Crews (2012) teaches the cell is a human cell (p. 20, 5th para.), which would have been obvious in light of the clinical significance.
In regard to claim 4, Crews (2016) teaches the target protein can be associated with a disease caused by overexpression of the protein or a dysregulated protein such as in cancer ([0138-0140]), and Crews (2012) teaches that the endogenous protein of interest is associated with disease such a cancer characterized by a gain of function mutation such as RasG12V (p. 73, last para. Fig. 3).
In regard to claim 6, Schneekloth evidences that the FKBP12 binding moiety of Crews (2013) is specific to FKBP12 F36V and therefore should not interfere with the function of the endogenous protein of interest (p. 3749, last para.). Furthermore, Crews (2012) teaches that the protein of interest fused to the dTag is stable in the absence of the degradation signal and should function normally until the heterobifunctional compound is provided (p. 35, last para., p. 75, last para.).
Hence, the claimed invention as a whole was prima facie obvious in the absence of evidence to the contrary.
RESPONSE TO ARGUMENTS
Applicant's arguments filed on 8/21/2025 are acknowledged and have been addressed above in so far that the primary reference of Crews (2016) has similar teaching to Crews (2013), and that the secondary references have been applied in the same fashion.
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 extension fee 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 date of this final action.
No claims are allowed.
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/ARTHUR S LEONARD/Examiner, Art Unit 1631