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 .
Election/Restrictions
Applicant’s election without traverse of the species of the ubiquitin ligase as RNF149 and the first and second extracellular non-native epitope tag as an alpha- and E6-tag, respectively, in the reply filed on 11/24/2025 is acknowledged. Upon further consideration, the species election requirements set forth in the Office action mailed 10/1/2025 are withdrawn because the claims are drawn to screening methods, which by definition encompass the testing of various embodiments. In view of the withdrawal of the species election requirements, applicant(s) are advised that if any claim presented in a divisional application is anticipated by, or includes all the limitations of, a claim that is allowable in the present application, such claim may be subject to provisional statutory and/or nonstatutory double patenting rejections over the claims of the instant application. Once the restriction requirement is withdrawn, the provisions of 35 U.S.C. 121 are no longer applicable. See In re Ziegler, 443 F.2d 1211, 1215, 170 USPQ 129, 131-32 (CCPA 1971). See also MPEP § 804.01.
Claims 1-21 are under examination.
Effective Filing Date
Applicant’s claims for the benefit of a prior-filed application under 35 U.S.C. 365(c) and for foreign priority are acknowledged. Based on the information given by Applicant and an inspection of the prior application, the examiner has concluded that the subject matter defined in the instant claims is supported by the disclosure in PCT/EP2021/066696. Further, the certified copies of the foreign priority applications are in English and support the claimed invention under 35 USC 112(a), therefore, the effective filing date of the instant application is 03/05/2020.
Nucleotide and/or Amino Acid Sequence Disclosures
It is noted that the Incorporation by Reference paragraph required by 37 CFR 1.821(c)(1) is missing from the instant specification. The applicant is required to explicitly reference:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
Applicant is reminded that in order to amend the specification, applicant must provide a substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required incorporation by reference paragraph, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. See p. 17, line 22. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Claim Objections
Claim 1-21 objected to because of the following informalities.
(i) The amendments to claims 1-21 contains a color font that renders the text difficult to read. The claims must have text written plainly and legibly in portrait orientation and presented in a form having sufficient clarity and contrast between the paper and the writing thereon to permit the direct reproduction of readily legible copies in any number by use of photographic, electrostatic, photo-offset, and microfilming processes and electronic capture by use of digital imaging and optical character recognition; and only a single column of text. See 37 CFR 1.52(a) and (b).
(ii) In claim 16, the phrase “overexpresses, optionally permanently overexpresses” in line 2 is grammatically awkward. It is suggested that “optionally” be replaced with “or”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-21 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
(i) Claims 1, 8, 10-15 and 20 recite the phrase “preferably”, which renders the claims indefinite because it is unclear whether the limitation(s) following the phrase is part of the claimed invention. Description of examples or preferences is properly set forth in the specification rather than the claims. If stated in the claims, examples and preferences may lead to confusion over the intended scope of a claim. See MPEP § 2173.05(d).
(ii) Claim 8 contains the trademark/trade name “nanobody”. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe a single domain antibody and, accordingly, the identification/description is indefinite.
(iii) Claim 9 depends from claim 8, which depends from claim 1. Claim 9 recites “wherein the first binding domain of the heterobifunctional molecule is an anti-Alpha VHH and the second binding domain is an anti-E6 VHH, or wherein the first binding domain of the heterobifunctional molecule is an anti-E6 VHH and the second binding domain is an anti-Alpha VHH”. There is insufficient antecedent basis for these limitations because Alpha and E6 are non-native epitope tags, and neither claim 1 nor claim 8 refers to or encompasses epitope tags. Rather, claim 1 recites that the first and second binding domains of the heterobifunctional molecule are specific for an extracellular portion of the transmembrane E3 ligase and an extracellular portion of the membrane bound protein, respectively, and claim 8 recites the heterobifunctional molecule is a bispecific antibody.
(iv) Claim 10 depends from claim 1 and recites the membrane bound protein comprises a third non-native epitope tag and/or the transmembrane ubiquitin E3 ligase comprises a fourth non-native epitope tag”. There is insufficient antecedent basis for these limitations because claim 1 makes no reference to epitope tags. Similarly, claims 18 and 19 depend from claim 17, which depends from claim 1. Claim 18 recites the clause: “wherein in the cell provided in step a) a genomic sequence encoding the transmembrane E3 ubiquitin ligase has been modified to incorporate a sequence encoding the first, and optional fourth, non-native epitope tag.” Claim 19 recites the clause: “wherein in the cell provided in step a) a genomic sequence encoding the membrane-bound protein has been modified to incorporate a sequence encoding the second, and optional third, non-native epitope tag”. There is insufficient antecedent basis for the limitations of “the first and optional fourth, non-native epitope tag” and “the second and optional third non-native epitope tag” in the claims because neither claims 1 nor 17, from which claims 18 and 19 depend, recite or encompass epitope tags.
Claims 2-21 are also included in this rejection for depending upon an indefinite claim without resolving the indefiniteness.
Claim Rejections - 35 USC § 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Scope of Enablement
Claims 1-21 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for the following:
a method for identifying an effective combination of a transmembrane E3 ubiquitin ligase and a membrane-bound protein, comprising
a) providing a cell, wherein the cell expresses the transmembrane E3 ubiquitin ligase and the membrane-bound protein at its cell surface, wherein the E3 ubiquitin ligase is attached to an Alpha epitope tag and the membrane-bound protein is attached to an E6 tag, and further wherein the E3 ubiquitin ligase and the membrane-bound protein are wild-type;
b) exposing the cell to a heterobifunctional molecule, wherein said heterobifunctional molecule is a bi-specific VHH antibody comprising:
i) a first binding domain capable of specific binding to the Alpha-tag;
ii) a second binding domain capable of specific binding to the E6 tag; and
c) determining the surface level of the membrane-bound protein of the cell, wherein a decrease in the surface level of the membrane-bound protein as compared to the surface level of the membrane-bound protein of the cell prior to step b) indicates that the combination is an effective combination.
Alternatively, the claims are enabled for proteolysis-targeting chimera (PROTAC) systems as disclosed in the prior art. The specification does not, however, reasonably provide enablement for the claims as broadly recited. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make or use the invention commensurate in scope with these claims.
There are many factors to be considered when determining whether there is sufficient evidence to support a determination that a disclosure does not satisfy the enablement requirement and whether any necessary experimentation is “undue.” (See In re Wands, 858 F.2d 731, 737, 8 USPQ2d 1400, 1404 Fed. Cir. 1988). These factors include, but are not limited to: (a) the breadth of the claims; (b) the nature of the invention; (c) the state of the prior art; (d) the level of one of ordinary skill; (e) the level of predictability in the art; (f) the amount of direction provided by the inventor; (g) the existence of working examples; and (h) the quantity of experimentation needed to make or use the invention based on the content of the disclosure.
The specification encompasses combinations in which the E3 ligases and membrane bound proteins need only share 60% sequence identity with the wild-type protein (see p. 43, lines 3-5 and p. 49, lines 11-20). The art teaches that identifying “suitable target/E3 ligase” combinations capable of being targeted by bifunctional molecules (proteolysis targeting chimeras or PROTACs) that result in the degradation of the target protein is complex (see abstract of Adhikari et al. (2024 eLife. https://doi.org/10.7554/eLife.98450.2; 34 pages total). Four years after the filing date of the instant invention, Adhikari et al. note that the failure of the E3 ligase and target protein to form a ternary complex to which the bifunctional molecule can bind to induce target degradation is a large hurdle:
A possible reason for this frequent failure could be the incompatibility of a particular E3 ligase with a given target. In fact, it has been observed that promiscuous kinase inhibitors exhibit very distinct degradation profiles when used as ligands for PROTACs, demonstrating that the efficacy of PROTAC-mediated degradation is not determined solely by the sheer affinity of the target and E3 ligand but rather by efficient ternary complex formation. (Citations omitted by examiner).
See also Marei et al. (Nature, 2022; 610: https://doi.org/10.1038/s41586-022-05235-6), who teach that when attempting to colocalize IGF1R with the ligase using bispecific antibodies, the affinity of IGF1R targeting antibody did not predict IGF1R degradation because the epitope and the geometry of the ternary complex influences target degradation (e.g. see p. 184, left column, 2nd full paragraph).
The specification teaches a proof-of-concept study in which forced dimerization of TβRII and RNF43 with an A/C dimerizer resulted in increased TβRII degradation (see Example 1, especially p. 70, lines 12-35). In the next study, the E6 epitope tag was fused to the extracellular domains (ECDs) of the membrane-bound proteins, TβRII and EGFR (i.e., the targets), and the Alpha tag was fused to the ECDs of the transmembrane E3 ubiquitin ligases, RNF43 and RNF167, and the bi-specific antibody, VHH Alpha - (G4S)3 - VHH E6, which targets Alpha and E6 resulted in “VHH-mediated dimerization” and induced removal of the target proteins from the plasma membrane. Further, in order “[t]o determine alterations in the localization of proteins”, a Myc epitope tag was fused to the E3 ligases and a Flag epitope tag was fused to the membrane bound receptors. See Example 2, pages 71-72 of the instant specification.
Next, the specification teaches that specific combinations of E3 ligase-membrane bound protein (target) combinations resulted in membrane bound protein (i.e., target) removal from the cell surface when contacted with the bi-VHH: “CTLA-4 and RNF167; FLT-3 and RNF43, RNF128 or RNF167, PD-1 and RNF128, RNF130 or RNF167 and PD-L1 and RNF43, RNF128 or RNF130” (see Example 3, p. 73, lines 1-14 and Figure 6 A-D). In the final working example, a Snorkel tag, which “is composed of a transmembrane domain (TMD) flanked by a linker region and two epitope tags”, was fused to the “multipsan receptor CMTM6” (see Example 4, p. 74, lines 5-26). Again, Alpha-Myc tags were attached to the E3 ligases and E6-Flag tags were attached to the targets. Treatment with the bi-VHH resulted in the removal of CMTM6 from the surface when paired with RNF43 “and to a lesser extent, RNF128”. Claims 1-20 are drawn to screening methods, thus, it is understood that not all combinations will be effective; indeed, the specification discloses this (see, for example, p. 73, lines 13-14). Nevertheless, given the recognized importance of the formation of the ternary complex between the E3 ligases and target proteins for degradation to be successful and guidance provided in the instant specification and art, the claims are not enabled for a screening method in which the proteins share as little as 60% identity with their wild-type counterparts.
Claim 21 recites a method for producing a heterobifunctional molecule in which a first domain binds to an extracellular portion of a transmembrane E3 ubiquitin ligase and a second domain binds to an extracellular portion of a transmembrane protein, and wherein the transmembrane E3 ligase and the transmembrane protein are an effective combination as determined by the method of claim 1. Thus, claim 21 requires that an effective combination has been determined and bases the method of producing the heterobifunctional molecule on this determined combination. The skilled artisan does not know how to make a heterobifunctional molecule that binds an extracellular portion of a transmembrane E3 ubiquitin ligase and an extracellular portion of a transmembrane protein, wherein said combination is not yet recited or identified. Rather, this represents a claim to a future invention based upon the currently disclosed screening method. However, patent protection is granted in return for an enabling disclosure, not for vague intimations of general ideas that may or may not be patentable. Tossing out the mere germ of an idea does not constitute an enabling disclosure. Reasonable detail must be provided in order to enable members of the public to understand and carry out the invention. See Genentech v. Novo Nordick A/S (CAFC) 42 USPQ2d 1001 (1997).
Due to the large quantity of experimentation necessary to establish which E3 ligases and membrane bound proteins that differ from their respective wild-type counterparts by up to 40% can be used in the recited screening methods as well as a method for producing a heterobifunctional molecule using an undefined E3 ubiquitin ligase-target protein combination, the lack of direction/guidance presented in the specification regarding and the absence of working examples directed to the same, the state of the art, which teaches that in PROTAC technology, the ternary complex that is formed by the E3 ligase and the target protein is extremely important for target degradation, the unpredictability of the effects of mutations and truncations of the proteins involved would have on the screening method, and the breadth of the recited heterobifunctional molecule, undue experimentation would be required of the skilled artisan to make and/or use the claimed invention in its full scope.
Written Description
Claims 1-21 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claims contain subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. This is a written description rejection.
The instant claims are drawn to a screening method for identifying an effective combination of a transmembrane E3 ubiquitin ligase and a membrane bound-protein, and encompasses a genus of heterobifunctional molecules which specifically bind to the E3 ubiquitin ligase and the membrane-bound protein. To support such heterobifunctional molecules, the instant specification discloses several working examples that employ a single a heterobifunctional molecule, a bi-VHH (bispecific nanobody), VHH Alpha - (G4S)3 - VHH E6, in which the first binding domain is an anti-Alpha VHH and the second binding domain is an anti-E6 VHH (see pages 71-72). The examples show that the Alpha and E6 epitope targets for the heterobifunctional molecule were recombinantly fused to a transmembrane E3 ubiquitin ligase and a transmembrane protein, respectively (e.g. see Example 1, pages 70-72). Therefore, based on the content of the disclosure, the VHH Alpha - (G4S)3 - VHH E6 heterobifunctional molecule binds non-native epitope tags on the membrane-bound proteins (targets) and not the targets themselves. Thus, the claimed genus of heterobifunctional molecules that bind an extracellular portion of a transmembrane E3 ubiquitin ligase and an extracellular portion of a membrane-bound protein do not have sufficient written description. Further, none of the claims at issue recite any structural limitations specific to the heterobifunctional molecules, such as specific CDR or VH and VL amino sequences.
The “heterobifunctional molecule” is defined broadly to be any molecule comprising two different functional binding domains having “a first functional binding domain for binding a transmembrane E3 ubiquitin ligase and a separate second functional binding domain for binding a second molecule…wherein the second molecule is not the same molecule, i.e. not the same transmembrane E3 ubiquitin ligase” (see p. 7, lines 19-26). There is insufficient written description encompassing any “heterobifunctional molecule” which specifically binds to a transmembrane E3 ubiquitin ligase and to a transmembrane protein. The “heterobifunctional molecules” encompass distinct and diverse structures and do not encompass common structural elements essential to the common utility of bi-specific binding to a transmembrane E3 ubiquitin ligase and to a transmembrane protein.
It is noted that the applicant has claimed a genus of heterobifunctional molecules that bind to a transmembrane E3 ubiquitin ligase and to a transmembrane protein to be used in a screening assay for targeted protein degradation. However, claim 1 does not indicate any specific structure for the genus of heterobifunctional molecules, nor does it indicate any specific species of transmembrane E3 ubiquitin ligase or transmembrane protein that the heterobifunctional molecule would bind nor where upon them it would bind. Claim 3 recites a list of possible transmembrane E3 ubiquitin ligases. Claims 4 and 13 encompass transmembrane E3 ubiquitin ligases comprising a first extracellular non-native epitope tag to which the first binding domain of the heterobifunctional molecule binds and the membrane-bound protein comprises a second extracellular non-native epitope tag, to which the second binding domain of the heterobifunctional molecule binds. Claim 5 recites the first and second non-native epitope tags are different and claim 6 recites that the first and or second tag may be either an Alpha or an E6 tag.
Nevertheless, knowledge of a given antigen (e.g., a transmembrane E3 ubiquitin ligase) provides no information concerning the sequence/structure of antibodies that bind the given antigen. It is well established in the art that the formation of an intact antigen-binding site generally requires the association of the complete heavy and light chain variable regions of a given antibody, each of which consists of three CDRs which provide the majority of the contact residues for the binding of the antibody to its target epitope. The amino acid sequences and conformations of each of the heavy and light chain CDRs are critical in maintaining the antigen binding specificity and affinity which is characteristic of the parent immunoglobulin. Townsend et al. (Frontiers in Immunology, 2016; 7: 388) teach “[v]ariability in the antigen binding site is achieved by V(D)J recombination via heavy and light chain pairing”, with the “most diverse” regions being the 6 CDR regions in the heavy and light chains. While the heavy chain is the most diverse, light chains are also important for binding specificity of antibodies, swapping light chains can “change the antigen specificity of the antibody” (see paragraph bridging pages 1-2). In addition, the light chain repertoire is extremely diverse, being encoded by kappa and lambda gene segments, each with different V and J genes (see Townsend, p. 2, left column, 1st two paragraphs; p. 4, right column, 1st paragraph). See also Janeway et al. (Chapter 4-The generation of diversity in immunoglobulins in Immunobiology: The Immune system in health and disease, 5th edition, New York, Garland Science, 2001), which teaches that the “antibody repertoire in humans is at least 1011”, with a large degree of diversity in both heavy and light chains (see 1st paragraph). Furthermore, the diversity of the immunoglobulin repertoire is mediated in part by different combinations of heavy and light chain V regions that pair to form a unique antibody binding site. See, for example, Rabia et al. (Biochem. Engin. J. 137, 365-374, 2018), which teaches that “the maximal chemical diversity of antibody CDRs is unimaginably large…[and] it is extremely challenging to define the sequence determinant of antibody specificity” (see p. 368 left column, 4th paragraph).
As such, it is not possible to predict the sequence/structure of an antibody that binds a given antigen, much less a heterobifunctional molecule that encompasses any or all molecules so long as it binds a transmembrane E3 ubiquitin ligase and a membrane-bound protein, as there does not appear to be any common or core structure present within all antibodies that gives rise to the function of antigen binding. It is noted that the specification does not appear to discuss any specific heterobifunctional molecules that bind to a transmembrane E3 ubiquitin ligase and to a membrane-bound protein that are found in the prior art or that were synthesized by applicant in the instant specification. Rather the specification discloses the bi-specific antibody, VHH Alpha - (G4S)3 - VHH E6, that binds to epitope tags that have been recombinantly fused to extracellular portions of the transmembrane E3 ubiquitin ligase and the membrane-bound protein, but do not bind to the targets themselves. Such a disclosure does not serve to provide a written description of a heterobifunctional molecule that binds to a transmembrane E3 ubiquitin ligase and to a membrane-bound protein as it does not identify any specific structural features or combination of features which give rise to the function of bispecific binding to a transmembrane E3 ubiquitin ligase and a transmembrane domain. Further, there does not appear to be any reasonable shared structure present in the genus of recited “heterobifunctional molecules” which gives rise to their functional activity. As such, the instant specification appears to disclose applicant’s wish for heterobifunctional molecules that bind to a transmembrane E3 ubiquitin ligase and to a transmembrane protein without informing artisans what such heterobifunctional molecules actually are.
Ultimately, identifying an antibody simply on the basis of what it binds rather than by identifying the sequence/structure of the antibody in question is generally insufficient to provide written description of the antibody in question. Therefore, in view of the generic nature of the instant specification, artisans would reasonably conclude that applicant was not in possession of the entire genus of heterobifunctional molecules that bind to the extracellular portions of a transmembrane E3 ubiquitin ligase and a membrane-bound protein at the time the instant application was filed.
Notice for all US Patent Applications filed on or after March 16, 2013: 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.
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.
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 1-3, 8, 11, 15-17 and 20 are rejected under 35 U.S.C. 103 as being unpatentable over Throsby et al. (WO2017069628—on IDS filed 11/21/2022) in view of Riching et al. (ACS Chem Biol. 2018; 13: 2758-2770) and Bondeson et al. (Cell Chemical Biology, 2018, 25, 78-87—on IDS 11/21/2022). The first factor to consider when making a rejection under 35 U.S.C. 103(a) is to determine the scope and contents of the prior art. Throsby et al. teach an in vitro cell culture system comprising a cell that expresses a membrane associated member of the epidermal growth factor receptor (EGFR) family, a membrane associated member of the WNT pathway and a bispecific antibody (p. 31, lines 1-18; claims 1-10 and 16). Throsby et al. teach further that the EGFR family member is Erbb-1 or Erbb-3, the membrane associated member of the WNT signaling pathway may be ZNRF3 or RNF43, among others, and the bispecific antibody binds to extracellular parts each of these membrane-bound proteins. Both ZNRF3 (Zinc And Ring Finger 3) and RNF43 (Ring Finger Protein 43) are transmembrane E3 Ubiquitin-Protein Ligases (e.g. see page 28, lines 9-29 of Throsby and colleagues; claim 4). The cell system can be used to detect growth responses of the cell (see claims 1-10 and 16; p. 31, lines 6-19; p. 67, lines 5-24 of Throsby and colleagues). Throsby et al. also teach a bispecific antibody that is a conjugate covalently joined, optionally by a linking region and that the bispecific antibody may also be a single domain antibody (i.e., a nanobody; see p. 10, lines 25-26; p. 11, lines 31-32; p. 23, lines 6-25).
Regarding instant claims 16 (the cell overexpresses the transmembrane E3 ubiquitin ligase or the membrane bound protein) and 17 (the cell expresses the transmembrane E3 ubiquitin ligase or the membrane bound protein at endogenous levels), Throsby et al. teach how to express the proteins on cells (see pages 95-97), thus those having ordinary skill in the art could choose to modulate the expression levels based on how robust a result they wish to induce and measure. For instance, overexpression could lead to more robust and easily detectable changes while endogenous expression more closely mimics the physiological cellular architecture.
The second factor to consider is to ascertain the differences between the prior art and the instant claims. Throsby et al. do not explicitly teach determining the surface level of the membrane-bound protein after the binding of the bispecific antibody, although they do exemplify the cell system being used to detect growth responses after bispecific antibody binding and in which an LGR5xEGFR bispecific antibody inhibited cell growth (see p. 145, lines 5-32). Riching et al. teach an “innovative, modular live cell platform” to screen proteolysis-targeting chimeras (PROTACs), which are bifunctional molecules, for their ability to “[target] proteins for degradation through recruitment to E3 ligases”, namely, VHL- and CRBN (see abstract; p. 2758, left column; p. 2759, paragraph bridging left and right columns). In addition, Bondeson et al. teach that there is “a strong correlation between [target] proteins that stably [interact] with VHL [an E3 ubiquitin ligase] and those that are degraded” and that “degradation potency” of a given protein depends on the ability of said protein to “form a stable ternary complex with the PROTAC [e.g., a bispecific antibody] and the recruited E3 ubiquitin ligase” (see p. 82, left column; p. 83, right column, last paragraph). It would have been obvious to the person of ordinary skill in the art at the time the invention was made to modify the in vitro cell culture system comprising a cell that expresses the ZNRF/EGFR or RNF43/EGFR combination as taught in Throsby et al. in order to determine the effectiveness of membrane protein degradation in response to bispecific antibody binding because Riching et al. teach that bispecific antibodies such as PROTACs “induce [target protein] degradation by simultaneously binding the target protein and the E3 ligase complex proteins, bringing the target protein into proximity for ubiquitination and targeting it for degradation through the UPS [ubiquitin proteasomal system]” (see p. 2758, 1st paragraph). In addition, the person having ordinary skill in the art would have recognized that UPS-based target protein degradation is correlated with a strong interaction (i.e., effective combination) between the E3 ligase and the target protein (see Bondeson and colleagues).
The person having ordinary skill in the art would have been motivated to use membrane-bound protein degradation to measure the bispecific antibody binding to transmembrane E3 ubiquitin ligase and a membrane-bound protein to induce protein degradation because Riching et al. teach targeting oncogenic proteins for degradation is a key goal in cancer treatment (see p. 2758, left column, 1st paragraph). Further, while Riching et al. teach cytoplasmic E3 ligases, they also teach that “active research efforts are underway to identify other efficacious E3 ligase components to serve as recruiters [which] will result in an expansion of options in the future, directly translating to increased chemical development and furthering the need for robust and relevant technologies to efficiently profile and triage PROTAC cellular activity” (see paragraph bridging pages 2764-2765). Thus, there was a motivation in the art to expand PROTAC assays to utilize other E3 ligases.
There is also a general motivation in the art to screen for combinations that could be useful in the treatment of cancer (see abstract of Throsby and colleagues). Throsby et al. provide an in vitro cellular platform expressing a transmembrane E3 ligase and membrane bound protein that screens the effectiveness of bispecific antibodies in inhibiting cancer growth, and Riching et al. teach an in vitro cellular platform expressing a cytoplasmic E3 ligase and membrane bound protein that screens the effectiveness of bispecific antibodies in promoting membrane bound protein degradation. As noted by the United States Supreme Court, if a person of ordinary skill can implement a predictable variation, §103 likely bars its patentability. For the same reason, if a technique has been used to improve one method (i.e., measuring a membrane-bound protein decrease), and a person of ordinary skill would recognize that it would improve similar methods (i.e., determining the effectiveness of the transmembrane E3 ubiquitin ligase-membrane bound protein combination) in the same way, using the technique is obvious unless its actual application is beyond his or her skill (KSR, 127 S. Ct. at 1740). “When there is a design need or market pressure to solve a problem and there are a finite number of identified, predictable solutions, a person of ordinary skill has good reason to pursue the known options within his or her technical grasp. If this leads to the anticipated success, it is likely the product is not of innovation but of ordinary skill and common sense. In that instance the fact that a combination was obvious to try might show it was obvious under 35 U.S.C. 103.” KSR Int'l Co. v. Teleflex Inc., 127 S. Ct. 1727, 1742, 82USPQ2d 1385, 1396 (2007). Finally, the person having ordinary skill in the art could have expected success, not only because the prior art provides a nexus between protein degradation and the formation of an effective E3 ubiquitin ligase-protein ternary complex, but also because measuring protein down-regulation is a straightforward, uncomplicated assay.
Thus, the claims do not contribute anything non-obvious over the prior art.
Conclusion
No claim is allowed.
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. Pillow et al. (WO 2017/201449—on IDS filed 11/21/2022) teach “antibody-PROTAC conjugates (PACs”—see abstract). See also p. 3, lines 23-28 of Pillow et al.:
[T]he subject matter described herein is directed to PROTAC-antibody conjugate (PAC) compositions that result in the ubiquitination of a target protein and subsequent degradation of the protein. The compositions comprise an antibody covalently linked to a linker (LI), which is covalently linked at any available point of attachment to a PROTAC, in which the PROTAC comprises an E3 ubiquitin ligase binding (E3LB) moiety, wherein the E3LB moiety recognizes a E3 ubiquitin ligase protein and a protein binding moiety (PB) that recognizes a target protein.
In addition, Cong et al. (WO2013054307) teach an isolated antibody or antigen binding fragment thereof that specifically binds to the extracellular domain of a transmembrane E3 ubiquitin ligase, wherein: (a) the transmembrane E3 ubiquitin ligase is selected from the group consisting of ZNRF3 and RNF43; and (b) binding of the antibody to the extracellular domain of the transmembrane E3 ubiquitin ligase, wherein the transmembrane E3 ubiquitin ligase is on the surface of a eukaryotic cell, increases Wnt signaling in the eukaryotic cell (claim 1).
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/CHRISTINA M BORGEEST/Primary Examiner, Art Unit 1675