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 Group II and SEQ ID NO:1 in the reply filed on 05/05/2026 is acknowledged.
Claims 1, 2, and 33 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention and species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 05/05/2026.
Status of Claims
Claims 3, 5-12, 21, 25, 29-30, 32, 35-42 were previously cancelled, in the amendment filed 12/18/2023. Claims 1, 2, 4, 13-20, 22-24, 26-28, 31, and 33-34 are pending. Claims 1, 2, and 33 are withdrawn. Claims 4, 13-20, 22-24, 26-28, 31, and 34 will be examined on the merits.
Information Disclosure Statement
The Information Disclosure Statement filed on 05/13/2024 has been considered. Signed copies are enclosed.
Claim Objections
Claims 4 and 23 are objected to because of the following informalities:
Claim 4 has three methods in one claim. While most of the steps for these methods are the same, step IV, specifically, appears to correlate the final step with the method being used. For clarity, Examiner suggests splitting claim 4 into three separate claims: Claim 4 remains a method for detecting modulator-dependent interaction(s) between an E3 ligase and one or more target(s), Claim 43 is a method of validating a predicted modulator-dependent interaction between an E3 ligase and target(s), and claim 44 is a method of identifying E3 ligase(s) that interact with target(s) in a modulator-dependent manner or not. Each method may recite the same steps I, II, and III, but the optional steps 1), 2), and 3) in step IV will be split into their individual claims: IV) 1) into claim 4 as step IV, IV) 2) into claim 43 as step IV, and IV) 3) into claim 44 as step IV). This will help clarify that the steps I, II option 1) and/or option 2), III, and IV are required in each claim. As currently recited, the numbering appears inconsistent, and it is confusing which steps are optional and which are required. For example, one would not use step IV), option 2) (validating), if performing the method of detecting. For the purposes of applying prior art, examiner is interpreting steps I, II, III, IV, and sub-steps a, b, c, and d are required, and steps labeled 1, 2, 3 as options to select from.
Claim 23 recites a list, which is missing commas after several options (specifically, DCAF16 and RNF4, as noticed by the Examiner). Please correct for consistency in the delineation of the list, so the list does not become indefinite.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
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 13 and 34 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.
Claim 13 recites the limitation "the target" in line 4 and 12. There is insufficient antecedent basis for this limitation in the claim. Claim 13 does not recite “a target” or any similar term earlier in the claim, and claim 13 is independent of all other claims.
Claim 34 recites “the modulator is a compound selected from those in Table 4 and Table 5.” Claims should be complete in themselves and not refer to external figures or tables. See MPEP §2173.05(s). Therefore, claim 34 is indefinite.
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.
Claim 13 is 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 claim(s) contains 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.
The instant claim is drawn to a method for identifying non-canonical E3 ligase substrate receptor binding sites, comprising the steps of (I) providing and incubating cells and a modulator and detecting labeled proteins, (II) providing and incubating cells and a negative control for the modulator and detecting labeled proteins, (III) comparing the presence and/or amount of labeled target(s), from step I to those in step II; and (IV) identifying non-canonical E3 binding sites that interact with a modulator and/or target based on the comparing of step III. Claim 13 has no dependent claims further modifying this method.
The recited steps in instant claim 13 do not describe a method of identifying binding sites. Steps (I) and (II) recite labeling proteins in the presence or absence of a modulator and detecting the presence of labeled proteins or the amount of labeled proteins. Steps (III) and (IV) disclose the comparison of the presence or the amount of labeled proteins found in steps (I) and (II). The presence of a labeled protein is simply a ‘yes’ or ‘no’ qualification. The amount of a protein is how much labeled protein there is. These parameters do not account for where the protein is labeled, or how the protein is labeled, or any other measure by which one might account for where the E3 ligase substrate receptor has bound. There is no parameter provided in any of steps I-IV wherein one would be reasonably be able to discern any binding site, let alone a non-canonical E3 ligase substrate receptor binding site.
The specification also does not provide any method of identifying non-canonical E3 ligase substrate receptor binding sites. The same steps as instant claim 13 are recited on page 6, second paragraph, with no further limitations, steps, or context provided. No working examples of this method are provided and no non-canonical binding site is identified in the specification from previous examples. Therefore, the specification does not support that this claimed method is a method capable of identifying non-canonical E3 ligase substrate receptor binding sites.
Taken together, no person of any skill level would be able to use the recited steps in order to identify a non-canonical binding site. Therefore, the method of claim 13 does not have sufficient written description support for a method of identifying non-canonical E3 ligase substrate receptor binding sites.
Claims 23, 24, and 26 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 claim(s) contains 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.
The instant claim 23 is drawn to a list of E3 ligase substrate receptors that may be investigated with the method of claim 4, and “an enzymatically active portion or variant of any one of the foregoing E3 ligase substrate receptors.” Claim 24 depends from claim 4 and recites that “the E3 ligase substrate receptor and/or the E3 ligase substrate receptor that does not bind the modulator at a canonical binding site has an amino acid sequence of at least 95% identity to CRBN (SEQ ID NO: 4).” Claim 26 depends from claim 24 and recites “wherein the E3 ligase that does not bind the modulator at canonical binding site comprises mutations Y384A and W386A”.
The specification provides the following definition on page 11, paragraph 2: an "enzymatically active portion" of an E3 ligase is one that retains the ability to ubiquitinate protein(s), e.g., to form an E3 ubiquitin ligase complex able to ubiquitinate protein(s).” Additionally, the specification recites that “the percent identity between the two sequences is a function of the number of identical positions shared by the sequences…”, and discloses that identity can be determined by methods known in the art (see page 28). The specification does not give a specific definition for the term ‘variant’, reciting only “in some embodiments, the fusion protein(s)… are at least 80%, e.g., at least 85%, 90%, 95%, 98%, or 100% identical to the amino acid sequence of an exemplary sequence (e.g., as described herein)” and “in preferred embodiments, the variant retains desired activity of the parent” (see pages 27-28). The recitation of the preferred embodiment indicates that there are embodiments wherein the variant does not have the activity of the parent.
Taken together, the specification does not provide support for the full scope of claim 23, 24, or 26. Claim 23 has written description support for the E3 ligase substrate receptor being any of the recited SEQ ID NOs or “an enzymatically active portion of any one of the foregoing E3 ligase substrate receptors”, as the specification provides a definition for ‘an enzymatically active portion’ that requires the receptor to retain its specific function. No such definition is provided for ‘variant’, and therefore there is no requirement that a “variant of any one of the foregoing E3 ligase substrate receptors” retains the function of the parent. The specification allows for up to 20% variation in the sequence of a variant as compared to the parent, and does not provide any limitation to the 20% variation that would require the function of the protein to be retained. Therefore, the method of claim 4 performed with “a variant of any one of the foregoing E3 ligase substrate receptors” lacks written description support. Claim 24 has written description support for a protein with amino acid sequence of SEQ ID NO: 4. However, for the reasons articulated above, claim 24 does not have written description support for a protein with “an amino acid sequence of at least 95% identity to CRBN (SEQ ID NO:4).” Similarly, claim 26 has support for a protein with SEQ ID NO:4 and mutations Y384A and W386A, but not a protein with “an amino acid sequence of at least 95% identity to CRBN (SEQ ID NO:4), wherein the E3 ligase….comprises mutations Y384A and W386A.”
Vas-Cath Inc. v. Mahurkar, 19 USPQ2d 1111, makes clear that "applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the 'written description' inquiry, whatever is now claimed." (See page 1117.) The specification does not "clearly allow persons of ordinary skill in the art to recognize that [he or she] invented what is claimed." (See Vas-Cath at page 1116.)
To fulfill the written description requirements set forth under 35 U.S.C. 112(a), the specification must describe at least a substantial number of the members of the claimed genus, or alternatively describe a representative member of the claimed genus, which shares a particularly defining feature common to at least a substantial number of the members of the claimed genus, which would enable the skilled artisan to immediately recognize and distinguish its members from others, so as to reasonably convey to the skilled artisan that Applicant has possession of the claimed invention. To adequately describe the genus of proteins, Applicant must adequately describe which combination of residues are required for the claimed function; i.e., “the ability to ubiquitinate protein(s)”. The instant specification, however, does not disclose distinguishing and identifying features of a representative number of members of the genus of E3 ligase substrate receptors so that the skilled artisan could immediately envision, or recognize, at least a substantial number of members of the claimed genus of E3 ligases. The specification fails to disclose which amino acids might be added, replaced or deleted within the 80% sequence identity requirement so that the resultant protein retains the function of its parent, or by which other amino acids the essential amino acids might be replaced so that the resultant protein retains the function of its parent. Therefore, the specification fails to adequately describe at least a substantial number of members of the genus of E3 ligase substrate receptors to which the claims refer; and accordingly, the specification fails to adequately describe at least a substantial number of members of the claimed genus of proteins.
As evidenced by the teachings of Skolnick et al., the art is unpredictable. Skolnick et al. (Trends in Biotechnology (2000) 18:34-39) discloses the skilled artisan is well aware that assigning functional activities for any particular protein or protein family based upon sequence homology is inaccurate, in part because of the multifunctional nature of proteins (see, e.g., the abstract; and page 34, Sequence-based approaches to function prediction). Even in situations where there is some confidence of a similar overall structure between two proteins, only experimental research can confirm the artisan's best guess as to the function of the structurally related protein (see, in particular, the abstract and Box 2). Thus, one skilled in the art would not accept the assertion, which is based only upon an observed similarity in amino acid sequence that a variant of a given polypeptide would necessarily retain a given function.
Overall, based on the disclosure, the state of the art at the time of filing, a skilled artesian would have recognized that the applicant was not in possession of the claimed invention at the time of filing. Consequently, in accordance with the MPEP, only the sequences recited in claims 23 and 24, but not the full breadth of claims 23 and 24 regarding any amino acid sequence having at least 80% sequence identity to these SEQ ID NOs, meets the written description provision of 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph.
Applicant is reminded that Vas- Cath makes clear that the written description provision of 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, is severable from its enablement provision. (See page 1115).
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 4, 13-20, 22-24, 27-28, and 31 are rejected under 35 U.S.C. 102(a)(1) and (a)(2) as being anticipated by WO 2021/074414, Winter et al., published 04/22/2021, as evidenced by Genbank Accession NO. NP-057386 and Branon et al., Nat Biotechnol 36, 880–887 (2018).
The instant claims are drawn to a method of detecting modulator-dependent interactions between an E3 ligase and one or more targets, comprising the steps of providing cells expressing a fusion protein comprising an E3 ligase substrate receptor and a proximity labeling enzyme and a modulator, incubating them together, and detecting what proteins were labeled, as well as repeating this process with a negative control for the modulator, or with a mutated E3 ligase substrate receptor unable to bind the modulator as a negative control, and comparing the labeled proteins to determine which proteins were labeled in a modulator-dependent manner (claims 4 and 13). Dependent claims refine the negative control (DMSO, claim 14), conditions for incubating as requiring the labeling substrate, or biotin (claims 15-16), and a proteasome inhibitor such as MG-132 (claims 17 and 18), the method of detecting labeled proteins (Western blot or mass spectrometry, claim 19), and the modulator itself (claim 34). Claims 23-26 provide options for the E3 ligase substrate receptor, and claims 27-28 provide options for the labeling enzyme. Claim 31 recites a SEQ ID NO: 1 for the fusion protein, comprising SEQ ID NO: 4 (CBRN) and SEQ ID NO: 18 (TurboID).
Winter et al. teach assessing the modulator-induced association of the E3 ligase complex via proximity labeling with TurboID using a vehicle control of DMSO for the modulator (page 119, 121) and comparing the two conditions, thereby teaching the method of claim 4. Fusion proteins comprising a component of an E3 ligase complex and a TurboID biotin ligase were expressed in cells incubated with a modulator compound or vehicle (DMSO) control in conditions including Carfilzomib treatment and a 30 minute biotin labeling pulse, teaching instant claims 14-18. Labeled proteins were quantified via Western blot (see page 122), teaching instant claim 19. The quantifications in the presence vs absence of the modulator were calculated and are displayed in tables 4-6, showing proteins with >1.5 fold change, teaching claims 20 and 22. The biotin ligase as TurboID, or mTurbo, teaches claims 27 and 28. Winter et al. teach that the fusion protein comprises a member of the E3 ligase complex, which may be a substrate receptor, on page 35, which also discloses that the substrate receptor may be CRBN or DCAF15.
Additionally, Winter et al. teach an in vivo method for identifying a compound having the ability to degrade one or more proteins, the method comprising contacted both wild type and mutated cells with a compound, wherein the mutated cell has a functional mutation to a member of an E3 ligase complex, wherein the compound is determined to degrade one or more proteins if the level of the one or more proteins is decreased as compared to the mutated cell (see claim 26). The mutant is defined as hypomorphic, which refers to a genetic mutation or allele that causes a partial loss of gene function, resulting in reduced activity or expression compared to the wild-type gene. This teaches a mutant protein that is unable to bind the modulator at the binding site, which can be used as a negative control in a similar experiment, thereby teaching the remaining limitations of claims 4 and 13. Winter also teaches, on page 50, that this mutated protein may be a substrate receptor, such as CRBN or DCAF15.
Winter et al. teach, on page 50, that the CRBN sequence may comprise the sequence of GenBank Accession No. NP-057386. This teaches the limitation of claims 23 and 24 (see attached sequence alignment 1 to SEQ ID NO:4). Winter et al. also teach, on page 119, Branon et al. as the source of the mTurbo protein sequence. Branon et al. disclose the sequence of this protein, which has the sequence of SEQ ID NO:18 (see alignment 2 attached), teaching the limitations of claims 27 and 28. Together, these sequences teach SEQ ID NO:1 (see alignment 3, attached), which anticipates claim 31.
Therefore, Winter et al. anticipate claims 4, 13-20, 22-24, 27-28, and 31.
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 4, 13-20, 22-24, 26-28, 31 and 34 are rejected under 35 U.S.C. 103 as being unpatentable over WO 2021/074414, Winter et al., published 04/22/2021, in view of WO 2021/069705, Flohr et al., published 04/15/2021, EFD 10/09/2019.
The instant claims are drawn to a method of detecting modulator-dependent interactions between an E3 ligase and one or more targets, comprising the steps of providing cells expressing a fusion protein comprising an E3 ligase substrate receptor and a proximity labeling enzyme and a modulator, incubating them together, and detecting what proteins were labeled, as well as repeating this process with a negative control for the modulator, or with a mutated E3 ligase substrate receptor unable to bind the modulator as a negative control, and comparing the labeled proteins to determine which proteins were labeled in a modulator-dependent manner (claims 4 and 13). Dependent claims refine the negative control (DMSO, claim 14), conditions for incubating as requiring the labeling substrate, or biotin (claims 15-16), and a proteasome inhibitor such as MG-132 (claims 17 and 18), the method of detecting labeled proteins (Western blot or mass spectrometry, claim 19), and the modulator itself (claim 34). Claims 23-26 provide options for the E3 ligase substrate receptor, and claims 27-28 provide options for the labeling enzyme. Claim 31 recites a SEQ ID NO: 1 for the fusion protein, comprising SEQ ID NO: 4 (CBRN) and SEQ ID NO: 18 (TurboID).
Winter et al. teach assessing the modulator-induced association of the E3 ligase complex via proximity labeling with TurboID using a vehicle control of DMSO for the modulator (page 119, 121) and comparing the two conditions, thereby teaching the method of claim 4. Fusion proteins comprising a component of an E3 ligase complex and a TurboID biotin ligase were expressed in cells incubated with a modulator compound or vehicle (DMSO) control in conditions including Carfilzomib treatment and a 30 minute biotin labeling pulse, teaching instant claims 14-18. Labeled proteins were quantified via Western blot (see page 122), teaching instant claim 19. The quantifications in the presence vs absence of the modulator were calculated and are displayed in tables 4-6, showing proteins with >1.5 fold change, teaching claims 20 and 22. The biotin ligase as TurboID, or mTurbo, teaches claims 27 and 28. Winter et al. teach that the fusion protein comprises a member of the E3 ligase complex, which may be a substrate receptor, on page 35, which also discloses that the substrate receptor may be CRBN or DCAF15.
Additionally, Winter et al. teach an in vivo method for identifying a compound having the ability to degrade one or more proteins, the method comprising contacted both wild type and mutated cells with a compound, wherein the mutated cell has a functional mutation to a member of an E3 ligase complex, wherein the compound is determined to degrade one or more proteins if the level of the one or more proteins is decreased as compared to the mutated cell (see claim 26). The mutant is defined as hypomorphic, which refers to a genetic mutation or allele that causes a partial loss of gene function, resulting in reduced activity or expression compared to the wild-type gene. This teaches a mutant protein that is unable to bind the modulator at the binding site, which can be used as a negative control in a similar experiment, thereby teaching the remaining limitations of claims 4 and 13.Winter also teaches, on page 50, that this mutated protein may be a substrate receptor, such as CRBN or DCAF15, and may comprise the sequence of GenBank Accession No. NP-057386 or NP-001166953. This teaches the limitation of claims 23 and 24 (see attached sequence alignment to SEQ ID NO:4). Winter et al. also teach, on page 119, Branon et al. as the source of the mTurbo protein sequence. Branon et al. disclose the sequence of this protein, which has the sequence of SEQ ID NO:18 (see alignment 2 attached), teaching the limitations of claims 27 and 28. Together, these sequences teach SEQ ID NO:1 (see alignment 3, attached), teaching claim 31.
Winter et al. do not teach that the modulator is one of those represented in Table 4 or Table 5, as recited in claim 34, or that CRBN comprises a mutation of Y384A and W386A, as in instant claim 26.
Flohr et al. teach compounds that are modulators of CRBN/cereblon activity that are listed in Table 4 and Table 5 (abstract, pg 1-3, claim 1). Flohr et al. also teach a YWAA mutant of CRBN that is unable to bind the compounds disclosed.
It would be obvious, to one of ordinary skill in the art before the effective filing date, to trial the compounds of Flohr et al. via the method of Winter et al., which discloses a method of investigating targets of the CRBN degron, in order to determine how the compounds of Flohr et al. impact the CRBN degron. One would have a reasonable expectation of success as Flohr et al. show these compounds affect CRBN, and Winter et al. disclose a method of determining CRBN targets, as well as modulating this method with a negative control, such as DMSO, or mutant proteins with impeded functionality. As Flohr et al. disclose a mutant unable to bind these modulators, it would be obvious to use this particular mutant as a negative control for these compounds in the method of Winter et al. Therefore, the combination of the method of Winter et al. and the compounds and mutant of Flohr et al. renders obvious instant claims 4, 13-20, 22-24, 26-28, 31, and 34.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Amelia Stephens whose telephone number is (571)272-1006. The examiner can normally be reached M-F 8-5 EST.
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/AMELIA STEPHENS/Examiner, Art Unit 1645
/ANNE M. GUSSOW/Supervisory Patent Examiner, Art Unit 1683
Prosecution Insights