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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 1/29/2026 has been entered.
Applicant's arguments filed 1/29/2026 have been fully considered but they are not persuasive.
Claims 2-4, 6, 8-10, 13, and 15-16 have been cancelled. Claims 17-22 have been newly added. Claims 1, 5, 7, 11-12, 14, and 17-22 are under consideration.
As set forth in the final Office action, dependent claims 5 and 11 are considered to be limited to the Fab antibody fragment embodiments of claims 1 and 7, respectively, in view of the recitation “Chothia numbering of the Fab domains.”
Claim 12 remains allowable for reasons of record.
Basis is seen for a cyclic peptide of 5-20 amino acids in paragraph [0020]. See new claims 17 and 20. Basis is seen for a cyclic peptide of 4 amino acids in paragraph [0024]. See claims 1 and 7.
Basis is seen for a cyclic peptide of 14 amino acids in SEQ ID NOS: 5 and 53. See claim 12 and new claims 19 and 22.
Basis is seen for a cyclic peptide of 15 amino acids in SEQ ID NO: 35. See claim 12 as and new claims 19 and 22.
Claim Objections
Applicant is advised that should claim 1 be found allowable, claim 14 will be objected to under 37 CFR 1.75 as being a substantial duplicate thereof. When two claims in an application are duplicates or else are so close in content that they both cover the same thing, despite a slight difference in wording, it is proper after allowing one claim to object to the other as being a substantial duplicate of the allowed claim. See MPEP § 608.01(m).
Claims 1 and 14 are directed to artificial proteins of the same scope.
Claim Rejections - 35 USC § 112
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.
Claims 1, 5, 7, 11, 14, and 17-22 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. This is a new matter rejection.
Independent claim 1 as currently amended recites:
An artificial protein comprising a peptide, which said peptide is a linearized form of a cyclic peptide that has 4 to 20 amino acids, was cyclized via thioether binding, and was obtained via Random non-standard Peptides Integrated Discovery (RaPID) and was thereby screened as a molecule bound to a desired target molecule, said peptide is fused to an antibody or a Fab antibody fragment having a given antigen-binding activity, wherein the peptide is exposed on a surface of the antibody or the Fab antibody fragment and is fused within the AB loop (CH1), CD loop (CH1), EF loop (CH1), AB loop (VH), C"D loop (VH), EF loop (VH), DE loop (CH1), FG loop (CH1), CC' loop (VH), AB loop (CL), CD loop (CL), EF loop (CL), AB loop (VL), C"D loop (VL), EF loop (VL), DE loop (CL), FG loop (CL), CC' loop (VL), GA loop (VH-CH1), or GA loop (VL-CL) of the antibody or the Fab antibody fragment, and wherein the artificial protein retains the given antigen-binding activity of the antibody or the Fab antibody fragment and exhibits the given binding activity of the cyclic peptide.
Independent claim 7 as currently amended recites:
A method of producing an artificial protein comprising an antibody or a Fab antibody fragment with a peptide presented on the surface of the antibody or the Fab antibody fragment, which comprises
fusing the peptide to the antibody or the Fab antibody fragment within a site that is the AB loop (CH1), CD loop (CH1), EF loop (CH1), AB loop (VH), C"D loop (VH), EF loop (VH), DE loop (CH1), FG loop (CH1), CC' loop (VH), AB loop (CL), CD loop (CL), EF loop (CL), AB loop (VL), C"D loop (VL), EF loop (VL), DE loop (CL), FG loop (CL), CC' loop (VL), GA loop (VH-CH1), or GA loop (VL-CL) of the antibody or the Fab antibody fragment which has a given antigen-binding activity, wherein the peptide is a linearized form of a cyclic peptide that has 4 to 20 amino acids, was cyclized via thioether binding, and was obtained via Random non-standard Peptides Integrated Discovery (RaPID) and was thereby screened as a molecule bound to a desired target molecule,
wherein the artificial protein retains the antigen-binding activity of the antibody or the Fab antibody fragment and exhibits the given biological binding activity of the cyclic peptide.
Claim 14 is not an original claim and was added by amendment on 6/27/2025.
Claims 17-22 are not original claims and were added by amendment on 1/29/2026.
While the specification discloses the name “RaPID method” in paragraph [0023], this paragraph does not spell out the name Random non-standard Peptides Integrated Discovery (RaPID). The acronym in paragraph [0023] is not identified as corresponding to this method.
Disclosure of the name or acronym RaPID and this paragraph do not provide basis for the screening limitations now set forth in the claims. There is no disclosure in the specification concerning the nature of this method or reference to any document disclosing anything about the method. Screening for binding to a desired target molecule is not disclosed anywhere in the specification. To the degree that applicant is attempting to incorporate information about method steps by reference to an uncited reference, applicant may not do so. Applicant may not add limitations to the claims without support within the specification.
In the 11/28/2025 after final response applicant submitted Bashiruddin (2015), Hayashi (2012), Jongkees (2017), Kawamura (2017), Yamagishi (2011), Hipolito (2012) and Cardote (2016). The instant specification does not reference any of Bashiruddin (2015), Hayashi (2012), Jongkees (2017), Kawamura (2017), Yamagishi (2011), Hipolito (2012) and Cardote (2016). None of these references are incorporated by reference to provide description of what applicant intended.
As set forth in the Advisory Action mailed 12/5/2025, Jongkees, Kawamura, and Cardote describe using a RaPID system/methodology without providing an overview of the features of this system/methodology. Yamagishi describes a RaPID system/methodology See at least Figure 1B. Hipolito describes a RaPID system/methodology referencing Yamagishi (reference 35). See at least Figure 4A and its legend on the bottom of page 201. Bashiruddin describes a RaPID system/methodology. See at least Figure 3. Hayashi describes a RaPID system/methodology. See at least Figure 1B. However, these various RaPID system/methodology overviews are not identical in their details and explanations. For example, Hayashi discloses using full length Akt2 protein and Ni²⁺-NTA magnetic beads. In contrast, Yamagishi discloses using biotin-Avidin(His)₆-GB1- HECT immobilized on streptavidin magnetic beads (SAvB). Bashiruddin discloses magnetic beads generally and counter selection. Hipolito discloses bead-bound target protein. Other differences exist.
Applicant has not established that the disclosure of “RaPID method” in paragraph [0023] would have conveyed to one of ordinary skill in the art at the time of the effective filing date a single, specific, art understood method having particular steps, particularly the screening limitations in claims 1 and 7. Applicant’s response does not address the differences in the methods of the prior art.
The specification provides insufficient information with respect to any method steps. The instant specification does not clearly identify what the “RaPID method” is and the prior art discloses different methods having the same acronym.
Claim 14 as amended 11/29/2025 now depends upon claim 7. As there is no basis for claim 7, there can be no basis for an artificial protein made by the method according to claim 7.
With respect to new claims 18 and 21, the specification does not disclose the range of 14-20 amino acids.
The claims constitute new matter.
In addition, even if there was basis for the claims, the claims would still lack adequate written description for the claimed products and methods. Claim 1 and its dependent claims are directed to products where the peptide portion of the product must be identified before fusing it to an antibody or a Fab fragment as recited in claim 1. Claim 7 is directed to a method of making the artificial protein product. Claim 14 is a product produced by the method of claim 7. It is a reach through claim. The peptide’s structure and characteristics are unknown beyond that it is of a certain size and must bind something unspecified. These peptides must be identified by a method that is not adequately described in the specification. The artificial protein product cannot be made without knowing what these peptides are. Applicant is particularly referred to University of Rochester V. G.D. Searle & Co., 358 F3d 916, 69 USPQ2d 1886 (Fed. Cir. 2004) and MPEP 2163(II)(3)(a) with respect to reach through claims.
The structures of the peptides required by the claims are not adequately described. The specification exemplifies three peptides (SEQ ID NOS: 5, 35, and 53; see claim 12) having the properties recited in the claims when fused to an antibody or a Fab antibody fragment as recited in claims 1 and 7 and the structural variability of the artificial proteins containing the structurally variable peptides is large. In addition, the specification does not identify any of peptides according to any RaPID method as recited in claims 1 and 7. No reasonable structure-function correlation has been established that is commensurate in scope with the claims. The specification does not describe representative examples to support the full scope of the claims. In particular, the only exemplified artificial proteins inserted linear peptides of 14 or 15 amino acids (SEQ ID NOS: 5, 35, and 53) which is not representative of fusing the smallest peptides (i.e.. 4 amino acids) or the largest peptides (i.e. 20 amino acids) where the resulting artificial protein retains the binding activity of the parent cyclic peptide as well as the binding activity of the antibody or Fab antibody fragment antigen-binding activity.
The claimed artificial proteins and methods of making them lack adequate written description.
Claim 1, 5, 7, 11, 14, and 17-22 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 enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
As set forth above, the specification does not adequately describe the RaPID method recited in the claims and thus does not enable this method. As set forth above, the instant specification does not incorporate by reference any documents with respect to this method.
The specification provides no examples of obtaining a cyclic peptide using the RaPID method where the cyclic peptide was screened as a molecule bound to a desired target molecule, where the cyclic peptide is then linearized for use in the product of claim 1 or method of claim 7. There is no direction or guidance provided for how to use the RaPID method in the context of the instant claims as the specification discloses no steps for this method, particularly screening steps.
Because the specification does not adequately describe “RaPID” and provide specific steps to perform, the claims are not enabled. It is unknown from the specification what steps to perform and what reagents to use. Note that none of the examples in the specification use any RaPID method or part thereof as set forth in the references provided by applicant. Puromycin conjugation is not performed. Magnetic beads are not used. Repeated cycles are not disclosed. The examples do not use DNA libraries, cDNA libraries, or mRNA libraries. These elements are not disclosed in the specification.
The claims are not enabled.
Applicant’s arguments regarding the RaPID method are unpersuasive for the reasons set forth above.
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, 5, 7, 11, 14, and 15-17 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.
Independent claims 1 and 7 recite “obtained via Random non-standard Peptides Integrated Discovery (RaPID) and was thereby screened as a molecule bound to a desired target molecule” Because the specification does not adequately describe RaPID and the particular steps and reagents intended, the metes and bounds of the claim cannot be determined.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MARIANNE P ALLEN whose telephone number is (571)272-0712. The examiner can normally be reached 7:00-3:30 EST Monday-Friday.
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/Marianne P Allen/Primary Examiner, Art Unit 1647
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