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 .
Objections/Rejections Withdrawn
Rejections and/or objections not reiterated from previous Office Actions are hereby withdrawn. The following rejections and/or objections are either reiterated or newly applied, and constitute the complete set presently being applied to the instant application.
Response to Arguments
Applicant’s arguments, see Pg 2-5, filed 5/21/20265, with respect to the rejection of claims 1-3, 7, and 16-18 under 35 U.S.C. 101 have been fully considered and are persuasive. Specifically, the argument that fava bean raw material, which comprises the full-length fava bean legumin protein, has no effect on S6 phosphorylation, whereas the instant SEQ ID NO: 3 does exhibit the ability to phosphorylate rpS6, as shown in Figure 1C of Cal et al. (cited on the IDS filed 5/21/2026), demonstrates a markedly different characteristic that distinguishes SEQ ID NO: 3 from the full-length, naturally-occurring protein is found persuasive. For these reasons, the rejection of the above claims have been withdrawn.
However, it is noted that the rpS6 phosphorylation activity limitation is not recited in independent claim 12. For this reason, the rejections of claims 12-14 and 19-21 under 35 U.S.C. 101 still stand. Rejection of these claims under this statute could be overcome through amending claim 12 to include the rpS6 phosphorylation activity limitation.
Applicant's arguments filed 5/21/2026 regarding the claim rejections under 35 U.S.C. 102 have been fully considered but they are not persuasive.
Applicant’s position is that the currently amended claim 1 overcomes the limitations of Wong and Kern because it now requires a peptide “consisting of a sequence having 1-3 amino acid alterations compared with SEQ ID NO: 3, wherein the or each amino acid alteration is independently selected from insertion, deletion, and substitution”. However, a peptide consisting of a sequence having 3 insertions compared with SEQ ID NO: 3 would necessarily result in a peptide 13 amino acids in length, which still reads on the peptide taught by Wong as it is also 13 amino acids. For this reason, the claim rejections under 35 U.S.C. 102 have been maintained/modified herein.
Election/Restrictions
Applicant’s election without traverse of Group I, claim(s) 1-7 and 12-14, drawn to isolated peptides, their variants, and compositions comprising the same and the species election by full sequence of the peptide SEQ ID NO: 3 in the reply filed on 1/30/2025 is acknowledged.
In the Office Action dated 3/18/2025, it was noted that the elected species was broadened to include SEQ ID NO: 20 along with previously elected SEQ ID NO: 3.
In the Office Action dated 11/24/2025, the elected species have been broadened to include SEQ ID NO: 9 and 19.
Claim Status
Claims 1-3 and 7-22 are pending. Claims 8-11 and 15 are withdrawn. Claims 1, 3, and 12 are currently amended. Claims 4-6 are cancelled. Claim 22 is new.
Priority
The instant application is the 371 of PCT/EP2020/072937, filed 8/14/2020, which claims foreign priority to EP19192689.8 with a filing date of 8/20/2019.
In the previous action, it was noted that there is a lack of support for peptides SEQ ID NO: 20, 8, 9, 11, and 19 within EP19192689.8, so the priority date had been set at 8/14/2020.
EP19192689.8 does provide support for SEQ ID NO: 3. Thus, the priority date for
the current claim set is set at 8/20/2019 for SEQ ID NO: 3 in claims 1-2, 7, 12-13, and 16-21 and 8/14/2020 for SEQ ID NO: 9, 19, and 20 in claims 3, 14, 18, and 21-22.
Claim Objections
Claim 1 is objected to because of the following informalities: the claim is difficult to comprehend because of the various combinations/possibilities recited in I) and II). The following amendment is suggested: A composition comprising a peptide having Ribosomal Protein S6 (rpS6) phosphorylation activity and a) having up to 50 amino acids and comprising a sequence of SEQ ID NO: 3 or b) consisting of a sequence having 1 to 3 amino acid alterations compared with SEQ ID NO: 3, wherein the or each amino acid alteration is independently selected from insertion, deletion, and substitution. Appropriate correction is required.
Claim Interpretation
Claim 1 recites a composition comprising a peptide I) a) having up to 50 amino acids and comprising SEQ ID NO: 3 or b) consisting of a sequence having 1-3 amino acid alterations compared with SEQ ID NO: 3 and II) having ribosomal protein S6 (rpS6) phosphorylation activity. Limitation “II)” of this claim is being interpreted as an inherent characteristic that meet the above structure requirements; in other words, the limitation of “II)” is met by either a) or b) as described above.
Additionally, the limitation I)b) is being interpreted as a peptide consisting of SEQ ID NO: 3 with 1-3 amino acid differences, whereby the introduction of 3 additional residues into SEQ ID NO: 3 would result in a peptide 13 residues in length and the deletion of 3 residues would result in a peptide of 7 residues in length.
New - Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 22 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. Claim 22 recites the composition according to claim 1, wherein the peptide comprises the sequence of SEQ ID NO: 20. SEQ ID NO: 20 has four amino acid deletions relative to SEQ ID NO: 3. Therefore, claim 22 does not recite all the limitations of its parent claim 1. Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
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 1-2, 7, and 16-17 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 claims are drawn to a composition comprising a peptide a) having up to 50 amino acids and comprising SEQ ID NO: 3 or consisting of a sequence having 1-3 amino acid alterations compared to SEQ ID NO: 3 and b) having ribosomal protein S6 (rpS6) phosphorylation activity. The rejection is based on the limitation “consisting of a sequence having 1-3 amino acid alterations compared to SEQ ID NO: 3 and having rpS6 phosphorylation activity”, which does not disclose sufficient structure-function relationship to meet the written description requirement.
The claims require any peptide with 1-3 insertions, deletions, or substitutions relative to SEQ ID NO: 3 have rpS6 phosphorylation activity. However, the core structure or the residue(s) of SEQ ID NO: 3 that facilitate this functionality is unknown. The claims do not indicate any positional information (i.e., where the insertions, deletions, or substitutions should occur in the sequence) nor restrict the type of amino acid used in an insertion or substitution (i.e., it does not specify that the substitution should be a conservative substitution).
Kelly et al. (US 20060058228, published 3/16/2006) discuss a phage display screen to identify peptides that distinguish between well-differentiated (HCT116) and poorly-differentiated (HT29) colon cancer cell lines. Analysis of the selected library resulted in the identification of a nine amino acid, disulfide-constrained peptide having a three amino acid (arg-pro-met, “RPM”) motif that specifically binds HT29 cells ([0032]). Substituting each of RPM with alanine significantly limited or abolished the ability of the peptide to compete with wild type RPM in a binding assay, indicating that these three residues alone accounted for the ability to bind to HT29 cells ([0034]). In contrast to this example, it is unknown which residues of SEQ ID NO: 3 facilitate rpS6 phosphorylation. Thus, one cannot extrapolate how 1-3 insertions, deletions or substitutions introduced to any position of SEQ ID NO: 3 might impact its functionality.
Further, Guo (Protein tolerance to random amino acid change, Proc. Natl. Acad. Sci. U.S.A. 101 (25) 9205-9210, (2004).) teaches that a protein’s tolerance to random substitutions ultimately depends on whether the residues at hand are involved the protein’s functional activity. For instance, regions that were highly substitutable in the human DNA repair enzyme 3-methyladenine DNA glycosylase (AAG) include the first 79 N-terminal residues previously demonstrated to be unnecessary for in vitro enzyme activity and DNA binding specificity. In contrast, residues that are involved in glycosylase function or DNA binding did not tolerate amino acid substitutions (“Substitutability and Structure”, Pg 9207-9209; Figure 1). Figure 1 of Guo also indicates that tolerated substitutions are generally conservative, i.e., a nonpolar residue is substituted for another nonpolar residue, etc. However, there are no explicit limitations in the instant claims regarding the type of insertions, deletions or substitutions that can be made relative to SEQ ID NO: 3.
Applicants have disclosed SEQ ID NO: 9 and 19 as variants of SEQ ID NO: 3 wherein 1-3 amino acids are deleted; no additional examples wherein amino acids are inserted or substituted are disclosed.
SEQ ID NO: 3 is amino acids in length. As there are no positional limitations on where the amino acid substitutions should be, this allows for more than (10!*19) + (10*19) = 6.89x10^7 possible variants where only 1-2 substitutions occur (10! possible combinations of two substitutions in a peptide with 10 positions * 19 naturally-occurring amino acids not including the amino acid present in the wild-type sequence; plus 10 possible positions wherein one substitution occurs * 19 naturally-occurring amino acids not including the amino acid present in the wild-type sequence).
Consequently, it is unknown whether all variants encompassed within the range of 1) up to 3 insertions, deletions, or substitutions in SEQ ID NO: 3 would retain the structural, chemical, and/or physical properties required to facilitate rpS6 phosphorylation. Therefore, the instant specification does not provide adequate written description to possess the broad genus described above since the specification does not disclose a correlation between the necessary structure of the sequence and the claimed function to be maintained.
Maintained/Modified - Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 12-14 and 19-21 are rejected under 35 U.S.C. 101 because they are directed to a judicial exception.
The Supreme Court has given a three-part test for patent eligibility (see flowchart of MPEP 2106(III)):
Are the claims drawn to a process, machine, manufacture, or composition of matter?
2a) If the claims pass the first test, are the claims drawn to a judicial exception (a law of nature, a natural phenomenon (product of nature), or an abstract idea)?
2b) If a judicial exception applies, do the claims recite additional elements that amount to significantly more than the judicial exception?
Applying the three-part test to the instant claims:
Regarding 1), the claims are drawn to peptides, which are compositions of matter.
Regarding 2a), the peptide claimed is a product of nature.
The claims above recite the following peptides, which read on the following natural products:
SEQ ID NO: 3:
Legumin (UniProt ID Q43674_VICFA)
Legumin B (UniProt IDs A0A392P037_9FABA, A0A392N2Z5_9FABA, A0A2K3MUH9_TRIPR, A0A2K3MUE0_TRIPR)
Legumin type B (UniProt IDs A0AAV1A036_VICFA, A0AAV1A1Q2_VICFA, A0AAV0ZYS1_VICFA, A0AAV0ZY58_VICFA, and LEGB4_VICFA)
Others not listed here
SEQ ID NO: 3 with 3 amino acid alterations:
Extension-like protein (UniProt ID Q9M3S8_ARATH)
C2H2-type domain-containing protein (UniProt ID A0A165FXF0_9APHY)
DUF1583 domain-containing protein (UniProt ID A0A517VZ61_9PLAN)
Others not listed here
SEQ ID NO: 3 with 2 amino acid alterations:
Legumin storage protein 2 (UniProt ID B5U8K1_LOTJA)
Legumin storage protein 3 (UniProt ID B5U8K2_LOTJA)
Peptide/nickel transport system permease protein (UniProt ID A0A1X7G7H4_9BACL)
Other not listed here
SEQ ID NO: 3 with 1 amino acid alteration:
Minor legumin (UniProt ID Q41035_PEA)
Legumin type B (UniProt ID Q41703_VICSA)
Cupin type-1 domain containing protein (UniProt ID A0A9D5A4B1_PEA, A0A9D4W410_PEA, A0A9D5A2F4_PEA, and A0A9D4W585_PEA)
Others not listed here
SEQ ID NO: 9:
Legumin (UniProt ID Q43674_VICFA)
Gp14 (UniProt ID K9K981_9CAUD)
Os12g0141400 protein (UniProt ID A0A0P0Y745_ORYSJ)
Others not listed here
SEQ ID NO: 19:
Legumin (UniProt ID Q43674_VICFA)
Legumin B (UniProt ID A0A392P037_9FABA)
Legumin type B (UniProt ID A0AAV1A036_VICFA)
Others not listed here
Of note, the modified SEQ ID NO: 3 described above have only taken into consideration 1-3 amino acid substitutions relative to SEQ ID NO: 3. Other alterations, such as additions or deletions, have the potential to also read on natural products.
While some of these proteins may be longer than the limit imposed by the claims, in Ass’n for Molecular Pathology v Myriad Genetics, the Supreme Court stated that fragments of a biopolymer still trigger this statute. Thus, the fact that these sequences are longer than those claimed does not make the rejection invalid, unless the fragment is significantly different from the full length polypeptide.
Regarding 2b), none of the claims above integrate the above peptide into a practical application. At most, the claims recite the peptides in a composition or as a comestible powder (claims 1 and 7, respectively) but without significantly more. As such, they do not contain elements added to the judicial exception sufficient to render the claims significantly more than the exception.
Taken together, the claims are drawn to patent ineligible subject matter and are rejected here.
Maintained/Modified - 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.
Claim(s) 1, 2, 7, 12, 13, 16, and 19 are rejected under 35 U.S.C. 102(a)(1) and (a)(2) as being anticipated by Wong et al. (US 2008/0305212 A1, published 12/11/2008).
Wong teaches protein hydrolysate compositions, processes of making, and food products generally comprising polypeptide fragments (Abstract). Wong teaches SEQ ID NO: 77, which is 13 residues in length, and shown below aligned to the instant SEQ ID NO: 3:
PNG
media_image1.png
176
628
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Greyscale
As stated above in the Claim Interpretation section, the above structural limitations read on the functional limitation of claim 1, wherein the peptide in the composition has rpS6 phosphorylation activity.
Thus, Wong anticipates claims 1, 2, 12, 13, 16, and 19.
Wong also teaches that the protein hydrolysate can be derived from plants powders, including soy, maize, barley, potato, rice, white, egg, and milk ([0029, 0035, 0036]). Thus, Wong also anticipates claim 7.
Allowable Subject Matter
A peptide having up to 50 amino acids, comprising SEQ ID NO: 3, and having rpS6 phosphorylation activity is free of the art. The closest art is 1) SEQ ID NO: 77 of Wong and/or 2) the naturally-occurring peptide Legumin (UniProt ID Q43674_VICFA), both of which are disclosed above. Wong does not provide teachings, suggestions, or motivations to substitute the Tyr and Arg residues at positions 8 and 10 for Ser and Gln residues, respectively. The legumin peptide comprises substantially more than 50 amino acids and there are no teachings, suggestions, or modifications to select the portion of the peptide comprising SEQ ID NO: 3.
Because SEQ ID NO: 3 comprises both SEQ ID NO: 9 and 19, peptides having 7 to 20 amino acids, comprising SEQ ID NO: 9 or 19, and having rpS6 phosphorylation activity are also free of the art.
Claims 3 and 18 are objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Conclusion
In summary, claims 1-2, 7, 12-14, 16-17, 19-22 are rejected and claims 3 and 18 are objected to.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Sara Konopelski Snavely whose telephone number is (571)272-1841. The examiner can normally be reached Monday - Friday 9-6pm EST.
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/SARA E KONOPELSKI SNAVELY/Examiner, Art Unit 1658
/Melissa L Fisher/Supervisory Patent Examiner, Art Unit 1658
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