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 .
Status of the Claims
Claims 1-20 were originally filed January 19, 2024.
The amendment received January 22, 2024 amended claims 3-9 and 12-20.
The amendment received July 7, 2026 changed the status identifiers only.
Claims 1-20 are currently pending.
Claims 1-4, 8-11, and 17-20 are currently under consideration.
Election/Restrictions
Applicant’s election without traverse of Group I (claims 1-11 and 17-20) in the reply filed on July 7, 2026 is acknowledged.
Please note: applicants elected Group I without traverse, but then proceeded to traverse the restriction based on the traversal that search and examination of all Groups would not be unduly burdensome. It is respectfully noted that the Requirement for Restriction/Election mailed on May 7, 2026 was based on Lack of Unity (i.e. search burden is not a factor and applicant did not traverse the prior art utilized to break unity of invention).
Claims 12-16 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected method, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on July 7, 2026.
Applicant’s election without traverse of SEQ ID NO: 1, negative charge, SEQ ID NO: 11, SEQ ID NO: 145, detecting legumain activity, detecting breast cancer, and thioflavin T dye in the reply filed on July 7, 2026 is acknowledged.
Please note: applicants elected the species without traverse, but then proceeded to traverse the species election based on the traversal that search and examination of all species would not be unduly burdensome. It is respectfully noted that the Requirement for Restriction/Election mailed on May 7, 2026 was based on Lack of Unity (i.e. search burden is not a factor and applicant did not traverse the prior art utilized to break unity of invention). In addition, it is unclear how applicants are of the opinion that searching 205 sequences is not burdensome.
Claims 5-7 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on July 7, 2026.
Potential Rejoinder
Applicant elected claims directed to a product. If a product claim is subsequently found allowable, withdrawn process claims that depend from or otherwise include all the limitations of the allowable product claim will be rejoined in accordance with the provisions of MPEP § 821.04. Process claims that depend from or otherwise include all the limitations of the patentable product will be entered as a matter of right if the amendment is presented prior to final rejection or allowance, whichever is earlier. Amendments submitted after final rejection are governed by 37 CFR 1.116; amendments submitted after allowance are governed by 37 CFR 1.312.
In the event of rejoinder, the requirement for restriction between the product claims and the rejoined process claims will be withdrawn, and the rejoined process claims will be fully examined for patentability in accordance with 37 CFR 1.104. Thus, to be allowable, the rejoined claims must meet all the criteria for patentability including the requirements of 35 U.S.C. 101, 102, 103, and 112. Until an elected product claim is found allowable, an otherwise proper restriction requirement between product claims and process claims may be maintained. Withdrawn process claims that are not commensurate in scope with an allowed product claim will not be rejoined. See “Guidance on Treatment of Product and Process Claims in light of In re Ochiai, In re Brouwer and 35 U.S.C. § 103(b),” 1184 O.G. 86 (March 26, 1996). Additionally, in order to retain the right to rejoinder in accordance with the above policy, applicant is advised that the process claims should be amended during prosecution either to maintain dependency on the product claims or to otherwise include the limitations of the product claims. Failure to do so may result in a loss of the right to a rejoinder. Further, note that the prohibition against double patenting rejections of 35 U.S.C. 121 does not apply where the restriction requirement is withdrawn by the examiner before the patent issues. See MPEP § 804.01.
Priority
The present application is a 371 (National Stage) of PCT/US2022/037769 filed July 20, 2022 which claims the benefit of 63/224,309 filed July 21, 2021 and 63/223,907 filed July 20, 2021.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on February 5, 2024 is being considered by the examiner.
Nucleotide and/or Amino Acid Sequence Disclosures
Summary of Requirements for Patent Applications Filed On Or After July 1, 2022, That Have Sequence Disclosures
37 CFR 1.831(a) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.831(b) must contain a “Sequence Listing XML”, as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.831-1.835. This “Sequence Listing XML” part of the disclosure may be submitted:
1. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter “Legal Framework”) in XML format, together with an incorporation by reference statement of the material in the XML file in a separate paragraph of the specification (an incorporation by reference paragraph) as required by 37 CFR 1.835(a)(2) or 1.835(b)(2) identifying:
a. the name of the XML file
b. the date of creation; and
c. the size of the XML file in bytes; or
2. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation by reference statement of the material in the XML format according to 37 CFR 1.52(e)(8) and 37 CFR 1.835(a)(2) or 1.835(b)(2) in a separate paragraph of the specification identifying:
a. the name of the XML file;
b. the date of creation; and
c. the size of the XML file in bytes.
DEFICIENCIES AND THE REQUIRED RESPONSE TO THIS NOTICE ARE AS FOLLOWS:
Specific deficiency - Sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.831(c). Sequence identifiers for sequences (i.e., “SEQ ID NO:X” or the like) must appear either in the drawings or in the Brief Description of the Drawings.
See Figures 1A, 1B, and 15A.
Required response – Applicant must provide:
Amended drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required sequence identifiers (i.e., “SEQ ID NO:X” or the like) into the Brief Description of the Drawings, 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.
Specific deficiency - Sequences appearing in the specification are not identified by sequence identifiers (i.e., “SEQ ID NO:X” or the like) in accordance with 37 CFR 1.831(c).
See the abstract and paragraphs 368 and 379.
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required sequence identifiers, 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 of the following informalities: paragraph 2 should include PCT/US2022/037769 filed July 20, 2022.
Appropriate correction is required.
The disclosure is objected to because of the following informalities: paragraph 17 should be split in two (i.e. one for Figure 10 and one for Figure 11).
Appropriate correction is required.
The disclosure is objected to because of the following informalities: Figures 15A-15B and 16A-16B are not described.
Appropriate correction is required.
The disclosure is objected to because of the following informalities: paragraph 21 should be split in two (i.e. one for Figures 15A-15B and one for Figures 16A-16B).
Appropriate correction is required.
The disclosure is objected to because of the following informalities: paragraph 23 should be split in three (i.e. one for Figure 18, one for Figure 19, and one for Figure 20).
Appropriate correction is required.
The disclosure is objected to because of the following informalities: paragraph 310 should be removed or should be part of the priority paragraph (i.e. paragraph 2).
Appropriate correction is required.
The lengthy specification has not been checked to the extent necessary to determine the presence of all possible minor errors. Applicant’s cooperation is requested in correcting any errors of which applicant may become aware in the specification.
Claim Objections
Claim 2 is objected to because of the following informalities: “from N-terminus to C-terminus” is unnecessary as one of skill in the art would assume the peptides are presented in N- to C-terminal orientation. Appropriate correction is required.
Claim 2 is objected to because of the following informalities: “selected from any one of” should read “selected from the group consisting of”. Appropriate correction is required.
Claim 2 is objected to because of the following informalities: “(SEQ ID NO: 2)” should be removed (i.e. due to the new sequence rules, the sequence is blank in the sequence listing). Appropriate correction is required.
Claim 4 is objected to because of the following informalities: “from N-terminus to C-terminus” is unnecessary as one of skill in the art would assume the peptides are presented in N- to C-terminal orientation. Appropriate correction is required.
Claim 4 is objected to because of the following informalities: “selected from any one of” should read “selected from the group consisting of”. Appropriate correction is required.
Claim 4 is objected to because of the following informalities: “(SEQ ID NO: 44)”, “(SEQ ID NO: 45)”, “(SEQ ID NO: 53)”, “(SEQ ID NO: 54)”, “(SEQ ID NO: 62)”and “(SEQ ID NO: 67)” should be removed (i.e. due to the new sequence rules, the sequences are blank in the sequence listing). Appropriate correction is required.
Claim 4 is objected to because of the following informalities: “and” between SEQ ID NO: 28 and SEQ ID NO: 29 should be removed (i.e. only a single conjunction should be present in the Markush group). Appropriate correction is required.
Claim 8 is objected to because of the following informalities: “selected from any one of” should read “selected from the group consisting of”. Appropriate correction is required.
Claim 10 is objected to because of the following informalities: “selected from any of ” should read “selected from the group consisting of”. Appropriate correction is required.
Claim 11 is objected to because of the following informalities: “selected from any of ” should read “selected from the group consisting of”. Appropriate correction is required.
Claim 17 is objected to because of the following informalities: “polypeptide” should read “polypeptide(s)” to correlate with “one or more”. Appropriate correction is required.
Claim 18 is objected to because of the following informalities: “selected from ” should read “selected from the group consisting of”. Appropriate correction is required.
Claim 19 is objected to because of the following informalities: “selected from any of ” should read “selected from the group consisting of”. Appropriate correction is required.
Claim 20 is objected to because of the following informalities: “selected from any of ” should read “selected from the group consisting of”. Appropriate correction is required.
Sequence Interpretation
The Office interprets claims comprising SEQ ID NOs: in the following manner: “comprising a sequence of SEQ ID NO: 1” requires only a 2mer of SEQ ID NO: 1, “comprising the sequence of SEQ ID NO: 1” requires the full-length sequence with 100% identity to SEQ ID NO: 1 with any N-/C-terminal additions or any 5’/3’ additions, “consisting of SEQ ID NO: 1” requires the full-length sequence with 100% identity to SEQ ID NO: 1 and the same length as SEQ ID NO: 1, and “selected from the group consisting of SEQ ID NOs: 1, 2, and 3” requires the full-length sequence with 100% identity to SEQ ID NOs: 1, 2, or 3 and the same length as SEQ ID NOs: 1, 2, or 3. Any claim requiring a specific percent identity, necessarily requires at least the recited percent identity.
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 1-4, 8-11, and 17-20 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. One of skill in the art would not be able to determine the scope of the presently claimed polypeptide. For example, it is unclear what “nominally identical” (see lines 2 and 8 of independent claim 1) means.
Claims 1-4, 8-11, and 17-20 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. One of skill in the art would not be able to determine the scope of the presently claimed polypeptide. For example, it is unclear if the one or more nominally identical b-strand motifs are required or not since the b-strand motif is only “configured to self-assemble” with the one or more nominally identical b-strand motifs (i.e. b-strand motif is only configured to self-assemble and not necessarily forming b-sheets).
Claims 1-4, 8-11, and 17-20 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. One of skill in the art would not be able to determine the scope of the presently claimed polypeptide. For example, it is unclear what the final structure is. The preamble of independent claim 1 refers to a “self-assembling polypeptide”, lines 2-5 requires the structure of a b-strand motif-protease substrate motif-hydrophilic motif and possibly one or more nominally identical b-strand motifs. Lines 5-9 of independent claim 1 refer to a potential product-by-process step of “whereby, when in an aqueous milieu and upon hybridization of the protease to the protease cleavage site, the protease cleaves the self-assembling polypeptide and disassociates the b-strand motif allowing the dissociated b-strand motif to self-assemble with the one or more nominally identical b-strand motifs and thereby from the anti-parallel b-sheet structure”.
Therefore, multiple structures are present in the claim and it is unclear which structure is required.
Self-assembling polypeptide wherein the functional limitation of self-assembling is only describing the polypeptide
b-strand motif-protease substrate motif-hydrophilic motif and possibly one or more nominally identical b-strand motifs
anti-parallel b-sheet structure made of a b-strand motif and one or more nominally identical b-strand motifs
Claims 1-4, 8-11, and 17-20 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 1 recites the limitation "the anti-parallel b-sheet structure " in line 9. There is insufficient antecedent basis for this limitation in the claim.
Claim 9 is 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. One of skill in the art would not be able to determine the scope of the presently claimed polypeptide. For example, it is unclear what structure is required by the claim. It is unclear what structure is required for detecting a protease. It is unclear how the protease, aqueous milieu, b-sheet intercalating dye are part of the “self-assembling polypeptide”. It appears that the claim is actually directed to an intended use (see MPEP § 2112.01) and/or a method of making (see MPEP § 2113).
Claim 9 is 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 9 recites the limitation "the enzyme-instructed self-assembly" in line 3. There is insufficient antecedent basis for this limitation in the claim.
Claim 10 is 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. One of skill in the art would not be able to determine the scope of the presently claimed polypeptide. For example, it is unclear what structure is required by the claim. It is unclear how the intended use as a means for detecting cancer alters the structure. It appears that the claim is actually directed an intended use (see MPEP § 2112.01) and/or a method of making (see MPEP § 2113).
Claim 11 is 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. One of skill in the art would not be able to determine the scope of the presently claimed polypeptide. For example, it is unclear what structure is required by the claim. It is unclear how the intended use as a means for detecting a disease, disorder, or syndrome alters the structure. It appears that the claim is actually directed to an intended use (see MPEP § 2112.01) and/or a method of making (see MPEP § 2113).
Claim 19 is 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. One of skill in the art would not be able to determine the scope of the presently claimed polypeptide. For example, it is unclear what structure is required by the claim. It is unclear how the intended use of detecting cancer alters the structure. It appears that the claim is actually directed an intended use (see MPEP § 2112.01) and/or an improper use claim (see MPEP § 2173.05(q)). Claim 19 is drawn to a kit, not a method of utilizing the kit. Also see withdrawn claim 14.
Claim 20 is 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. One of skill in the art would not be able to determine the scope of the presently claimed polypeptide. For example, it is unclear what structure is required by the claim. It is unclear how the intended use of detecting a disease, disorder, or syndrome alters the structure. It appears that the claim is actually directed to an intended use (see MPEP § 2112.01) and/or an improper use claim (see MPEP § 2173.05(q)). Claim 20 is drawn to a kit, not a method of utilizing the kit. Also see withdrawn claim 15.
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 19 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 19 is dependent on claim 17 which is dependent on independent claim 1. Independent claim 1 is drawn to a self-assembling polypeptide. Dependent claim 17 is drawn to a kit comprising one or more self-assembling polypeptides and a b-sheet intercalating dye. Dependent claim 19 simply refers to the intended use of the kit and not to any structural changes to the components of the kit. 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.
Claim 20 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 20 is dependent on claim 17 which is dependent on independent claim 1. Independent claim 1 is drawn to a self-assembling polypeptide. Dependent claim 17 is drawn to a kit comprising one or more self-assembling polypeptides and a b-sheet intercalating dye. Dependent claim 20 simply refers to the intended use of the kit and not to any structural changes to the components of the kit. 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.
Claim 2 is rejected on the basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
The Markush grouping of SEQ ID NOs: 1-10 is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: the sequences do not share a common core structure which provides the function/structure of a b-strand motif.
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims and/or present convincing arguments that the group members recited in the alternative within a single claim in fact share a single structural similarity as well as a common use.
Claim 4 is rejected on the basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
The Markush grouping of SEQ ID NOs: 11-72 is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: the sequences do not share a common core structure which provides the function/structure of a hydrophilic motif. Please also see SEQ ID NOs: 73-108 of withdrawn claim 6 and SEQ ID NOs: 109-144 in withdrawn claim 7.
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims and/or present convincing arguments that the group members recited in the alternative within a single claim in fact share a single structural similarity as well as a common use.
Claim 8 is rejected on the basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
The Markush grouping of SEQ ID NOs: 145-205 is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: the sequences do not share a common core structure which provides the function/structure of a protease substrate motif.
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims and/or present convincing arguments that the group members recited in the alternative within a single claim in fact share a single structural similarity as well as a common use.
Claims 9-11 in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action.
This application includes one or more claim limitations that use the word “means” or “step” (see claims 9-11) but are nonetheless not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph because the claim limitation(s) recite(s) sufficient structure, materials, or acts to entirely perform the recited function. Such claim limitation(s) is/are: anti-parallel b-sheet structure and, potentially, protease, aqueous milieu, and b-sheet intercalating dye in claim 9; anti-parallel b-sheet structure and, potentially, protease, aqueous milieu, and b-sheet intercalating dye in claim 10 due to the dependency on claim 9; and anti-parallel b-sheet structure and, potentially, protease, aqueous milieu, and b-sheet intercalating dye in claim 11 due to the dependency on claim 9.
Because this/these claim limitation(s) is/are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, it/they is/are not being interpreted to cover only the corresponding structure, material, or acts described in the specification as performing the claimed function, and equivalents thereof.
If applicant intends to have this/these limitation(s) interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to remove the structure, materials, or acts that performs the claimed function; or (2) present a sufficient showing that the claim limitation(s) does/do not recite sufficient structure, materials, or acts to perform the claimed function.
Please note: due to the plethora of objections and 35 USC 112 issues with the claims, applicants are respectfully requested to carefully review the claims for any additional issues.
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 1, 3, 9-11, and 17-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to anti-parallel b-sheet structures formed via b-strand polypeptides without significantly more. The claims recite anti-parallel b-sheet structures formed via b-strand polypeptides (i.e. any b-strand polypeptide, any anti-parallel b-sheet structure) with (claims 17-20) or without dyes (claims 1, 3, and 9-11) which are known to be naturally occurring. See Camino et al., 2020, The extent of protein hydration dictates the preference for heterogeneous or homogeneous nucleation generating either parallel or antiparallel b-sheet a-synuclein aggregates, Chem Sci, 11: 11902-11914. This judicial exception is not integrated into a practical application because the present claims are not drawn to a method. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because it is unclear how the dyes in the kit are associated with the anti-parallel b-sheet structures formed via b-strand polypeptides (i.e. not clear if a structural relationship is present). In addition, dyes are well-understood, routine, and conventional in the art.
Claim Rejections - 35 USC § 102
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.
Claims 1, 3, 9-11, and 17-20 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Camino et al., 2020, The extent of protein hydration dictates the preference for heterogeneous or homogeneous nucleation generating either parallel or antiparallel b-sheet a-synuclein aggregates, Chem Sci, 11: 11902-11914.
For present claims 1, 3, 9-11, and 17-20, Camino et al. teach anti-parallel b-sheet structures formed via b-strand polypeptides with dyes including thioflavin T (please refer to the entire reference particularly the abstract; Introduction; pages 11907, 11908, 11909; “Aggregation assays”).
Therefore, the teachings of Camino et al. anticipate the presently claimed self-assembling polypeptide.
Claims 1-3 and 9-11 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Jiang et al., February 26, 2021, Formation Mechanism and Biomedical Applications of Protease-Manipulated Peptide Assemblies, Frontiers in Bioengineering and Biotechnology, 9: 598050 (7 pages).
For present claims 1-3 and 9-11, Jiang et al. teach self-assembling polypeptides comprising building block/b-strand-protease-recognizing linker-hydrophilic moiety wherein the building block can form b-sheets and can be Fmoc-FFF (please refer to the entire reference particularly the abstract; Introduction; Protease-Instructed Assembly Mechanism, Assembly by Bond-Cleaving Reactions; Assembly by Bond-Forming Reactions; Figure 1; Table 1).
Compounds which are homologs (compounds differing regularly by the successive addition of the same chemical group, e.g., by -CH2- groups) are generally of sufficiently close structural similarity that there is a presumed expectation that such compounds possess similar properties. See In re Wilder, 563 F.2d 457, 195 USPQ 426 (CCPA 1977).
Therefore, the teachings of Jiang et al. anticipate the presently claimed self-assembling polypeptide.
Claims 1, 3, 9-11, and 17-20 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Chen et al. WO 2009/026729 published March 5, 2009.
For present claims 1, 3, 9-11, and 17-20, Chen et al. teach anti-parallel b-sheet structures formed via b-strand polypeptides including phenylalanine dipeptide (i.e. FF) with dyes including thioflavin T (ThT) and kits; N-termini acetylation and C-termini amidation (please refer to the entire reference particularly the abstract; pages 1-11, 21-24, 27-33).
Therefore, the teachings of Chen et al. anticipate the presently claimed self-assembling polypeptide.
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.
Claims 1-4, 8-11, and 17-20 are rejected under 35 U.S.C. 103 as being unpatentable over Jiang et al., February 26, 2021, Formation Mechanism and Biomedical Applications of Protease-Manipulated Peptide Assemblies, Frontiers in Bioengineering and Biotechnology, 9: 598050 (7 pages); Saiani et al. WO 2012/045822 published April 12, 2012; Luyt et al. WO 2011/150495 published December 8, 2011; Pohlmann et al. WO 2016/023974 published February 18, 2016; and Chen et al. WO 2009/026729 published March 5, 2009.
For present claims 1-4, 8-11, and 17-20, Jiang et al. teach self-assembling polypeptides comprising building block/b-strand-protease-recognizing linker-hydrophilic moiety wherein the building block can form b-sheets and can be Fmoc-FFF (please refer to the entire reference particularly the abstract; Introduction; Protease-Instructed Assembly Mechanism, Assembly by Bond-Cleaving Reactions; Assembly by Bond-Forming Reactions; Figure 1; Table 1).
For present claims 1-4, 8-11, and 17-20, Saiani et al. teach self-assembling polypeptides comprising as the building block/b-strand of FKFE (100% identify and the same length as present SEQ ID NO: 1) and Fmoc which form anti-parallel b-sheets (please refer to the entire specification particularly pages 1-7, 15, 22; claim 6).
For present claims 1-4, 8-11, and 17-20, Luyt et al. teach SEQ ID NO: 21 (hydrophilic moiety; 100% identity and the same length as present SEQ ID NO: 22).
For present claims 1-4, 8-11, and 17-20, Pohlmann et al. teach present SEQ ID NO: 145 (100% and the same length) as a protease substrate/protease cleavage site (please refer to the entire specification particularly page 29).
For present claims 1-4, 8-11, and 17-20, Chen et al. teach anti-parallel b-sheet structures formed via b-strand polypeptides including phenylalanine dipeptide (i.e. FF) with dyes including thioflavin T (ThT) and kits; N-termini acetylation and C-termini amidation (please refer to the entire reference particularly the abstract; pages 1-11, 21-24, 27-33).
All the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in the respective functions and the combination would have yielded predictable results to one of ordinary skill in the art at the time of the invention (i.e. b-sheet formation after cleavage). The claims would have been obvious because the substitution of one known element (i.e. genus of b-strand peptide, genus of protease substrate motif, genus of hydrophilic motif) for another (i.e. present SEQ ID NOs: 1, 22, and 145) would have yielded predictable results (i.e. fusion polypeptide and/or antiparallel b-sheet) to one of ordinary skill in the art at the time of the invention. The claims would have been obvious because a particular known technique (i.e. making fusion polypeptides; b-strands making antiparallel sheets) was recognized as part of the ordinary capabilities of one skilled in the art. The claims would have been obvious because a person of ordinary skill has good reason to pursue the known options within their technical grasp. If this leads to the anticipated success, it is likely the product no of innovation but of ordinary skill and common sense. See KSR International Co v. Teleflex Inc., 82 USPQ2d 1385 (U.S. 2007).
Claims 1-4, 8-11, and 17-20 are rejected under 35 U.S.C. 103 as being unpatentable over Law et al., 2007, Protease Sensitive Fluorescent Nanofibers, Bioconjug Chem, 18(6): 1701-1704; Saiani et al. WO 2012/045822 published April 12, 2012; Luyt et al. WO 2011/150495 published December 8, 2011; Pohlmann et al. WO 2016/023974 published February 18, 2016; and Chen et al. WO 2009/026729 published March 5, 2009.
For present claims 1-4, 8-11, and 17-20, Law et al. teach self-assembling polypeptides comprising b-strand peptide-protease sensitive domain-hydrophilic moiety wherein the b-strand can form b-sheets and FITC labels/dyes (please refer to the entire reference particularly the abstract; Introduction; The synthesis of nanofibers 1, 2, 3; Enzyme digestion study by fluorescence imaging; Figure 1).
For present claims 1-4, 8-11, and 17-20, Saiani et al. teach self-assembling polypeptides comprising as the building block/b-strand of FKFE (100% identify and the same length as present SEQ ID NO: 1) and Fmoc which form anti-parallel b-sheets (please refer to the entire specification particularly pages 1-7, 15, 22; claim 6).
For present claims 1-4, 8-11, and 17-20, Luyt et al. teach SEQ ID NO: 21 (hydrophilic moiety; 100% identity and the same length as present SEQ ID NO: 22).
For present claims 1-4, 8-11, and 17-20, Pohlmann et al. teach present SEQ ID NO: 145 (100% and the same length) as a protease substrate/protease cleavage site (please refer to the entire specification particularly page 29).
For present claims 1-4, 8-11, and 17-20, Chen et al. teach anti-parallel b-sheet structures formed via b-strand polypeptides including phenylalanine dipeptide (i.e. FF) with dyes including thioflavin T (ThT) and kits; N-termini acetylation and C-termini amidation (please refer to the entire reference particularly the abstract; pages 1-11, 21-24, 27-33).
All the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in the respective functions and the combination would have yielded predictable results to one of ordinary skill in the art at the time of the invention (i.e. b-sheet formation after cleavage). The claims would have been obvious because the substitution of one known element (i.e. genus of b-strand peptide, genus of protease substrate motif, genus of hydrophilic motif) for another (i.e. present SEQ ID NOs: 1, 22, and 145) would have yielded predictable results (i.e. fusion polypeptide and/or antiparallel b-sheet) to one of ordinary skill in the art at the time of the invention. The claims would have been obvious because a particular known technique (i.e. making fusion polypeptides; b-strands making antiparallel sheets) was recognized as part of the ordinary capabilities of one skilled in the art. The claims would have been obvious because a person of ordinary skill has good reason to pursue the known options within their technical grasp. If this leads to the anticipated success, it is likely the product no of innovation but of ordinary skill and common sense. See KSR International Co v. Teleflex Inc., 82 USPQ2d 1385 (U.S. 2007).
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-4, 9-11, 17, 19, and 20 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 6-9, 15, 29, 31-33, 35, 37, 40, 51-53, 57, 60, 68, 69, 71, 72, 74, and 75 of copending Application No. 18/290,755 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because both the present claims the claims of copending Application No. 18/290,755 (reference application) are drawn to self-assembling polypeptides comprising a b-strand motif of FF or Fmoc-FF, a hydrophilic motif of EGEE, and a dye.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 1-4, 8-11, and 17-20 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 6-9, 15, 29, 31-33, 35, 37, 40, 51-53, 57, 60, 68, 69, 71, 72, 74, and 75 of copending Application No. 18/290,755 in view of Luyt et al. WO 2011/150495 published December 8, 2011; Pohlmann et al. WO 2016/023974 published February 18, 2016; and Chen et al. WO 2009/026729 published March 5, 2009.
Copending Application No. 18/290,755 claims self-assembling polypeptides comprising a b-strand motif of FF or Fmoc-FF, a hydrophilic motif of EGEE, and a dye.
Luyt et al. teach SEQ ID NO: 21 (hydrophilic moiety; 100% identity and the same length as present SEQ ID NO: 22).
Pohlmann et al. teach present SEQ ID NO: 145 (100% and the same length) as a protease substrate/protease cleavage site (please refer to the entire specification particularly page 29).
Chen et al. teach anti-parallel b-sheet structures formed via b-strand polypeptides including phenylalanine dipeptide (i.e. FF) with dyes including thioflavin T (ThT) and kits; N-termini acetylation and C-termini amidation (please refer to the entire reference particularly the abstract; pages 1-11, 21-24, 27-33).
All the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in the respective functions and the combination would have yielded predictable results to one of ordinary skill in the art at the time of the invention (i.e. b-sheet formation after cleavage; adding a dye to a kit). The claims would have been obvious because the substitution of one known element (i.e. genus of protease substrate motif, genus of hydrophilic motif) for another (i.e. present SEQ ID NOs: 22 and 145) would have yielded predictable results (i.e. fusion polypeptide and/or antiparallel b-sheet) to one of ordinary skill in the art at the time of the invention. The claims would have been obvious because a particular known technique (i.e. making fusion polypeptides; b-strands making antiparallel sheets) was recognized as part of the ordinary capabilities of one skilled in the art. The claims would have been obvious because a person of ordinary skill has good reason to pursue the known options within their technical grasp. If this leads to the anticipated success, it is likely the product no of innovation but of ordinary skill and common sense. See KSR International Co v. Teleflex Inc., 82 USPQ2d 1385 (U.S. 2007).
This is a provisional nonstatutory double patenting rejection.
Allowable Subject Matter
The hydrophilic motifs requiring 100% identity and the same length as present SEQ ID NOs: 10-17, 19-21, and 23-25 are free of the prior art.
The protease substrate motif requiring 100% identity and the same length as present SEQ ID NO: 201 is free of the prior art.
Please note: prior art exists for hydrophilic motifs and protease substrate motif requiring 100% identify and longer sequences.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. The SEQ ID NOs:/sequences in the prior art below all have 100% identity and the same length as the present indicated SEQ ID NOs:. Please note: prior art also exists for sequences requiring 100% identify with a longer length.
Present SEQ ID NO: 1 U.S. Patent 9,849,174 (SEQ ID NO: 62)
Present SEQ ID NO: 1 U.S. Patent Application Publication 2013/0281602 (SEQ ID NO: 9)
Present SEQ ID NO: 3 U.S. Patent Application Publication 2008/0112926 (SEQ ID NO: 1070)
Present SEQ ID NO: 3 U.S. Patent 7,807,413 and U.S. Patent Application Publication 2009/0005541 (SEQ ID NO: 1071)
Present SEQ ID NO: 4 U.S. Patent 7,902,144 (SEQ ID NO: 13)
Present SEQ ID NO: 4 U.S. Patent Application Publication 2012/0244575 (SEQ ID NO: 3030)
Present SEQ ID NO: 4 WO 01/68142 (page 15)
Present SEQ ID NO: 5 U.S. Patent 7,399,831 and U.S. Patent Application Publication 2006088510 (SEQ ID NO: 85)
Present SEQ ID NO: 6 U.S. Patent 7,449,180 and U.S. Patent Application 20020160471 (SEQ ID NO: 15)
Present SEQ ID NO: 6 WO 02/062969 (page 20; Table 1)
Present SEQ ID NOs: 7-9 U.S. Patent 8,486,621 and U.S. Patent Application Publication 20070148246 (SEQ ID NO: 24)
Present SEQ ID NOs: 7-9 WO 2006/014570 (page 11; Table 1)
*Present SEQ ID NO: 18 U.S. Patent 10,706,955 and U.S. Patent Application Publication 2013/0330335 (SEQ ID NO: 445420)
*Present SEQ ID NO: 22 U.S. Patent 10,706,955 and U.S. Patent Application Publication 2013/0330335 (SEQ ID NO: 2362239)
*Present SEQ ID NO: 145 U.S. Patent 10,706,955 and U.S. Patent Application Publication 2013/0330335 (SEQ ID NO: 1104032)
Future Communications
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/AMBER D STEELE/Primary Examiner, Art Unit 1658
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