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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 12/22/2025 has been entered.
Status of Claims
Claims 1, 3-7 and 11-27 are pending following the Reply filed 12/22/2025. Claims 1, 3-7 and 11-17 have been amended without adding new matter. Claim 9 has been cancelled by Applicant. Claims 23-27 remain withdrawn. Accordingly, claims 1, 3-7 and 11-22 are presently considered.
Election/Restrictions
Applicant’s election without traverse of Group I and the species, Glutamine (Gln) for A, BACE for B, Alzheimer’s Disease for C and Adeno-associated Virus (AAV) for D, remains in effect. Claims 23-27 stand withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 01/06/2025.
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55. All pending claims of the instant application are entitled to the effective filing date of 11/08/2019.
Withdrawn
Any rejection of claim 9 is moot because the claim has been cancelled.
Objection of claim 6 is withdrawn in light of the amendments.
The rejection of claims 1, 3-7 and 11-22 under 35 U.S.C. 112(a) for failing to comply with the Written Description requirement is withdrawn in light of the amendments. As discussed under Claim Interpretation and 35 U.S.C. 112(b) below, the claims now require the NIa protease fragments and variants to comprise the full-length of one of the amino acid sequences recited in claim 1.
Claim Objections
Claim 1 is objected to for the following informalities: on line 13, the claim recites, “n, and q are each 0 or 1, m, o, and p are each 1” in line 13. For clarity and consistency, please remove the comma (“,”) that follows “n” and separate line 13 to read as follows:
n and q are each 0 or 1;
m, o, and p are each 1;
Appropriate correction is required.
Claim 1 is objected to for the following informalities: the claim recites “13, and 15;” in line 17. Please remove the comma (“,”) which follows “13”, so the claim reads “13 and 15;” in line 17. Appropriate correction is required.
Claim Interpretation
Claim 1 recites the limitation, “the NIa protease has any one of the amino acid sequences represented by SEQ ID NOs: 13, and 15” in lines 16-17. It is reasonably interpreted that this limitation requires that the NIa protease comprises (“has”) the full-length of one of the recited sequences.
Claim 1 also recites the limitation, “the fragment of the NIa protease is a polypeptide having any one of the amino acid sequences represented by SEQ ID NOs: 13 to 21” in lines 18-19. It is reasonably interpreted that this limitation requires that the fragment of the NIa protease is a polypeptide comprising (“having”) the full-length of one of the recited sequences.
If applicant does not intend to have these limitations interpreted as presented above, applicant may amend the claim and/or provide an explanation in response to the office action.
Maintained Rejections and New Rejections Necessitated by Amendment
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 1 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 1 recites the limitation, wherein “the variant of the NIa protease is one in which one of the N-glycosylation sites of the NIa protease is substituted with another amino acid having any one of the amino acid sequences represented by SEQ ID NOs: 19 to 21” in lines 20-22. This renders the claim indefinite because it is unclear how an “amino acid” (i.e., a single residue) can have an “amino acid sequence” (i.e., two or more residues).
Suggestion to obviate the rejection: Applicant may amend the limitation to recite, for example, “the variant of the NIa protease is a polypeptide having any one of the amino acid sequences represented by SEQ ID NOs 19 to 21, in which one of the N-glycosylation sites of the variant is substituted with another amino acid.”
In the interest of compact prosecution, the claim is interpreted accordingly, wherein the variant of the NIa protease is a polypeptide comprising (“having”) the full-length of any one of the amino acid sequences represented by SEQ ID NOs 19 to 21. Examiner notes that these sequences already comprise the recited substitution in view of Applicant’s disclosure (see, e.g., instant specification at pg. 11, lines 19-21).
Claim Rejections - 35 USC § 103
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.
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.
Claims 1, 3-7 and 13-22 are rejected under 35 U.S.C. 103 as being unpatentable over Park (US 9,498,519 B2; previously cited), and further in view of Yan (US 20030017991 A1; previously cited).
Regarding claim 1, Park teaches a pharmaceutical composition for preventing or treating an amyloid β-caused disease, which comprises as an active ingredient an NIa (nuclear inclusion a) protease, effective to treat a variety of diseases or disorders including Alzheimer’s disease (see Abstract), wherein the NIa protease may be fused to a protein transduction domain (PTD) for effectively penetrating cells, which may include a growth factor signal peptide sequence (see col. 5, lines 26-28 and 31-33). Hence, Park teaches a fusion protein comprising an NIa protease (A). Additionally, Park teaches that accumulating evidence suggests that intracellular amyloid β (Aβ) is critical for the development of Alzheimer’s disease, as it has been found that Aβ is present in a diverse set of subcellular organelles, including early endosomes, the trans-Golgi network, the rough endoplasmic reticulum, the outer mitochondrial membrane, and the nuclear envelope (see col. 1, lines 45-46 and 50-54). Park teaches the NIa protease cleaves intracellular or extracellular amyloid β (see claim 1), therefore having “an activity to degrade amyloid β”.
Regarding the limitation, wherein “the NIa protease has any one of the amino acid sequences represented by SEQ ID NOs: 13 and 15”, Park teaches the NIa protease derived from TuMV consists of the amino acid sequence of SEQ ID NO: 1 (see claim 1). As shown in the following alignment, Park’s SEQ ID NO: 1 (bottom) comprises (“has”) the full-length of instant SEQ ID NO: 13 (top):
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Park does not teach the fusion protein wherein the signal sequence is derived from β-secretase.
Yan teaches novel compositions for monitoring the β-secretase activity of human Asp2 protease, useful in the identification of agents that modulate β-secretase activity and the therapeutic intervention of disorders characterized by the presence of amyloid plaques (see pg. 1, para. [0002]), including Alzheimer’s disease (see pg. 1, para. [0003]). It is understood in view of Yan’s disclosure that “Asp2 protease” is a “β-secretase” which Yan teaches is also a membrane-bound aspartyl protease (pg. 1, para. [0006]). Yan teaches that amyloid beta (Aβ) is the primary component of amyloid plaques (see pg. 1, para. [0003]) and is produced from the cleavage of amyloid protein precursor (APP) at the β-secretase cleavage site by human aspartyl protease (Hu-Asp2) (see pg. 1, col. 2, para. [0006]). Yan teaches that the amyloid protein precursor (APP) localizes to the cell surface (see pg. 1, para [0004]), and its β-secretase cleavage site (an Asp2 target) is located near the plasma membrane luminal surface and as such is a favored therapeutic target (see pg. 1, para. [0005]). Yan also teaches that the processing of the beta-secretase site can occur in both the endoplasmic reticulum (in neurons) and in the endosomal/lysosomal pathway after re-internalization of cell surface APP (in all cells) (see pg. 1, para. [0005]).
Yan also teaches the design of fusion proteins, wherein such fusions typically employ leader sequences from other species to permit the recombinant expression of a protein or peptide in a heterologous host and that useful protein fusions include the linking of functional domains, such as the active sites from enzymes, cellular targeting signals or transmembrane regions (see pg. 11, para. [0085]). Yan teaches the Asp2 amino acid sequence includes a putative signal peptide comprising residues 1 to 21 (see pg. 14, para. [0110]), i.e., a signal sequence (X) derived from beta-secretase.
Regarding the limitation, wherein “m, o, and p are each 1”, this limitation requires the fusion protein to have a signal sequence (X) and a transmembrane domain (Y), wherein the linker (L2) separates the NIa protease (A) and the transmembrane domain (Y). (i.e., X-A-L2-Y). Yan teaches fusion polypeptides further comprising a transmembrane domain which may be separated by a linker (see pg. 3, para. [0023]). Yan teaches that the transmembrane domain anchors the polypeptide to an intracellular membrane, such as the Golgi or the endoplasmic reticulum (see pg. 3, para. [0023]).
It would have been obvious at the time of filing for a person of ordinary skill in the art to have combined the teachings of Yan and Park to make an NIa fusion protein comprising the signal peptide and transmembrane domains of a β-secretase, because Yan teaches Asp2 to localize to regions containing amyloid proteins which Park teaches can be degraded by NIa proteases. One would have recognized that Park teaches signal peptide sequences can be useful for effectively penetrating into cells by NIa protease to cleave amyloid proteins, which Yan teaches are effectively targeted by Asp2 (i.e., a beta-secretase). Furthermore, one would have recognized that Yan teaches fusion proteins containing the active site of other enzymes to be useful, and that it would have been possible to simply replace the active site of a beta-secretase with that of an NIa protease, or an active fragment thereof, rendering a fusion protein that may localize in vivo to the desired therapeutic target. Such a protein would have necessarily comprised signal (X) and transmembrane (Y) domains N- and C-terminal to an NIa protease (A). Further, Yang teaches the active site (“A”) can be separated from the transmembrane domain (“Y”) by a linker (“L2”). Because each reference teaches these respective elements can be used in constructing fusion proteins, with each element expected to perform the same function as it does separately, the results of the combination would have been predictable with a reasonable expectation of success. Hence, the combination would have been readily apparent and deemed to be a mere (A) combining of prior art elements according to known methods to yield predictable results (see MPEP 2143(I): Rationales to support rejections under 35 U.S.C. 103).
Regarding claim 3, Yan teaches the putative signal peptide of Asp2 to comprise residues 1 to 21 of SEQ ID NO: 2. As shown in the following alignment, instant SEQ ID NO: 3 (top) is identical to Yan’s SEQ ID NO: 2 (bottom) from residues 1 to 21:
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Regarding claim 4, Yan teaches fusion polypeptides comprising peptide linkers comprising 20 to about 40 amino acids. This range overlaps with the claimed range from 20 to 24 amino acids. In view of the instant specification, there is no apparent support showing the criticality of the claimed range. In fact, the specification states, “[t]he linker merely has a role of linking these monomers, and it has a very limited effect on the structure and impact” (see pg. 7, lines 21-22). Applicant also discloses an embodiment wherein L1 comprises instant SEQ ID NO: 4 (see pg. 7, lines 23-25) which is 34 amino acids in length and outside the claimed range. Further, the Examples in the specification do not specify the length of the linker regions used, only that “SAS was prepared by fusing the N-terminus and C-terminus of NIa with the pro domain and the transmembrane domain of β-secretase” (see pg. 25, lines 1-2; Emphasis added). Hence, the overlapping range of 20-24 amino acids is sufficient to support a prima facie case of obviousness, particularly when there is no showing of criticality of the claimed range or evidence of unexpected results using the claimed range. See MPEP 2144.05(I).
Regarding claim 5, as discussed regarding instant claim 1, it would have been obvious to have fused the leader signal peptide of β-secretase (taught by Yan) to an NIa protease (taught by Park) for more effective penetration of the fusion protein into cells. As discussed regarding instant claim 4, Yan teaches peptide linkers may be used to fuse separate elements of a fusion polypeptide. Yan also teaches that the region immediately following the signal peptide is a putative pre-propeptide domain that extends through residue 45 of β-secretase (see pg. 14, para. [0110]) which is 24 residues in length. As the linker merely serves the purpose of attaching different segments of a fusion protein, and is not intended to have any impact on the structure or function of the protein, it would have been obvious to have simply included this segment of the β-secretase, or any other segment of the β-secretase, so long as it did not impact protein function.
Regarding claim 6, as shown in the following alignment, instant SEQ ID NO: 5 (top) is identical to Yan’s SEQ ID NO: 2 from residues 142 to 163 (bottom):
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The Examples of Applicant’s disclosure do not state which linker regions were used, only that “SAS was prepared by fusing the N-terminus and C-terminus of NIa with the pro domain and the transmembrane domain of β-secretase” (see pg. 25, lines 1-2). As discussed regarding claim 5, because there is no criticality of the linker region regarding protein structure or function, it would have been obvious when constructing a β-secretase fusion protein to have selected any segment from the β-secretase to use as a peptide linker so long as it did not impact protein function.
Regarding claim 7, Park teaches the NIa protease is derived from Turnip mosaic virus (TuMV) (see claim 1) which is disclosed as a Potyvirus (see Sequence Listing, SEQ ID NO: 1, “Organism”).
Regarding claim 13, Yan teaches that human aspartyl protease (Hu-Asp2) has an activity responsible for the processing of APP at the beta-secretase cleavage site (see pg. 1, para. [0006]), and is therefore understood to be a beta-site APP cleaving enzyme, i.e., a “BACE”. Yan teaches that Asp2 is also a membrane-bound protease (pg. 1, para. [0006]) that features a transmembrane domain near the C-terminus comprising residues 455-477 (see pg. 14, para. [110]) which anchors the protease to the membrane and is essential for the enzyme to function in cells (see pg. 1, para. [0006]). Yan also teaches the transmembrane domain anchors the polypeptide to intracellular membranes, such as the Golgi or the endoplasmic reticulum (see, e.g., claim 32).
Hence, it would have been obvious in view of Park and Yan to have included the transmembrane domain of Asp2 in the NIa fusion protein, because this element helps localize the enzyme to regions containing amyloid proteins. Furthermore, as previously discussed regarding instant claim 1, one of ordinary skill would have recognized that an NIa protease, or an active fragment thereof, could simply be fused within a β-secretase resulting in a fusion protein which would have necessarily included this region near the C-terminus.
Regarding claim 14, as shown in the following alignment, the full length of instant SEQ ID NO: 29 (top) is identical to the transmembrane domain of Yan’s SEQ ID NO: 2 from residues 458-478 (bottom):
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Regarding claim 15, Yan teaches that Asp2, a β-secretase, has a cytoplasmic domain immediately following the transmembrane domain comprising residues 478-501 comprising the C-terminus of the protein (see pg. 14, para. [0110]). As discussed regarding instant claims 1 and 13, one would have recognized that an NIa protease, or an active fragment thereof, could simply be fused within a β-secretase that includes the transmembrane domain. Hence, it would have been obvious to include the C-terminal portion of the protein that includes both transmembrane and cytoplasmic domains.
Regarding claim 16, as shown in the following alignment, the full length of instant SEQ ID NO: 30 (top) is identical to the cytoplasmic domain of Yan’s SEQ ID NO: 2 from residues 479 to 501 (bottom):
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Regarding claim 17, Park teaches a pharmaceutical composition comprising an NIa protease, or alternatively, a gene carrier containing a nucleotide sequence encoding the synthesized NIa protease (see claim 1), while Yan teaches it may be necessary to express the fusion proteins of the disclosure by employing vectors comprising polynucleotide molecules which encode the proteins (see pg. 18, para. [0152]). Hence, it would have been obvious to have provided a polynucleotide that encodes the fusion NIa protein.
Regarding claim 18, instant SEQ ID NO: 42 translates to the following amino acid sequence:
1 MAQALPWLLL WMGAGVLPAH GTQHGIRLPL RSGLGGAPLG LRLPRETDEE
51 PEEPGRDYNP ISNNICHLTN VSDGASNSLY GVGFGPLILT NRHLFERNNG
101 ELVIKSRHGE FVIKNTTQLH LLPIPDRDLL LIRLPKDIPP FPQKLGFRQP
151 EKGERICMVG SNFQTKSITS VVSETSTIMP VENSQFWKHW ISTKDGQCGS
201 PMVSTKDGKI LGLHSLANFQ NSINYFAAFP DDFAEKYLHT IEAHEWVKHW
251 KYNTSAISWG SLNIQASQPN IPQTDESTLM TIAYVMAAIC ALFMLPLCLM
301 VCQWRCLRCL RQQHDDFADD ISLLKEQKLI SEEDL
As discussed above, Park teaches the TuMV NIa polypeptide represented by SEQ ID NO: 1 and a polynucleotide sequence encoding it, while Yan teaches the beta-secretase polypeptide represented by SEQ ID NO: 2. As shown in the following alignments, the full length of the translated amino acid sequence (top) encoded by instant SEQ ID NO: 42 is identical to specific regions of the sequences taught by Yan and Park.
First, amino acids 1-56 of the translated polypeptide (top) are identical to the first 56 amino acids of the beta-secretase, SEQ ID NO: 2, taught by Yan (bottom):
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Examiner notes that Yan teaches the propeptide region of Asp2, which follows the leading signal sequence, to extend to about residue 57 based on the GRR-GS sequence which has the characteristics of a protease recognition site (see pg. 14, para. [0110]).
Next, amino acids 56-269 of the translated polypeptide (top) are identical to amino acids 9-222 of the TuMV NIa, SEQ ID NO: 1, taught by Park (bottom):
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Finally, amino acids 270-335 of the translated polypeptide (top) are identical to amino acids 446-501 of the beta-secretase, SEQ ID NO: 2, taught by Yan (bottom):
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For clarity, the translated polypeptide is shown below, with Yan’s SEQ ID NO:2 in bold and Park’s SEQ ID NO: 1 underlined:
1 MAQALPWLLL WMGAGVLPAH GTQHGIRLPL RSGLGGAPLG LRLPRETDEE
51 PEEPGRDYNP ISNNICHLTN VSDGASNSLY GVGFGPLILT NRHLFERNNG
101 ELVIKSRHGE FVIKNTTQLH LLPIPDRDLL LIRLPKDIPP FPQKLGFRQP
151 EKGERICMVG SNFQTKSITS VVSETSTIMP VENSQFWKHW ISTKDGQCGS
201 PMVSTKDGKI LGLHSLANFQ NSINYFAAFP DDFAEKYLHT IEAHEWVKHW
251 KYNTSAISWG SLNIQASQPN IPQTDESTLM TIAYVMAAIC ALFMLPLCLM
301 VCQWRCLRCL RQQHDDFADD ISLLKEQKLI SEEDL
Hence, the claimed instant SEQ ID NO: 42 encodes a polypeptide that consists of the N-terminus of a beta-secretase (including signal sequence and inactive prodomain), the active site of an NIa protease, and the C-terminus of beta-secretase (including the transmembrane and cytoplasmic domains). Accordingly, for the reasons discussed regarding instant claims 1, 13 and 15, it would have been obvious to fuse an NIa protease, or an active fragment thereof, within a β-secretase to arrive at the claimed fusion protein.
Regarding claim 19, Park teaches that the gene carrier containing the NIa protease-encoding nucleotide is a suitable “expression construct” (see col. 5, lines 44-46) and may be a “viral vector” (see claim 1). Yan also teaches vectors comprising polynucleotide molecules for encoding the fusion proteins (see pg. 18, [0152]).
Regarding claim 20, Park teaches the viral vector is a recombinant AAV virus (see col. 7, lines 39-43). Yan also teaches the vectors employed may be viral vectors (see pg. 19, para. 0166).
Regarding claim 21, Park teaches that the NIa gene was cloned into the expression vector, pTYB12, and transformed into a host cell to produce recombinant NIa protein (see col. 9, lines 26-30). Yan also teaches the vector comprising the polynucleotide encoding the fusion protein is expressed in a host cell transfected with said vector (see claims 36, 38 and 42).
Regarding claim 22, Park teaches that the pTYB12-NIa vector was transformed into the E. coli strain BL21 (DE3) (see col. 9, lines 28-30). Yan also teaches that mammalian cells useful in recombinant protein production include Chinese hamster ovary (CHO) cell lines (see pg. 15, para. [0123]), and useful prokaryotic cells include E. coli (see pg. 15, para. [0124]).
Claims 11-12 are rejected under 35 U.S.C. 103 as being unpatentable over Park and Yan as applied to claims 1, 3-7 and 13-22 above, and further in view of Cesaratto 2015 (previously cited), and as further evidenced by NP734212.1 (previously cited).
Regarding claim 11, the claim recites “wherein the another amino acid…” which refers to the variant of the NIa protease recited in lines 20-22 of claim 1, wherein “the variant of the NIa protease is one in which one of the N-glycosylation sites of the NIa protease is substituted with another amino acid having any one of the amino acid sequences represented by SEQ ID NOs: 19 to 21.” As discussed under 35 U.S.C. 112(b), it is reasonably interpreted that the variant comprises one of the amino acid sequences represented by one of SEQ ID NOs 19-21, each of which comprises a substitution at an N-glycosylation site. As shown in the following alignment, Park’s SEQ ID NO: 1 (bottom) comprises the full length of instant SEQ ID NO: 19 (top) with only one mismatch, as annotated below:
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Note that the mismatch above is at position 15 (Q15) in instant SEQ ID NO: 19, which corresponds to position 23 (N23) in Park’s SEQ ID NO: 1.
Park does not explicitly teach a variant of the NIa protease in which one of the N-glycosylation sites of the NIa protease is substituted with another amino acid.
Cesaratto 2015 teaches the tobacco etch virus Nuclear Inclusion a (NIa) gene which encodes a protease named tobacco etch virus protease (TEVp) (see pg. 159, col. 1, para. 1) which is widely used as a purified protein for in vitro applications and as a biological tool that that can be directly expressed in living cells (see Abstract). Cesaratto 2015 teaches that TEVp mutants with different stabilities and enzymatic properties have been reported in adapting the protease to a diverse range of applications (see Abstract). With the aim of targeting TEVp to the endoplasmic reticulum (ER) for biotechnological applications, Cesaratto 2015 engineered a mutated TEVp that showed strong cleavage activity on substrates localized to the ER lumen (see pg. 160, col. 1, para. 3). Cesaratto 2015 teaches that while the wild type TEVp targeted to the secretory pathway of mammalian cells is synthetized as an N-glycosylated and catalytically inactive enzyme, a TEVp mutant with selected mutations at two verified N-glycosylation sites was highly efficient and very active in the ER and can be used as a biotechnological tool to cleave proteins within the secretory pathway (see Abstract).
Examiner notes that Applicant appears to acknowledge Cesaratto 2015’s teachings on pg. 28, lines 6-10 of the instant specification: “It has been reported that when TEV NIa, which is an intracellular protease similar to TuMV, was secreted out of the cell, glycosylation, which did not occur in the original cell, proceeded, and as a result it affected the activity of TEV Nia (Cesaratto et al., 2015).”
Cesaratto 2015 teaches the substitution of N23Q in TEVp NIa, which NP734212.1 is relied upon to represent. Cesaratto 2015 teaches that the N23Q mutation was much more active and similarly resistant to auto-cleavage in cells, compared to the S219P mutant, previously claimed to have higher stability (see pg. 165, col. 1, para. 3).
The GenBank entry for NP734212.1 identifies this sequence as a “NIa-Pro protein” from the “Tobacco etch virus” (see “DEFINITION”). Hence, this sequence represents the TEV NIa of Cesaratto 2015’s disclosure. As shown in the following alignment, position N23 of the TEV NIa protease (bottom) corresponds to position Q15 of instant SEQ ID NO: 19 (top):
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Hence, Cesaratto 2015 teaches a variant NIa protease in which one of the N-glycosylation sites of the NIa protease is substituted with another amino acid, wherein the another amino acid is a glutamine (Gln), and the resulting substitution in Park’s SEQ ID NO: 1 renders a sequence that is identical to instant SEQ ID NO: 19.
It would have been obvious at the time of filing for a person of ordinary skill in the art to have arrived at the claimed invention by combining the teachings of Park, Yan and Cesaratto 2015 by modifying Park’s NIa protease by the removal of an N-glycosylation site via an amino acid substitution, because Cesaratto 2015 teaches that doing so may increase the cleavage activity of the protease in the ER lumen which, as taught by Park, may be a critical site for targeting intracellular Aβ. One would have recognized that both Park and Cesaratto 2015 teach the use of NIa proteases in biotechnology applications for its ability to cleave substrates, while Cesaratto 2015 teaches substitutions at specific sites that enhance the protease’s activity. Furthermore, one would have recognized that the N23Q mutation in the NIa protease taught by Cesaratto 2015 corresponds to the N15 position in Park’s NIa protease, and there would have been a reasonable expectation that this substitution would have resulted in higher activity and stability. One would have also recognized that the TEVp NIa taught by Cesaratto 2015 has a publicly available amino acid sequence which could be readily used for reference when applying this substitution in the NIa protease taught by Park. Hence, the combination would have been readily apparent and deemed to be a mere (A) combining of prior art elements according to known methods to yield predictable results (see MPEP 2143(I): Rationales to support rejections under 35 U.S.C. 103).
Regarding claim 12, the examiner notes that SEQ ID NO: 31 is the translated product of SEQ ID NO: 42 (see, e.g., instant specification at pg. 15, lines 21-25), previously discussed regarding claim 18.
Cesaratto 2015 teaches the substitution N23Q in TEVp NIa, which NP734212.1 is relied upon to represent. Cesaratto 2015 teaches that the N23Q mutation was much more active and similarly resistant to auto-cleavage in cells, compared to the S219P mutant, previously claimed to have higher stability (see pg. 165, col. 1, para. 3).
The GenBank entry for NP734212.1 identifies this sequence as a “NIa-Pro protein” from the “Tobacco etch virus” (see “DEFINITION”). Hence, this sequence represents the TEV NIa of Cesaratto 2015’s disclosure. As shown in the following alignment, position N23 of the TEV NIa protease (bottom) corresponds to position N70 of instant SEQ ID NO: 31 (top):
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Hence, it would have been obvious to have made this substitution in the NIa fusion protein at the position corresponding to N70 in instant SEQ ID NO: 31.
Response to Arguments
Regarding the rejection of claims under 35 U.S.C. 112(a) as failing to comply with the written description requirement, Applicant argues that the claims are amended to comply with the written description requirement and are supported from paragraph 0069, Formula 2-4 and Examples 3, 6 and 7 of the present application.
Applicant’s arguments have been fully considered and are persuasive. Specifically, the limitations of “a fragment” and “a variant” of an NIa protease have been narrowed in scope to the species which are adequately described in Applicant’s disclosure. Accordingly, the rejection under 35 U.S.C. 112(a) has been withdrawn.
Regarding the rejections under 35 U.S.C. 103, Applicant argues that “a prima facie case of obviousness cannot be established, because the Office failed to properly determine the scope and content of the applied references”. Applicant proceeds to present evidence from the instant specification, stating, “[v]arious fusion protein SAS have been synthesized in the Examples of the present specification (see paras. [0080] to [0091], [0135], [0136], [0144] to [0146], and Figs. 2, 6, 9 and 10).”
Applicant’s argument is not persuasive, because it fails to specifically point out the alleged deficiencies of the applied references. It is particularly unclear how the “various fusion protein SAS” proteins of the specification relates to the “scope and content” of the applied references, because Applicant does not compare any of the cited information from the specification with the prior art references which were used in the rejection.
Applicant further argues that “[t]he Office admitted Park fails to teach the fusion protein wherein the signal sequence is derived from β-secretase” and “Park fails to teach ‘the NIa protease has any one of the amino acid sequences represented by SEQ ID NOs: 13, and 15; or the fragment of the NIa protease is a polypeptide having any one of the amino acid sequences represented by SEQ ID NOs 13 to 21’ as recited in claim 1.”
In response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). In the instant case, Park does teach an NIa protease comprising SEQ ID NO: 13, which may also include a growth factor signal peptide sequence, as discussed in the present rejection. The rejection further relies upon the teachings of Yan, who teaches a signal sequence derived from a beta-secretase.
Applicant further argues that Yan provides a compound that is cleaved by Hu-Asp2 to confirm the β-secretase activity of human Asp2 protease (see Yan, paragraph [0045]), and does not disclose the NIa protease fusion protein of synthetic α-secretase at all. Specifically, Yan relates to β-secretase, which performs a function completely opposite to synthetic α-secretase (SAS) of claim 1. Yan fails to teach the signal sequence is derived from β-secretase in the fusion protein of synthetic α-secretase (SAS) as recited in claim 1.
Applicant’s arguments have been full considered but are not persuasive for the following reasons.
First, Applicant is reminded that one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. It is apparent in view of the prior art, that NIa protease (as taught by Park) and β-secretase (as taught by Yan) are relevant to the formation/degradation of amyloid plaques. As discussed in the rejections under 35 USC 103, a person of ordinary skill would have recognized the advantage of combining elements of NIa and β-secretase in a fusion protein based on the relevant teachings of both references. Furthermore, Yan teaches the β-secretase includes a putative signal peptide (see pg. 14, para. [0110]), while Park teaches the NIa protease may be fused to a signal peptide sequence for effectively penetrating cells (see col. 5, lines 26-28 and 31-33), as discussed in the rejection.
Second, Applicant’s argument that the present invention relates to “synthetic α-secretase” (SAS) while “Yan relates to β-secretase” is misleading. The present inventors explicitly disclose that “SAS was prepared by fusing the N-terminus and C-terminus of NIa with the prodomain and transdomain of β-secretase” (see instant specification at pg. 25, lines 1-2). The fact that Applicant refers to the claimed fusion protein as a “synthetic alpha-secretase” does not change its underlying structure, which is explicitly derived from β-secretase, even in view of the claims.
Finally, Applicant is reminded that "The use of patents as references is not limited to what the patentees describe as their own inventions or to the problems with which they are concerned. They are part of the literature of the art, relevant for all they contain." In re Heck, 699 F.2d 1331, 1332-33, 216 USPQ 1038, 1039 (Fed. Cir. 1983) (quoting In re Lemelson, 397 F.2d 1006, 1009, 158 USPQ 275, 277 (CCPA 1968)). In the instant case, the Yan reference was relied upon for its teachings of beta-secretase translocation and activity in vivo and the structure- function relationships of its respective components (signal sequence, transmembrane domain, etc.) for constructing fusion proteins. From these teachings, a person of ordinary skill would have recognized that the active site of beta-secretase has a function that is, in a sense, “opposite” of an NIa protease (i.e., it cleaves APP to generate amyloid-beta which contributes to disease) and would have recognized the therapeutic potential of replacing this site with an NIa protease, which Park teaches to cleave amyloid-beta in a manner that significantly prevents such diseases (see, e.g., Park at col. 2, lines 34-40).
Applicant further argues that the Office failed to apply Cesaratto 2015 in a manner sufficient to cure the above noted deficiencies of Park in view of Yan. Therefore, one of ordinary skill in the art could not have a motivation and could not combine Park into Yan, and Cesaratto 2015. Amended claim 1 is not obvious to one of ordinary skill in the art over the applied references. Thus, for at least the above reasons, independent claim 1 is patentable over the combination of Park, Yan, and Cesaratto 2015. Dependent claims 3-7, and 11-22 are patentable over the applied references, for the same reason as independent claim 1 is patentable, as well as for the additional features this claim recites.
Applicant's arguments fail to comply with 37 CFR 1.111(b) because they amount to a general allegation that the claims define a patentable invention without specifically pointing out how the language of the claims patentably distinguishes them from the references. In the instant case, Applicant does not specifically point out (1) how the Office “failed” to apply Cesaratto 2015, (2) why one of ordinary skill could not have a motivation to combine the references, and (3) why one of ordinary skill “could not combine” Park with Yan and Cesaratto 2015.
Furthermore, Applicant does not specifically point out what “additional features” recited in the claim make the claims patentable over the recited references. This fails to comply with 37 CFR 1.111(c) because Applicant’s argument does not clearly point out the patentable novelty which he or she thinks the claims present in view of the state of the art disclosed by the references cited or the objections made. Further, they do not show how the amendments avoid such references or objections.
Finally, in response to applicant’s argument that there is no motivation to combine the references, the examiner recognizes that obviousness may be established by combining or modifying the teachings of the prior art to produce the claimed invention where there is some teaching, suggestion, or motivation to do so found either in the references themselves or in the knowledge generally available to one of ordinary skill in the art. See In re Fine, 837 F.2d 1071, 5 USPQ2d 1596 (Fed. Cir. 1988), In re Jones, 958 F.2d 347, 21 USPQ2d 1941 (Fed. Cir. 1992), and KSR International Co. v. Teleflex, Inc., 550 U.S. 398, 82 USPQ2d 1385 (2007). In this case, both Park and Yan relate to amyloid-beta-related pathologies, such as Alzheimer’s disease, and describe the structure-function relationships of amyloid beta and beta-secretase. One would have recognized the advantage of fusing an NIa protease active site into a beta-secretase protein to effectively enhance the translocation of NIa to sites in vivo for the degradation of amyloid-beta (as discussed regarding claim 1). One would have also recognized from Cesaratto 2015 the advantage of removing an N-glycosylation site to increase the cleavage activity of the NIa protease in the endoplasmic reticulum (as discussed regarding claims 11-12).
Conclusion
No claims are allowed.
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/DENNIS IGNATIUS ARMATO JR/Examiner, Art Unit 1651
/MELENIE L GORDON/Supervisory Patent Examiner, Art Unit 1651