DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
Applicant’s election without traverse of Group IV, drawn to a reaction mixture comprising a first aminopeptidase having a sequence at least 92% identical to SEQ ID NO: 3 and a tag sequence in the reply filed on 4/27/2026 is acknowledged. Claims 64-65 and 75-91 encompass the elected invention. Claims 1-2, 4-5, 7-10, 12, 15-16, 22, 26, 30-31, 63, 66-67, and 73-74 were canceled.
Claim 92 is withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 4/27/2026.
Priority
This application claims benefit of 63/418,287 (10/21/2022).
Information Disclosure Statement
The information disclosure statement filed 4/27/2026 fails to comply with 37 CFR 1.98(a)(2), which requires a legible copy of each cited foreign patent document; each non-patent literature publication or that portion which caused it to be listed; and all other information or that portion which caused it to be listed. The references not considered by the examiner are lined through on the IDS form.
The information disclosure statement (IDS) filed on 5/22/2024 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 64-65 and 75-91 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Regarding written description, 35 U.S.C. 112(a) and the first paragraph of pre-AlA 35 U.S.C. 112 require that the "specification shall contain a written description of the invention ...." This requirement is separate and distinct from the enablement requirement. Ariad Pharm., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1340, 94 USPQ2d 1161, 1167 (Fed. Cir. 2010). To satisfy the written description requirement, a patent specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention (MPEP § 2163(I)).
MPEP 2163(II)(A)(3)(a)(i and ii) states that the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus.
A "representative number of species" means that the species which are adequately described are representative of the entire genus. See AbbVie Deutschland GmbH & Co., KG v. Janssen Biotech, Inc., .759 F.3d 1285, 1300, 111 USPQ2d 1780, 1790 (Fed. Cir. 2014). Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus.
In the instant case, claim 64 recites a first cleaving reagent with a sequence at least 92% identical to SEQ ID NO: 3, and claim 76 recites that the first aminopeptidase sequence is at least 94% identical to SEQ ID NO: 3. Claim 78 recites that the second aminopeptidase comprises an amino acid sequence that is at least 80% identical to SEQ ID NO: 1. Claim 88 recites that the third aminopeptidase comprises an amino acid sequence that is at least 80% identical to SEQ ID NO: 7.
There is not sufficient written description support for aminopeptidases having the claimed percent sequence identities and maintaining the function of peptide cleavage. SEQ ID NO: 3 has 353 amino acid residues, meaning that ~21-28 residues may differ from SEQ ID NO: 3 within the range of 92-94% identity. This encompasses a large number of potential amino acid sequences, including substitutions at one or more of 21-28 residues, as well as insertions or deletions. There is not a disclosure of which residues or regions are important for activity, i.e. which residues may or may not differ from the original sequence while maintaining the enzyme cleavage activity. There are no examples of aminopeptidases with sequences in the range of 92-94% identity and having aminopeptidase activity.
Similarly, SEQ ID NO: 1 has 353 amino acids, and SEQ ID NO: 7 has 445 amino acids. This means that ~70 or ~89 amino acids may differ from the original SEQ ID NOs: 1 and 7, respectively, within the range of 80% identity, encompassing a vast number of potential amino acid sequences having substitutions at one or more of 70 or 89 residues, as well as insertions or deletions. There is not a disclosure of which residues are important for activity, i.e. which residues may or may not differ from the original sequence while maintaining the enzyme cleavage activity. There are no examples of aminopeptidases with sequences within the range of 80% identity which maintain peptide cleavage activity.
For this reason, the aminopeptidases as set forth in claims 64, 76, 78, and 88 do not have sufficient written description support to show that the applicant was in possession of the entire genus of aminopeptidases as claimed.
Claims 65, 75, 77, 79-87, and 89-90 are included in this rejection because they depend on a rejected claim and do not clarify the issue.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 64-65 and 75-91 are rejected under 35 U.S.C. 103 as being unpatentable over Franzetti et al., US 2021/0380960 A1 in view of Reed et al., US 2020/0209257 A1.
Regarding claim 64, Franzetti teaches a composition for hydrolyzing polypeptides comprising at least one first aminopeptidase and at least one second aminopeptidase, which are enzymes exhibiting amino acid cleavage activity, i.e. cleaving reagent (Franzetti Abstract; p. 1 para. 9). Franzetti teaches that the two aminopeptidases may be PhTET2 and PhTET3 (Franzetti p. 2 para. 18). PhTET3 has a sequence according to SEQ ID NO: 3, which is 99.4% identical to instant SEQ ID NO: 3 (see sequence alignment in OA appendix). PhTET2 has a sequence according to SEQ ID NO: 2 (Franzetti p. 2 para. 18), which is less than 80% identical to PhTET3, or SEQ ID NO: 3 of Franzetti (see sequence alignment in OA appendix). Thus, Franzetti teaches a composition which is used for enzymatic reactions (Franzetti p. 7 para. 96), i.e. a reaction mixture, comprising a first aminopeptidase cleaving reagent (PhTET3) with a sequence that is at least 92% identical to instant SEQ ID NO: 3, and a second aminopeptidase cleaving reagent (PhTET2) with a sequence that is less than 80% identical to the first aminopeptidase.
Regarding claim 75, Franzetti teaches that the amino acid sequences of the first and second aminopeptidases, PhTET3 and PhTET2, are less than 60% identical (50.6% identical, see sequence alignment in OA appendix).
Regarding claim 76, Franzetti teaches that the amino acid sequences of the first aminopeptidase, PhTET3, is at least 94% identical (99.4% identical) to instant SEQ ID NO: 3 (see sequence alignment in OA appendix).
Regarding claim 77, Franzetti teaches that the second aminopeptidase, PhTET2, is from Pyrococcus horikoshii (Franzetti p. 1 para. 7).
Regarding claim 78, Franzetti teaches that the second aminopeptidase, PhTET2, is at least 80% identical (100% identical) to instant SEQ ID NO: 1 (see sequence alignment in OA appendix).
Regarding claim 83, the first cleaving reagent as set forth in claim 64 is PhTET3 as taught by Franzetti (sequence is at least 92% identical to instant SEQ ID NO: 3). Franzetti teaches that the aminopeptidases are present in a ratio ranging from 1:99 to 40:60 by weight relative to the total weight of the composition (Franzetti p. 2 para. 13). Thus, in an embodiment as taught by Franzetti, the composition may comprise PhTET2 and PhTET3 at a ratio of 1:99 by weight. As PhTET3 is the first cleaving reagent as recited in claim 64 (sequence is at least 92% identical to instant SEQ ID NO: 3), the concentration of first cleaving reagent PhTET3 is at least two-fold higher than the second, PhTET2.
Regarding claim 86, Franzetti teaches that the reaction mixture further comprises a third aminopeptidase (Franzetti p. 3 para. 34).
Regarding claim 90, Franzetti teaches that a first, second, and third aminopeptidase may be in a composition in a ratio of 10/10/80 by weight relative to the total weight of the composition (Franzetti p. 4 para. 37). The aminopeptidases of Franzetti may be a 10/10/80 ratio of PhTET1/PhTET2/PhTET3 (Franzetti p. 3 para. 34). Thus, the first cleaving reagent of claim 64 (PhTET3) is at a concentration at least two-fold higher than the second cleaving reagent and at least five-fold higher than the third cleaving reagent.
Franzetti does not teach that the aminopeptidase with a sequence at least 92% identical to SEQ ID NO: 3 comprises a tag sequence (claim 64), that the second aminopeptidase cleaving reagent comprises a tag sequence (claim 79), that the first and second tag sequences are between 2-100 amino acids in length (claim 80), that the tag sequences are attached to the terminal end of the aminopeptidases (claim 81), that the tag sequences are a polyhistidine or biotinylation tag (claim 82), or that the third cleaving reagent comprises a third tag sequence (claim 89).
Regarding claims 64, 79, and 89, Reed teaches a reaction mixture for polypeptide analysis with a composition comprising one or more terminal amino acid recognition molecules and a cleaving reagent (Reed p. 2 para. 10). Reed teaches that the amino acid recognition molecule comprises a tag sequence which provides functions other than amino acid binding, including purification or modification of the recognition molecules (Reed p. 15 para. 109). Reed teaches that the amino acid recognition molecule or affinity reagent is a peptidase, and that suitable peptidases for recognition molecules include aminopeptidases (Reed p. 15 para. 110; p. 16 para. 115). One suitable aminopeptidase is Pyrococcus horikoshii TET Aminopeptidase which has a sequence according to SEQ ID NO: 59, and is 100% identical to instant SEQ ID NO: 1 (see sequence alignment in OA appendix; Reed p. 19 Table 4). Reed teaches embodiments wherein the recognition molecule peptidase has not been modified to inactivate the peptidase activity (Reed pp. 15-16 para. 110). Thus, Reed teaches aminopeptidases which have cleaving activity (cleaving reagent) and a tag sequence.
Regarding claim 80, Reed teaches that the tag sequences are between 2-100 amino acids in length (Reed p. 15 Table 2).
Regarding claim 81, Reed teaches that the tag sequences are attached to the N- or C- terminus (Reed p. 15 para. 108).
Regarding claim 82, Reed teaches that the tag sequences may be polyhistidine tags or biotinylation tags, or a combination thereof (Reed p. 15 Table 2; para. 109).
It would have been obvious for a skilled artisan to modify the aminopeptidases of Franzetti to include a tag sequence such as a polyhistidine tag or biotinylation tag at the terminal end of the protein. Both Franzetti and Reed teach reaction mixtures including aminopeptidases from Pyrococcus horikoshii, including an aminopeptidase with a sequence according to instant SEQ ID NO: 1. It would have been obvious that the aminopeptidases as taught by Franzetti could have been modified with a polyhistidine or biotinylation tag in the same way as the aminopeptidases of Reed.
A person of ordinary skill in the art would have been motivated to modify the aminopeptidases of Franzetti with a tag as taught by Reed because polyhistidine or biotinylation tags provide additional function and are useful for purification and modification of the polypeptides (Reed p. 15 para. 109). It would therefore be considered advantageous to modify the aminopeptidases of Franzetti with tag sequences that are known to confer beneficial functions to the modified polypeptide, such as facilitating purification.
A skilled artisan would have had a reasonable expectation of success in making this modification because tag sequences, in particular polyhistidine and biotinylation tags, are established in the art as common protein modifications to allow for purification and other functional features (Reed p. 15 para. 109; Table 2). As Reed teaches that aminopeptidases, including aminopeptidases from Pyrococcus horikoshii such as those taught by Franzetti, can be modified in this way, a skilled artisan could expect success in modifying the aminopeptidases taught by Franzetti to include a polyhistidine or biotinylation tag.
Franzetti does not teach that the reaction mixture further comprises an amino acid binding protein not having peptide cleavage activity (claim 65).
Regarding claim 65, Reed teaches that the reaction mixture may contain a peptidase affinity reagent that has been modified to inactivate exopeptidase or endopeptidase activity, allowing the peptidase to selectively bind without cleaving the polypeptide (Reed p. 15 para. 110). Thus, Reed teaches a reaction mixture with one or more binding proteins that do not have peptide cleavage activity.
It would have been obvious for a skilled artisan to modify the mixture of Franzetti and include an amino acid binding protein that does not have peptide cleavage activity based on the teachings of Reed. Both Franzetti and Reed are directed to reaction mixtures comprising aminopeptidases. Reed teaches that the aminopeptidases can be modified to be inactivated in order to selectively bind without cleaving the polypeptide, which is useful for certain sequencing applications wherein detection of the polypeptide without cleavage is desired. It would have been obvious that the reagents taught by Franzetti could be similarly modified to eliminate cleavage activity, resulting in a reaction mixture that has cleaving reagents and additional binding proteins without cleaving activity.
A person of ordinary skill in the art would have been motivated to modify the reaction mixture of Franzetti to include binding proteins without peptide cleavage activity by inactivating the cleavage activity of an aminopeptidase, because aminopeptidases which have been modified to eliminate peptide cleavage activity are able to bind selectively for use as a labeled affinity reagent for detection of a polypeptide without cleaving the polypeptide (Reed p. 16 para. 111; 114).
A skilled artisan would have had a reasonable expectation of success in making this modification to the reaction mixture of Franzetti because Reed teaches similar reaction mixtures comprising aminopeptidases, some of which are active cleaving reagents and some of which have been inactivated to become binding proteins without cleavage activity. Thus, a skilled artisan could expect success in creating such a reaction mixture with the similar aminopeptidases as taught by Franzetti, using techniques for catalytic inactivation of the aminopeptidases that are known in the art (Reed p. 16 para. 111).
Franzetti does not teach the concentrations of cleaving reagents as recited in claims 84, 85 and 91.
Regarding claims 84, 85, and 91, Reed teaches that the reaction mixture comprises an amino acid recognition molecule/affinity reagent at a concentration of 10 nM to 10 µM and a cleaving reagent at a concentration of 500 nM to 500 µM (Reed p. 25 para. 151). Reed teaches that the amino acid recognition molecule or affinity reagent is a peptidase, and that suitable peptidases for recognition molecules include aminopeptidases, which may retain cleaving activity (Reed p. 15 para. 110; p. 16 para. 115). Thus, Reed teaches a mixture comprising two aminopeptidases with cleaving activity, wherein one has a concentration within the range of 10 nM (0.01 µM) to 10 µM and the other has a concentration in a range of 500 nM (0.5 µM) to 500 µM. When claimed ranges "overlap or lie inside the ranges disclosed by the prior art" and even when the claimed ranges and prior art ranges do not overlap but are close enough that one skilled in the art would have expected them to have similar properties, a prima facie case of obviousness exists. See MPEP 2144.05(I).
Further, Franzetti teaches that the concentrations of aminopeptidases in the composition may be modified and used at various ratios of different aminopeptidases depending on the desired outcome and specific aminopeptidases used (Franzetti p. 2 para. 13) and Reed teaches that the concentrations of aminopeptidases in the reaction mixture can be optimized depending on the desired use and outcome of the reaction mixture (Reed p. 25 para. 150). This means that the concentrations of aminopeptidases (cleaving reagents) used in the mixture are result-effective variables. Result-effective variables would be optimized through routine experimentation by one having ordinary skill in the art. It would have been obvious for a skilled artisan, given the teachings of Franzetti and Reed, to optimize the concentrations of each of the aminopeptidases in the reaction mixture. Especially given the teachings of Reed using concentrations of aminopeptidases overlapping with the concentration ranges set forth in claims 84-85 and 91, a skilled artisan would have found it obvious to arrive at a reaction mixture with aminopeptidases at the claimed concentrations. Furthermore, differences in concentration will not support the patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration is critical. See MPEP 2144.05(II)(A).
Franzetti does not teach that the third aminopeptidase is an aminopeptidase from Yersinia pestis (claim 87) which comprises an amino acid sequence that is at least 80% identical to SEQ ID NO: 7 (claim 88).
Regarding claim 87, Reed teaches that the cleaving reagent may be an aminopeptidase from Yersinia pestis (Reed p. 16 Table 3).
Regarding claim 88, the aminopeptidase from Yersinia pestis taught by Reed has a sequence according to SEQ ID NO: 48, which is 99.6% identical to instant SEQ ID NO: 7 (see sequence alignment in OA appendix, Reed p. 16 Table 3).
It would have been obvious for a skilled artisan to substitute the third aminopeptidase as taught by Franzetti with the Yersinia pestis aminopeptidase with a sequence 99.6% identical to SEQ ID NO: 7 as taught by Reed. Both Franzetti and Reed teach compositions comprising multiple aminopeptidases. The aminopeptidases suitable for use as cleaving reagents as taught by Reed include Y. pestis aminopeptidases as well as Pyrococcus horikoshii TET Aminopeptidases (Reed Tables 3-4). It would have been obvious for a skilled artisan to substitute an aminopeptidase from Y. pestis as the third aminopeptidase in the composition of Franzetti, as both the aminopeptidases of Franzetti and Reed are suitable for the same function of polypeptide binding and cleavage.
A person of ordinary skill in the art would have been motivated to make this substitution because each of the aminopeptidases as taught by Franzetti and Reed have different selective binding activity and would thus be useful for different binding and cleavage purposes depending on the desired use of the reaction mixture. It would be considered beneficial to use different combinations of aminopeptidases with distinct binding interactions in order to create various reaction mixtures with broad cleavage and/or binding capabilities to different polypeptides.
A skilled artisan would have had a reasonable expectation of success in making this substitution because Franzetti teaches that three aminopeptidases may be used in a single reaction mixture, and Reed teaches that the Y. pestis aminopeptidase is suitable as a cleavage reagent. Thus, it could reasonably be expected that the aminopeptidases taught by Franzetti could be used in combination with those of Reed, especially given the overlap in aminopeptidases taught by both references, i.e. Pyrococcus horikoshii aminopeptidases.
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 64-65, 75-76, 79-88, and 90-91 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 142-154 of copending Application No. 19/009,859 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because both are directed to compositions comprising aminopeptidase cleaving reagents.
Regarding instant claim 64, claims 142 and 143 of ‘859 recites a composition comprising: a first cleaving reagent comprising an aminopeptidase from Pyrococcus horikoshii; and a second cleaving reagent comprising an aminopeptidase from Streptomyces griseus, wherein the first cleaving reagent comprises an amino acid sequence that is at least 85% identical to SEQ ID NO: 3. SEQ ID NO: 3 of ‘859 is 100% identical to instant SEQ ID NO: 3. Claim 146 of ‘859 recites that the second aminopeptidase is at least 85% identical to SEQ ID NO: 101. SEQ ID NO: 3 and SEQ ID NO: 101 of ‘859 are less than 80% identical to each other. Claim 144 of ‘859 recites that the first cleaving reagent comprises a tag sequence attached to the terminal end of the aminopeptidase.
Regarding instant claims 65, 75-76, 79-88, and 90-91, all the limitations of these dependent claims are recited in claims 142-154 of ‘859.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
Claims 64-65 and 75-91 are rejected. No claims are allowed.
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/EMILY F EIX/Examiner, Art Unit 1653
/SHARMILA G LANDAU/Supervisory Patent Examiner, Art Unit 1653
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