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 with traverse of claims 1-14 in the reply filed on 1/16/2026 is acknowledged. The traversal is on the ground(s) that a search of the claimed invention of one group will identify references that are material to the other group and would not pose an undue burden. This is not found persuasive because the instant application is a national stage application submitted under 35 U.S.C. 371, and therefore requires unity of invention analysis rather than the independent and distinct analysis required for applications filed under 35 U.S.C. 111(a). Applicant is directed to MPEP § 823. The unity of invention analysis does not require establishment of undue burden.
The requirement is still deemed proper and is therefore made FINAL.
Claims 15-17 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 1/16/2026.
Applicant did not respond to the species election requirement. However, in view of the prior art search, the species election is withdrawn.
Priority
This application is a 371 of PCT/EP2022/062467 (5/9/2022) which claims priority to GB2106771.5 (5/12/2021) as reflected in the filing receipt issued on 6/4/2025.
Information Disclosure Statement
The information disclosure statement(s) (IDS) filed on 10/17/2023 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement(s) is/are being considered by the examiner.
Claim Objections
Claims 3-5, 8, and 12-13 are objected to because of the following informalities:
Claims 3 and 4 recite “amino acid that provide increased solubility is”. This should instead be “amino acid that provides increased solubility is”.
Claim 5 recites “non-Cystein”. This should instead be “non-Cysteine”.
Claim 8 recites “solid phased”. This should instead by “solid phase”.
Claims 12 and 13 recite “proein variant”. This should instead be “protein variant”.
Appropriate correction is required.
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 1-14 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.
In claim 1, the limitation “An N-intein protein variant derived from wildtype Nostoc punctiforme (Npu) or sequences having at least 95% homology therewith” is unclear. There are multiple interpretations of the alternatives presented by this limitation.
It is unclear if the claim is directed to the options:
An N-protein variant derived from wildtype Npu
or
Sequences having at least 95% homology therewith
Or if the claim is directed to an N-protein variant that is alternatively:
Derived from wildtype NPU
or
Derived from sequences having at least 95% identity therewith
Further, claim 1 recites “sequences having at least 95% homology therewith”. However,
claim 1 does not recite a sequence. For this reason, it is not clear which sequence the sequences are homologous to.
Additionally, the use of “homology” in claim 1 is unclear. As set forth in the specification,
p. 12:
"Sequence homology" can refer to the situation where nucleic acid or protein
sequences are similar because they have a common evolutionary origin. "Sequence
homology" can indicate that sequences are very similar. Sequence similarity is observable;
homology can be based on the observation. "Very similar" can mean at least 70% identity,
homology or similarity; at least 75% identity, homology or similarity; at least 80% identity,
homology or similarity; at least 85% identity, homology or similarity; at least 90% identity,
homology or similarity; such as at least 93% or at least 95% or even at least 97% identity,
homology or similarity.
Based on the above, and as commonly understood in the art, “homology” refers to whether or not two sequences share a common evolutionary origin, which is determined based on quantitative measurements of percent identity or similarity. However, it is not clear based on the disclosure if applicant is using the terms homology, similarity, and identity interchangeably (i.e., to mean number of identical positions between two sequences), or if similarity and identity are the quantitative measure of homology. For this reason, it is unclear what is meant by “95% homology”. If the terms are meant to be interchangeable, this would be taken to mean 95% of positions are the same amino acids. However, if homology is a characteristic determined based on similarity/identity, then two sequences would either be considered homologous or not homologous, and a percentage homology does not make sense. As the specification does not define homology, but only sets forth exemplary embodiments of what sequence homology can refer to, the meaning of this term in claim 1 is not clear. For purposes of examination, it is considered that this limitation refers to 95% of residues being identical between two sequences.
A broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c).
In the present instance, claim 6 recites the broad recitation “a single point mutation”, and the claim also recites “preferred N or non-positive amino acid” which is the narrower statement of the range/limitation. Claim 9 recites “a natural or synthetic resin”, and the claim also recites “preferably a polysaccharide”, which is the narrower statement of the range/limitation. Claim 14 recites “per ml solid phase”, and the claim also recites “preferably chromatography resin” which is the narrower statement of the range/limitation. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims.
Regarding claims 7 and 9, the phrase "such as" renders the claim indefinite because it is unclear whether the limitations following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
Claim 14 recites “preferably chromatography resin (ml swollen gel)”. The parentheses around “ml swollen gel” renders this limitation indefinite, as it is unclear if “ml swollen gel” is a required or optional feature of the claim.
Claims 2-5, 8, and 10-13 are included in this rejection because they depend on a rejected claim and do not clarify the issue.
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.
(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.
Claims 1-3 and 5-6 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Muir et al., WO 2017/132580 (hereinafter Muir ‘580).
Regarding claim 1, Muir ‘580 teaches a Cfa split intein derived from Npu, with a mutation of K24E compared to the wildtype Npu DnaE sequence (Muir ‘580 Fig. 1; p. 15 para. 65).
The limitation “wherein the substituted amino acid provides increased solubility in aqueous buffers compared to the native N-intein protein sequence or a consensus N-intein sequence” is a functional limitation of the claimed variant protein. Any N-intein variant having the claimed structure is considered capable of performing this function. Thus, the intein variant of Muir ‘580 anticipates claim 1.
Regarding claims 2 and 3, Muir ‘580 teaches that the substituted amino acid is a non-positive amino acid, specifically K24E (Muir ‘580 Fig. 1).
Regarding claim 5, the structure of the claimed N-intein protein variant is a protein with the substitutions K24E and R25N relative to SEQ ID NO: 1. Muir ‘580 teaches an N-intein according to SEQ ID NO: 257, which is homologous to the Npu DnaE N-intein and comprises substitutions of both K to E at position 24 and R to N at position 25 relative to instant SEQ ID NO: 1 (see sequence alignment in OA appendix, Muir p. 35 para. 444 and p. 36 para. 445). As set forth in the instant specification, p. 8, "variant" refers to a molecule that retains a biological activity that is the same or substantially similar to that of the original sequence. Thus, this protein anticipates the structure of claim 5, as the N-intein of SEQ ID NO: 257 is homologous to the wildtype Npu DnaE N-intein and is therefore considered a variant of the Npu DnaE N-intein with a sequence according to instant SEQ ID NO: 1.
The limitation “to increase solubility in aqueous buffers” is an intended use of the claimed protein. Any protein having the same structure is capable of performing this intended use. Therefore, the N-intein protein variant of Muir ‘580 reads on claim 5.
Regarding claim 6, the solubility of the protein in an aqueous buffer is a functional limitation of the claimed protein. Any N-intein variant having the claimed structure is considered capable of performing this function. Thus, the intein variant of Muir ‘580, Cfa split intein, is considered to have a solubility as claimed for an N-intein with mutation K24E.
Claim Rejections - 35 USC § 102/103
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:
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.
Claim 4 is rejected under 35 U.S.C. 102(a)(1) as anticipated by or, in the alternative, under 35 U.S.C. 103 as obvious over Muir et al., WO 2017/132580 (hereinafter Muir ‘580).
Muir ‘580 teaches an N-intein protein variant derived from Npu that includes a mutation in position 24, and thus anticipates claim 1, as discussed above. This embodiment in Muir ‘580 does not include a mutation of R25N relative to the wildtype Npu, as required by claim 4.
Regarding claim 4, Muir ‘580 teaches an N-intein protein, with a sequence according to SEQ ID NO: 257, which has mutations K24E and R25N relative to instant SEQ ID NO: 1, as discussed regarding claim 5 above (see sequence alignment in OA appendix, Muir p. 36 para. 445). The N-intein according to SEQ ID NO: 257 taught by Muir ‘580 is a DnaE N-intein from Cyanothece sp. ATCC 51142 (Muir ‘580 p. 35 para. 444).
Claim 4, including the limitations of claim 1, is directed to an N-intein protein variant, which is produced by the claimed process, i.e. derived from wildtype Nostoc punctiforme (Npu) or sequences having at least 95% homology therewith, and having a mutation of R25N. The N-intein in this embodiment, SEQ ID NO: 257, was not derived from Npu or sequences having 95% homology therewith.
However, "[E]ven though product-by-process claims are limited by and defined by the process, determination of patentability is based on the product itself. The patentability of a product does not depend on its method of production. If the product in the product-by-process claim is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process." In re Thorpe, 777 F.2d 695, 698, 227 USPQ 964, 966 (Fed. Cir. 1985).
Here, Muir ‘580 teaches an N-intein (SEQ ID NO: 257) that is homologous to the Npu DnaE intein (Muir ‘580 p. 15 para. 65). Therefore, functionally, the N-intein of Muir ‘580 represented by SEQ ID NO: 257 is the same as the claimed N-intein. As set forth in the instant specification, p. 8, "variant" refers to a molecule that retains a biological activity that is the same or substantially similar to that of the original sequence. As such, the N-intein variant of Muir ‘580 is the same as, or would have rendered obvious, the N-intein produced by the claimed process with a substitution of R25N.
"The Patent Office bears a lesser burden of proof in making out a case of prima facie obviousness for product-by-process claims because of their peculiar nature" than when a product is claimed in the conventional fashion. In re Fessmann, 489 F.2d 742, 744, 180 USPQ 324, 326 (CCPA 1974). Once the examiner provides a rationale tending to show that the claimed product appears to be the same or similar to that of the prior art, although produced by a different process, the burden shifts to applicant to come forward with evidence establishing an unobvious difference between the claimed product and the prior art product. In re Marosi, 710 F.2d 798, 802, 218 USPQ 289, 292 (Fed. Cir. 1983).
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 7-11 and 14 are rejected under 35 U.S.C. 103 as being unpatentable over Muir ‘580 et al. in view of Ohman et al., WO 2018/091424 as evidenced by Strancar et al., Modern Advances in Chromatography; 14:49-85.
Muir ‘580 teaches the N-intein variant of claim 1 as discussed above. Muir ‘580 does not teach that the N-intein is attached to a solid phase as set forth in claims 7-11 and 14.
Regarding claim 7, Ohman teaches Nostoc punctiforme DnaE N-intein fragments immobilized/attached to a solid support, which can be any solid support, including a surface, particle or bead (Ohman p. 7 lines 2-3).
Regarding claims 8-9, Ohman teaches that the N-intein fragments are immobilized/attached to a chromatography resin (Ohman p. 1 lines 1-9; p. 5 lines 7-9). Ohman teaches that the chromatography resin is of natural or synthetic origin, i.e. agarose, polystyrene, methacrylate or cellulose beads, preferably agarose (Ohman p. 6 lines 4-5).
Regarding claim 10, Ohman teaches that the solid phase comprises magnetic beads (Ohman p. 6 lines 14-16).
Regarding claim 11, Ohman teaches that the solid phase chromatography resin includes porous monoliths (Ohman p. 6 lines 14-15). As evidenced by Strancar, monoliths are a non-diffusional resin, as diffusional constraints limit separation speed in conventional columns whereas the mobile phase is forced to flow through in monoliths resulting in fast separation (Strancar p. 51 para. 2; p. 53 Section 1.3).
Regarding claim 14, Ohman teaches that the ligand density on the chromatography resin is 2-10 mg ligand/ml resin (Ohman p. 6 lines 11-12). Ohman teaches that the molecular weight of Npu N-intein ligand is 12.8 kDa, or 12800 g/mol (Ohman p. 19 lines 10-11). Thus, the range taught by Ohman corresponds to 0.16-0.78 µmol/ml resin (2-10 mg / 12800g/mol). Therefore, the range taught by Ohman is within the claimed range.
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). 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).
It would have been obvious for a skilled artisan, before the effective filing date, to combine the teachings of Muir ‘580 and Ohman, resulting in an N-intein as taught by Muir ‘580 attached to a solid support as taught by Ohman. Both Muir ‘580 and Ohman are directed to Npu N-intein compositions. It would have been obvious to a skilled artisan that the N-intein as taught by Muir ‘580 could be attached to a solid phase, specifically a chromatography resin as instantly claimed, given the teachings of Ohman directed to a wildtype Npu N-intein.
A person of ordinary skill in the art would have been motivated to modify the teachings of Muir ‘580 and attach the N-intein to a solid support because the improved affinity resin taught by Ohman allows for predictable purifications, preferably in formats such as columns or filters for use together with chromatography systems for increased versatility and efficiency (Ohman p. 5 lines 1-5). Further, the chromatography resin with immobilized/attached N-terminal intein fragments provides higher ligand densities and enables multiple re-use even after harsh cleaning procedures (Ohman p. 5 lines 6-9). Ohman teaches that other Npu N-intein purification systems are a two-step procedure and the highly exposed hydrophobic surface of the intein N-fragment of DnaE tends to interfere with the folding and/or solubility during expression, potentially causing aggregation and loss of yield, thus limiting the use of this split intein system, and there is a need for an improved production method for the split intein ligand to get higher yields (Ohman p. 4 lines 14-19, lines 25-26). Thus, it is considered advantageous for a skilled artisan to utilize the solid support taught by Ohman for purification of DnaE N-inteins such as that of Muir ‘580.
A skilled artisan would have had a reasonable expectation of success in utilizing the solid supports of Ohman with the N-intein of Muir ‘580 because Ohman teaches the successful use of such solid supports with wildtype Npu N-intein, which is highly similar to the N-intein of Ohman, see sequence alignment in OA appendix. Thus, a skilled artisan could expect to successfully use this system in combination with the intein of Muir ‘580.
Claims 12-13 are rejected under 35 U.S.C. 103 as being unpatentable over Muir ‘580 in view of Ohman, as applied to claims 7-11 and 14 above, and further in view of Muir et al., WO 2014/004336 (hereinafter Muir ‘336).
Muir ‘580 and Ohman teach the N-intein protein attached to a solid support, as discussed above. These references do not teach that the N-intein is coupled to the solid support via a Lys or Cys-tail on the C-terminal as set forth in claims 12-13.
Regarding claims 12-13, Muir ‘336 teaches split inteins immobilized on solid supports including resins, particles, and beads (Muir ‘336 p. 17 para. 60). Muir ‘336 teaches that the split intein fragment can be attached to the solid support via linkers, and that the C-terminus residue
of a peptide linker can be modified to introduce an appropriately reactive functional group to
attach the split intein C-fragment to a surface of choice, e.g., Lys to react via an amine or Cys
to react via a thiol (Muir ‘336 p. 14 para. 49).
It would have been obvious for a skilled artisan to modify the teachings of Muir ‘580 and Ohman and couple the intein to the solid support via a Lys or Cys-tail attached to the C-terminal. Muir ’336 is similarly directed to split inteins attached to solid support systems such as chromatography resins. Given the teachings of Muir ‘336 that the C-terminus can be modified with a Lys or Cys to facilitate attachment of the intein to the solid support, it would have been obvious to a skilled artisan that the N-intein of Muir ‘580 and Ohman could similarly be attached in this way.
A person of ordinary skill in the art would have been motivated to utilize a Lys or Cys tail attachment as taught by Muir ‘336 because the choice of Lys or Cys introduces different functional groups for attachment of the split intein to various surfaces, and would therefore be considered advantageous to incorporate this technique in the intein of Muir ‘580 and Ohman to allow for attachment to different types of supports.
A skilled artisan would have had a reasonable expectation of success in making this modification because Muir ‘336 teaches this technique for a similar split intein system as that of Muir ‘580 and Ohman, and therefore a skilled artisan could expect to implement a Lys or Cys tail attachment with the intein and solid support of Muir ‘580 and Ohman with an expectation of predictable results.
Conclusion
Claims 1-14 are rejected. No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to EMILY F EIX whose telephone number is (571)270-0808. The examiner can normally be reached M-F 8am-5pm ET.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Sharmila Landau can be reached at (571)272-0614. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/EMILY F EIX/Examiner, Art Unit 1653
/JENNIFER M.H. TICHY/Primary Examiner, Art Unit 1653
