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
The restriction and species election requirement of 11/27/2024 was previously withdrawn following the reply filed on Jan 27, 2025.
Priority
The priority date for this application is: 3/19/2019.
Amendments
This action is in response to papers filed 5/6/2026, in which claims 1, 4, 7 – 8, and 10 were amended, claims 2-3 and 12-17 were canceled, and no new claims were added. All of the amendments have been thoroughly reviewed and entered.
The amendments have overcome previous objections and rejections. However, in view of amendments to claim 1, a new 103 rejection is made in this office action. In addition, a new 103 rejection of claim 18, not necessitated by amendment is made in this office action.
Response to Arguments
Applicant’s arguments, also filed 5/6/2026, with respect to:
rejections of claims 1, 4, 5 – 11, and 18-19 under 35 USC § 103 have been fully considered and are partially persuasive for the reasons discussed in this office action. Significantly, the amendments have overcome previous 35 USC § 102 and 103 rejections. However, a new 35 USC § 103 rejection in view of Sharma (previously cited) and Yokohama (new) has been presented in this office action.
Arguments applicable to newly applied rejections to amended claims are addressed below. Arguments that are no longer relevant are not addressed.
Objections and Rejections not reiterated here are withdrawn.
Status of the Claims
Claims 1, 4, 5 – 11, and 18-19 are under consideration.
Withdrawn Claim Objections
Claims 7 - 8 and 10 are amended to remove the word derivative.
The objection is withdrawn.
Withdrawn Claim Rejections - 35 USC § 112
Claim 4 has been rewritten in independent form.
The 112d rejection is withdrawn.
Withdrawn Claim Rejections - 35 USC § 102
Claim 1 has been amended to remove the limitation of the wild-type lysyl-tRNA synthetase. The 102(a)(1) rejection of Claim(s) 1-10, 12, and 15-17 is withdrawn.
New Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 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 text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claim 1, 4, 5 – 10, and 18 are rejected under 35 U.S.C. 103 as being unpatentable over Sharma (Chembiochem, 2018 Jan 4;19(1):26-30., Epub 2017 Nov 16, IDS of 11/22/2022) as applied to claims 1-10, 12, and 15-17 above in view of Yokohama (US 9,133,449 B2).
This is a new rejection necessitated by amendment for claims 1, 4, 5 –10 and a new rejection not necessitated by amendment for claim 18.
Sharma teach the pyrrolysyl-tRNA synthetase system is known and previously demonstrated to function in the incorporation of unnatural amino acid, e.g., Pyrrolysine (abstract). By mutating the N-terminal domain of this enzyme, further improvements in the enzyme’s function of recognizing and binding to tRNAPyl and incorporation of Nε-(tert-butoxycarbonyl)-L-lysine up to three-fold more than the wild type was identified. See abstract.
Thus, Sharma teaches a mutant lysyl-tRNA synthetase with improved functionality.
Regarding claims 1 and 18, Sharma teaches mutating the wild-type sequence of the enzyme, pyrrolysyl-tRNA synthetase (M. mazei PylRS, supplementary materials, section 5., pg. S-5), to create various mutants. Sharma teaches mutations such as R19H, H29R, T122S mutation (The identified mutations are R19H/H29R/T122S, 4th line of abstract; R3-11 mm PylRS in 11th row of Table S1). The results of this mutant clone show improved amber suppression efficiency for the genetic incorporation of Nε-(tert-butoxycarbonyl)-L-lysine three-fold more than the wild type was identified (abstract, 1st sentence).
See the list of mutations from Supplementary table of Sharma, row 11 consists of the clone that bears mutations being discussed.:
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Sharma state about their improved results, such mutations in the N-terminal non-catalytic domain (title, first para on pg. 2), while effective in improving efficacy of lysyl-tRNA synthetases, a dramatically higher yield was not obtained. See recitation below from bottom of pg.4:
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Sharma also did not disclose any mutations in the catalytic domain, such as Y384F as required by instant claim.
Thus, Sharma does not teach a mutant lysyl-tRNA synthetase, wherein the amino acid sequence of the wild-type lysyl-tRNA synthetase consists of SEQ ID NO: 4.
However, before the effective filing date of instant invention, Yokohama resolve the deficiency of Sharma by teaching mutations in the catalytic domain of lysyl-tRNA synthetase. Yokohama had taught Y384F.
Yokohama taught a mutant pyrrolysine tRNA with single mutations such as the Y384F mutation and this mutation in combination with other mutations. Yokohama taught the nucleic acid sequence wherein the codons of the amino acid chain at positions 306 and 384 are codons corresponding to alanine and phenylalanine (col 8, lines 35-45). Yokohama taught the single Y384F mutation imparts the ability of the pyrrolysine tRNA synthetase to aminoacylate a tRNA with t-butoxycarbonyl-lysine, Nε-benzyloxycarbonyl-lysine, allyoxycarbonyl-lysine, or Nε-ortho-azide-benzyloxycarbonyl-lysine more efficiently than the wild type pyrrolysyl-tRNA synthetase. See Fig. 6; Fig. 78, right two columns; Fig. 8, left two columns; Column 15. On the other hand, 5 mutants in which alanine was substituted correspondingly for leucine at position 305, tyrosine at position 306, asparagine at position 346, Valine at position 401 and tryptophan at position 417, the catalytic activities were decreased drastically (Column 14, lines 50-60). Therefore, Yokohama suggest NOT to make certain mutants, such as the 5 mutations discussed above in the catalytic domain of the enzyme.
It would have been obvious to one of ordinary skill in the art before the instant invention to modify the lysyl-tRNA synthetase of Sharma consisting of R19H, H29R, and T122S mutations (the R3-11 clone) known to improve efficacy of lysyl-tRNA synthetase with the further addition of Y384F also known to improve efficacy of lysyl-tRNA synthetase as shown by Yokohama because it is prima facie obvious to combine known mutations into a single composition. By incorporating R19H, H29R, and T122S as already demonstrated by Sharma to be effective in improving lysyl-tRNA synthetase function to a certain extent, one would also be motivated to incorporate at least one mutation within the catalytic domain, such as Y384F mutation, as shown by Yokohama, and arrive at instant SEQ ID NO: 4, for the advantage of further improved efficacy; i.e., R3-11 clone of Sharma (consisting of R19H, H29R, and T122S) + Y384F mutation of Yokohama = instant SEQ ID NO: 4.
There would have been a reasonable expectation of success in making this modification because both the mutations of Sharma and Yokohama are known mutations that independently and effectively (to different extents) increase efficacy of lysyl-tRNA synthetases. One would be motivated to make this combination of mutations, because Sharma’s mutations are in the non-catalytic domain, known to effect association, and Yokohama’s mutations are in the catalytic domain known to improve functionality. One of skill in the art can see that the combination would improve efficacy to a greater extent than a combination of mutations restricted to one domain or the other. MPEP 2144 II and 2143 I A.
Thus, Sharma in view of Yokohama make obvious the combination of mutations: R19H, H29R, T122S, and Y384F, i.e., SEQ ID NO: 4, as required by claim 1.
The MPEP states: "It is prima facie obvious to combine two compositions each of which is taught by the prior art to be useful for the same purpose, in order to form a third composition to be used for the very same purpose.... [T]he idea of combining them flows logically from their having been individually taught in the prior art." In re Kerkhoven, 626 F.2d 846, 850, 205 USPQ 1069, 1072 (CCPA 1980).
Regarding claims 4 - 5, Sharma teaches the nucleotide sequence of the wild-type and primers for mutants, (pg. S-4); i.e., the isolated polynucleotide encoding a mutant lysyl-tRNA synthetase (claim 4) and a plasmid encoding the same (6. Construction of pEVOL-R3-11 AcKRS and pEVOL-R3-11 AcdKRSa, pg. S-6); i.e., a vector (claim 5).
Regarding claim 6, Sharma teaches co-transforming E. coli Top10 cells with the vector described (pg. S-7); i.e., a host cell containing a vector that comprises a polynucleotide that encodes the mutant lysyl-t-RNA synthetase.
Regarding claim 7, Sharma teaches E. coli (a host cell) comprising:(a) a mutant lysyl-tRNA synthetase (as discussed above); and (b) in a vector wherein the vector, pEVOL-PylRS, (pEVOL-PylRS is derived from a pEVOL vector developed by Schultz et al.[10] was constructed to contain genes coding tRNAPyl, middle of para on pg. 3; and vector map, pg. S-3) (an orthogonal tRNA capable of binding to a lysine derivative in the presence of the mutant lysyl-tRNA synthetase); and optionally (c) sfGFP134X, where X is the site for BocK, AcK or AcdK, which are lysine derivatives(for e.g., sfGFP134X on pg. S-7) (a target nucleic acid sequence encoding a target protein (GFP), which includes a codon recognized by the orthogonal tRNA at a position for introducing a lysine derivative; wherein the lysine derivative is BOC-lysine (t-butyloxycarboryl -L-lysine).
Other derivatives recited in claim 7 have not been examined because they are recited as being optional (selected from the group consisting of..).
Regarding claim 8, Sharma teach an improved expression system for ncAA incorporation (see summary line, end of pg. 5). Further, the discussion for claim 7 is incorporated herein.
Claim Interpretation for claim 9, " kit " in claim 9 is being interpreted to encompass any collection of parts and reagents that includes all of the elements of the claims including a suitable container to contain the collection because the specification does not define this term. Any further interpretation of the word is considered an “intended use” and does not impart any further structural limitation of on the claimed subject matter.
Regarding claim 9, Sharma does not expressly teach a “kit”. However, as discussed above, Sharma teach all the components of claim 9. One of skill in the art knows these must be contained in a container.
Claim Interpretation for claim 10, the claim will be interpreted as a method, wherein the step is: providing the mutant lysyl-tRNA synthetase of claim 1 to a host cell. This interpretation is consistent with the specification pg. 19, where various host cells are discussed but no in vitro or any other examples are discussed.
Regarding claim 10, that recites A method for incorporating an unnatural amino acid into a target protein or for preparing a target protein containing an unnatural amino acid, comprising a step of: … is being interpreted as: a method for incorporating an unnatural amino acid into a target protein or for preparing a target protein containing an unnatural amino acid by providing the mutant lysyl-tRNA synthetase of claim 1; wherein the unnatural amino acid is a BOC-lysine (t- butyloxycarboryl -L-lysine), to a cell.
Sharma teaches a method of incorporation of several unnatural amino acids (supplementary methods) using variants of pyrrolysyl-tRNA synthetase/tRNAPyl pairs in E.coli (Summary of Invention). Sharma teaches the steps involved in a method to incorporate such unnatural amino acids into a protein as discussed for claims 7 and 8. See also citations: 11. The Expression of Ub48BocK and Ub, pg. S-8 and Fig. S6. Thus, Sharma teaches a method of using a mutant lysyl-tRNA synthetase for incorporating an unnatural amino acid into a target protein or for preparing a target protein containing an unnatural amino acid, as per the requirements of claim 10.
Thus, Sharma in view of Yokohama make obvious instant claims 1, 4, 5 – 10, and 18.
Claim 11 is rejected under 35 U.S.C. 103 as being unpatentable over Sharma (Chembiochem, 2018 Jan 4;19(1):26-30., Epub 2017 Nov 16, IDS of 11/22/2022) in view of Yokohama (US 9,133,449 B2) as applied to claims 1, 4, 5 – 10, and 18 above and further in view of Chin (WO 2012/038706 A1, of record).
Regarding claim 11, the teachings of Sharma and Yokohama as discussed above are incorporated herein. Sharma further teach the portability of lysyl-tRNA synthetase between cell types. See recitation from pg. 2:
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Sharma does not teach a host cell genome with a polynucleotide encoding a mutant lysyl-t-RNA synthetase integrated into its genome.
However, before the effective filing date of instant, Chin had taught that the lysyl-tRNA synthetase system was known and previously demonstrated to function in the incorporation of unnatural amino acids. See recitation from pg. 42 below:
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Chin had taught a host cell genome with a polynucleotide encoding a mutant lysyl-t-RNA synthetase integrated into its genome (We have tested constructs in cell culture (Drosophila S2) and subsequently used those constructs to make transgenic lines (with the constructs genomically integrated), Chin lines 20-21 of pg.51).
It would have been obvious to one of ordinary skill in the art before the time of the invention to have made a stable integrand out of the polynucleotide of claim 4 for the advantage to be gained from a stable and inheritable genetic modification, and arrive at the limitation required by instant claim 11. For one of ordinary skill in the art, such integration would merely mean a combination of prior art elements, a known polynucleotide treated in the same manner as another known polynucleotide by a known method, wherein the latter was disclosed by Chin, to make a novel yet functional host cell with an integrated polynucleotide encoding an enzyme, lysyl-tRNA synthetase. One of ordinary skill in the art would have a reasonable expectation of success in doing so since all of Sharma, Yokohama, and Chin teach orthogonal tRNA synthetases in host cells for non-canonical biological activities. See MPEP 2144 II and 2143 I.(A).
Thus, Sharma and Yokohama in view of Chin make obvious instant claim 11.
Therefore the invention as a whole would have been prima facie obvious to one ordinary skill in the art before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains.
III. Withdrawn Claim Rejections - 35 USC § 103
Claim 1 has been amended to remove the limitation of wild-type Lysyl tRNa synthetase.
Therefore, the 103 rejection of claims 1-11 made over Chin (WO 2012/038706 A1) in view of Neumann (Neumann et al., Nature chemical biology, 2008-04, Vol.4 (4), p.232-234) and Wikipedia (Wikipedia webpage, Retrieved from the Internet on 2025-03-19: https://en.wikipedia.org/wiki/Amino_acid, cited from a 2015 reference, 29 pages) is withdrawn.
Allowable Subject Matter
Claim 19 is objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Claims 1 and 18-19 are directed to sequences carrying amino acid substitutions at various positions.
SEQ ID NO:4 has mutations at position 19 arginine, 29 histidine, threonine (T) at position 122 and Tyrosine at position 384 (Y); i.e., R19H, H29R, T122S, and Y384F.
SEQ ID NO: 5 has mutations at position 19 arginine, 29 histidine, Leucine (L) at position 309 and Cysteine at position 348 (C); i.e., R19H, H29R, L309A, and C348S.
SEQ ID NO: 4 has been rendered obvious over Sharma in view of Yokohama. However, no motivation could be gleaned from the prior art to combine mutations and arrive at SEQ ID NO: 5. Therefore, SEQ ID NO: 5 is free of the prior art of record.
Response to Arguments
Applicant's arguments filed 6th May 2026 to claim rejections under 35 USC § 103 have been fully considered but are not fully persuasive. Applicants argue:
A. Pgs. 3-5: the Prior Art Fails to Teach all the Claimed Mutations (Sharma, Schneider, and Soll).
and
B. Unexpected Results are argued: Pgs. 3-4, SEQ ID NO: 4 provides a surprising and significant increase in the production of Boc lysine fusion protein and insulin derivatives, which could not have been foreseen by a person of ordinary skill in the art. Pgs. 4-5, SEQ ID NO: 5 provides an unexpectedly high yield of butynoxycarbonyl human insulin, which is not suggested or made obvious by the prior art. last sentence on pg. 5: Unexpected Improvements are shown.
A. In detail, Applicants argue:
1. As to SEQ ID NO: 4 (Rejection: Sharma+ Schneider):
Schneider discloses only a synergistic triple mutant (Y306G + Y384F + l405R). Y384F of instant invention requires the other mutations to function.
Schneider's mutations are specific for norbornene-containing amino acids, structurally distinct from the Boc-lysine and butynoxycarbonyl lysine substrates of the present invention.
There is no motivation to apply such mutations to the present invention.
Regarding 1 i., this argument is persuasive because one of skill in the art would not be motivated to take one element (mutation) out of context.
Regarding 1 ii. and iii., this argument is not persuasive because Claims 1, 4, 5 – 6, 11, and 18-19 are not drawn to any particular Lysyl-tRNA synthetase that aminoacylates any particular lysine analogue and Claims 8 and 10 that require a particular lysine substrate (alkynyloxycarbonyl lysine, the Boc-lysine (t-butynoxycarbonyl lysine), fatty acylated lysine) would require a corresponding tRNAlysine derivative which subsequently is incorporated into a desired protein. The specification teaches Lysyl-tRNA synthetase comprising a specific mutations e.g., R19H, H29R, L309A, and C348S, that more efficiently aminoacylates Boc-lysine and subsequently is incorporated into a desired protein, than for e.g., R19H or H29R or the two in combination. However the instant claims are drawn to a genus of structural variants of a lysine tRNA synthetase wherein the variations are in different domains of the synthetase. The claims are not limited to specific variants of Lysyl-tRNA synthetase that correlate with the ability to aminoacylate a specific lysine analogue. Further, norbornene-containing amino acids used by Schneider are Boc-lysine derivatives.
Applicants argue, Sharma is limited to mutagenesis of the N-terminal non-catalytic domain and provides no motivation to combine N-terminal mutations with catalytic domain mutations as in SEQ ID NO: 4.
This argument is not persuasive because one of skill in the art would be motivated to include other mutations, especially in the catalytic domain because Sharma explicitly suggest doing so. See Sharma’s 4th line of abstract where they say R3-11 clone carrying the R19H/H29R/T122S mutations, exhibit three-fold more activity than the wild type; and then. Sharma state about their improved results, such mutations in the N-terminal non-catalytic domain (title, first para on pg. 2), didn’t provide the dramatically increased performance they were hoping to see (bottom of pg. 4).
Also, 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).
Applicants argue, mutational effects are non-additive and unpredictable. As shown in Example 3 of the present specification, the triple mutant Rl9H/I26V/H29R produces a lower yield than the double mutant RI 9H/H29R (790 mg/L vs. 810 mg/L ). Adding more mutations does not guarantee improved activity.
This argument is not persuasive because as per MPEP 716.02(b), the burden is on the applicant to establish significance of the results:
"The evidence relied upon should establish "that the differences in results are in fact unexpected and unobvious and of both statistical and practical significance." Ex parte Gelles, 22 USPQ2d 1318, 1319 (MPEP 716.02(b)).
In instant case, the differences Applicant argues about do not show statistical or practical significance.
2. As to SEQ ID NO: 5 (Rejection: Sharma+ Soll):
In Soll, L309A and C348S are found in two different mutants (MmAcKRS1 and MmAcKRS2) and never coexist in the same enzyme. The Examiner's combination is based solely on impermissible hindsight.
Soll's mutations require the presence of L301M and Y306L to function. Neither L309A nor C348S is functional alone or in the absence of these additional mutations.
Soll's mutants are specific for N-acetyl lysine (AcK), a substrate entirely different from the lysine derivatives of the present invention.
Soll only mutates the catalytic active site and provides no teaching or suggestion to combine catalytic domain mutations with the N-terminal mutations Rl9H + H29R from Sharma.
Soll's screening system (CcdB/CAT selection for AcK incorporation) is completely different from the high-density fermentation system for insulin production of the present invention. No result could be reasonably predicted. •
Regarding 2 i., this argument is not persuasive because: Table 1 of Soll shows the two mutations to exist together in MmAcKRS1:
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Regarding 2 ii., this argument is persuasive because Soll: a. does not create/show individual mutant performance, b. Fig. 2 of Soll shows MmAcKRS1 outperforming other combinations of mutants, and c. one of skill in the art would not be motivated to take one element (mutation) out of context.
Regarding 2 iii., this argument is persuasive because as explained regarding 1 ii. and iii., above.
Regarding 2 iv., this argument is not persuasive because Soll provides plenty of teaching or suggestion to combine catalytic domain mutations with other mutations. Fig. 2 of Soll shows MmAcKRS1 outperforming other combinations of mutants in vivo. But then Soll goes on to say the rate of catalysis (kcat) of the evolved AcKRSs (MmAckRS1) showed a comparable value to the wild-type enzyme but with a lower substrate affinity (higher Km values). See recitation from pg. 732:
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Surely, one of skill in the art would be motivated to not accept the mutants as is rather modify the mutants further to achieve lower Km and higher kcat.
Regarding 2 v., this argument is not persuasive because claims 1, 4, 5 – 11, and 18-19 are not drawn to any particular screening system.
Regarding B., unexpected results, Applicants arguments are not persuasive for the reasons discussed below.
As MPEP states, any differences between the claimed invention and the prior art may be expected to result in some differences in properties. The issue is whether the properties differ to such an extent that the difference is really unexpected." See MPEP §716.02. In the instant case, Applicants have created point mutations and shown that such change has resulted in a (small) change in activity. This is expected.
See In re Klosak, 455 F.2d 1077, 1080 (CCPA 1972): "It is not enough to show that results are obtained which differ from those obtained in the prior art: that difference must be shown to be an unexpected difference".
See In re Baxter Tavenol Labs., 952 F.2d 388,392 (Fed. Cir. 1991): "When unexpected results are used as evidence of nonobviousness, the results must be shown to be unexpected compared with the closest prior art."
In view of the foregoing, and because Applicants have not provided any evidence showing there was no reasonable expectation of success, Applicants arguments in B. are not dispositive.
However, in view of amendments, new references have been applied and rejection of claims 1, 18, and other dependent claims made.
The rejection of claim 19 is withdrawn. Claim 19 is drawn to SEQ ID NO: 5, which has mutations at position 19 arginine, 29 histidine, Leucine (L) at position 309 and Cysteine at position 348 (C); i.e., R19H, H29R, L309A, and C348S. One of skill would not “break up” the mutations described in Soll, and cherry-pick mutations described by Sharma to arrive at the combination of mutations in SEQ ID NO: 5, as discussed in the Response to Arguments section.
Conclusion
No claims are allowed.
Correspondence
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SHABANA MEYERING, Ph.D. whose telephone number is (703)756-4603. The examiner can normally be reached M - F: 9am to 5pm EST.
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SHABANA S. MEYERING, Ph.D.
Examiner
Art Unit 1635
/SHABANA S MEYERING/Examiner, Art Unit 1635
/CATHERINE KONOPKA/Primary Examiner, Art Unit 1635
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