DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of Claims
Receipt of Arguments/Remarks filed on 1/21/2026 is acknowledged. Claims 1, 2, 4, 5, 7-9, 11, 12, 15, 16, 21-23, and 29-33 are pending. Claims 1, 2, 4, 7, 8, and 31 were amended. Claims 9, 11, 12, 15, 16, 21-23, 29, and 30 are withdrawn.
Applicant elected Actinobacillus sp., SEQ ID NO: 1, in response to the species election requirement on 7/10/2025. SEQ ID NO: 2 is withdrawn from consideration as being drawn to a non-elected species.
Withdrawn Objections and Rejections
The objections to the sequence listing, drawings, and specification are withdrawn.
The rejection of claims 1, 2, 4, 5, 7, and 8 under 35 U.S.C. § 102/103 is withdrawn.
Modified rejections necessitated by amendment
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 1-2, 4-5, 7-8, and 31-33 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.
Claims 1 and 31 recite the limitation “modified Actinobacillus pleuropneumoniae N-glycosyltransferase (NGT) of SEQ ID NO: 1”. This limitation is unclear. Specifically, it is not clear what is meant by “of SEQ ID NO: 1”, for example, it is not clear if this means that the NGT comprises the amino acid sequence of SEQ ID NO: 1. The claims should be amended to clarify the structure of the NGT.
Claims 2, 4, 31, and 33 recite a modified NGT comprising amino acid substitutions at one or more positions, with reference to SEQ ID NO: 1, wherein possible substitutions include A469 (Q469) (claims 2, 31) or A469G, A469I, A469G-H495D, and A469I-H495D (claims 4, 33).
In claims 2 and 31, the use of parentheses around Q469 is unclear. Elected SEQ ID NO: 1 comprises a Q at position 469. However, the parentheses make it unclear if the Q469 limitation is optional or required, and the scope of claim 2 is indefinite. Further, the elected SEQ ID NO: 1 has a Q at position 469, so the recitation of “A469” is not clear.
Similarly, claims 4 and 33 are unclear. As recited in claims 4 and 31, the amino acid substitutions are made with reference to SEQ ID NO: 1, which has a Q at position 469. Thus, the use of A469 in these claims is unclear, because if SEQ ID NO: 1 is the reference sequence there is not an A at position 469.
Q is the amino acid at position 469 in the wildtype sequence corresponding to SEQ ID NO: 1. For the purposes of examination, it is considered that A469 and Q469 are interchangeable (i.e., if prior art teaches a substitution at Q469, this reads on A469 substitutions as well, because SEQ ID NO: 1 has a Q at this position).
Claims 5, 7-8, and 32 are included in this rejection because they depend on a rejected claim and do not clarify the issue.
Claim Rejections - 35 USC § 103
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claims 1-2, 5, and 31-33 are rejected under 35 U.S.C. 103 as being unpatentable over Kawai et al., Journal of Biological Chemistry; 286(44):38546-57 (cited in IDS 5/1/2023).
Regarding claim 1, Kawai teaches the structure and glycosyltransferase activity of the Actinobacillus pleuropneumoniae HMW1C-like Protein (Kawai “Abstract”). The sequence of HMW1C (GenBank Accession Number WP_005605627.1) is 100% identical to instant SEQ ID NO: 1 (see GenBank WP_005605627.1 reference). Kawai teaches a substitution at position T438, T438A (Kawai pg. 38553 Table 2).
Regarding claim 2, Kawai teaches amino acid mutations to an NGT having SEQ ID NO: 1 at positions F39, H214, D215, H219, H272, H277, K441, Y498, N521, and D525 (Kawai pg. 38553 Table 2).
Kawai does not expressly teach the specific substitutions at position T438 as recited in claim 1.
However, it is recognized in the art that conservative amino acid substitutions are expected to maintain the structure of the polypeptide backbone, the charge or hydrophobicity, and the bulk of the side chain (see instant specification pg. 31 para. 103). Conservative substitutions of a Thr residue include Ser and Val (see instant specification pg. 31). Thus, a skilled artisan would expect that a substitution of T438S or T438V, which are known to be conservative substitutions, would maintain the structure and function of the enzyme. For this reason, it would have been obvious to a skilled artisan to arrive at an NGT with the sequence according to SEQ ID NO: 1 and a substitution of T438S or T438V, in view of Kawai’s disclosure of SEQ ID NO: 1, as an NGT with these amino acid sequence substitutions are considered conservative variants of this sequence. Thus, introducing a substitution of valine or serine at this position would be considered a simple substitution of one known element for another having similar properties, with a reasonable expectation that such a substitution would result in a protein having similar properties to the wildtype.
Regarding claim 31, a “panel” as understood based on the disclosure is a collection of multiple modified NGTs. It would have been obvious to a skilled artisan to obtain a panel of modified NGTs comprising (a) at least one modified NGT of claim 1 and (b) one or more additional NGTs derived from an Actinobacillus spp. and having substitutions at the recited positions. As set forth above, Kawai teaches a modified NGT of claim 1 and teaches NGTs with substitutions at residues F39, H214, D215, H219, H272, H277, K441, Y498, N521, and D525 (Kawai pg. 38553 Table 2). Thus, it would be considered obvious for a skilled artisan to obtain a collection of these NGTs in a panel, as these modified glycosyltransferases are obvious in view of the prior art teachings.
Regarding claims 5 and 32, the “wherein” clause recites a functional limitation of the glycosyltransferase of claim 1 or the panel of glycosyltransferases of claim 31, regarding acceptor peptide sequences that the glycosyltransferases are capable of recognizing. As discussed above, the structure of the modified NGT of claim 1 and the panel of claim 31 is taught by Kawai. It is expected that any glycosyltransferase having this same structure would be capable of the claimed function, and therefore the NGT taught by Kawai reads on the NGT of claim 5 and the NGT panel of claim 32.
Regarding claim 33, as set forth above, a panel comprising modified NGTs as recited in claim 31 is obvious in view of Kawai. The specific mutation T438S is obvious in view of Kawai, as discussed above regarding claim 1. Thus, it would have been obvious for a skilled artisan to obtain a panel comprising a modified NGT comprising a T438S mutation.
Claims 4 and 7-8 are rejected under 35 U.S.C. 103 as being unpatentable over Kawai et al., Journal of Biological Chemistry; 286(44):38546-57 (cited in IDS 5/1/2023) in view of Song et al., Journal of Biological Chemistry; 292(21):8856-63 (cited in IDS 5/1/2023).
Kawai teaches the NGT of claim 1 as set forth above.
Kawai does not teach the specific substitutions recited in claim 4, or the acceptor peptide sequences as recited in claims 7 and 8.
Regarding claim 4, Song teaches a mutation of ApNGT at position Q469 (Song “Abstract”). The amino acid sequence of the wild-type NGT from A. pleuropneumoniae comprises a Q at position 469 (see SEQ ID NO: 1, instant specification pg. 32). Song teaches that site-directed mutagenesis of position 469 results in valuable mutants with enhanced glycosylation efficiency and expanded acceptor specificity (Song pg. 8857 first partial para.). Song teaches 17 mutated ApNGTs with a substitution at position 469, including Q469G and Q469I (Song Table 1).
Regarding claims 7 and 8, Song teaches that the WT ApNGT has activity against a variety of acceptor peptide sequences, including the peptide GGANVTKTIER containing the optimal motif ANVTK (Song pg. 8858 para. 1). Song teaches that ApNGT is known to transfer UDP and GDP-glucose to an asparagine (Asn, N) in a conserved Asn-X-Ser/Thr sequon, where X is not equal to Pro (Song pg. 8856 para. 3). Thus, the acceptor peptide sequence glycosylated by an NGT derived from Actinobacillus has the structure of [X-2-]-[X-1-]-[N]-[X+1]-[X+2]-[X+3], (GANVTK), wherein X is any canonical amino acid and [X+1] is not P.
It would have been obvious to a skilled artisan to modify the NGT taught by Kawai to have an additional mutation at residue 469, specifically Q469G or Q469I as taught by Song. Kawai teaches mutation of many residues in the active site of the NGT, including F39, H214, D215, H219, H272, H277, T438, K441, Y498, N521, and D525, as set forth above. Kawai additionally teaches that Q469 is located in the enzyme active site (Kawai Fig. 3). Thus, it would have been obvious to a skilled artisan that a mutation to an active site residue in addition to T438, such as Q469I or Q469G, could be made in the enzyme taught by Kawai.
A person having ordinary skill in the art would have been motivated to modify the NGT taught by Kawai to have an additional substitution of Q469G or Q469I, because the replacement of Q469 with small hydrophobic amino acids, such as Gly, Ala, Val, Ile, and Leu, results in more flexible residue selectivity for the acceptor peptide (Song pg. 8858 “Site-saturated mutagenesis”). Expanded acceptor selectivity is advantageous to allow for more efficient N-glycosylation in both in vivo and in vitro glycosylation techniques (Song pg. 8861 para. 4).
A skilled artisan would have a reasonable expectation of success in obtaining an NGT with a substitution at position 469 in the NGT enzyme taught by Kawai, given the teachings of Song directed to a successful mutation of Q469 to G or I in NGT from A. pleuropneumoniae.
Response to Arguments
In light of amendments to the claims, the rejection of claims 1-2, 4-5, and 7-8 under 35 U.S.C. § 102/103; and the rejection of claims 1-2, 5, and 31-33 under 35 U.S.C. § 103 in view of Kawai and Song, have been withdrawn. However, upon further consideration, new grounds of rejection of claims 1-2, 5, and 31-33 are made under 35 U.S.C. § 103 in view of Kawai as set forth above. Given these new grounds of rejection, the arguments presented regarding claims rejected under 35 U.S.C. § 102/103 or claims 1-2, 5, and 31-33 under 35 U.S.C. § 103 in view of Kawai and Song are moot. Responses to pertinent arguments are set forth below.
Applicant argues that Kawai and Song, alone or in combination, fail to teach or suggest a modified Actinobacillus pleuropneumoniae NGT of SEQ ID NO: 1 with the claimed T438 substitutions. Applicant argues that the Office appears to equate the lack of specific UDP contact by T438 (reported in Kawai) with the minimal change to UDP-Glc donor specificity produced by the Q469 substitution of Song, which is not reasonable. Applicant argues that Kawai and Song describe a specific interaction between Q469 and UDP. Applicant argues that the sole teaching in either reference relating to T438 is the express indication in Kawai that it does not impact glycosylation, and the assertion that a skilled artisan would have interpreted the Q469 mutant results of Song as suggesting anything regarding a T438 mutant is unreasonable.
In response to these arguments, it is first noted that the substitution of T438S or T438V are considered conservative substitutions, which are known in the art to generally maintain the overall function and structure of the enzyme, and therefore it would have been obvious to a skilled artisan to arrive at an NGT with the sequence according to SEQ ID NO: 1 and a substitution of T438S or T438V, in view of Kawai's disclosure of SEQ ID NO: 1, as an NGT with these amino acid sequence substitutions are considered conservative variants of this sequence, as set forth in the above rejection under 35 U.S.C. § 103.
Song is relied upon to teach mutation of another active site residue, Q469. It would have been obvious to obtain a conservative variant, T438S or T438V in view of Kawai, given Kawai’s teaching of a substitution at this position. The teachings of Song were previously applied to claim 1 to provide additional motivation to substitute a residue within the active site, as both Q469 and T438 are in the active site. However, ultimately, the substitution of T438S or T438V is considered to be obvious as these are conservative variants and Kawai teaches a substitution at this position, as reflected in the current rejection of amended claim 1 under 35 U.S.C. § 103.
Applicant argues that absent impermissible hindsight, a skilled artisan viewing Kawai and Song would have no reason to modify T438, nor could they have reasonably expected that the specific claimed T438 mutations could impact glycosylation specificity and/or activity.
In response to this argument, it is noted that Kawai teaches a substitution of T438. Thus, obtaining an NGT with a conservative substitution at this position (T438S or T438V) would have been obvious, as discussed above. Further, the invention of claim 1 is directed to a modified NGT of SEQ ID NO: 1 with a substitution at T438. It is not required that this NGT have any particular functional features such as glycosylation specificity or activity. Song is relied upon in the rejection under 35 U.S.C. § 103 to teach an additional modification of Q469G or Q469I.
Conclusion
Claims 1-2, 4-5, 7-8, and 31-33 are rejected. No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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.
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/EMILY F EIX/Examiner, Art Unit 1653
/JENNIFER M.H. TICHY/Primary Examiner, Art Unit 1653
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