DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claims 1, 3-10 are pending in the instant application. Claims 3-10 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention.
Claim 1 is under consideration in this Office Action.
In view of the claim amendment and arguments filed 10/23/2025, all previous claim objections and claim rejections have been withdrawn in favor of the claim objections and claim rejections stated in the instant Office Action.
Claim Objection
Claim 1 is objected for reciting the phrase “SEQ ID No: 2”, which should be recited as “SEQ ID NO: 2”. Appropriate correction is required.
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 of this title, 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.
Claim 1 is rejected under 35 U.S.C. 103 as being unpatentable over Accession A0A6N4SMB5 (07-OCT-2020; reference of record) in view of Nocek et al. (ACS Catalysis 2018, 8 (11), 10746-10760; reference of record), Bornscheuer et al. (Curr Protoc Protein Sci. 2011 Nov;Chapter 26:Unit26.7; reference of record), Yoshikuni et al. (Curr Opin Chem Biol. 2007 Apr;11(2):233-9; reference of record).
Accession A0A6N4SMB5 teaches the Cytophaga hutchinsonii polyphosphate kinase having 97% identity to SEQ ID NO: 2 (see attached record). The teachings of the reference differ from the claims in that the reference does not teach the claimed polyphosphate kinase having the recited single- or multi-site mutations.
Nocek et al. teach biochemical and structural studies on polyphosphate (polyp) kinases from bacteria including CHU0107 from Cytophaga hutchinsonii, which is a member of the PPK2 class III family and can be used for polyphosphate-dependent ATP regeneration. Nocek et al. teach that structure-based site-directed mutagenesis of CHU0107 from Cytophaga hutchinsonii demonstrated the critical role of several conserved residues from the PPK2 core and lid domains, which are involved in the coordination of both substrates and two Mg2+ ions. Nocek et al. teach a two-times higher activity is observed following deletion of the C-terminal in the CHU0107 mutant protein L285Stop. Nocek et al. teach that the polyphosphate kinase CHU0107 has the Walker A loop which is involved in the binding of polyphosphate (polyP) kinase and the Mg2+ ion, and the Walker B loop which coordinates the nucleotide phosphate groups, where the loops are located at residues 75-81 and 131-136, respectively. Nocek et al. teach the conservative substitutions of the Walker-A Gly to Ala (Ala75 in CHU0107) and Walker-B Asp to Asn (Asn132 in CHU0107) in phylogenetic analysis of the PPK2 family of polyP kinases (see Fig. 1). Nocek et al. teach structure of the CHU0107-ADP complex demonstrated binding of the adenine base and ribose, with the two phosphates of ADP forming ionic interactions with the side chains of Lys103, Arg133, Lys81, and Asp82. Nocek et al. teach polyP and ADP are bound in the active site in close proximity to each other with two Mg2+ ions coordinated by conserved aspartates Asp77 and Asp222 in CHU0107 (see Fig. 7). Nocek et al. teach the Lys81, Arg133, Arg208, Lys214 and Lys217 in CHU0107 are involved in phosphate binding, orientation, transfer and charge compensation; and the Asp77 and Asp222 are involved in the coordination of Mg2+. Nocek et al. teach the mutation analysis provides information for engineering highly-activity polyphosphate kinases for use in biocatalytic applications. See entire publication and abstract especially MATERIALS AND METHODS section, RESULTS AND DISCUSSION section, Figs. 1-7, and pages 10748-10757.
Bornscheuer et al. teach protein engineering strategies to improve or change the properties of proteins, teach concepts for protein engineering using rational design including substitution and/or deletion of amino acids, directed evolution, and combinations of them where different strategies are presented for identifying the best mutagenesis method, how to identify desired variants by screening or selection, and examples for successful applications are shown which enable researchers to choose the most promising tools to solve their protein engineering challenges (see entire publication especially pages 26.7.1- 26.7.10 and Tables 26.7.1, 26.7.2, and 26.7.3).
Yoshikuni et al. (Curr Opin Chem Biol. 2007 Apr;11(2):233-9; PTO 892) teach protein engineering methodology to redesign enzyme function which was developed on the basis of the theories of divergent molecular evolution: (i) enzymes with more active and specialized functions have evolved from ones with promiscuous functions; (ii) this process is driven by small numbers of amino acid substitutions (plasticity); and (iii) the effects of double or multiple mutations are often additive (quasi-additive assumption). Yoshikuni et al. teach the impact of multiple mutations can be calculated by first determining the effects of a mutation at a single position and subsequently summing these effects using the quasi-additive assumption where the shape of the fitness landscape of a particular enzyme function can be estimated, and the combinations of mutations predicted to yield global optima for desired functions can then be selected and introduced into the enzymes. Yoshikuni et al. teach that the methodology has been demonstrated to be very powerful to redesign enzyme function. See entire publication and abstract especially pages 234-7 and Fig. 2.
The arguments filed 10/23/2025 have been considered but are not persuasive. According to MPEP 2111 while claims must be given their broadest reasonable interpretation consistent with the specification, limitations of the specification cannot be read into the claims to thereby narrow the scope of the claims. The claims do not recite that the polyphosphate kinase mutants have specific enzyme activity that is 2.7-17.9 times higher than that of the parent polyphosphate kinase as show in experimental data as stated on pages 5-6 of the remarks filed 10/23/2025.
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify and/or combine the reference teachings to make the claimed invention by using the protein engineering strategies and protein engineering methodology of taught by Bornscheuer et al. and Yoshikuni et al. on the the Cytophaga hutchinsonii polyphosphate kinase of Accession A0A6N4SMB5 to make the claimed polyphosphate kinase mutant having the amino acid substitutions recited in amended claim 1.
One of ordinary skill in the art before the effective filing date of the claimed invention would have been motivated to do this in order to obtain a polyphosphate kinase mutant that can be used in methods for producing products including mononucleotides, where Nocek et al. teach the mutation analysis provides information for engineering highly-activity polyphosphate kinases for use in biocatalytic applications. One of ordinary skill in the art at the time the invention was made would have a reasonable expectation of success because using protein engineering strategies and protein engineering methodology to improve or change the properties of enzymes are known in the art as shown by the above reference teachings including the teachings of Nocek et al. Hence, the claimed invention as a whole is prima facie obvious.
Amending the claims to recite that the polyphosphate kinase mutants have specific enzyme activity that is 2.7-17.9 times higher than that of the parent polyphosphate kinase would aid in overcoming the rejection.
Conclusion
No claim is allowed.
THIS ACTION IS MADE FINAL 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 extension fee 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.
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/CHRISTIAN L FRONDA/Primary Examiner, Art Unit 1652
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