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 .
The Response of 20 May 2026 has been entered.
Claims 1 and 4-22 are currently pending. Claims 6-9, 12-14 and 18-22 are withdrawn as being drawn to a nonelected invention (claims 12-14, 18 and 22) and species (claims 6-9 and 19-21).
Claims 1, 4, 5, 10, 11 and 15-17 are considered here with respect to the elected species of: an ammonia oxidase domain as the active domain; amoB1 and amoB2 (SEQ IDs 1 and 2) as the ammonia oxidase domain(s); C-terminus of ferritin as the fusion site; E. coli as the host cell; and duroquinol as the reducing agent.
Any rejection not reiterated herein has been withdrawn.
Response to Arguments
Applicant's arguments filed 20 May 2026 have been fully considered but they are not persuasive.
Applicant argues that neither Kim nor Taher teaches the specific residue ranges of the claimed AMOB1 and AMOB2 subunits consisting of SEQ IDs 1 and 2. This is not persuasive because Taher teaches that AMO of N. Europa is a methane to methanol converting enzyme that is structurally and functionally homologous to MMO, and the alignment of MMO as taught by Kim vs. AMO from N. europaea shows that the fragments used by Kim (residues 33-172 and 265-414 of MMO) correspond to AMO residues 38-177 as set forth in SEQ ID 1 and AMO residues 270-417 of SEQ ID 2. While the attached alignment extends only to residue 417 of AMO, the pmoB2 fragment used by Kim extend to the C-terminus of MMO and it would have been obvious to similarly extend the corresponding fragment of AMO to the C-terminus (i.e. to residue 420). Alternatively, it would have been obvious to use routine experimentation to determine the optimal/workable ranges for the length/sequence of the domains, e.g. using the methodology taught by Kim for measuring the resulting enzyme activity. Thus, one of ordinary skill in the art would have selected the claimed fragments as being homologous to the minimal structural catalytic units taught by Kim, with a reasonable expectation of success.
Applicant further argues that neither Kim nor Taher identifies the specific location of the methane oxidation active site within the much longer full-length AMO sequence. This is not persuasive because AMO of N. Europa is structurally and functionally homologous to MMO, and it would have been obvious for one of ordinary skill to use sequence alignment of the proteins to identify the corresponding regions of AMO with a reasonable expectation of success.
Applicant further argues that the claimed fragments were obtained through advanced multiple sequence alignments and AlphaFold 3D structural predictions, not through routine experimentation. This is not persuasive because the criteria and processes for selecting the claimed fragments are not set forth in the specification, and thus the above arguments are considered unsupported arguments of counsel (see MPEP 716.01(c) - Arguments presented by the applicant cannot take the place of evidence in the record).
Applicant further argues that "the instant specification confirms that fusing only these specific minimal domains prevents structural interference that would occur if longer, non-specific sequences were used. This precise structural modification provides unpredictable and remarkable technical advantages over the prior art, including (i) Stable formation of spherical nanoparticles (confirmed by TEM and DLS in FIG. 3) and (ii) Maximized methane oxidation activity (confirmed in FIG. 5)." This is not persuasive because the specification does not provide any comparison of different fragments nor any other evidentiary basis for concluding that the specific fragment boundaries recited in the claims provide any unexpected benefits. The examples of the specification describe only expression of the claimed fragments (Spec., Table 2) and the use of such fragments to make nanoparticles and convert methane to methanol, and do not provide any comparative data or analysis regarding other fragments.
To the extent Applicant wishes to establish that the claimed fragment boundaries provide unexpected results, Applicant is reminded that Applicant bears the burden of producing objective evidence establishing that the differences in results are in fact unexpected and unobvious and of both statistical and practical significance (MPEP 716.02(b)). Such evidence must be factually supported by an appropriate affidavit or declaration to be of probative value (MPEP 716.01 (a)), and any unexpected results must be commensurate in scope with the claims the evidence is offered to support (MPEP 716.02(d)).
Applicant further cites caselaw (In re Deuel) for the argument that conception of a specific protein fragment from a full-length protein is non-obvious. This is not persuasive because i) the cited case deals with whether an amino acid sequence suggests a particular DNA sequence encoding it, which is not applicable to the facts of the instant case (where the issue is whether knowledge of active fragments of a known protein is suggestive of corresponding fragments in a homologous protein); and ii) the claimed fragments in the instant obviousness rejection are not selected arbitrarily or via hindsight, but rather based on being homologous to known fragments as taught by Kim.
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.
Claims 1, 4, 5, 10, 11 and 15-17 are rejected under 35 U.S.C. 103 as being unpatentable over the combination of Kim et al., Nature Catalysis 2.4 (2019): 342-353 in view of Taher et al., Environmental science & technology 47.7 (2013): 3167-3173 and AMOB_NITEU (Ammonia monooxygenase beta subunit from Nitrosomonas europaea, Accession No. Q04508) (1995), as evidenced by Lawton et al., Proteins: Structure, Function, and Bioinformatics 82.9 (2014): 2263-2267 and (in the case of claims 16 and 17) Shears et al., FEMS Microbiology letters 33.2-3 (1986): 281-284.
Regarding claim 1, Kim teaches a protein nanoparticle comprising self-assembled ferritin monomers, comprising a ferritin monomer fused with an active domain having methane oxidation activity (p. 342, 3rd ¶ to p. 343, last ¶; Table 1). The domain(s) having methane oxidation activity comprise domains from particulate methane monooxygenase (pMMO) of M. capsulatus (Bath), comprising residues 33-172 (pmoB1) and 265-414 (pmoB2), which were determined to be the minimal structural units for pMMO catalytic activity (p. 343, 1st and 2nd ¶; p. 350-351, under Biosynthesis of recombinant proteins including pMMO-mimics; Table 1 and Supp. Table 1). Kim teaches that recombinant forms of pMMO are typically inactive due to the membrane-anchored structure of the enzyme, and that expressing pMMO as a fusion construct with ferritin allows for expression of active pMMO by providing a self-assembling particulate scaffold that mimics the native membrane-embedded structure (p. 342, 3rd ¶ to p. 343, last ¶; p. 349, 1st ¶ under Discussion to p. 350, 1st ¶). Kim further teaches that pMMO is of high interest in academia and industry due to its ability to oxidize carbon feedstocks, including the conversion of methane to methanol (p. 342, 1st – 3rd ¶).
Regarding claim 4, Kim teaches that the pmoB1 and pmoB2 domains can each be fused to a single ferritin monomer, and that multiple such monomers can self-assemble to form a catalytically active nanoparticle (Table 1, pMMO-m1; p. 345-347, under Biocatalytic conversion of methane to methanol by pMMO-mimics).
Regarding claim 5, Kim teaches that the pmoB1 and pmoB2 domains can each be fused separately to a ferritin monomer, and that multiple such monomers can self-assemble to form a catalytically active nanoparticle (Table 1, pMMO-m2-pMMO-m4; p. 345-347, under Biocatalytic conversion of methane to methanol by pMMO-mimics).
Regarding claim 10, Kim teaches that the ferritin can be human heavy chain ferritin (p. 343, 1st full ¶; p. 350-351, under Biosynthesis of recombinant proteins including pMMO-mimics; Table 1 and Supp. Table 1).
Regarding claim 11, Kim teaches that the pmoB1 and pmoB2 domains are fused to the C-terminus of the ferritin (p. 343, 1st full ¶; p. 350-351, under Biosynthesis of recombinant proteins including pMMO-mimics; Table 1 and Supp. Table 1).
Regarding claims 15-17, Kim further teaches compositions for converting methane to methanol comprising the ferritin-pMMO construct and duroquinol as a reducing agent (p. 345-347, under Biocatalytic conversion of methane to methanol by pMMO-mimics). Kim teaches that duroquinol is essential for pMMO activity, and binds directly to the catalytic core of the enzyme (p. 346, 1st full ¶).
Claims 1, 4, 5, 10, 11 and 15-17 differ from Kim in that: the domain(s) having methane oxidation activity comprise an ammonia oxidase active domain comprising amoB1 and amoB2 consisting of SEQ ID 1 and SEQ ID 2 (claim 1; elected species of domain having methane oxidation activity and elected species of ammonia oxidase domain).
Taher teaches that ammonia-oxidizing bacteria can oxidize methane to methanol via the action of ammonia monooxygenase (AMO), and that such conversion is of great industrial interest (p. 3167, under INTRODUCTION). Taher further teaches that the capability of ammonia-oxidizing bacteria to convert methane to methanol is due to the broad substrate base of AMO and its evolutionary relationship with MMO (p. 3168, under Fortuitous Oxidation of Organic Compounds by AOB). Taher exemplifies the AMO-based conversion of methane to methanol with N. europaea (under MATERIALS AND METHODS).
It would have been obvious to one of ordinary skill in the art at the time the invention was made to make an enzyme construct capable of converting methane to methanol by fusing a methane oxidizing enzyme (pMMO) to ferritin to make a self-assembled enzyme nanoparticle as taught by Kim wherein the methane oxidizing enzyme is AMO as taught by Taher because it would have been obvious to combine prior art elements according to known methods to yield predictable results. One of ordinary skill would have been motivated to make an enzyme construct as taught by Kim wherein the enzyme is AMO because oxidation of carbon feedstocks, including conversion of methane to methanol, is of great commercial interest. Moreover, making a construct with AMO would provide an additional source of enzyme (in addition to MMO) that could expand the range of potential operating conditions, substrates, etc. Making an enzyme construct as taught by Kim wherein the enzyme is AMO would have led to predictable results with a reasonable expectation of success because Taher teaches that AMO is evolutionarily related to MMO, and Kim teaches that the general approach of using a ferritin scaffold to assemble enzyme nanoparticles can be used for other enzymes (Kim, p. 350, last ¶ under Discussion). Moreover, the pMMO from M. capsulatus as taught by Kim has substantial sequence homology with AMO of N. europaea as taught by Taher (41.3% identity; see attached alignment of NCBI Accession Nos. AAB51066 (pMMO) and Q04508 (AMO)), and Lawton further evidences that pMMO and AMO are phylogenetically and structurally homologous (Lawton, Fig. 1 and under RESULTS AND DISCUSSION).
Regarding the recitation in claim 1 that the active domains are amoB1 and amoB2 consisting of SEQ ID 1 and SEQ ID 2, Taher teaches the use of AMO from N. europaea and instant SEQ IDs 1 and 2 correspond to residues 38-177 and 270-420 of the AMO of N. europaea (Spec., Table 2). The alignment of MMO as taught by Kim vs. AMO from N. europaea (Accession Nos. AAB51066 and Q04508, cited above) shows that the fragments used by Kim (residues 33-172 and 265-414 of MMO) correspond to AMO residues 38-177 as set forth in SEQ ID 1 and AMO residues 270-417 of SEQ ID 2 (while the attached alignment extends only to residue 417 of AMO, the pmoB2 fragment used by Kim extend to the C-terminus of MMO and it would have been obvious to similarly extend the corresponding fragment of AMO to the C-terminus (i.e. to residue 420); alternatively, it would have been obvious to use routine experimentation to determine the optimal/workable ranges for the length/sequence of the domains, e.g. using the methodology taught by Kim for measuring the resulting enzyme activity). Since AMO as taught by Taher is structurally and functionally homologous with MMO as taught by Kim, it would have been obvious to use the domains of AMO (corresponding to SEQ IDs 1 and 2) that correspond to the MMO domains shown by Kim to be the minimal structural units for MMO catalytic activity.
Regarding claims 16-17, Kim teaches that duroquinol is essential for pMMO activity and teaches compositions for converting methane to methanol comprising the ferritin-enzyme construct plus duroquinol. Since AMO as taught by Taher is structurally and functionally homologous with MMO as taught by Kim, it would have been obvious to use the same reducing agent in the composition of the cited combination. One of ordinary skill would have had a reasonable expectation of success in doing so because Shears evidences that duroquinol (i.e. tetramethylhydroquinone) stimulates AMO catalytic activity in the same manner as for MMO (Shears, Table 1 and related text).
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 1, 4, 5, 10, 11 and 15-17 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12442022 in view of Taher, AMOB_NITEU and Kim as evidenced by Lawton and Shears (each cited in the 103 rejection above). Claim 1 of the ‘022 patent recites an enzyme nanoparticle useful for converting methane to methanol comprising first and second active domains of MMO fused to human ferritin heavy-chain protein, wherein the active domains are identical to those taught by Kim above (Kim is an inventor on the ‘022 patent). Taher and AMOB_NITEU teach that AMO is structurally and functionally homologous to MMO and can be used to catalyze the same conversion of methane to methanol as taught by the ‘022 patent. It would have thus been obvious to make a ferritin-fusion nanoparticle as in the ‘022 claim wherein the active domains comprise the corresponding regions of AMO. Regarding claims 16-17, Kim teaches that duroquinol is essential for MMO activity and teaches compositions for converting methane to methanol comprising duroquinol. Since AMO is structurally and functionally homologous with MMO, it would have been obvious to use the same reducing agent in the AMO enzyme nanoparticle, and there would have been a reasonable expectation of success in doing so because Shears evidences that duroquinol (i.e. tetramethylhydroquinone) stimulates AMO catalytic activity in the same manner as for MMO (Shears, Table 1 and related text).
Claims 1, 10, 11 and 15 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 2, 4, 13, 14 and 20 of copending Application No. 18288490. Although the claims at issue are not identical, they are not patentably distinct from each other because the claims of the ‘490 App anticipate claims 1, 10, 11 and 15. The ‘490 claims recite a protein comprising self-assembled ferritin monomers in which a methane oxidation active domain is fused, wherein the active domain is ammonia oxidase domain amoB1 (‘490, claims 1, 2, 4). The ‘490 claims further recite that the ferritin is human heavy chain ferritin (‘490, claim 13), that the active domain can be fused to the C-terminus of ferritin (‘490, claim 14), and compositions comprising the protein for preparing methanol (‘490, claim 20).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
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 ROBERT J YAMASAKI whose telephone number is (571)270-5467. The examiner can normally be reached M-F 930-6 PST.
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/ROBERT J YAMASAKI/Primary Examiner, Art Unit 1657
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