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 .
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.
DETAILED ACTION
Claim 4, 6, 8, 13, 15, 17-18, 21-23, 25, 29-40, 43-44, and 46-51 are cancelled. Claims 1-3, 5, 7, 9-12 14, 16, 19-20, 24, 26-28, 41-42, and 45 are pending.
Election/Restrictions
Applicant’s election without traverse of Group I, claims 1-5, 7, 9-12 14, and 16, and the species of beta-lactamase, in the reply filed on 2/10/2026 is acknowledged.
Claims 19-20, 24, 26-28, 41-42, and 45 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.
Claims 1-3, 5, 7, 9-12 14, and 16 are examined herein.
Claim Objections
Claims 3 and 14 are objected to because of the following informalities:
In claim 3, “where both parts of the enzyme are needed” should be corrected to “wherein both parts of the enzyme are needed.”
In claim 14, the conjunction “or” is italicized.
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 5, 7, 9-12, 14, and 16 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.
Claim 5 recites “wherein the first and second constructs encode the first and second parts of the enzyme as first and second fusion polypeptides, each comprising a
respective member of a specific binding pair.” This claim limitation has multiple reasonable interpretations, rendering the claim indefinite. In one interpretation, the first and second parts of the enzyme are the fusion polypeptide (i.e. the first and second parts of the enzyme are the specific binding pair). In a second interpretation, the first part of the polypeptide forms a fusion polypeptide with another, unnamed part, the second part of the enzyme forms a fusion polypeptide with another, unnamed part, and the two fusion polypeptides together form the specific binding pair.
Claims 5 and 7 are indefinite for “specific binding pair.” In one interpretation, this limitation refers to a binding pair with members of the binding pair that specifically bind to each other. In a second interpretation, “specific” is a synonym for “particular.” Under the second interpretation, the person of ordinary skill in the art would have been unable to ascertain the metes and bounds of the claim since the specific binding pair is not named.
Claim 9 is rejected for “gene enzyme activity” The combination of “gene” with the name of the gene in non-italics (which typically denotes a protein) and “enzyme” leads to ambiguity in the claim scope since it is unclear whether the gene or the enzyme is required.
Claims 10-11 are rejected for depending from a rejected base claim and not rectifying the source of indefiniteness discussed above.
Claim 12 contains the trademark/trade name SpyTag and SpyCatcher (see specification line 1 on page 3, which should trademark symbols next to each name). Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe two specific peptide sequences and, accordingly, the identification/description is indefinite.
Claim 12 is indefinite for “wherein the first and second constructs encode the first and second parts of the enzyme as first and second fusion polypeptides, respectively, each comprising a respective member of the SpyTag/SpyCatcher specific binding pair.” In one interpretation, “each” refers to the first and second constructs. In a second interpretation, “each” refers to the first and second fusion polypeptides. Under the first interpretation, each construct encodes first or second parts of the enzyme as a fusion polypeptide and each construct encodes SpyTag or SpyCatcher. Under this interpretation, the first and second parts of the enzyme are first and second fusion polypeptides but are not required to be fusion polypeptides with SpyTag or SpyCatcher. Under the second interpretation, the fusion polypeptides are the first part of the enzyme fused with SpyTag or SpyCatcher and the second part of the enzyme fused with SpyTag or SpyCatcher.
Claim 12 is further indefinite because SpyTag and SpyCatcher are separated by a slash. This slash can be interpreted as requiring SpyTag and SpyCatcher in the alternative or as requiring both SpyTag and SpyCatcher.
Claim 14 is indefinite for “wherein the microorganism is an engineered lactic acid bacterium or an engineered non-pathogenic or probiotic yeast selected from Saccharomyces cerevisiae, Saccharomyces boulardii, Saccharomyces pastorianus, Saccharomyces bavanus, or Kluvveromvces marxianus.” The claim does not present a closed group of alternatives. Applicant may consider amending to “wherein the microorganism is an engineered lactic acid bacterium or an engineered non-pathogenic or probiotic yeast selected from Saccharomyces cerevisiae, Saccharomyces boulardii, Saccharomyces pastorianus, Saccharomyces bavanus, and Kluvveromvces marxianus.”
Claim 16 recites “The composition of claim 1, in a formulation for oral delivery.” The claim is indefinite because it is unclear whether the claim further comprises additional formulation components or whether the composition is merely intended for oral delivery (intended use).
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.
Claims 1-3, 5, 7, and 9-10 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Park et al. (Journal of microbiology and biotechnology 17.10 (2007): 1607; cited in the Restriction Requirement mailed on 8/15/2025) as evidenced by Brevnova (US 2017 /0204401 A1; cited on the IDS filed on 6/31/2023).
Claim 1 is given its broadest reasonable interpretation as requiring that the microorganism is capable of degrading an antibiotic at least partially in the mammalian gut, such as by secreting an antibiotic-degrading enzyme.
Regarding claims 1-3 and 9, Park teaches separate plasmids (nucleic acids) expressing fragments of beta-lactamase (antibiotic-degrading enzyme): see Fig. 1. These plasmids are recombinantly expressed in Escherichia coli (page 1608, Materials and Methods, left column, Cell Lines paragraph and Construction of Plasmids first paragraph). Park detects beta-lactamase activity on antibiotics such as nitrocefin (page 1608, right column, beta-lactamase activity assay), so the enzyme fragments together are necessarily capable of degrading an antibiotic in the mammalian gut. Park uses beta-lactamase activity as a reporter in a protein-protein fragment complementation assay in order to detect protein-protein interactions (Abstract and page 1607, right column, middle paragraph), so each fragment by itself is necessarily inactive (i.e. unable to degrade antibiotics).
Expressing the fragments in separate plasmids necessarily reduces the likelihood of horizontal transmission as evidenced by Brevnova (Abstract: “the risk of horizontal gene transfer of a functional protein is reduced by separately encoding domains of a protein on at least two spatially distinct nucleic acid sequences”).
Regarding claim 5, the first and second fusion polypeptides each comprise a respective member of a specific binding pair: see Fig. 1(B) caption. hFasDD is a cognate binding partner for hFADD.
Regarding claim 7, Park measures beta-lactamase activity (page 1608, right column, beta-lactamase activity assay) in order to detect the interacting protein pair hFADD and hFasDD (Title and Abstract). Therefore, binding of the first and second fusion polypeptides via the protein interaction between hFasDD and hFADD necessarily promotes the physical interaction between the first and second fragments of the beta-lactamase enzyme resulting in detectable beta-lactamase activity (i.e. reconstitution of antibiotic-degrading enzymatic activity).
Regarding claim 10, the beta-lactamase is a TEM-1 β-lactamase (Abstract).
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 1-3, 5, 7, 9, 14 and 16 are rejected under 35 U.S.C. 103 as being unpatentable over Mao et al. (US 2018/0328923 A1; cited on the IDS filed on 6/31/2023) in view of Kokai-Kun et al. (International journal of toxicology 35.3 (2016): 309-316), and Brevnova et al. (US 2018/0328923 A1; cited on the IDS filed on 6/31/2023) as evidenced by Pandey et al. (2023 website).
Regarding claims 1-3, Mao teaches an engineered Lactococcus lactis comprising a beta-lactamase ([0093]) to detect the presence of other microorganisms, such as pathogenic V. cholerae using an invitro colorimetric assay ([0094]). Mao also teaches an engineered Lactococcus lactis that activates expression of a target gene, such as a gene encoding an antimicrobial peptide, by detecting the quorum-sensing molecule CAI-1 produced by Vibrio cholerase ([0081] and [0087]).
Mao does not teach that the Lactococcus lactis is engineered to degrade an antibiotic in the mammalian gut.
Kokai-Kun teaches that antibiotics exposure causes dysbiosis and can result in antibiotic-associated diarrhea as well as the emergence of opportunistic pathogens such as Clostridium difficile (page 66, Introduction, paragraph bridging left and right column). Kokai-Kun teaches SYN-004, which is a recombinant β-lactamase that degrades β-lactam antibiotics and has been formulated to be administered orally to patients receiving intravenous β-lactam antibiotics including cephalosporins (Abstract). SYN-004 is intended to degrade unmetabolized antibiotics excreted into the intestines and thus has the potential to protect the gut microbiome from disruption by these antibiotics (Abstract). Kokai-Kun administers SYN-004 to beagle dogs and suggests advancing SYN-004 into human clinical trials (Abstract). Both dogs and humans have mammalian guts.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to replace the beta-lactamase of Mao with the recombinant beta-lactamase SYN-004 of Kokai-Kun in order to engineer the Lactococcus lactis of Mao to degrade unmetabolized antibiotics excreted into the intestines and thus protect the gut microbiome from disruption by antibiotics. The person of ordinary skill in the art would have had a reasonable expectation of success in replacing Mao’s beta- lactamase with the beta-lactamase of Kokai-Kun.
Mao and Kokai-Kun do not teach that the microorganism is also engineered to reduce the likelihood of horizontal transmission of its engineered antibiotic-degrading capacity by encoding the enzyme in first and second parts on separate, first and second nucleic acid constructs, wherein neither construct on its own encodes active antibiotic-degrading enzyme, and wherein both parts of the enzyme are needed to provide antibiotic-degrading activity.
Brevnova teaches reducing horizontal gene transfer of a functional protein by separately encoding domains of the protein on at least two spatially distinct nucleic acid sequences, where each individual domain alone is non-functional, but co-expression of the encoded domains results in their association to form a functional protein (Abstract). Brevnova teaches that the domains are encoded by sequences on two different polynucleotides, such as two plasmids ([0007]). In some embodiments, the protein is an enzyme ([0012]). In other embodiments, the protein confers resistance to antibiotics such as amoxicillin, ampicillin, and penicillin ([0048]), which are all beta-lactams as evidenced by Pandey (middle of page 2, top third of page 3). Brevnova teaches that the different domains of the protein associate via protein binding motifs ([0014] and Fig. 4).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to further modify the engineered bacterium of Mao modified by Kokai-Kun by separately encoding the β-lactamase into two parts, each part adjacently fused to a protein binding motif and on a different plasmid, per the teaching of Brevnova in order to reduce the likelihood of horizontal gene transfer. The person of ordinary skill in the art would have had a reasonable expectation of success in applying the teaching of Brevnova to the engineered bacterium of Mao modified by Kokai-Kun.
Regarding claims 5 and 7, the protein binding motifs fused to each β-lactamase fragment would have specifically bound the two β-lactamase fragments produced by the engineered microorganism of Mao modified by Kokai-Kun (see Brevnova Fig. 4, which shows the protein binding motifs adjacent to the nucleotide sequence encoding each protein domain). Thus, the two protein binding motifs promote the physical interaction of the first and second parts of the enzyme and reconstitution of the beta-lactamase (antibiotic-degrading) enzymatic activity.
Regarding claim 9, SYN-004 is a β-lactamase (Kokai-Kun Abstract).
Regarding claim 14, Mao teaches that Lactococcus lactis is a lactic acid bacterium (Mao [0034]).
Regarding claim 16¸ although Mao teaches administering an engineered Lactococcus lactis (Mao claim 22), Mao does not teach the engineered Lactococcus lactis in a formulation for oral delivery.
Kokai-Kun’s SYN-004 has been formulated to be administered orally to patients receiving intravenous β-lactam antibiotics including cephalosporins (Abstract).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to formulate the engineered L. lactis bacteria of Mao modified by Kokai-Kun and Brevnova for oral delivery given the teaching of Kokai-Kun, who suggests administering the recombinant β-lactamase SYN-004 orally. The person of ordinary skill in the art would have had a reasonable expectation of success in formulating the engineered L. lactis for oral delivery.
Claim 12 is rejected under 35 U.S.C. 103 as being unpatentable over Mao et al. (US 2018/0328923 A1; cited on the IDS filed on 6/31/2023) in view of Kokai-Kun et al. (International journal of toxicology 35.3 (2016): 309-316), and Brevnova et al. (US 2018/0328923 A1; cited on the IDS filed on 6/31/2023) as evidenced by Pandey et al. (2023 website), as applied to claims 1-3, 5, 7, 9, 14 and 16 above, further in view of Zakeri et al. (Proceedings of the National Academy of Sciences 109.12 (2012): E690-E697; cited on the IDS filed 2/10/2026).
See discussion of Mao, Kokai-Kun, and Brevnova above, which is incorporated into this rejection as well.
Mao, Kokai-Kun, and Brevnova do not teach that the first and second constructs encode a first fusion polypeptide and a second fusion polypeptide, each fusion polypeptide comprising a respective member of the SpyTag or SpyCatcher peptides.
Rather, Brevnova teaches that the different domains of the protein associate via a protein binding motif fused to each respective domain ([0014], [0018], Figure 4).
Zakeri teaches a peptide SpyTag which forms an amide bond to its protein partner SpyCatcher in high yield simply upon mixing and amidst diverse conditions of pH, temperature, and buffer (Abstract). Zakeri teaches that the SpyTag and SpyCatcher module is a stable module for new protein architectures (Abstract). Zakeri teaches a fusion polypeptide of SpyTag with green fluorescent protein-labeled intracellular adhesion molecule-1 (page E693, right column, SpyTag Reaction was Specific at the Mammalian Cell Surface). The fusion polypeptide binds to SpyCatcher labeled with a fluorescent dye (Fluor 555): see Figure 4C.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to improve the engineered Lactococcus lactis bacterium of Mao modified by Kokai-Kun, and Brevnova by replacing each of the protein binding motifs fused to the first and second beta-lactamase fragments with SpyTag and SpyCatcher, respectively. The person of ordinary skill in the art would have been motivated to increase the binding affinity of the beta-lactamase fragments to each other in order to increase the amount of reconstituted enzyme within the gastrointestinal tract. The person of ordinary skill in the art would have had a reasonable expectation of success given that Zakeri teaches that SpyTag and SpyCatcher are capable of spontaneously binding to each other amidst diverse conditions of pH, temperature, and buffer.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CANDICE LEE SWIFT whose telephone number is (571)272-0177. The examiner can normally be reached M-F 8:00 AM-4:30 PM (Eastern).
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/LOUISE W HUMPHREY/Supervisory Patent Examiner, Art Unit 1657
/CANDICE LEE SWIFT/Examiner, Art Unit 1657