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
Applicant’s election without traverse of Group II, claims 108-111 and species: N-acetylglucosaminyltransferase in claim 124 and bacterium in claim 126 in the reply filed on 02/10/2026 is acknowledged.
Priority
This application is a 371 of PCT/EP2021/072263 filed 08/10/2021. Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged.
Acknowledgment is made of applicant’s claim for foreign priority under 35 U.S.C. 119 (a)-(d) based on applications EP190201.2 filed 08/10/2020, EP20190198.0 filed 08/10/2020, EP20190200.4 filed 08/10/2020, EP20190202.0 filed 08/10/2020 and EP20190203.8 filed 08/10/2020. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 03/23/2023, 11/29/2023, 01/19/2024, 07/15/2024 and 01/30/2025 comply with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements are being considered by the examiner.
Status of the Claims
Claims 108-129 are pending. Claims 109 and 111 are amended. Claims 112-129 are new.
Claims 108-129 (claims set filed 02/10/2026) are examined on the merits herein.
Nucleotide and/or Amino Acid Sequence Disclosures
Claim 123 and the specification recite sequences of the membrane proteins MdfA from different species and identify these sequences by UniProt ID numbers. These sequences are not included in the Sequence Listing and do not have SEQ ID Nos.
According to 37 CFR 1.821(c): ”Patent applications that contain disclosures of nucleotide and/or amino acid sequences, as defined in paragraph (a) of this section, must contain a "Sequence Listing," which is a separate part of the specification containing each of those nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of §§ 1.822 and 1.823.” Although the “Sequence Listing” is present in the application, it does not contain the sequences recited in claim 123.
According to 37 CFR 1.821(d):” Where the description or claims of a patent application discuss a sequence that is set forth in the "Sequence Listing," in accordance with paragraph (c) of this section, reference must be made to the sequence by use of the sequence identifier (§ 1.823(a)(5) ), preceded by "SEQ ID NO:" or the like, in the text of the description or claims, even if the sequence is also embedded in the text of the description or claims of the patent application.”
Applicant is requested to follow 37 CFR 1.821 rule and submit the corresponding sequences and have SEQ ID NOs for each sequence.
Claim Objections
Claim 123 is objected to because of the following informalities:
Claims 123 recites “E. coli”. Although it is known what E. coli is stands for, Applicant is suggested to provide complete species name: “Escherichia coli”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claim 123 is rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
First, claim 123 is directed to membrane proteins, i.e. MdfA from different species or their variants having at least 80% overall sequence identity to the full-length MdfA. For instance: “E. coli MdfA with UniProt ID POAEY8 or a variant having at least 80% overall sequence identity to the full-length of the E. coli MdfA”. Please note the requirement for sequences above. The specification describes MdfA polypeptides recited in claim 123, however, does not mention variants with 80% identity (paragraph 0261). Therefore, recitation of MdfA membrane protein variants having at least 80% sequence identity to the full-length of the corresponding MdfA is not supported by the specification. Thus, since the support for the claim 123 is not provided, claim 123 contains new matter. One of ordinary skill in the art would not conclude that the applicant would have been in possession of the subject matter of claim 123 at the time of filing application.
Second, claim 123 recites the limitation for the variants of membrane protein MdfA proteins from different species with the corresponding UniProt ID number to have at least 80% sequence identity to the corresponding full-length MdfA. The membrane proteins are involved in the secretion of neutral oligosaccharides outside the cells as described in the specification (paragraphs 0252, 0261 and claim 121). Claim 123 is interpreted as directed to the polypeptides wherein 20% or less of the sequence of MdfA proteins vary from the sequence identified by UniProt ID numbers and the polypeptides retain function of secreting neutral oligosaccharides.
Thus, claim 123 broadly encompasses genera of the MdfA proteins with 80% or more sequence identity to the corresponding sequences identified by UniProt ID numbers. This would represent large pools of variant amino acid sequences encoding the respective polypeptides which are functional. At the same time proteins can have 20% or less of sequences that can differ from the corresponding sequences identified by UniProt ID numbers. The Specification does not provide structure function correlation for the MdfA proteins and does not describe domains and/or amino acid residues essential for the function of polypeptides in secretion of neutral oligosaccharides and domains and/or amino acid residues which can be modified without loss of MdfA function. Further, applicants have not shown possession of a representative number of species for the functional MdfA as specification does not provides examples of using MdfA proteins besides general description. The prior art of Heng (Heng et al. Cell Research, 2015, 25, 1060-1073) teaches the structure of E. coli MdfA (Abstract) and shows that mutation of single amino acid residues, D34A, Y30A, N33A and others, results in significant reduction of a substrate binding (p. 1065, Figure 2, p. 1066, left column, 1st paragraph, Figure 4). Thus, modification of a single residue of MdfA can lead to a significant functional change.
Therefore, one of ordinary skill in the art would not be able to identify which polypeptide sequences that have 80% identity to MdfA protein sequences identified by UniProt ID numbers encode for functional MdfA proteins. One of ordinary skill in the art would conclude based on the lack of representative number of species and the lack of describing the domains or amino acid residues of MdfA proteins critical for its function, that the Applicant was not in possession of the claimed genera and that the specification fails to satisfy the requirements of written description under 35 U.S.C. 112 (a).
Therefore, claim 123 is rejected.
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 122-124 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.
The term “improved production” in claim 122 is a relative term which renders the claim indefinite. The term “improved production” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. It is not clear what parameter of production is considered for improvement and to what extent that parameter needs to be changed to be considered improved. The scope and boundaries of claim 122 are not certain making claim 122 indefinite.
Claim 122 and 123, dependent on claim 120, recites the limitation "the membrane protein". There is insufficient antecedent basis for this limitation in the claim since claim 120 does not recite “a membrane protein”. At the same time “A membrane protein” is recited in claim 121. The scope and boundaries of claims 122 and 123 are not certain making claims 122 and 123 indefinite.
Claim 124 recites: “an additional enzyme involved in carbohydrate and nucleotide-sugar biosynthesis”. Claim 124 depends on claim 108 that recites: “at least one additional glycosyltransferase”. It is not clear if claims 124 refers to additional glycosyltransferase of claim 108 or to another additional enzyme. The scope and boundaries of claim 124 are not certain making claim 124 indefinite.
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 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 108-122 and 124-127 are rejected under 35 U.S.C. 103 as being unpatentable over Papadakis (WO 2017101958 A1 on record in IDS).
Regarding claims 108, 109 and 111, Papadakis teaches production of human milk oligosaccharides (HMO) using a genetically modified microorganism (Abstract). The term “genetically modified” is used interchangeably with “metabolically engineered” as defined in the specification (paragraph 0017). Production method of Papadakis includes expression of recombinant glycosyltransferase necessary for synthesis of oligosaccharide in the cell, production of monosaccharide nucleotide donor in the cell suitable to be transferred by the glycosyltransferase to the acceptor and culturing the cell in the presence of acceptor (p. 2, lines 3-25). Papadakis describes that the cell can express different glycosyltransferases including fucosyltransferase (p. 11, lines 4-8) and provides example of the presence of two glycosyltransferases in the cell, α-1,2-fucosyltransferase and α-1,3-fucosyltranferase (p. 16, lines 17, 18, 24) capable of producing three neutral fucosylated oligosaccharides, 2’-FL, DFL and 3-FL (p. 15, lines 16-17). Papadakis describes production of other neutral fucosylated oligosaccharides depending on the glycosyltransferases expressed (p. 17, line 3-32). Papadakis mentions that the cell is capable to produce activated nucleotide sugars, GDP-Fuc, UDP-Gal, UDP-GlcNAc suitable to be transferred by the corresponding glycosyltransferase (p. 11, lines 21-24).
Papadakis does not explicitly teach production of a mixture of four different neutral fucosylated oligosaccharides. However, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention that combination of glycosyltransferases can be selected based on Papadakis teaching to produce mixture of at least four different neutral fucosylated oligosaccharides. One would have been motivated to do that since Papadakis describes production of different neutral fucosylated oligosaccharides in a cell and provides instructions for the selection of the necessary glycosyltransferases. A skilled artisan would have reasonably expected success in this combination following the description of the prior art. Thus, Papadakis teaching renders claims 108, 109 and 111 obvious.
Regarding claim 110, similar to the described above, Papadakis does not explicitly teach production of a mixture of five different neutral fucosylated oligosaccharides. However, it would have been obvious to one of ordinary skill in the art that combination of glycosyltransferases can be selected based on Papadakis teaching to produce mixture of at least five different neutral fucosylated oligosaccharides. One would have been motivated to do that since Papadakis describes production of different neutral fucosylated oligosaccharides, including 2’-FL, DFL and 3-FL (p. 15, lines 16-17), LNFP-I-III, LNDFH-I-III (p. 17, lines 3-30) and teaches glycosyltransferases producing the specific oligosaccharides or their combination. A skilled artisan would have reasonably expected success in this combination following the instruction of the prior art. Thus, Papadakis teaching renders claim 110 obvious.
Regarding claims 112-115, Papadakis teaches that the cell can produce neutral non-fucosylated oligosaccharides such as LNT and LNnT (p. 12, lines 28-29). Papadakis further describes that these oligosaccharides can be fucosylated to neutral fucosylated oligosaccharides, such as LNFP-I, LNFP-II, LNFP-III, LNDFH-I, LNDFH-II and LNDFH-II depending on the galactosyltransferase and fucosyltransferase used (p. 17, lines 15-30). It would have been obvious to one of ordinary skill in the art that the mixture would contain both the fucosylated oligosaccharide as the products and non-fucosylated oligosaccharides, the substrates. Thus, Papadakis teaching renders claims 112-115 obvious.
Regarding claims 116 and 117, Papadakis teaches that the preferable oligosaccharide produced is HMO (p. 2, line 17) and provides examples of the neutral fucosylated HMO (p. 6, lines 1-7). Thus, Papadakis teaching renders claims 116 and 117 obvious.
Regarding claims 118-120, 124 and 125, Papadakis teaches production of the recited neutral fucosylated oligosaccharides, such as 2’-FL, 3’-FL, LNFP-I, LNFP-II, LNFP-III (p. 6, lines 1-4). Papadakis describes that 2’-FL, 3’-FL are produced with α-1,2-fucosyltransferase and α-1,3-fucosyltranferase (p. 16, lines 27-28) and when in addition to fucosyltransferases, two additional glycosyltransferases, i.e. β-1,3-N-acetylglucosaminyltransferase (elected species in claim 124) and galactosyltransferases, are present, LNFP-I, LNFP-II, LNFP-III are produced (p. 17, lines 3-29). Thus, Papadakis teaching renders claims 118-120, 124 and 125 obvious.
Regarding claims 121 and 122, Papadakis teaches that the cell can have sugar efflux transporter that promotes secretion of the oligosaccharide produced from the cell to the supernatant and that this promoter can be overexpressed indicating genetic modification of the cell. Papadakis mentions that the transporter enhances export of the oligosaccharides (p. 12, lines 10-15).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention that the transporter secreting oligosaccharides outside the cell is a membrane protein and that overexpression of the transporter will improve oligosaccharide production. One would have been motivated to reasonably expect that since separation of the produced oligosaccharides from the medium will require less steps than from the cells and presence of the produced oligosaccharides in medium can support continuous production of oligosaccharides by collection of medium. Thus, Papadakis teaching renders claims 121 and 122 obvious.
Regarding claim 126, Papadakis teaches that the cell is preferably bacterial cell, e.g. E. coli (p. 3, lines 6-7). Thus, Papadakis teaching renders claim 126 obvious.
Regarding claim 127, Papadakis teaches that the oligosaccharides are produced intracellularly by providing the cell, culturing the cell and separating oligosaccharides from the cell (p. 2, lines 3-4, 24-26). Papadakis further describes that glucosyltransferases necessary for the production of oligosaccharide are able to transfer glycosyl residue to the acceptor intracellularly (p. 6, lines 12-14). Thus, Papadakis teaching renders claim 127 obvious.
Claim 123 is rejected under 35 U.S.C. 103 as being unpatentable over Papadakis (WO 2017101958 A1 on record in IDS) as applied to claims 108, 110 and 120 above, and further in view of Putman (Putman et al. Microbiol. Molec. Biol. Reviews, 2000, 64, 672-693), GenBank Y08743.1 ( GenBank Y08743.1 [retrieved on 05/01/2026]. Retrieved from the Internet: <E.coli mdfA gene - Nucleotide - NCBI>) as evidenced by UniProt P0AEY8 (UniProt P0AEY8 [retrieved on 05/01/2026]. Retrieved from the Internet: <mdfA - Multidrug transporter MdfA - Escherichia coli (strain K12) | UniProtKB | UniProt>).
The teaching of Papadakis has been set forth above.
Regarding claim 123, Papadakis teaches that the cell can have overexpressed sugar efflux transporter that enhances export of the oligosaccharides (p. 12, lines 10-15) as described for claims 121 and 122 above. Papadakis does not teach the recited MdfA membrane proteins.
Putman teaches major facilitator superfamily (MFS) of membrane transport proteins found from bacteria to higher eukaryotes and involved in transport of various substrates including oligosaccharides (p. 673, right column, 2nd paragraph). Table 1 (p. 675) presents various MFS transporters, including MdfA transporter of E. coli with the accession numbers Y08743 and U44900. The sequence of the MdfA with accession number Y08743 has 99.8% identity to instantly claimed MdfA of E. coli with UniProt ID P0AEY8 according to BLAST analysis as evidenced by UniProt P0AEY8.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to overexpress MdfA transporter of E. coli from Putman teaching during production of neutral fucosylated oligosaccharides based on Papadakis teaching and use the sequence of MdfA from GenBank Y08743. One would have been motivated to do that since Putman describes that MdfA is one of the membrane protein involved in transport of various substrates including oligosaccharides and provides the sequence and Papadakis teaches that transporter facilitates export of the oligosaccharides from the cell providing easier separation of the produced oligosaccharides from the medium and supporting continuous production of oligosaccharides by collection of medium. A skilled artisan would have reasonably expected success in this combination because Papadakis and Putman describe bacterial oligosaccharide efflux transporters. Thus, Papadakis, Putman and GenBank Y08743 teachings as evidenced by UniProt P0AEY8 render claims 123 obvious.
Claims 128 and 129 are rejected under 35 U.S.C. 103 as being unpatentable over Papadakis (WO 2017101958 A1 on record in IDS) as applied to claim 108 above, and further in view of Faijes (Faijes et al. Biotechn. Advances, 2019, 37, 667-697).
The teaching of Papadakis has been set forth above.
Regarding claims 128 and 129, Papadakis teaches production of fucosylated LNT or LNnT, involving taking lactose from the cultivation by the function of lactose permease, expressing fucosyltransferase, β-1,3-N-acetylglucosaminyltransferase and β-1,3-galactosyltransferase or β-1,4-galactosyltransferase and having the cell synthesizing GDP-fucose, UDP-Gal and UDP-GlcNac (p. 17, lines 3-29). However, Papadakis does not explicitly teach the galactose β-1,3-acetylglucosaminyltransferase, N-acetylglucosamine β-1,3-galactosyltransferase and N-acetylglucosamine β-1,4-galactosyltransferase.
Faijes teaches human milk oligosaccharides (HMO) and enzymatic approaches for their production (Abstract). Faijes describes biosynthesis of different neutral complex HMO and discloses enzymes involved in their biosynthesis (p. 672-673, Figure 3). Faijes describes that “N-acetylglucosaminyltransferases (GlcNAcT) attach N-acetylglucosamine (GlcNAc) to terminal galactose (Gal) at the β1,3 position”. That corresponds to instant galactose β-1,3-acetylglucosaminyltransferase. Faijes further describes galactosyltransferases: “ Galactosyltransferases (GalT): β3GalT attaches Gal to GlcNAc at the β1,3 position and β4GalT attaches Gal to the β1,4 position of GlcNAc.” (p. 672-673, Figure 3). That corresponds to instant N-acetylglucosamine β-1,3-galactosyltransferase and N-acetylglucosamine β-1,4-galactosyltransferase.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention that to use galactose β-1,3-acetylglucosaminyltransferase and β3GalT and β4GalT of Faijes teaching during production of neutral fucosylated oligosaccharides based on Papadakis teaching. One would have been motivated to do that to increase variability of produced human milk oligosaccharides since Faijes describes various HMO and enzymes necessary for their production. A skilled artisan would have reasonably expected success in this combination because Papadakis and Faijes describe enzymatic production of HMO. Thus, Papadakis and Faijes teachings render claims 128 and 129 obvious.
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 108, 109, 111, 112, 116, 117, 121, 122 and 125-127 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 100-103, 105-109 and 113-117 of copending Application No. 18/040,332 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because claims overlap in scope.
Claim 108 of instant application is directed to a method of producing a mixture of at least four neutral fucosylated oligosaccharides comprising providing and cultivating cell expressing a glycosyltransferase being a fucosyltransferase and at least one additional glycosyltransferase and cell being capable of synthesizing GDP-fucose and at least one more nucleotide sugar as a donor for additional glycosyltransferase. Claim 109 is directed to the cell metabolically engineered for producing the mixture, expressing fucosyltransferase, at least one additional glycosyltransferase and capable of synthesizing GDP-fucose and at least one more nucleotide sugar as a donor for additional glycosyltransferase. Claim 111 is directed to a method of producing a mixture of at least four neutral fucosylated oligosaccharides in a metabolically engineered cell comprising expressing a fucosyltransferase and at least one additional glycosyltransferase and cell being capable of synthesizing GDP-fucose and at least one more nucleotide sugar as a donor for additional glycosyltransferase and cultivating the cell.
Regarding claims 108, 109 and 111, reference claim 100 teaches a cell producing a mixture of at least three mammalian milk oligosaccharides, metabolically engineered, expressing at least two glycosyltransferases and is capable of synthesizing one or more nucleotide-sugar as donor for glycosyltransferase. Reference claim 105 is directed to one of glycosyltranferases being fucosyltransferase and one of nucleotide-sugars being GDP-fucose. Reference claim 109 is directed to at least two glycosyltransferases producing the mixture. Reference claim 114 is directed to a cell producing a mixture of at least three mammalian milk oligosaccharides comprising producing a cell capable of expressing at least two glycosyltransferases and synthesizing one or more nucleotide-sugar donors and cultivating the cell. Reference claim 116 is drawn to the metabolically engineered cells expressing at least two glycosyltransferases and synthesizing one or more nucleotide-sugar donors. Reference claims 103 and 117 are drawn to a mixture comprising at least four mammalian milk oligosaccharides. Reference claims 102 and 115 are drawn to the mixture comprising neutral fucosylated and neutral non-fucosylated oligosaccharides. Thus, the reference claims 100, 102, 103, 105, 109 and 114-117 recite the method steps and the limitations of instant claims 108, 109 and 111 except that the reference claims do not explicitly teach producing the mixture of at least four neutral fucosylated oligosaccharides.
However, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention that at least four neutral fucosylated oligosaccharides can be produced based on the reference claims. One would have been motivated to expect that with reasonable success since the reference claims teach production of neutral fucosylated oligosaccharides (claims 102, 115), do not exclude production of more than four mammalian milk oligosaccharides (claims 103, 117), teach expression of at least two glycosyltransferases one of which is fucosyltransferase (claim 105) in the cell synthesizing GDP-fucose serving as fucose donor and therefore the cell of the reference application is capable of production of four neutral fucosylated oligosaccharides. Thus, reference claims 100, 102, 103, 105, 109 and 114-117 render instant claims 108, 109 and 111 obvious.
Claim 112 of instant application is directed to the mixture comprising at least one neutral non-fucosylated oligosaccharide. Reference claims 102 and 115 are drawn to the mixture comprising neutral fucosylated and neutral non-fucosylated oligosaccharides and hence including at least one non-fucosylated oligosaccharide.
Instant claim 116 is directed to at least one of the neutral oligosaccharides being a mammalian milk oligosaccharide. Instant claim 117 is directed to at least four neutral oligosaccharides being a mammalian milk oligosaccharides. Reference claims 100, 114 and 116 teach production of at least three mammalian milk oligosaccharides, claims 103 and 117 of at least four mammalian milk oligosaccharides and claims 102 and 115 are drawn to the mixture containing neutral fucosylated mammalian milk oligosaccharides. Reference claim 105 is directed to one of glycosyltransferases being fucosyltransferase and one of nucleotide-sugars being GDP-fucose. As described above, production of at least four mammalian milk oligosaccharides would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention based on the reference claims. One would have been motivated to expect that with reasonable success since the reference claims teach production of fucosylated oligosaccharides (claims 102, 115), do not exclude production of more than four mammalian milk oligosaccharides (claims 103, 117), teach expression of at least two glycosyltransferases one of which is fucosyltransferase (claim 105) and therefore the cell of reference application is capable of production of four neutral fucosylated mammalian milk oligosaccharides. Thus, reference claims 100, 102, 103, 105 and 114-117 render instant claims 116 and 117 obvious.
Instant claim 121 is directed to the cell further genetically modified for expression of a membrane protein involved in secretion of neutral fucosylated oligosaccharides outside the cell. Reference claim 106 is drawn to the cell further genetically modified for expression of a membrane protein involved in secretion of mammalian milk oligosaccharides outside the cell. Since mammalian milk oligosaccharides of the reference claims include neutral fucosylated as recited in claim 102, reference claims 106 and 102 render instant claim 121 obvious.
Instant claim 122 is directed to the membrane protein providing improved production of neutral fucosylated oligosaccharides. Reference claim 107 is drawn to the improved production of mammalian milk oligosaccharides. Since mammalian milk oligosaccharides of the reference claims include neutral fucosylated as recited in claim 102, reference claims 107 and 102 render instant claim 122 obvious.
Instant claim 125 is directed to expression of at least two additional glycosyltransferases. Reference claim 101 is drawn to expression of at least three glycosyltransferases and therefore covers instant claim 125.
Instant claim 126 is directed to the cell being bacterium (elected species), fungus, yeast, plant cell, animal cell or protozoan cell. That corresponds to reference claim 108.
Instant claim 127 is directed to the oligosaccharides mixture produced intracellularly. That corresponds to reference claim 113.
Therefore, since instant claims 108, 109, 111, 112, 116, 117, 121, 122 and 125-127 encompass the subject matter of the reference claims 100-103, 105-109 and 113-117, they are rejected under obviousness double patenting.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 108, 109, 111, 116, 117, 121, 125-127 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 105-107, 109, 111-113, 115-117, 124-126 and 128 of copending Application No. 18/040,378 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because claims overlap in scope.
Claim 108 of instant application is directed to a method of producing a mixture of at least four neutral fucosylated oligosaccharides comprising providing and cultivating cell expressing a glycosyltransferase being a fucosyltransferase and at least one additional glycosyltransferase and cell being capable of synthesizing GDP-fucose and at least one more nucleotide sugar as a donor for additional glycosyltransferase. Claim 109 is directed to the cell metabolically engineered for producing the mixture, expressing fucosyltransferase, at least one additional glycosyltransferase and capable of synthesizing GDP-fucose and at least one more nucleotide sugar as a donor for additional glycosyltransferase. Claim 111 is directed to a method of producing a mixture of at least four neutral fucosylated oligosaccharides in a metabolically engineered cell comprising expressing a fucosyltransferase and at least one additional glycosyltransferase and cell being capable of synthesizing GDP-fucose and at least one more nucleotide sugar as a donor for additional glycosyltransferase and cultivating the cell.
Regarding claims 108, 109 and 111, reference claim 105 teaches a cell producing a mixture of at least three oligosaccharides, including neutral oligosaccharides wherein the cell is metabolically engineered, is capable of expressing at least two glycosyltransferases and synthesizing one or more nucleotide-sugar as a donor for the glycosyltransferase. Reference claim 109 is directed to one of glycosyltranferases being fucosyltransferase and one of nucleotide-sugars being GDP-fucose. Reference claim 117 is drawn to at least two glycosyltransferases involved in producing the mixture. Reference claim 124 is directed to a cell producing a mixture of at least three oligosaccharides including neutral oligosaccharides comprising producing a cell capable of expressing at least two glycosyltransferases and synthesizing one or more nucleotide-sugar donors and cultivating the cell. Reference claim 125 is drawn to the metabolically engineered cells expressing at least two glycosyltransferases and synthesizing one or more nucleotide-sugar donors. Reference claims 106 and 126 are drawn to the mixture comprising at least four oligosaccharides. Thus, the reference claims 105, 109, 117 and 124 -126 recite the method steps and the limitations of instant claims 108, 109 and 111 except that the reference claims do not explicitly teach producing the mixture of at least four neutral fucosylated oligosaccharides.
However, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention that at least four neutral fucosylated oligosaccharides can be produced based on the reference claims. One would have been motivated to expect that with reasonable success since the reference claims teach producing of at least four oligosaccharides, expression of at least two glycosyltransferases one of which is fucosyltransferase and cell capable of synthesizing GDP-fucose which is the substrate of fucosyltransferase catalyzing oligosaccharides fucosylation. Thus, reference claims 105, 106, 109, 117 and 124-126 render instant claims 108, 109 and 111 obvious.
Instant claim 125 is directed to expression of at least two additional glycosyltransferases. Reference claim 107 is drawn to expression of at least three glycosyltransferases and therefore covers instant claim 125.
Instant claim 121 is directed to the cell further genetically modified for expression of a membrane protein involved in secretion of neutral fucosylated oligosaccharides outside the cell. That corresponds to the reference claim 111 drawn to the cell further genetically modified for expression of a membrane protein involved in secretion of any oligosaccharides outside the cell.
Instant claim 116 is directed to at least one of the neutral fucosylated oligosaccharides being a mammalian milk oligosaccharide. Instant claim 117 is directed to at least four neutral fucosylated oligosaccharides being a mammalian milk oligosaccharide. Reference claims 112 and 128 teaches production of at least one mammalian milk oligosaccharides and reference claim 113 – production of all oligosaccharides as mammalian milk oligosaccharides. Since producing of at least four neutral fucosylated oligosaccharides is obvious over reference claims as described above, reference claims 112, 113 and 128 make obvious producing of at least four neutral fucosylated oligosaccharides as mammalian milk oligosaccharides.
Instant claim 126 is directed to the cell being bacterium (elected species), fungus, yeast, plant cell, animal cell or protozoan cell. That corresponds to reference claim 115.
Instant claim 127 is directed to the oligosaccharides mixture produced intracellularly. That corresponds to reference claim 116.
Therefore, since instant claims 108, 109, 111, 116, 117, 121, 125-127 encompass the subject matter of the reference claims 105, 106, 107, 109, 111-113, 115-117, 124-126 and 128, they are rejected under obviousness double patenting.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 108, 109, 110 and 121 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 62, 66, 71 and 75 of copending Application No. 18/041,022 (reference application) in view of Papadakis (WO 2017101958 A1 on record in IDS).
Claim 108 of instant application is directed to a method of producing a mixture of at least four neutral fucosylated oligosaccharides comprising providing and cultivating cell expressing a glycosyltransferase being a fucosyltransferase and at least one additional glycosyltransferase and cell being capable of synthesizing GDP-fucose and at least one more nucleotide sugar as a donor for additional glycosyltransferase. Claim 109 is directed to the cell metabolically engineered for producing the mixture, expressing fucosyltransferase, at least one additional glycosyltransferase and capable of synthesizing GDP-fucose and at least one more nucleotide sugar as a donor for additional glycosyltransferase. Claim 111 is directed to a method of producing a mixture of at least four neutral fucosylated oligosaccharides in a metabolically engineered cell comprising expressing a fucosyltransferase and at least one additional glycosyltransferase and cell being capable of synthesizing GDP-fucose and at least one more nucleotide sugar as a donor for additional glycosyltransferase and cultivating the cell.
Regarding claims 108, 109 and 111, reference claim 62 teaches a method of producing DiFL by providing at least two fucosyltransferases and a GDP-fucose donor and resulting in a mixture of DiFL with 2’FL and 3’FL. Reference claim 66 is directed to expression of at least two fucosyltransferases in a cell providing GDP-fucose as a donor and cultivating the cell producing in a mixture of DiFL with 2’FL and 3’FL. Reference claim 71 is drawn to the cell being a metabolically engineered cell. Thus, the reference claims teach production of three neutral fucosylated oligosaccharides in a metabolically engineered cell providing GDP-fucose and expressing two fucosyltransferases which are glycosyltransferases.
The reference claims do not teach production of a mixture of at least four neutral fucosylated oligosaccharides and the cell capable of synthesizing one or more nucleotide-sugar donors.
Regarding claims 108, 109 and 111, Papadakis teaches production of human milk oligosaccharides (HMO) by expression of recombinant glycosyltransferases necessary for synthesis of oligosaccharide in the cell, production of monosaccharide nucleotide donor in the cell suitable to be transferred by the glycosyltransferase to the acceptor and culturing the cell in the presence of acceptor (p. 2, lines 3-25). Papadakis describes that the cell can produce different neutral fucosylated oligosaccharides, such as 2’-FL, 3’-FL, LNFP-I, LNFP-II, LNFP-III (p. 6, lines 1-4). Papadakis discloses that 2’-FL, 3’-FL are produced with α-1,2-fucosyltransferase and α-1,3-fucosyltranferase (p. 16, lines 27-28) and when in addition to fucosyltransferases, two additional glycosyltransferases, i.e. β-1,3-N-acetylglucosaminyltransferase and galactosyltransferases, are present, LNFP-I, LNFP-II, LNFP-III are produced (p. 17, lines 3-29). Papadakis mentions that the cell is capable to produce activated nucleotide sugars, GDP-Fuc, UDP-Gal, UDP-GlcNAc suitable to be transferred by the corresponding glycosyltransferase (p. 11, lines 21-24).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention that additional glycosyltransferases and additional nucleotide-sugar donors can be provided in the cell taught in reference claims based on Papadakis teaching. One would have been motivated to do that to produce additional neutral fucosylated oligosaccharides since Papadakis describes production of different neutral fucosylated oligosaccharides in a cell and provides instructions for the selection of the necessary glycosyltransferases and reference claims do not exclude presence of additional glycosyltransferases. A skilled artisan would have reasonably expected success in this combination because the reference claims and Papadakis describe enzymatic production of neutral fucosylated oligosaccharides. Thus, reference claims 62, 66 and 71 and Papadakis teaching render claims 108, 109 and 111 obvious.
Claim 121 of instant application is directed to the cell further genetically modified for expression of a membrane protein involved in secretion of neutral fucosylated oligosaccharides outside the cell. That corresponds to the reference claim 75 drawn to the cell further genetically modified for expression of a membrane protein involved in secretion of 2’FL, 3’FL and DiFL oligosaccharides outside the cell.
Therefore, since instant claims 108, 109, 111 and 121 encompass the subject matter of the reference claims 62, 66, 71 and 75, they are rejected under obviousness double patenting.
This is a provisional nonstatutory double patenting rejection.
Claims 108, 109, 111, 112, 116, 117, 121, 122 and 126 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 5, 7, 9, 20, 21, 26, 27, 31, 34, 40 and 42 of copending Application No. 18/041064 (reference application) in view of Papadakis (WO 2017101958 A1 on record in IDS).
Claim 108 of instant application is directed to a method of producing a mixture of at least four neutral fucosylated oligosaccharides comprising providing and cultivating cell expressing a glycosyltransferase being a fucosyltransferase and at least one additional glycosyltransferase and cell being capable of synthesizing GDP-fucose and at least one more nucleotide sugar as a donor for additional glycosyltransferase. Claim 109 is directed to the cell metabolically engineered for producing the mixture, expressing fucosyltransferase, at least one additional glycosyltransferase and capable of synthesizing GDP-fucose and at least one more nucleotide sugar as a donor for additional glycosyltransferase. Claim 111 is directed to a method of producing a mixture of at least four neutral fucosylated oligosaccharides in a metabolically engineered cell comprising expressing a fucosyltransferase and at least one additional glycosyltransferase and cell being capable of synthesizing GDP-fucose and at least one more nucleotide sugar as a donor for additional glycosyltransferase and cultivating the cell.
Regarding claims 108, 109 and 111, reference claim 1 teaches a method for producing a mixture of at least two oligosaccharides, comprising providing cell capable of expressing glycosyltransferase and synthesizing a nucleotide-sugar donor and cultivating the cell. Reference claim 3 is drawn to the metabolically engineered cell. Reference claim 5 is directed to the cell producing three or more oligosaccharides. Reference claim 9 is drawn to glycosyltransferase being fucosyltransferase and the nucleotide-sugar being GDP-fucose. Reference claim 7 teaches various glycosyltransferases. Reference claim 20 is directed to the cell producing charged or neutral oligosaccharides. Reference claim 26 is directed to the mixture of all fucosylated oligosaccharides. Reference claim 27 is drawn to the cell producing three fucosylated oligosaccharides.
The reference claims do not teach expression of additional glycosyltransferase and nucleotide-sugar donor and do not teach producing at least four neutral fucosylated oligosaccharides.
Regarding claims 108, 109 and 111, Papadakis teaches production of human milk oligosaccharides (HMO) by expression of recombinant glycosyltransferases necessary for synthesis of oligosaccharide in the cell, production of monosaccharide nucleotide donor in the cell suitable to be transferred by the glycosyltransferase to the acceptor and culturing the cell in the presence of acceptor (p. 2, lines 3-25). Papadakis describes that the cell can produce different neutral fucosylated oligosaccharides, such as 2’-FL, 3’-FL, LNFP-I, LNFP-II, LNFP-III (p. 6, lines 1-4). Papadakis discloses that 2’-FL, 3’-FL are produced with α-1,2-fucosyltransferase and α-1,3-fucosyltranferase (p. 16, lines 27-28) and when in addition to fucosyltransferases, two additional glycosyltransferases, i.e. β-1,3-N-acetylglucosaminyltransferase and galactosyltransferases, are present, LNFP-I, LNFP-II, LNFP-III are produced (p. 17, lines 3-29). Papadakis mentions that the cell is capable to produce activated nucleotide sugars, GDP-Fuc, UDP-Gal, UDP-GlcNAc suitable to be transferred by the corresponding glycosyltransferase (p. 11, lines 21-24).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention that additional glycosyltransferases and additional nucleotide-sugar donors can be provided in the cell taught in reference claims based on Papadakis teaching. One would have been motivated to do that to produce additional neutral fucosylated oligosaccharides since Papadakis describes production of different neutral fucosylated oligosaccharides in a cell and provides instructions for the selection of the necessary glycosyltransferases and glycosyltransferases described by Papadakis, such as N-acetylglycosaminyltransferase and galactotransferases are taught in the reference claim 7. A skilled artisan would have reasonably expected success in this combination because the reference claims and Papadakis describe enzymatic production of neutral fucosylated oligosaccharides. Thus, reference claims 1, 5, 7, 9, 20, 26 and 27 and Papadakis teaching render claims 108, 109 and 111 obvious.
Claim 112 of instant application is directed to the mixture comprising at least one neutral non-fucosylated oligosaccharide. That corresponds to reference claim 20 directed to the cell producing neutral oligosaccharides and reference claim 21 teaching the cell producing fucosylated, non-fucosylated or mixture of fucosylated and non-fucosylated oligosaccharides.
Instant claim 116 is directed to at least one of the neutral oligosaccharides being a mammalian milk oligosaccharide. Instant claim 117 is directed to at least four neutral oligosaccharides being a mammalian milk oligosaccharide. That corresponds to reference claim 40 drawn to any one of oligosaccharides being mammalian milk oligosaccharides.
Claim 121 of instant application is directed to the cell further genetically modified for expression of a membrane protein involved in secretion of neutral fucosylated oligosaccharides outside the cell. That corresponds to the reference claim 31 drawn to the cell further metabolically engineered for expression of a membrane protein involved in secretion of any oligosaccharides outside the cell.
Instant claim 122 is directed to the membrane protein providing improved production of neutral fucosylated oligosaccharides. That corresponds to reference claim 34 is drawn to the improved production of at least two oligosaccharides.
Instant claim 126 is directed to the cell being bacterium (elected species), fungus, yeast, plant cell, animal cell or protozoan cell. That corresponds to reference claim 42.
Therefore, since instant claims 108, 109, 111, 112, 116, 117, 121, 122 and 126 encompass the subject matter of the reference claims 1, 5, 7, 9, 20, 21, 26, 27, 31, 34, 40 and 42, they are rejected under obviousness double patenting.
This is a provisional nonstatutory double patenting rejection.
Conclusion
No claims are allowed.
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/L.G.K./Examiner, Art Unit 1653
/SHARMILA G LANDAU/Supervisory Patent Examiner, Art Unit 1653
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