DETAILED CORRESPONDENCE
Application Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
2. A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 05/26/2026 has been entered.
3. Claims 5-6, 22, and 41-42 are cancelled.
4. Claims 1-4, 7-21, 23-31, 33-35, 37-40, and 46-50 are pending.
5. Applicant’s remarks filed on 05/26/2026 in response to the Final Rejection mailed on 03/13/2026 have been fully considered and are deemed persuasive to overcome at least one of the rejections and/or objections as previously applied.
The text of those sections of Title 35 U.S. Code not included in the instant action can be found in the prior Office Action.
Claim Rejections - 35 USC § 112(b)
6. The rejection of claims 1-31 and 41-42 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, for the relative term “reduced” is withdrawn in view of applicants’ amendment to the claims to recite “as compared to a recombinant cell that does not have reduced activity of the disulfide reductase enzyme”.
7. The rejection of claim 6 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, is withdrawn in view of applicants’ amendment to the claims to cancel claim 6.
8. The rejection of claims 37-42 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, is withdrawn in view of applicants’ amendment to the claims for claim 37 to depend upon claim 33.
Claim Rejections - 35 USC § 112(a)
9. The written description rejection of claims 1-31 and 33-42 under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, is withdrawn in view of applicants’ amendment to the claims to recite “wherein the recombinant cell has a gor mutation of a disulfide reductase enzyme that creates a reduced activity of the disulfide reductase enzyme”.
10. The scope of enablement rejection of claims 1-31 and 33-42 under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, is withdrawn in view of applicants’ amendment to the claims to recite “wherein the recombinant cell has a gor mutation of a disulfide reductase enzyme that creates a reduced activity of the disulfide reductase enzyme”.
11. The enablement rejection of claim 6 under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, is withdrawn in view of applicants’ amendment to the claims to cancel claim 6.
Claim Rejections - 35 USC § 103
12. The rejection of claims 5-6 and 22 under 35 U.S.C. 103 as being unpatentable over Oganesyan et al. (WO 2015/117093 A1; cited on IDS filed on 03/10/2025) in view of Norby et al. (US Patent Application Publication 2009/0253900 A1; cited on IDS filed on 08/24/2023) is withdrawn in view of applicants’ amendment to the claims to cancel claims 5-6 and 22.
13. The rejection of claims 41-42 under 35 U.S.C. 103 as being unpatentable over Peters et al. (US Patent Application Publication 2013/0281671 A1; cited on PTO-892 mailed on 08/22/2025) in view of Norby et al. (US Patent Application Publication 2009/0253900 A1; cited on IDS filed on 08/24/2023) as applied to claims 33-35 and 37-40 above, and further in view of Oganesyan et al. (WO 2015/117093 A1; cited on IDS filed on 03/10/2025) is withdrawn in view of applicants’ amendment to the claims to cancel claims 41-42.
14. The rejection of claims 1-4, 7-21, 23-29, 31, and 46-50 under 35 U.S.C. 103 as being unpatentable over Oganesyan et al. (WO 2015/117093 A1; cited on IDS filed on 03/10/2025) in view of Norby et al. (US Patent Application Publication 2009/0253900 A1; cited on IDS filed on 08/24/2023) is maintained for the reasons of record and the reasons set forth below. The rejection has been modified in order to address applicants’ amendment to the claims.
15. With respect to claim 1, Oganesyan et al. teach a method for producing a soluble CRM197 protein from E. coli comprising expressing the protein from an E. coli (interpreted as containing a genome) containing an expression vector that encodes the protein sequence, wherein the recombinant cell has a mutation in one or more disulfide reductase genes such that the activity is reduced, and purifying the expressed protein [see Abstract; p. 3]. Oganesyan et al. teach the method wherein the recombinant E. coli comprises a gor mutation [see Abstract; p. 3-4; p. 7; p. 9].
With respect to claim 2, Oganesyan et al. teach the method wherein the protein expressed is CRM197, which is a diphtheria toxin [see p. 2, lines 3-10].
With respect to claim 3, Oganesyan et al. teach the method wherein the recombinant cell has a reduced activity of only one disulfide reductase enzyme [see p. 3].
With respect to claim 4, Oganesyan et al. teach the method wherein the recombinant cell has a reduced activity of more than one disulfide reductase enzyme [see p. 3].
With respect to claim 6, Oganesyan et al. teach the method wherein the recombinant E. coli comprises a deletion of gor gene [see p. 4, lines 11-12; p. 9]. Although Oganesyan et al. does not explicitly teach wherein the cell is obtained or derived from ATCC Deposit No. PTA-126975, given the indefiniteness of this claim, it is the examiner’s position that the Oganesyan et al. strain can be interpreted as derived from said strain.
With respect to claim 8, Oganesyan et al. teach the method wherein the expression vector contains a ribosome binding site, an initiation codon, and/or an expression enhancer region [see p. 4, lines 8-9].
With respect to claim 9, Oganesyan et al. teach the method wherein the expression vector contains an inducible first promoter and expressing the protein comprises inducing the inducible promoter with a first inducing agent [see p. 4, lines 3-24].
With respect to claim 10, Oganesyan et al. teach the method wherein the expression vector comprises one or more inducible promoters [see p. 4, lines 3-24; p. 7, bottom; p. 12].
With respect to claim 11, Oganesyan et al. teach the method wherein the expression vector contains expressible sequences, an inducible first promoter and expressing the protein comprises inducing the inducible first promoter with a first inducing agent, the gene contains an inducible second promoter and inducing with a second inducing agent, wherein the first and second inducing agents are the same [see 4, lines 3-24; p. 7, bottom; p. 11, bottom bridging to p. 12].
With respect to claim 13, Oganesyan et al. teach the method wherein the isolating comprises chromatography [see p. 4, lines 25-27].
With respect to claim 14, Oganesyan et al. teach the method wherein the chromatography comprises a dextran sulfate resin, an active sulfate resin, a phosphate resin, a heparin resin, or a heparin-like resin [see p. 4, lines 25-27].
With respect to claim 15, Oganesyan et al. teach the method further comprising conjugating the isolated protein with a chemical compound [see p. 4, bottom; p. 14, lines 22-24].
With respect to claim 16, Oganesyan et al. teach the method wherein the chemical compound comprises a polysaccharide, protein, peptides, oligosaccharides and haptens [see p. 14, lines 22-24].
With respect to claim 17, Oganesyan et al. teach a method of producing a CRM peptide from E. coli comprising expressing the protein from an E. coli (interpreted as containing a genome) containing an expression vector that encodes the peptide sequence, wherein the recombinant cell has a mutation in one or more disulfide reductase genes such that the activity is reduced, wherein the reducing activity results in a shift in the redox status of the cytoplasm to a more oxidative state, and purifying the expressed peptide [see Abstract; p. 3-4]. Oganesyan et al. teach the method wherein the recombinant E. coli comprises a gor mutation [see Abstract; p. 3-4; p. 7; p. 9].
With respect to claim 18, Oganesyan et al. teach the method wherein the protein expressed is CRM197 peptide, which is a diphtheria toxin [see p. 2, lines 3-10].
With respect to claim 19, Oganesyan et al. teach the method wherein the recombinant cell has a reduced activity of only one disulfide reductase enzyme [see p. 3].
With respect to claim 20, Oganesyan et al. teach the method wherein the recombinant cell has a reduced activity of more than one disulfide reductase enzyme [see p. 3].
With respect to claim 21, Oganesyan et al. teach the method wherein the one or more disulfide reductase enzymes comprises one or more of an oxidoreductase, a dihydrofolate reductase, a thioredoxin reductase, or a glutathione reductase [see p. 4, lines 12-15].
With respect to claim 23, Oganesyan et al. teach the method wherein the expression vector comprises one or more inducible promoters [see p. 4, lines 3-24; p. 7, bottom; p. 12].
With respect to claim 24, Oganesyan et al. teach the method wherein the expression vector contains expressible sequences, an inducible first promoter and expressing the protein comprises inducing the inducible first promoter with a first inducing agent, the gene contains an inducible second promoter and inducing with a second inducing agent, wherein the first and second inducing agents are the same [see 4, lines 3-24; p. 7, bottom; p. 11, bottom bridging to p. 12].
With respect to claim 25, Oganesyan et al. teach the method wherein the isolating comprises chromatography [see p. 4, lines 25-27].
With respect to claim 26, Oganesyan et al. teach the method wherein the chromatography comprises a dextran sulfate resin, an active sulfate resin, a phosphate resin, a heparin resin, or a heparin-like resin [see p. 4, lines 25-27].
With respect to claim 27, Oganesyan et al. teach the method further comprising conjugating the isolated protein with a chemical compound [see p. 4, bottom; p. 14, lines 22-24].
With respect to claim 28, Oganesyan et al. teach the method wherein the chemical compound comprises a polysaccharide, protein, peptides, oligosaccharides and haptens [see p. 14, lines 22-24].
With respect to claim 29, Oganesyan et al. teach the method wherein the reducing activity results in a shift in the redox status of the cytoplasm to a more oxidative state (interpreted as an oxidizing agent) [see Abstract; p. 3-4].
With respect to claim 31, Oganesyan et al. teach a method of producing a CRM peptide from E. coli comprising expressing the protein from an E. coli (interpreted as containing a genome) containing an expression vector that encodes the peptide sequence, wherein the recombinant cell has a mutation in one or more disulfide reductase genes such that the activity is reduced, wherein the reducing activity results in a shift in the redox status of the cytoplasm to a more oxidative state, and purifying the expressed peptide from the cytoplasm [see Abstract; p. 3-4, p. 7]. Oganesyan et al. teach wherein CRM contains two disulfide bonds that are important for correct folding, function and solubility [see p. 7]. Oganesyan et al. teach the method wherein the recombinant E. coli comprises a gor mutation [see Abstract; p. 3-4; p. 7; p. 9].
With respect to claim 46, Oganesyan et al. teach a method for producing a soluble CRM197 protein from E. coli comprising expressing the protein from an E. coli (interpreted as containing a genome) containing an expression vector that encodes the protein sequence, wherein the recombinant cell has a mutation in one or more disulfide reductase genes such that the activity is reduced, and purifying the expressed protein [see Abstract; p. 3]. Oganesyan et al. teach the method wherein the recombinant E. coli comprises a gor mutation [see Abstract; p. 3-4; p. 7; p. 9].
With respect to claim 50, Oganesyan et al. teach the method wherein the recombinant cell is an E. coli cell [see p. 4, lines 11-12].
However, Oganesyan et al. does not teach the methods of claims 1-4, 7-21, 23-28, 31, and 46 of expressing a peptidase from a gene in the recombinant cell, wherein the peptidase removes the methionine from the N-terminus of the protein or peptide expressed; the method of claims 7 and 49, wherein the peptidase comprises a methionine aminopeptidase; and the method of claims 12, 17, and 48, wherein the peptidase gene is integrated into the genome of the recombinant cell.
Norby et al. teach that production of peptides by recombinant techniques using either prokaryotic or eukaryotic systems inherently yields the peptide with a leading methionine amino acid residue that may not be present in the native protein [see paragraph 0003]. Norby et al. teach a method of producing a peptide comprising expressing the peptide in a recombinant cell, wherein the expressed peptide contains an N-terminal methionine, and the recombinant cell contains a gene that encodes a peptidase; expressing the peptidase gene such that the N-terminal methionine is cleaved from the expressed peptide; and isolating the peptide [see Abstract; paragraphs 0006-0011; 0051-0062]. Norby et al. further teach the method wherein the peptidase gene and peptide gene is integrated into the genome of the recombinant cell [see paragraphs 0051-0062].
With respect to claim 47, Norby et al. teach the method wherein the peptide is expressed from another gene that is integrated into the genome of the recombinant cell [see paragraphs 0051-0062].
With respect to claim 48, Norby et al. teach the method wherein the peptidase gene is integrated into the genome of the recombinant cell [see paragraphs 0051-0062].
With respect to claim 49, Norby et al. teach the method wherein the peptidase is a methionine amino peptidase [see paragraphs 0051-0062].
Before the effective filing date of the claimed invention, it would have been obvious for one of ordinary skill in the art to combine the teachings of Oganesyan et al. and Norby et al. according to the teachings of Norby et al. to include a methionine aminopeptidase in the recombinant cell of Oganesyan et al. because Oganesyan et al. teach methods for producing high quantities of soluble CRM proteins and peptides by reducing the activity of disulfide reductase activity in an E. coli cell. Norby et al. teach that production of peptides by recombinant techniques using either prokaryotic or eukaryotic systems inherently yields the peptide with a leading methionine amino acid residue that may not be present in the native protein and teach coexpressing a methionine aminopeptidase with a protein in order to cleave the initiator methionine. One of ordinary skill in the art desiring to produce a soluble protein in its native form would look to combine the teachings of Oganesyan et al. and Norby et al. with a reasonable expectation of success and a reasonable level of predictability because Norby et al. acknowledges that coexpressing a methionine aminopeptidase with a protein of interest can result in processing and removal of the initiator methionine. Therefore, the above invention would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
RESPONSE TO REMARKS: Beginning on p. 9 of applicants’ remarks, applicants in summary contend that those skilled in the art could not have known what effect the amino peptidase would have on a disulfide containing protein absent actual experimentation, and such assertion can only be made using hindsight.
This argument is found to be not persuasive because it must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. See In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971). As stated above, Norby et al. teach that production of peptides by recombinant techniques using either prokaryotic or eukaryotic systems inherently yields the peptide with a leading methionine amino acid residue that may not be present in the native protein [see paragraph 0003]. Norby et al. teach a method of producing a peptide comprising expressing the peptide in a recombinant cell, wherein the expressed peptide contains an N-terminal methionine, and the recombinant cell contains a gene that encodes a peptidase; expressing the peptidase gene such that the N-terminal methionine is cleaved from the expressed peptide; and isolating the peptide. As stated above, One of ordinary skill in the art desiring to produce a soluble protein in its native form would look to combine the teachings of Oganesyan et al. and Norby et al. with a reasonable expectation of success and a reasonable level of predictability because Norby et al. acknowledges that coexpressing a methionine aminopeptidase with a protein of interest can result in processing and removal of the initiator methionine.
16. The rejection of claim 30 under 35 U.S.C. 103 as being unpatentable over Oganesyan et al. (WO 2015/117093 A1; cited on IDS filed on 03/10/2025) in view of Norby et al. (US Patent Application Publication 2009/0253900 A1; cited on IDS filed on 08/24/2023) as applied to claims 1-4, 7-21, 23-29, 31, and 46-50 above, and further in view of Thom et al. (Bioconjugate Chemistry, 2011; cited on PTO-892 mailed on 08/22/2025) is maintained for the reasons of record and the reasons set forth below.
17. The relevant teachings of Oganesyan et al. and Norby et al. as applied to claims 1-4, 7-21, 23-29, 31, and 46-50 are set forth above.
With respect to claim 30, Oganesyan et al. teach the method of producing a CRM peptide from E. coli comprising expressing the protein from an E. coli (interpreted as containing a genome) containing an expression vector that encodes the peptide sequence, wherein the recombinant cell has a mutation in one or more disulfide reductase genes such that the activity is reduced, wherein the reducing activity results in a shift in the redox status of the cytoplasm to a more oxidative state, and purifying the expressed peptide from the cytoplasm [see Abstract; p. 3-4, p. 7]. Oganesyan et al. teach wherein CRM contains two disulfide bonds that are important for correct folding, function and solubility [see p. 7]. , Oganesyan et al. further teach conjugating the isolated protein with a chemical compound, wherein the chemical compound comprises a polysaccharide, protein, peptides, oligosaccharides and haptens for vaccines [see p. 4; p. 14, lines 22-24].
However, the combination of Oganesyan et al. and Norby et al. do not each the method of claim 30, wherein the oxidizing agent comprises a hydrazide, a hydrazine, an aminoxy group, N-terminal 1-amino, 2-alcohol amino acid, or a combination thereof.
Thom et al. teach that recombinant protein therapeutics have emerged as effective treatment for a variety of conditions and teach that the covalent attachment of PEG to a therapeutic protein increasing the half-life of the protein in vivo by decreasing renal clearance [see p. 1017, column 1]. Thom et al. further teach that PEGylation of a target protein can improve its solubility and stability [see p. 1017, column 1]. Thom et al. teach a method for site specific C-terminal PEGylation of recombinant proteins that exploits the chemical cleavage of intein-fusion proteins with hydrazine to directly produce recombinant protein hydrazides that permits the site-specific C-terminal modification by hydrazone-forming ligation reactions [see Abstract].
Before the effective filing date of the claimed invention, it would have been obvious for one of ordinary skill in the art to combine the teachings of Oganesyan et al., Norby et al. and Thom et al. according to the teachings of Thom et al. to use an oxidizing agent such as hydrazine to conjugate a PEG molecule to the peptides of Oganesyan et al. and Norby et al. because Oganesyan et al. and Norby et al. teach methods for production of high amounts of soluble proteins for therapeutic purposes. Thom et al. teach a method for site specific C-terminal PEGylation of recombinant proteins that exploits the chemical cleavage of intein-fusion proteins with hydrazine to directly produce recombinant protein hydrazides. One of ordinary skill in the art would have had a reasonable expectation of success, a reasonable level of predictability and would have been motivated to combine the teachings of Oganesyan et al., Norby et al. and Thom et al. because Thom et al. acknowledges that the covalent attachment of PEG to a therapeutic protein increasing the half-life of the protein and solubility. Therefore, the above invention would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
RESPONSE TO REMARKS: Beginning on p. 10 of applicants’ remarks, applicants in summary contend that the use of oxidizing agents as recited in claim 30 is novel and nonobvious.
This argument is found to be not persuasive for the reasons set forth above.
18. The rejection of claims 33-35 and 37-40 under 35 U.S.C. 103 as being unpatentable over Peters et al. (US Patent Application Publication 2013/0281671 A1; cited on PTO-892 mailed on 08/22/2025) in view of Norby et al. (US Patent Application Publication 2009/0253900 A1; cited on IDS filed on 08/24/2023) is maintained for the reasons of record and the reasons set forth below.
19. With respect to claim 33, Peters et al. teach a method of producing a preprotein, Factor VIII, comprising co-transfecting a host cell with a polynucleotide encoding Factor VIII and a polynucleotide encoding a protein convertase, inducing (translation induction sequence) expression of Factor VIII and proprotein convertase, wherein the proprotein convertase cleaves the Factor VIII to produce a processed Factor VIII, and isolate the processed Factor VIII [see Abstract; paragraphs 0004-0022; 0035-0037].
With respect to claim 34, Peters et al. teach the method wherein the preprotein is Factor VIII (interpreted as proprotein of the coagulation system) [see Abstract; paragraphs 0004-0022; 0035-0037].
With respect to claim 35, Peters et al. teach the method wherein the vector is a viral vector or plasmid vector designed to integrate the nucleotide sequence encoding the protease into the genome of the host cell [see paragraphs 0129-0134].
With respect to claims 37-40, Peters et al. teach a method of producing a preprotein, Factor VIII, comprising co-transfecting a host cell with a polynucleotide encoding Factor VIII and a polynucleotide encoding a protein convertase, inducing (translation induction sequence) expression of Factor VIII and proprotein convertase, wherein the proprotein convertase cleaves the Factor VIII to produce a processed Factor VIII, and isolate the processed Factor VIII [see Abstract; paragraphs 0004-0022; 0035-0037]. Peters et al. teach the method wherein the preprotein is Factor VIII (interpreted as proprotein of the coagulation system) [see Abstract; paragraphs 0004-0022; 0035-0037] and wherein the vector is a viral vector or plasmid vector designed to integrate the nucleotide sequence encoding the protease into the genome of the host cell under control of inducible promoters and enhancer sequences [see paragraphs 0127-0134].
However, Peters et al. does not teach the method of claims 33-40, wherein a methionine aminopeptidase gene is integrated into the genome of the recombinant cell and the method of claim 37, wherein expression of the methionine aminopeptidase gene removes an N-terminal methionine from the preprotein or the protein.
Norby et al. teach that production of peptides by recombinant techniques using either prokaryotic or eukaryotic systems inherently yields the peptide with a leading methionine amino acid residue that may not be present in the native protein [see paragraph 0003]. Norby et al. teach a method of producing a peptide comprising expressing the peptide in a recombinant cell, wherein the expressed peptide contains an N-terminal methionine, and the recombinant cell contains a gene that encodes a peptidase; expressing the peptidase gene such that the N-terminal methionine is cleaved from the expressed peptide; and isolating the peptide [see Abstract; paragraphs 0006-0011; 0051-0062]. Norby et al. further teach the method wherein the peptidase gene and peptide gene is integrated into the genome of the recombinant cell [see paragraphs 0051-0062].
Before the effective filing date of the claimed invention, it would have been obvious for one of ordinary skill in the art to combine the teachings of Peters et al. and Norby et al. according to the teachings of Norby et al. to include a methionine aminopeptidase in the recombinant cell of Peters et al. because Peters et al. teach methods for producing high quantities of processed Factor VIII proteins. Norby et al. teach that production of peptides by recombinant techniques using either prokaryotic or eukaryotic systems inherently yields the peptide with a leading methionine amino acid residue that may not be present in the native protein and teach coexpressing a methionine aminopeptidase with a protein in order to cleave the initiator methionine. One of ordinary skill in the art desiring to produce a soluble protein in its native form would look to combine the teachings of Peters et al. and Norby et al. with a reasonable expectation of success and a reasonable level of predictability because Norby et al. acknowledges that coexpressing a methionine aminopeptidase with a protein of interest can result in processing and removal of the initiator methionine. Therefore, the above invention would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
RESPONSE TO REMARKS: Beginning on p. 10 of applicants’ remarks, applicants in summary contend that Peters is directed to a protein convertase and not a methionine peptidase, wherein protein convertases are serine proteases that cleave specific sequences off precursor proteins to activate them, and thus the combination is inaccurate.
This argument is found to be not persuasive because one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). In the instant case, one of ordinary skill in the art desiring to produce a soluble protein in its native form would look to combine the teachings of Peters et al. and Norby et al. with a reasonable expectation of success and a reasonable level of predictability because Norby et al. acknowledges that coexpressing a methionine aminopeptidase with a protein of interest can result in processing and removal of the initiator methionine.
Conclusion
20. Status of the claims:
Claims 1-4, 7-21, 23-31, 33-35, 37-40, and 46-50 are pending.
Claims 1-4, 7-21, 23-31, 33-35, 37-40, and 46-50 are rejected.
No claims are in condition for an allowance.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to PAUL J HOLLAND whose telephone number is (571)270-3537. The examiner can normally be reached Monday to Friday from 8AM to 5PM.
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/PAUL J HOLLAND/Primary Examiner, Art Unit 1656
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