Ex Parte Kato et alDownload PDFPatent Trial and Appeal BoardMar 23, 201712310258 (P.T.A.B. Mar. 23, 2017) Copy Citation United States Patent and Trademark Office UNITED STATES DEPARTMENT OF COMMERCE United States Patent and Trademark Office Address: COMMISSIONER FOR PATENTS P.O.Box 1450 Alexandria, Virginia 22313-1450 www.uspto.gov APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO. 12/310,258 07/06/2009 Shigeo Kato 392.1006 7352 23280 7590 03/27/2017 Davidson, Davidson & Kappel, LLC 589 8th Avenue 16th Floor New York, NY 10018 EXAMINER TREPTOW, NANCY ANN ART UNIT PAPER NUMBER 1636 NOTIFICATION DATE DELIVERY MODE 03/27/2017 ELECTRONIC Please find below and/or attached an Office communication concerning this application or proceeding. The time period for reply, if any, is set in the attached communication. Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the following e-mail address(es): ddk @ ddkpatent .com PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE BEFORE THE PATENT TRIAL AND APPEAL BOARD Ex parte SHIGEO KATO, YOICHI KUMADA, TOMOMI KAWASAKI, and YASUFUMI KIKUCHI Appeal 2016-003542 Application 12/310,25s1 Technology Center 1600 Before JEFFREY N. FREDMAN, TIMOTHY G. MAJORS and DAVID COTTA, Administrative Patent Judges. COTTA, Administrative Patent Judge. DECISION ON APPEAL This is an appeal under 35 U.S.C. § 134 involving claims to a process for producing an intracellular soluble fraction of an antibody fragment, and a related vector allowing for this production. The Examiner rejected the claims on appeal as obvious under 35 U.S.C. § 103(a). We affirm. 1 According to Appellants, the real parties in interest are National University Corporation Kobe University and Chugai Seiyaku Kabushiki Kaisha. App. Br. 2. Appeal 2016-003542 Application 12/310,258 STATEMENT OF THE CASE Claims 16, 18, 19, 23—27, and 29 are on appeal. Claim 16 is illustrative and reads as follows: 16. A process for producing an intracellular soluble fraction of an antibody fragment comprising two or more polypeptide domains and a polypeptide linker joining the domains, comprising culturing a prokaryotic host cell transformed by a vector comprising a polynucleotide inserted into the vector to allow the polynucleotide to be expressed in the host cell, wherein the polynucleotide encodes the antibody fragment, and wherein the sequence of the polynucleotide encoding the polypeptide linker is such that the nucleotide encoding the polypeptide linker contains one or more rare codons in the host cell; and recovering the antibody fragment thus produced. The Examiner rejected claims 16, 18, 19, 23—27, and 29 under 35 U.S.C. § 103(a) as unpatentable over the combination of Smallshaw,2 Huston,3 Komar,4 Purvis5 and Khan.6 2 Smallshaw et al., Synthesis, Cloning and Expression of the Single-Chain Fv Gene of the HPr-Specific Monoclonal Antibody, Jel42, 12(7) Protein Engineering 623-630 (1999) (“Smallshaw”). 3 Huston et al., Protein Engineering of Antibody Binding Sites: Recovery of Specific Activity in an Anti-Digoxin Single-Chain Fv Analogue Produced in Escherichia Coli, 85 Proc.Natl. Acad. Sci. USA, 5879-83 (1988) (“Huston”). 4 Komar et al., Kinetics of Translation of yB Crystallin and its Circularly Permutated Variant in an in Vitro Cell-Free System: Possible Relations to Codon Distribution and Protein Folding, 376 Federation of European Biochemical Societies Letters 195-98 (1995) (“Komar”). 5 Purvis et al, The Efficiency of Folding of Some Proteins is Increased by Controlled Rates of Translation in Vivo, 193 J. Mol. Biol. 413—417 (1987) (“Purvis”). 6 Khan et al., US Patent No. 6,680,182 Bl, issued Jan. 20, 2004 (“Khan”). 2 Appeal 2016-003542 Application 12/310,258 FINDINGS OF FACT 1. The Examiner finds, and Appellants do not dispute, that: Smallshaw et al. and Huston et al. disclose a method of producing a large amount of single chain Fv fragments by creating a DNA encoding a single chain Fv fragment, in which a heavy chain and a light chain of an antibody [are] connected by a peptide linker, and expressing the DNA using E. coli transformed with a vector comprising a polynucleotide encoding said antibody (see abstract, page 626 of Smallshaw; see abstract and pages 5881—5882 [of Huston]). Ans. 2—3. 2. Komar discloses: As a consequence of the irregular distribution of rare codons along the polypeptide chain of yB-crystallin, translation of the two-domain protein is a non-uniform process characterized by specific pauses. ... In this connection, the pause in the linker region between the domains provides a delay allowing the correct folding of the N-terminal domain and its subsequent assistance in the stabilization of the C-terminal one. Komar Abstract (emphasis added). 3. Purvis discloses: It is possible that some genes have evolved translation pauses through the development of strings of infrequently used codons, or sequences that are capable of forming strong secondary structures, or both. Selective advantages might have been gained by the introduction of specific translational pauses in mRNAs that encode proteins with potential problems in their folding pathway (for example, polypeptides with alternative, kinetically feasible folding pathways that lead to aberrant, but stable conformations). Purvis 414 (emphasis added). 3 Appeal 2016-003542 Application 12/310,258 4. Khan discloses: Codons which are infrequently utilised in E. coli [H. Grosjean et al, Gene 18, 199-209, 1982] and Salmonella are selected to encode for the hinge, as such rare codons are thought to cause ribosomal pausing during translation of the mess[e]nger RNA and allow for the correct folding of polypeptide domains. Khan col. 4,11. 35—40 (emphasis added). 5. Khan discloses: “The hinge region is a region designed to promote the independent folding of both the first and second proteins by providing both spatial and temporal separation between the domains.” Id. at col. 3,11. 57-60. 6. Khan discloses: The fusion protein was stably expressed in a number of different genetic backgrounds including E. coli (TG2) and S. typhimurium (SLB338,SL3261) as judged by SDS-PAGE and Western blotting. Of interest was a minor band of 50 kDal which co-migrates with the TetC-Hinge protein alone and cross-reacts exclusively with the anti-TetC sera is visible in a Western blot. As the codon selection in the hinge region has been designed to be suboptimal, the rare codons may cause pauses during translation which may occasionally lead to the premature termination of translation, thus accounting for this band. Id. at col. 9,11. 17-27. 7. Khan discloses: “In summary the antibody responses against the repitopes improved dramatically with increasing copy number, with the tetrameric and octameric repitope fusions being the most potent.” Id. at col. 11,11. 19-24. 8. Khan discloses: “Improved constructs consisting of codon optimised hinge regions, codon optimized P28, and multiple copies of full length P28, are currently in preparation.” Id. at col. 12,11. 25—29. 4 Appeal 2016-003542 Application 12/310,258 9. Kane7 discloses: Within Escherichia coli and other species, a clear codon bias exists among the 61 amino acid codons found within the population of mRNA molecules, and the level of cognate tRNA appears directly proportional to the frequency of codon usage. Given this situation, one would predict translational problems with an abundant mRNA species containing an excess of rare low tRNA codons. Such a situation might arise after the initiation of transcription of a cloned heterologous gene in the E. coli host. Recent studies suggest clusters of AGG/AGA, CUA, AUA, CGA or CCC codons can reduce both the quantity and quality of the synthesized protein. In addition, it is likely that an excess of any of these codons, even without clusters, could create translational problems. Kane Abstract. 10. Smallshaw discloses: Once the amino acid sequence of the gene product had been determined by translation of the corrected DNA sequence (see Results), a DNA sequence using the codons found in highly expressed E.coli genes (Sharp and Li, 1987) was made, incorporating codon redundancy where appropriate. The sequence was then searched for potential restriction endonuclease sites, and changes were made that did not introduce unfavourable codons. Smallshaw 624. 11. Huston discloses: “Design of the 744-base sequence for the synthetic sFv gene was derived from the sFv protein sequence by choosing codons preferred by E. coli.'” Huston 5879. 7 Kane, Effects of Rare Codon Clusters on High-Level Expression of Heterologous Proteins in Escheria Coli, 6 Current Opinion in Biotechnology 494—500 (1995). Kane was cited by Appellants as evidence that “at the time of filing of the present application it was recognized that rare codons reduce the quantity and quality of synthesized proteins and could create translational problems.” App. Br. 10. 5 Appeal 2016-003542 Application 12/310,258 ANALYSIS Claims 16, 18, 19, 23, 24, 26, 27, and29 Appellants argue claims 16, 18, 19, 23, 24, 26, 27, and 29 as a group. We designate claim 16 as representative for the group. The Examiner found that Smallshaw and Huston disclosed a method of producing a large amount of single chain Fv fragments by creating a DNA encoding a single chain Fv fragment, in which a heavy chain and a light chain of an antibody are connected by a peptide linker, and expressing the DNA using E. coli transformed with a vector comprising a polynucleotide encoding said antibody. FF1. Neither Smallshaw nor Huston, however, discloses that the nucleotide encoding the polypeptide linker contains one or more rare codons. Ans. 3. The Examiner found that it was well known in the art that “rare codons in the DNA encoding [the] interdomain region of polypeptides cause[] pausing in translation, which allows proper folding of the domains.” Id. As evidence, the Examiner cited Komar, Purvis, and Khan. Id. The Examiner concluded: it would have been obvious to one of ordinary skill in the art to provide a rare codon in the DNA encoding the polypeptide linker region and adjust the translation speed of any domain located downstream of another domain, including two portions of a fusion protein or antibody, so as to become slower in the linker region, compared to that of a domain located upstream thereof, in order to produce a protein being correctly folded and stable, as described by the references. Id. 6 Appeal 2016-003542 Application 12/310,258 We adopt the Examiner’s findings of fact and reasoning regarding the scope and content of the prior art (Ans. 2—11; Final Act. 2—8) and agree that the claims would have been obvious over Smallshaw, Huston, Komar, Purvis and Khan. We address Appellants’ arguments below. Appellants argue that Huston teaches to choose “codons preferred by E. coir rather than rare codons and that Smallshaw teaches ‘“not to introduce unfavorable codons’ during gene design.” App. Br. 9 (citing material quoted at FF10 and FF11). Appellants assert that “[a]t the time of filing of the present application, rare codons were recognized to be ‘unfavorable’, because it was recognized that rare codons reduce the quantity and quality of synthesized proteins and could create translational problems.” Id. (citing Kane (see FF 9)). Appellants thus contend that because “the cited references teach[] not to utilize rare codons in a process for producing an intracellular soluble fraction of an antibody fragment in a prokaryotic host cell,” the references cannot be combined to achieve the claimed invention. Id. at 8. We are not persuaded. Smallshaw and Huston disclose all of the elements of claim 16 except for “the nucleotide encoding the polypeptide linker contains one or more rare codons.” See FF1; Ans. 2—3. Komar and Khan disclose that the use of rare codons in the linker (or “hinge”) region provides translational “pauses” that allow the “correct folding” of the encoded protein. FF2 and FF4. Consistent with this teaching, Purvis discloses that “infrequently used codons” may provide “[selective advantages ... by the introduction of specific translational pauses . . . .” FF3. In view of these teachings, we agree with the Examiner that it would have been obvious to “provide a rare 7 Appeal 2016-003542 Application 12/310,258 codon in the DNA encoding the polypeptide linker region ... in order to produce a protein being correctly folded and stable.” Ans. 4. [A] given course of action often has simultaneous advantages and disadvantages, and this does not necessarily obviate motivation to combine. See [Winner Inti Royalty Corp. v. Wang, 202 F.3d 1340, 1349 n.8 (Fed. Cir. 2000)] (“The fact that the motivating benefit comes at the expense of another benefit, however, should not nullify its use as a basis to modify the disclosure of one reference with the teachings of another. Instead, the benefits, both lost and gained, should be weighed against one another.”). Where the prior art contains “apparently conflicting” teachings (i.e., where some references teach the combination and others teach away from it) each reference must be considered “for its power to suggest solutions to an artisan of ordinary skill. . . . considering] the degree to which one reference might accurately discredit another.” In re Young, 927 F.2d 588, 591 (Fed. Cir. 1991). Medichem, S.A. v. Rolabo, S.L., 437 F.3d 1157, 1165 (Fed. Cir. 2006). We acknowledge Appellants’ argument that Huston and Smallshaw suggest a preference for commonly used codons in designing a gene sequence for a synthetic protein. See FF10 and FF11. We similarly acknowledge Appellants’ argument that Kane teaches that rare codons can create translational problems. See FF9. In the obviousness analysis however, these references are not considered alone. Considering Huston and Smallshaw together with the clear teaching of Komar, Khan and Purvis that using rare codons in the linking region ensures proper protein folding, the ordinary artisan would have had reason to include some rare codons in order to obtain the advantage of improved protein folding, without adding large clusters of rare codons that could reduce protein quantity and quality as taught by Kane. FF9. Because claim 16 is open to “one or more rare codons”, we find that a preponderance of the evidence supports the 8 Appeal 2016-003542 Application 12/310,258 Examiner’s conclusion that the claimed process would have been obvious over the cited references. Appellants dispute the Examiner’s finding that Khan teaches to include rare codons at the linking region. Appellants contend that Khan teaches the opposite — i.e. to “avoid” rare codons because “the use of rare codons in the region[s] between domains is suboptimal.” App. Br. 11. We disagree. As the Examiner explains, Khan uses the term “suboptimal” to indicate that translation in the linking/hinge region occurs at less than maximum possible speed due to the use of rare codons. FF6; Ans. 7. This causes a “pause,” which, as the Examiner also points out, “is the desired effect.” FF5 and FF6 (“the hinge region has been designed to be suboptimal”) (emphasis added); Ans. 7. Accordingly, Khan does not teach to “avoid” rare codons. To the contrary, Khan teaches that the use of rare codons “ allow [s] for the correct folding of polypeptide domains.” FF4. Appellants argue that Komar and Purvis are silent on the expression of an antibody fragment in a prokaryotic cell and thus cannot overcome Smallshaw’s and Huston’s preference for not using rare codons in a prokaryotic host. Appellants assert: At the priority date of the claimed invention, it was recognized that proper folding in a cell-free system does not necessarily translate to proper folding in E. Coli, and that folding in E. Coli is affected by many factors. There is nothing in Komar that indicates that the technique described in Komar can be used to make functional antibodies in E. Coli as described in Smallshaw and Huston App. Br. 12. We are not persuaded. As an initial matter, Khan discloses the use of rare codons in prokaryotic cells. FF6. Komar’s disclosure regarding rare codons is 9 Appeal 2016-003542 Application 12/310,258 cumulative of and consistent with Khan. Moreover, as explained in the Examiner’s Answer, Komar makes general statements about protein folding and translation without any limiting language suggesting that the statements apply only in the context of in vitro translation methods. See, Ans. 9—10. Finally, Appellants do not provide persuasive evidence to support their position that folding in a cell-free system would not translate to folding in E. coli. See Johnston v. IVAC Corp., 885 F.2d 1574, 1581 (Fed. Cir. 1989) (“Attorneys’ argument is no substitute for evidence.”); In re Pearson, 494 F.2d 1399, 1405 (CCPA 1974). Accordingly, we affirm the Examiner’s decision to reject claim 16. Because they were not argued separately, claims 18, 19, 23, 24, 26, 27, and 29 fall with claim 16. Claim 25 Claim 25 depends from claim 16 and adds the requirement “wherein the nucleotide encoding the polypeptide linker has a sequence set forth in SEQ ID NO: 6, 8, 10, 12, or 24.” In the Appeal Brief, Appellants argued that the Examiner did not provide “any evidence or explanation of how and why the combination of the cited references teaches or suggests SEQ ID NO: 6, 8, 10, 12, or 24.” App. Br. 13. In the Examiner’s Answer, the Examiner asserted that Huston disclosed “using the linker region comprising (Gly-Gly-Gly-Gly-Ser)3” and that “[t]his is the same polypeptide as the polypeptide sequence encoded by SEQ ID NO: 24 of the instant claim.” Ans. 10. Appellants’ Reply Brief does not contest that Huston discloses SEQ ID NO: 24, instead arguing that claim 25 is patentable for the same reasons discussed with respect to claim 16. Accordingly, we affirm the 10 Appeal 2016-003542 Application 12/310,258 Examiner’s decision to reject claim 25 under 35 U.S.C. § 103(a) for the reasons provided in connection with claim 16. SUMMARY For these reasons and those set forth in the Examiner's Answer, and the Final Office Action, the Examiner’s decision to reject claims 16, 18, 19, 23—27, and 29 is affirmed. No time period for taking any subsequent action in connection with this appeal may be extended under 37 C.F.R. § 1.136(a)(1). AFFIRMED 11 Copy with citationCopy as parenthetical citation