Ex Parte ReedDownload PDFPatent Trial and Appeal BoardNov 26, 201311834897 (P.T.A.B. Nov. 26, 2013) 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. 11/834,897 08/07/2007 Thomas D. Reed 2584.0280001/RWE/GER 1472 80011 7590 11/27/2013 Sterne, Kessler, Goldstein & Fox P.L.L.C. 1100 New York Avene N.W. Washington, DC 20005 EXAMINER LEAVITT, MARIA GOMEZ ART UNIT PAPER NUMBER 1633 MAIL DATE DELIVERY MODE 11/27/2013 PAPER 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. PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE ____________ BEFORE THE PATENT TRIAL AND APPEAL BOARD ____________ Ex parte THOMAS D. REED ____________ Appeal 2012-0055191 Application 11/834,897 Technology Center 1600 ____________ Before DONALD E. ADAMS, ANNETTE R. REIMERS, and SUSAN L. C. MITCHELL, Administrative Patent Judges. ADAMS, Administrative Patent Judge. DECISION ON APPEAL2 This appeal under 35 U.S.C. § 134 involves claims 166-170 and 174- 176 (App. Br. 7).3 Examiner entered rejections under the written description and enablement provisions of 35 U.S.C. § 112, first paragraph. We have jurisdiction under 35 U.S.C. § 6(b). We affirm. 1 This Appeal is related to Appeal No. 2012-005520, Application No. 11/836,563 (see App. Br. 5). 2 The Real Party in Interest is Intrexon Corporation (App. Br. 4). 3 Pending claims 171-173 stand “withdrawn from consideration” (App. Br. 7). Examiner found the subject matter of claim 177 allowable if rewritten in independent form (Ans. 5). Appeal 2012-005519 Application 11/834,897 2 STATEMENT OF THE CASE The claims are directed to an isolated polynucleotide. Claims 166 and 176 are representative and are reproduced in the Claims Appendix of Appellant’s Brief. Claims 166-170 and 174-176 stand rejected under the written description and enablement provisions of 35 U.S.C. § 112, first paragraph. ISSUES Does the preponderance of evidence on this record support Examiner’s: 1. finding that Appellant’s Specification fails to provide written descriptive support for the full scope of Appellant’s claimed invention; and 2. conclusion that undue experimentation would be required to practice the full scope of claimed invention? FACTUAL FINDINGS (FF) FF 1. “Protein Kinase A or PKA … can phosphorylate serine and threonine residues” (Spec. 1: ¶ [0004]). FF 2. During the November 14, 2013 Oral Hearing, Appellant’s representative explained that: (1) “protein kinase A,” as that term is used in Appellant’s claimed invention, represents a genus of isoforms and (2) the polypeptide encoded by the polynucleotide of Appellant’s claimed invention may inhibit one or more of the protein kinase A isoforms (see Ans. 13 (“There are two classes of PKA, types I and II, which contain … regulatory subunits…. Multiple isoforms of the regulatory subunits … and catalytic subunits … are expressed and may contribute to the specificity of PKA”)). Appeal 2012-005519 Application 11/834,897 3 FF 3. Appellant’s “invention intends to capture all combinations of homopolyligands and heteropolyligands without limitation to the examples” provided in Appellant’s Specification (id. at 4: ¶ [0010]; see also id. at 7: ¶ [0032] (“The instant invention is directed to all possible combinations of homopolyligands and heteropolyligands without limitation”); see also id. at 13: ¶ [0051]). FF 4. Appellant discloses that “ligands of the invention are optionally linked to additional molecules or amino acids that provide an epitope tag, a reporter, and/or a cellular localization signal,” wherein each may represent the same or “different molecules” (id. at 4-5: ¶ [0015]; see also id. at 13: [0052]). FF 5. Appellant discloses that “[p]olyligands may comprise any two or more of SEQ ID NOS: 55-216, wherein Xaa is any amino acid” (id. at 7: ¶ [0032]). FF 6. Appellant discloses that “SEQ ID NOS: 55-132 are subsequences of SEQ ID NOS: 12-54, where … the locations of the PKA phosphorylatable residues are represented by Xaa,” wherein “Xaa can be any amino acid,” including naturally and non-naturally occurring amino acids (id. at ¶ [0033]). FF 7. Appellant discloses that “[t]here are numerous ways to combine SEQ ID NOS: 55-216 into homopolymeric or heteropolymeric ligands” (id. at ¶ [0032]). FF 8. Appellant discloses that “[t]he length and composition of the spacer may vary” (id. at 13: ¶ [0051]). Appeal 2012-005519 Application 11/834,897 4 FF 9. Appellant exemplifies the structure of three heteropolyligands, wherein: [T]he PKA polyligand of SEQ ID NO: 1 is encoded by SEQ ID NO:2, SEQ ID NO:3 and by SEQ ID NO:4, wherein the codons of SEQ ID NO:3 and SEQ ID NO:4 have been optimized for vector insertion. SEQ ID NO:4 includes flanking restriction sites. . . . SEQ ID NO: 1 is an embodiment of a polyligand of the structure A-S1-B-S2-C-S3-D, wherein A is SEQ ID NO:142, B is SEQ ID NO:143, C is SEQ ID NO:144, and D is SEQ ID NO:145, and wherein S1 is a spacer of the amino acid sequence PGAGA, S2 is a spacer of amino acid sequence GGGG, and S3 is a spacer of amino acid sequence AAGGAA. A polyligand of structure A-S1-B-S2-C-S3-D is also called herein a heteropolyligand. SEQ ID NO:5 is an embodiment of a polyligand of the structure X-S4-Y-S5-Z, wherein X is SEQ ID NO:153, Y is SEQ ID NO:154, and Z is SEQ ID NO:155, and wherein S4 is a spacer of amino acid sequence GAGA, and S5 is a spacer of amino acid sequence AGAG. The PKA polyligand of SEQ ID NO:5 is encoded by SEQ ID NO:6 and by SEQ ID NO:7, wherein the . . . codons of SEQ ID NOS:6 and 7 have been optimized for vector insertion. SEQ ID NO:7 includes flanking restriction sites. A polyligand of structure X-S4-Y-S5-Z is also called herein a heteropolyligand. SEQ ID NO:8 is an embodiment of a polyligand of the structure X-S6-Y-S7-Z-S8-A-S9-B, wherein X is SEQ ID NO:146, Y is SEQ ID NO:147, Z is SEQ ID NO:148, A is SEQ ID NO:149, and B is SEQ ID NO:150, and wherein S6 is a four amino acid spacer with the sequence PGAG, S7 is an eight amino acid spacer with the sequence PAAAGGGP, S8 is a seven amino acid spacer with sequence PAGAGAG, and S9 is a five amino acid spacer with the sequence AAAAP. The PKA polyligand of SEQ ID NO:8 is encoded by SEQ ID NO:9, SEQ ID NO:10, and by SEQ ID NO:11, wherein the . . . codons of SEQ ID NOS:10 and 11 have been optimized for vector insertion. SEQ ID NO:11 includes flanking restriction sites. A Appeal 2012-005519 Application 11/834,897 5 polyligand of structure X-S6-Y-S7-Z-S8-A-S9-B is also called herein a heteropolyligand. (Id. at 22-23: ¶¶ [0088]-[0090].) FF 10. Examiner finds that Appellant’s Specification fails to provide written descriptive support for, or provide an enabling description of, [A] genus of isolated nucleic acid sequences encoding a PKA polyligand comprising a structure selected from the group consisting of X-S-X and X-S-Y, wherein X and Y are different polypeptide monomers, wherein X and Y are monomers selected from an amino acid sequence having at least 85% (claim 166), 90% (claim 174), 95% (claim 175)[,] and 98% (claim 176) sequence identity to any of the polypeptides of SEQ ID NOS: 55-201 . . . , able to inhibit PKA activity. (Ans. 7.) FF 11. Examiner finds that Appellant fails to disclose a “core structure” that is representative of the “full scope of the claimed genera” (id. at 12-13; see also id. at 11 (Examiner finds “no evidence of record that the polypeptides/ligands of SEQ ID NOS: 55-216 share a common structural motif or a common active site mechanism to define the genus of PKA substrates other than being substrates of PKA”)). FF 12. Examiner finds that While one of skill in the art can readily envision numerable species of nucleic acid sequences that are at least a given % identity to a reference nucleotide sequence and . . . encode a polypeptide monomer at least of a given % identity to a recited reference amino acid sequence i.e., SEQ ID NOS: 142, 143, 144[,] and 145, one cannot envision which of these also encode a polypeptide with a specified activity in the context of the polyligand structure X-S-X or X-S-Y. (Id. at 17.) Appeal 2012-005519 Application 11/834,897 6 FF 13. Examiner finds that Appellant’s Specification fails to disclose “how the linker segments in the context of a polyligand comprising the claimed variants of inhibitory peptides interact with particular PKAc [(protein kinase A catalytic subunit)] sites” (id. at 18). FF 14. Examiner finds that “excessive trial and error experimentation would have been required to identify” a polynucleotide that encodes a polypeptide that inhibits protein kinase A activity as set forth in Appellant’s claimed invention (id. at 18-19). FF 15. Appellant discloses that “[i]hibition of PKA activity is demonstrated by measuring phosphorylation of endogenous substrates against controls” (Spec. 21: ¶ [0079]). FF 16. Kimchi-Sarfaty discloses that The amino acid sequence of proteins is generally believed to determine protein expression, folding, and function; mutations that alter the primary structure of a protein can affect these properties. The important question addressed by this study is the role of silent mutations (i.e., those that do not affect amino acid sequence) in protein folding and function. Recent theoretical studies have suggested that codon usage is not random, and experimental studies in prokaryotes suggest that this may be so. Here we show that a silent mutation in a complex, mammalian membrane transport protein alters the substrate specificity. We hypothesize that when frequent codons are changed to rare codons in a cluster of infrequently used codons, the timing of cotranslational folding is affected and may result in altered function. (Kimchi-Sarfaty4 527: col. 3, ll. 36-53 (endnotes omitted); see generally Ans. 13-16.) 4 Chava Kimchi-Sarfaty, et al., “A ‘Silent’ Polymorphism in the MDR1 Gene Changes Substrate Specificity,” 315 SCIENCE 525-528 (2007). Appeal 2012-005519 Application 11/834,897 7 ANALYSIS Initially, we note that there is some confusion on this record as to the exact scope of the claims before this Panel for review (see, e.g., Ans. 6 (While the claims before this Panel for review are drawn to polynucleotides, Examiner states that “[t]he claims are rejected to the extent that the[y] read on the elected species: the polypeptide of SEQ ID NO: 1”); Cf. App. Br. 14). Nevertheless, during the November 14, 2013 Oral Hearing, Appellant’s representative confirmed that the full scope of Appellant’s claimed invention is before this Panel for review. Claim Interpretation: Appellant’s claims 166 and 176 are directed to: (1) a polynucleotide of any sequence and length (2) that encodes a polypeptide of any length, (3) wherein the polypeptide includes within its sequence (4) at least one region represented by the formula X-S-X or X-S-Y and (5) any number of additional molecules (e.g., an epitope tag, reporter, cellular localization signal, X or Y monomers, and spacers (S)) attached to the polypeptide in some manner (FF 4-6; Claims 166 and 176). Appellant defines the components of the X-S-X and X-S-Y formulas as a polypeptide monomer (a) of any length that (b) contains an amino acid sequence at least 85% (claim 166) or 98% (claim 176) identical to any one of SEQ ID NOS: 55-216, wherein (c) “Y” is a different polypeptide monomer than “X,” and (d) the Xaa recited in SEQ ID NOS: 55-216 represents a naturally or non-naturally occurring amino acid (FF 5 and 6; Claims 166 and 176). Appeal 2012-005519 Application 11/834,897 8 The “S” component of Appellant’s formula is (i) optionally present and (ii) may be of any length and composition (FF 8; Claims 166 and 176). According to Appellant’s Specification, variants of SEQ ID NOS: 55- 216 may be combined in any number of ways and with any number of additional molecules of any length to realize the intended scope of Appellant’s claimed invention, which is “to capture all combinations of homopolyligands and heteropolyligands without limitation” (FF 3 and 7; Claims 166 and 176). The remaining limitation of Appellant’s claimed invention requires the foregoing highly variable polynucleotide to encode a polypeptide that inhibits at least one isoform of protein kinase A activity (FF 2; Claims 166 and 176). Representative Species: Appellant discloses three heteropolyligands that fall within the scope of Appellant’s claimed invention and comprise a structure having the formula, A-S1-B-S2-C-S3-D; X-S4-Y-S5-Z; and X-S6-Y-S7-Z-S8-A-S9-B (FF 9). Appellant fails to identify which protein kinase A isoform is inhibited by the representative heteropolyligands (see FF 9; Cf. FF 2 and 15). Instead, Appellant discloses that “[i]hibition of PKA activity is demonstrated by measuring phosphorylation of endogenous substrates against controls” (FF 15). Written Description: Examiner finds that Appellant’s Specification fails to provide written descriptive support for the genus of isolated nucleic acid sequences, Appeal 2012-005519 Application 11/834,897 9 encompassed by Appellant’s claims 166 and 176, that encode a polypeptide that inhibits the activity of at least one isoform of protein kinase A (FF 10; see also FF 2). According to Examiner, “one cannot envision which of the [highly variable polynucleotides encompassed by Appellant’s claimed invention] encode[s] a polypeptide with a specified activity in the context of the polyligand structure X-S-X or X-S-Y (FF 12 (emphasis added)). In this regard, Examiner finds that variability in both nucleic acid and amino acid sequence contribute to the unpredictability associated with protein functionand Appellant failed to disclose a “core structure” that is representative of the “full scope of the claimed genera” (FF 11, 13, and 16). Claim 166: Appellant contends that because it would have been obvious to make and test a polynucleotide within the genus of Appellant’s claimed invention, Appellant had possession of every polynucleotide sequence contained therein that is capable of inhibiting the activity of at least one protein kinase A isoform (App. Br. 15-16; FF 2). We are not persuaded. “[A] description that merely renders the invention obvious does not satisfy the requirement.” Ariad Pharmaceuticals, Inc. v. Eli Lilly and Co., 598 F.3d 1336, 1352 (Fed. Cir. 2010) (en banc). Appellant contends that the law does not require a correlation between structure and function (App. Br. 25). While we agree with Appellant in that the written description requirement of 35 U.S.C. § 112, first paragraph, may be satisfied in a number of ways, the Specification must “itself … demonstrate[s] possession” of the claimed invention. Ariad, 598 F.3d at 1352. For the reasons set forth above, Appellant’s Specification fails to Appeal 2012-005519 Application 11/834,897 10 demonstrate possession of the entire claimed genus of polynucleotides that encode a protein that is capable of inhibiting the activity of at least one isoform of protein kinase A. For the same reasons, we are not persuaded by Appellants’ contention that “one need not disclose what amino acid modifications are permissible” (App. Br. 25; Cf. FF 16). We recognize, but are not persuaded by, Appellant’s reliance on Example 14 of the “REVISED INTERIM WRITTEN DESCRIPTION GUIDELINES TRAINING MATERIALS” (see e.g. App. Br. 16-19 and 25- 26; see also Appellant’s Exhibit A). Appellant’s contentions fail to account for the revised “TRAINING MATERIALS”5 dated prior to the filing date of Appellant’s Briefs. We recognize, but are not persuaded by, Appellant’s contention that Examiner’s written description rejection is contrary to Federal Circuit Case Law (App. Br. 19-22). See e.g., Ariad; see also University of Rochester v. G.D. Searle & Co., Inc., 358 F.3d 916, 925 (Fed. Cir. 2004) (“[e]ven with the three-dimensional structures of enzymes such as COX-1 and COX-2 in hand, it may even now not be within the ordinary skill in the art to predict what compounds might bind to and inhibit them”). Simply stated, contrary to the disclosure set forth in Appellant’s Specification and Appellant’s contentions, the written description requirement “requires a description of an invention, not an indication of a result that one might achieve if one made that invention.” Regents of the University of California v. Eli Lilly & Co., 119 F.3d 1559, 1568 (Fed. Cir. 1997); see also Novozymes A/S v. DuPont 5 “WRITTEN DESCRIPTION TRAINING MATERIALS,” 33-35, (Revision 1, March 25, 2008) (see http://www.uspto.gov/web/menu/ written.pdf). Appeal 2012-005519 Application 11/834,897 11 Nutrition Biosciences APS, 723 F.3d 1336, 1350 (Fed. Cir. 2013) (“A patent … ‘is not a reward for the search, but compensation for its successful conclusion.’ … For that reason, the written description requirement prohibits a patentee from ‘leaving it to the … industry to complete an unfinished invention.’” (citations omitted)). Claim 176: We recognize Appellant’s contention that Appellant’s Specification provides written descriptive support for the genus encompassed by Appellant’s claim 176, because the recited monomers “are at least 98% identical to SEQ ID NOS: 55-216” (App. Br. 26-27). We are not persuaded for the reasons set forth above. To be clear, as discussed above, the claimed polynucleotide comprises any number of different components that vary, inter alia, in size, composition, and sequence, in addition to at least two monomer units that vary to some degree relative to the recited SEQ ID NOS. Enablement: Examiner finds that Appellant’s Specification fails to provide an enabling description of the genus of isolated nucleic acid sequences, as set forth in Appellant’s claims 166 and 176, that encode a polypeptide able to inhibit the activity of at least one isoform of protein kinase A (FF 11; see also FF 2). Examiner finds that “excessive trial and error experimentation would have been required to identify” a polynucleotide that encodes a polypeptide that inhibits protein kinase A activity as set forth in Appellant’s claimed invention (FF 14). Appeal 2012-005519 Application 11/834,897 12 Claim 166: “Appellants submit that one of ordinary skill in the art would be able to make and derive the claimed isolated polynucleotide of claim 166 based on the specification as filed” (App. Br. 32). Appellant’s claims are not, however, limited to a polynucleotide that encodes a protein. Instead, Appellant’s claims require the polynucleotide to encode a protein that inhibits the activity of at least one protein kinase A isoform (see, e.g., FF 2 and 13). Appellant’s Specification fails to disclose which polypeptides encoded by a polynucleotide, within the scope of Appellant’s claimed invention, would be capable of inhibiting the activity of at least one protein kinase A isoform or, if not all isoforms, which particular isoform such an encoded polypeptide would inhibit. At best, Appellant’s Specification directs one to make polynucleotides that fall within the extremely large scope of Appellant’s claim and then figure out, through trial and error testing, which of these polynucleotides encode a polypeptide capable of inhibiting the activity of at least one protein kinase A isoform (see FF 15). As Examiner explains, this activity would require “excessive trial and error experimentation” (FF 14). See In re ʼ318 Patent Infringement Litigation, 583 F.3d 1317, 1327 (Fed. Cir. 2009) (“[A]t the end of the day, the specification, even read in light of the knowledge of those skilled in the art, does no more than state a hypothesis and propose testing to determine the accuracy of that hypothesis. That is not sufficient.”). We acknowledge Appellant’s concession that “it would . . . require[] experimentation in order to modify the claimed polynucleotide to encode a PKA ligand across the full scope of the claims” (Reply Br. 18). See In re Appeal 2012-005519 Application 11/834,897 13 Vaeck, 947 F.2d 488, 495 (Fed. Cir. 1991) (“That some experimentation may be required is not fatal; the issue is whether the amount of experimentation required is ‘undue.’”) However, notwithstanding Appellant’s contention to the contrary, we agree with Examiner’s conclusion that making and testing every possible species that falls within the scope of Appellant’s claimed invention to identify those polynucleotides that encode a polypeptide exhibiting the claimed activity would require undue experimentation (See Ans. 20 and 28-29; Cf. Reply Br. 18;). “[T]o be enabling, the specification of a patent must teach those skilled in the art how to make and use the full scope of the claimed invention without ‘undue experimentation.’” Genentech, Inc. v. Novo Nordisk, A/S, 108 F.3d 1361, 1365 (Fed. Cir. 1997) (quoting In re Wright, 999 F.2d 1557, 1561 (Fed. Cir. 1993)). Claim 176: We recognize Appellant’s contention that Appellant’s Specification provides written descriptive support for the genus encompassed by Appellant’s claim 176, because the recited monomers “are at least 98% identical to SEQ ID NOS: 55-216” (App. Br. 33-34). We are not persuaded for the reasons set forth above. CONCLUSION OF LAW The preponderance of evidence on this record supports Examiner’s: 1. finding that Appellant’s Specification fails to provide written descriptive support for the full scope of Appellant’s claimed invention; and 2. conclusion that undue experimentation would be required to practice the full scope of claimed invention. Appeal 2012-005519 Application 11/834,897 14 The rejection of claims 166 and 176 under the written description and enablement provisions of 35 U.S.C. § 112, first paragraph is affirmed. Claims 167-170, 174, and 175 fall together with claim 166. TIME PERIOD FOR RESPONSE No time period for taking any subsequent action in connection with this appeal may be extended under 37 C.F.R. § 1.136(a). AFFIRMED lp Copy with citationCopy as parenthetical citation