Xencor, Inc.

Patent Trials and Appeals Board

Mar 4, 2022

2020004863 (P.T.A.B. Mar. 4, 2022)

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. 15/167,822 05/27/2016 Gregory Alan Lazar 067461-5121-US25 9984 67374 7590 03/04/2022 MORGAN, LEWIS & BOCKIUS LLP (SP) ONE MARKET, SPEAR STREET TOWER, SUITE 2800 SAN FRANCISCO, CA 94105 EXAMINER DAHLE, CHUN WU ART UNIT PAPER NUMBER 1644 NOTIFICATION DATE DELIVERY MODE 03/04/2022 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): DONALD.MIXON@MORGANLEWIS.COM SFIPDOCKETING@MORGANLEWIS.COM PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE BEFORE THE PATENT TRIAL AND APPEAL BOARD Ex parte GREGORY ALAN LAZAR, ARTHUR J. CHIRINO, WEI DANG, JOHN DESJARLAIS, STEPHEN K. DOBERSTEIN, ROBERT J. HAYES, SHER BAHADUR KARKI, and OMID VAFA Appeal 2020-004863 Application 15/167,822 Technology Center 1600 Before TAWEN CHANG, TIMOTHY G. MAJORS, and DAVID COTTA, Administrative Patent Judges. CHANG, Administrative Patent Judge. DECISION ON APPEAL Pursuant to 35 U.S.C. § 134(a), Appellant1 appeals from the Examiner’s decision to reject claims 68-101.2 We have jurisdiction under 35 U.S.C. § 6(b). We AFFIRM. 1 We use the word “Appellant” to refer to “applicant” as defined in 37 C.F.R. § 1.42. Appellant identifies the real party in interest as Xencor, Incorporated. Appeal Br. 1. 2 Appellant purports to cancel claims 75, 76, 85, 86, 92, 93, 100, and 101 in the Reply Brief. Reply Br. 3. However, a new amendment must be Appeal 2020-004863 Application 15/167,822 2 STATEMENT OF THE CASE According to the Specification, “[t]he present invention relates to novel optimized Fc variants, engineering methods for their generation, and their application, particularly for therapeutic purposes.” Spec. ¶ 2. CLAIMED SUBJECT MATTER The claims are directed to a nucleic acid encoding a polypeptide comprising an Fc variant of a parent Fc polypeptide and a method of producing a polypeptide. Claim 68 is illustrative: 68. A nucleic acid encoding a polypeptide comprising an Fc variant of a parent Fc polypeptide, said Fc variant comprising an amino acid substitution at position 332 in the Fc region, wherein numbering is according to the EU index. Appeal Br. 27 (Claims App.). submitted in a separate paper, and entry of a new amendment in an application on appeal is not a matter of right. MPEP § 1206(I). Furthermore, an Examiner’s refusal to admit an amendment is a petitionable, rather than an appealable matter. 37 C.F.R. § 41.37(c)(1)(2). As Appellant does not appear to have submitted such a separate paper, and as the amendment has not been entered, we include claims 75, 76, 85, 86, 92, 93, 100, and 101 in our decision. Appeal 2020-004863 Application 15/167,822 3 REJECTION(S)3 Claims 68-101 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-24 of U.S. Patent No. 9,102,739 (the “’739 patent”) in view of Presta.4 Ans. 3. OPINION A. Issue The Examiner asserts that the claims on appeal are “drawn to a nucleic acid encoding an Fc variant comprising an amino acid substitution at position 332, a vector, a host cell, and a method of producing the polypeptide by culturing the host cell and purifying the peptide,” including wherein the amino acid substitution is 332E and the Fc variant exhibits increased FcγRIIA binding, or to a nucleic acid encoding a heavy chain of an antibody comprising such an Fc variant. Ans. 3. The Examiner asserts that “[t]he claims in the ’739 Patent are drawn to an anti-glypican-3 antibody comprising an Fc region having” a variety of amino acid substitutions, including glutamic acid at position 332 (i.e., 332E), a method for producing and isolating the antibody, and a method for treating 3 Appellant and the Examiner disagree as to whether a terminal disclaimer is appropriate in this case. See, e.g., Appeal Br. 5-6, Ans. 5, Reply Br. 3. We decline to offer an opinion on this issue: As no terminal disclaimer has been filed, any opinion would be advisory in nature. We further note that whether a terminal disclaimer should be entered is a petitionable matter outside of the jurisdiction of the Board. 37 C.F.R. § 1.181; MPEP § 1201 (explaining that “[t]he line of demarcation between appealable matters for the Board and petitionable matters for the Director of the U.S. Patent and Trademark Office (Director) should be carefully observed” and that “[t]he Board will not ordinarily hear a question that should be decided by the Director on petition”). 4 Presta, US 6,737,056 B1, issued May 18, 2004. Appeal 2020-004863 Application 15/167,822 4 a patient with hepatic cancer comprising administering to the patient a composition comprising the antibody. Id. at 3-4. The Examiner finds that Presta teaches “polypeptides comprising an Fc variant comprising amino acid modifications” and further teaches recombinant production of the polypeptide by isolating and inserting the nucleic acid encoding the polypeptide into a replicable vector, transfecting the vectors into host cells, culturing the cells in conditions suitable for producing the polypeptide, and purifying the polypeptide from cell culture. Ans. 4. The Examiner concludes that the claims on appeal are obvious variations of the claims in the reference ’739 patent, because a skilled artisan “would use the methodology of Presta, including recombinant nucleic acids, vectors and host cells, to make the polypeptides of the ’739 patent,” and “the present claimed inventions . . . would be made as part of producing the peptides of the issued ’739 patent.” Id. at 5. Appellant first argues that “the ‘739 patent is not ‘prior’ art to which an ODP can be applied,” because the claims on appeal have an earlier priority date than the claims of the ’739 patent. Appeal Br. 17. Appellant also contends that, “taken as a whole, the claims of the present application directed to nucleic acids (and expression vector, etc.) are ‘patentably distinct’ from the claims of the ’739 patent, taken as a whole, which are directed to ‘. . . anti-glypican-3 antibodies’ (and methods of producing, using, etc.).” Appeal Br. 24. More particularly, Appellant argues that the rejection is inconsistent with the PTO’s position, in issuing restriction and election requirements, that proteins and the nucleic acids encoding them are “patentably distinct.” Id. at 17-20. Appellant further contends that the rejection uses the claims of the ’739 patent as prior art, Appeal 2020-004863 Application 15/167,822 5 which is impermissible in an obviousness-type double patenting rejection. Id. at 20; Reply Br. 4-7. Appellant does not separately argue the claims. Accordingly, we focus our analysis on claim 68 as representative. The issues with respect to this rejection are (1) whether the ’739 patent may be used as a reference patent in a double patenting rejection, and, if so, (2) whether a restriction requirement in a related patent application precludes the issuance of the double patenting rejection, and (3) whether claim 68 is an obvious variant of the claims of the ’739 patent. B. Analysis 1. Whether the ’739 patent may be used as a reference patent in a double patenting rejection We are not persuaded by Appellant’s argument that a patent having a later priority date cannot be a reference patent in an obviousness-type double patenting rejection of an application having an earlier priority date. Appeal Br. 17. As our reviewing court has explained, a “crucial purpose” of the double patenting doctrine is to “prevent an inventor from securing a second, later expiring patent for the same invention.” Abbvie Inc. v. Mathilda & Terence Kennedy Inst. of Rheumatology Trust, 764 F.3d 1366, 1373 (Fed. Cir. 2014). As our reviewing court has further explained, “[p]atents claiming overlapping subject matter that were filed at the same time still can have different patent terms due to examination delays at the PTO.” Id. It is the patent expiration dates that is relevant in a double patenting rejection, not the priority dates. Cf. Gilead Sciences, Inc. v. Natco Pharma Ltd., 753 F.3d 1208, 1215 (Fed. Cir. 2014) (explaining that, in a double patenting rejection Appeal 2020-004863 Application 15/167,822 6 analysis, “it is the comparison of . . . patent expiration dates that should control, not merely the issuance dates”). Appellant contends that “the ’739 patent expires roughly 3 years later, and thus there is no improper extension of patent exclusivity to the present claims.” Appeal Br. 17. However, Appellant has not directed us to persuasive evidence that any patent issued from the present application will necessarily expire before the ’739 patent. For instance, certain delays, including in actions after appeal, may result in patent term adjustment under 35 U.S.C. § 154(b). On this record, we decline to speculate on when a patent issued from the present application, if it were deemed allowable, would expire.5 Finally, as the Examiner points out, Ans. 7-8, in addition to preventing unjustified timewise extension of a patent’s right to exclude, the double patenting doctrine is also intended to “prevent multiple infringement suits by different assignees asserting essentially the same patented invention.” In re Hubbell, 709 F.3d 1140, 1145 (Fed. Cir. 2013). This rationale would apply to the double patenting rejection on appeal regardless of the relative priority (or expiration) dates of the patents. 5 We further note that, as the Examiner points out, Ans. 7-8, in addition to preventing unjustified timewise extension of a patent’s right to exclude, the double patenting doctrine is also intended to “prevent multiple infringement suits by different assignees asserting essentially the same patented invention.” In re Hubbell, 709 F.3d 1140, 1145 (Fed. Cir. 2013). This rationale would apply to the double patenting rejection on appeal regardless of the relative priority (or expiration) dates of the patents. Appeal 2020-004863 Application 15/167,822 7 2. Whether the restriction requirement in the related ’604 patent precludes the double patenting rejection Appellant contends that the present application is a divisional of application 13/773,485 (the ’485 application), which is in turn a divisional of the 13/346,604 application (the ’604 application). Appeal Br. 18. Appellant contends that the Patent Office issued a restriction requirement in the ’604 application requiring restriction to (1) claims drawn to a polypeptide comprising a variant Fc domain, (2) claims drawn to a nucleic acid encoding a polypeptide, a host cell and a method of making a polypeptide, or (3) claims drawn to a method of treating a patient by administering an antibody. Id. Appellant contends that, in issuing the restriction requirement, “the Office took the position that claims directed to proteins . . . are patentably distinct from claims directed to nucleic acids . . . for a number of reasons . . . , including that the claims are patentably distinct.” Id. at 19-20. As an initial matter, we note that Section 121 states: A patent issuing on an application with respect to which a requirement for restriction . . . has been made, or on an application filed as a result of such a requirement, shall not be used as a reference either in the Patent and Trademark Office or in the courts against a divisional application or against the original application or any patent issued on either of them, if the divisional application is filed before the issuance of the patent on the other application. 35 U.S.C. § 121. Appellant acknowledges that the “safe harbor” provision of 35 U.S.C. § 121 does not apply in the present case. Appeal Br. 16. To the extent Appellant’s argument is that, despite the inapplicability of the Section 121 safe harbor, the double patenting rejection should nevertheless be reversed because it is inconsistent with the Examiner’s Appeal 2020-004863 Application 15/167,822 8 position in issuing a restriction requirement in an earlier, related application, we are not persuaded. To the extent there is any inconsistency between the restriction requirement in the ’604 application and the instant double patenting rejection, the Examiner is permitted to change his viewpoint regarding the patentability of the claims as prosecution progresses as warranted by the evidence. See In re Ruschig, 379 F.2d 990, 992-93 (CCPA 1967) (“There is nothing unusual, certainly, about an examiner changing his viewpoint as to the patentability of claims as the prosecution of a case progresses, and, so long as the rules of Patent Office practice are duly complied with, an applicant has no legal ground for complaint because of such change in view”). Finally, to the extent Appellant’s argument is that the rationale supporting the restriction requirement in the ’604 application shows the double patenting rejection to be in error, we are not persuaded for the reasons discussed below. 3. Whether claim 68 is patentably distinct from the claims of the reference ’739 patent We agree with the Examiner that claim 68 on appeal is an obvious variation of the claims of the reference ’739 patent. To facilitate our discussion, we reproduce below (1) claim 68 on appeal and (2) claim 1 of the reference ’739 patent (emphasis added): Appealed claim Reference claims 68. A nucleic acid encoding a polypeptide comprising an Fc variant of a parent Fc polypeptide, said Fc variant comprising an 1. An anti-glypican-3 antibody comprising an Fc region having aspartic acid at EU numbering position 239, threonine at EU numbering position 326, alanine at EU numbering position 330, and glutamic acid at EU numbering position 332 of the Fc region, Appeal 2020-004863 Application 15/167,822 9 amino acid substitution at position 332 in the Fc region, wherein numbering is according to the EU index. wherein the anti-glypican-3 antibody comprises a H-chain CDR1 as set forth in SEQ ID NO:23, a H-chain CDR2 as set forth in SEQ ID NO:24, and a H-chain CDR3 as set forth in SEQ ID NO:25, and comprises a L-chain CDR1 as set forth in SEQ ID NO:26, a L-chain CDR2 as set forth in SEQ ID NO:27, and a L-chain CDR3 as set forth in SEQ ID NO:28. Appellant has not disputed that a glutamic acid at EU numbering position 332 of the Fc region of an anti-glypican-3 antibody constitutes an amino acid substitution. See also ’739 patent, Abstract (describing the invention as “[a]n anti-glypican-3 antibody comprising one or more amino acid substitutions introduced in the Fc region,” preferably at positions 239, 298, 326, 330, and 332 in the Fc region). Thus, a nucleic acid encoding the anti-glypican-3 antibody of claim 1 of the reference ’739 patent would be a species of nucleic acids claimed by claim 68 on appeal. Reference claim 1 teaches an antibody with a variant Fc region comprising an amino acid substitution at position 332. Presta similarly teaches “polypeptides comprising a variant Fc region,” and further teaches methods of producing such polypeptides by expressing nucleic acid encoding the variant in a cultured host cell as well as methods of producing such nucleic acids. See, e.g., Presta Abstract, 6:33-41, 18:45-19:40 (describing methods of generating nucleic acid sequence encoding a polypeptide variant, including by determining the desired amino acid sequence encoding a polypeptide variant and synthetically generating a nucleic acid sequence encoding such amino acid sequence variant). We agree with the Examiner that, in light of the teachings of Presta, claim 68 is Appeal 2020-004863 Application 15/167,822 10 an obvious variation of the claims of reference ’739 patent. See, e.g., In re Kubin, 561 F.3d 1351, 1360 (Fed. Cir. 2009) (finding claim to polynucleotides encoding specified polypeptides to be obvious over prior art disclosing protein comprising such a polypeptide, a monoclonal antibody for the protein, and methods for obtaining DNA and amino acid sequences for the protein). Citing to General Foods Corp. v. Studiengesellschaft Kohle mbH, 972 F.2d 1272 (Fed. Cir. 1992), Appellant contends that the Examiner improperly applied only part of the reference claim in a double patenting rejection. Appeal Br. 21. In particular, Appellant contends that, in contrast to claim 68, claim 1 of the reference ’739 patent, recited above, “has three additional amino acid positions, . . . is directed to a single 332E amino acid substitution,” and further recites “CDRs of the anti-glypican antibody,” whereas the Examiner “has only focused on a single element of the claim, the 332 amino acid variant.” Id. at 22. We are not persuaded. In General Foods, the reference ’619 patent recited “[a] process for obtaining caffein[e] from green coffee” comprising a series of steps a through h and j. General Foods, 972 F.2d at 1277. Claim 1 of the ’639 patent, which was found by the lower court to be invalid on the ground of obviousness-type double patenting, recited “[a] process for the decaffeination of raw coffee” comprising a caffeine removal step and a decaffeinated-coffee recovery step. Id. at 1276. The lower court held that claim 1 of the ’639 patent was obvious over “claim 1(a)” of the ’619 patent - i.e., step (a) of claim 1 of the ’619 patent. General Foods, 972 F.2d at 1280. The Federal Circuit agreed that step of claim 1 of the ’619 patent “recites the essence of the very same process Appeal 2020-004863 Application 15/167,822 11 claimed in the ’639 patent,” but held that, “in accordance with the principles of claim construction discussed early in this opinion, step (a) is not ‘claimed’ in the ’619 patent” and that “[w]hat is patented by claim 1 of ’619 [patent] is a 9-step caffeine recovery process, nothing more and nothing less.” Id. Accordingly, the Federal Circuit held that the lower court erred by “using nothing but the disclosure of clause (a) of claim 1 as though it were prior art, and in not reading claim 1 to determine what invention it defines.” Id. at 1281. In contrast, here the Examiner’s rejection is based on what the claims of the ’739 patent define, not on what they disclose. In this regard, we find In re Metoprolol Succinate Patent Litigation to be instructive. 494 F.3d 1011, 1018 (Fed. Cir. 2007). The Federal Circuit in that case affirmed the district court’s holding that a claim to “a compound (A1) is an obvious variation of [the reference claim] claiming a composition comprised of one compound of an enumerated list (A1, A2, A3, etc.), an inner layer (B), and an outer layer (C).” Id. at 1017. In particular, the Federal Circuit noted that [t]he language of General Foods and of the precedents cited in the decision explain . . . that what is claimed, as opposed to what is disclosed to one skilled in the art, remains critical. Indeed, adopting [Appellant’s] argument that there can never be “double patenting simply because a later claimed element is set forth in an earlier claim to the combination” would require that this court eviscerate obviousness-type double patenting, thereby reducing invalidity based on double patenting to the § 101 statutory prohibition against claims of the same invention. Id. at 1018 (citations omitted). “A later patent claim is not patentably distinct from an earlier patent claim if the later claim is obvious over, or anticipated by, the earlier claim.” Appeal 2020-004863 Application 15/167,822 12 Eli Lilly & Co. v. Barr Labs., Inc., 251 F.3d 955, 968 (Fed. Cir. 2001). For the above reasons, we are not persuaded by Appellant’s contention that the claims of the present application directed to nucleic acids (and expression vector, etc.) are ‘patentably distinct’ from the claims of the ’739 patent, taken as a whole, which are directed to ‘an anti-glypican-3 antibodies’ (and methods of producing, using, etc.) under the case law cited above, as well as under M.P.E.P. 802.01, 803, 804, and 805. Appeal Br. 24. For the same reasons, we are not persuaded by Appellant’s contention that “the present claims, directed to nucleic acids, are patentably distinct from the proteins of the ’739 patent” for the same reasons cited by the Patent Office in requiring restriction, namely that polypeptide, nucleic acid and host cell differ with respect to their structures, physicochemical properties and/or mode of action . . . , and they do not share a common structure that is disclosed to be essential for common utility. Furthermore, the inventions as claimed do not encompass overlapping subject matter and there is nothing of record to show them to be obvious variants. Appeal Br. 20; see also id. at 24 (arguing that the Office acknowledged that an invention directed to polypeptide(s) is patentably from that directed to nucleic acid, expression vector and method of making a polypeptide because the claimed polypeptide can be made by another, materially different process than that claimed, e.g., by using “protein synthesizer . . . and various recombinant techniques”), Reply Br. 7 (noting that, for claims 68 and 87 in particular, “it should be noted that Fc domains encoded by the nucleic acids Appeal 2020-004863 Application 15/167,822 13 of the invention can be used in constructs that do not contain variable heavy nad variable light domains, e.g. non-antibody related inventions).6 Accordingly, we affirm the Examiner’s rejection of claim 68 on the ground of nonstatutory double patenting as being unpatentable over claims 1-24 of the ’739 patent in view of Presta. Claims 69-101, which are not separately argued, fall with claim 68. CONCLUSION In summary: Claim(s) Rejected 35 U.S.C. § Reference(s)/Basis Affirmed Reversed 68-101 Nonstatutory Double Patenting: US 9,102,739, Presta 68-101 6 In this regard, we also note that claims 3 and 4 of the reference ’739 patent, recite, respectively, “[a] method for producing an anti-glypican-3 antibody, the method comprising: (i) culturing a host cell engineered to express nucleic acid encoding the anti-glypican-3 antibody of claim 1 [or claim 2]; and (ii) isolating said antibody from the culture.” ’739 patent claim 3. Each of claims 75, 76, 85, 86, 92, 93, 100, and 101 on appeal also recites a method of producing a polypeptide. Appeal Br. 28-31. Claim 75, for example, recites “[a] method of producing a polypeptide comprising (a) culturing a host cell according to claim 73 under conditions wherein said polypeptide is produced; and b) purifying said polypeptide,” wherein claim 73 recites “[a] host cell comprising the nucleic acid according to claim 68,” i.e., “[a] nucleic acid encoding a polypeptide Id. at 28. As the Examiner points out, therefore, at least certain of the appealed claims appear to overlap with, e.g., claims 3 and 4 of the reference ’739 patent. Ans. 8. Although Appellant does not “acquiesc[e] on the merits of the rejections” as to claims 75, 76, 85, 86, 92, 93, 100, and 101, Appellant also has not provided persuasive arguments or evidence to address the Examiner’s determinations with respect to these specific claims. Reply Br. 3. Appeal 2020-004863 Application 15/167,822 14 Claim(s) Rejected 35 U.S.C. § Reference(s)/Basis Affirmed Reversed Overall Outcome 68-101 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). See 37 C.F.R. § 1.136(a)(1)(iv). AFFIRMED