Ex Parte Hutchins et alDownload PDFPatent Trial and Appeal BoardJun 7, 201712959941 (P.T.A.B. Jun. 7, 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. 12/959,941 12/03/2010 CHARLES W. HUTCHINS 029996-1026 (10263USO1) 6155 17567 7590 06/09/2017 Michael Best & Friedrich LLP (AbbVie) 444 West Lake Street Suite 3200 Chicago, IL 60606 EXAMINER RAO, MANJUNATH N ART UNIT PAPER NUMBER 1656 NOTIFICATION DATE DELIVERY MODE 06/09/2017 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): chiipdocket @ michaelbest. com abb vie_patents_abt_prk @ abb vie .com llczech@michaelbest.com PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE BEFORE THE PATENT TRIAL AND APPEAL BOARD Ex parte CHARLES W. HUTCHINS, DAVID A. DEGOEY, WARREN M. KATI, ALLAN C. KRUEGER, JOHN T. RANDOLPH, ROLF WAGNER, and PAMELA L. DONNER1 Appeal 2015-006253 Application 12/959,941 Technology Center 1600 Before ULRIKE W. JENKS, RICHARD J. SMITH, and DEVON ZASTROW NEWMAN, Administrative Patent Judges. SMITH, Administrative Patent Judge. DECISION ON APPEAL This is an appeal under 35U.S.C. § 134 involving claims to a method of identifying NS5A inhibitors. We have jurisdiction under 35 U.S.C. § 6(b). We affirm. 1 According to Appellants, the real party in interest is Abbvie Inc. (Appeal Br. 3.) Appeal 2015-006253 Application 12/959,941 STATEMENT OF THE CASE Background “The nonstructural protein NS5 A ... is a critical component of [Hepatitis C virus (“HCV”)] replication. . . . NS5A has been identified as a promising therapeutic target for treating HCV.” (Spec. 1,11. 22—23 and 32.) Claims on Appeal Claims 1, 2, 4—7, 9, 10, 12, 13, 15, and 16 are on appeal.2 (Claims Appendix, Appeal Br. 14—18.) Claim 1 is illustrative and reads as follows: 1. A method of identifying NS5 A inhibitors, comprising docking a compound to an NS5A dimer using a computer docking program, wherein the NS5A dimer comprises two NS5A monomers and an interaction site, and the amino acid residues that form the interaction site comprise amino acids 37, 38, 39 and 58 of both said monomers, wherein whether said compound comprises a moiety that fits to the interaction site is indicative of whether said compound is an NS5 A inhibitor, and wherein each said monomer comprises amino acids 36—198 of SEQ ID NO: 1, 2, 3, 4, 5, 6 or 8 or amino acids 36-197 of SEQ ID NO:7. (Appeal Br. 14 (emphasis added).) Examiner’s Rejection Claims 1, 2, 4—7, 9, 10, 12, 13, 15, and 16 stand rejected under 35 U.S.C. § 103(a) as unpatentable over Rice.3 (Ans. 2—3.)4 2 Claims 18—24 are withdrawn. (Final Act. 2, dated June 4, 2013.) 3 Rice et al., WO 2006/093867 Al, pub. Sept. 8, 2006 (“Rice”). 4 The claims on appeal were rejected under 35 U.S.C. § 102(b) or, in the alternative, under 35 U.S.C. § 103(a), based on Rice (Final Act. 3), but the rejection of claims 1, 2, 4—7, 10, 12, 13, 15, and 16 under 35 U.S.C. § 102(b) was withdrawn in the Answer (Ans. 3). The Answer inadvertently omits claim 9 from the withdrawal under Section 102 and the restatement of the rejection under Section 103. (Compare Final Act. 3 and Ans. 2—3.) 2 Appeal 2015-006253 Application 12/959,941 FINDINGS OF FACT We adopt the Examiner’s findings as our own, including with regard to the scope and content of the prior art. The following findings are included for emphasis and reference purposes. FF 1. The Examiner finds that: [Rice] teaches the crystallization of the N-terminus domain of NS5 A of SEQ ID NO:4 to produce the tetragonal crystal in space group P4i22 having the unit cell dimension of a,b=55.28 Angstrom, c=312.3 Angstrom, and a=P=gamma=90 degree. [] The amino acid sequence of SEQ ID NO:4 comprises residues 36-198 of SEQ ID NO: 1 of the instant application. (Ans. 2, citing Rice H 147—149 and 151.) FF 2. The Examiner finds that Rice teaches “numerous program[s] available for rational drug design and the processes of computer modeling, model building, and computationally identifying, selecting, and evaluating potential inhibitors of dimerized NS5A proteins of hepatitis C virus.” (Ans. 2, citing Rice 161.) FF 3. The Examiner finds that Rice identifies “several target areas of the [NS5A] structure for drug design and development including the groove area, the zinc binding domain, and the dimerization domain.” (Ans. 7, citing Rice 111.) FF 4. Rice teaches that “[i]n another embodiment [of the invention], the inhibitor is positioned within a groove formed between two subdomain IB regions of N-terminal domains of dimerized NS5A.” (Rice 111.) DISCUSSION We adopt as our own the Examiner’s findings, analysis, and conclusions as set forth in the Final Action (Final Act. 2-4) and Answer (Ans. 2—7). We discern no error in the rejection of the claims as obvious. 3 Appeal 2015-006253 Application 12/959,941 Issue Whether a preponderance of evidence of record supports the Examiner’s rejection under 35 U.S.C. § 103(a). Analysis The issue in this appeal turns on whether the identification and claiming of certain “amino acid residues that form the interaction site” render the claims patentably distinct from the teachings of Rice. (Appeal Br. 14.) The Examiner’s position is that: “[t]he only difference between the teaching of [Rice] and the claimed invention is the binding site of the inhibitor as defined by the atomic coordinates of the specific amino acid residues of the claims. Data, which are fed into known algorithm[s] such as QUANTA whose purpose is to compare or modify those data using [a] series of processing steps, do not impose a change in processing steps and are thus nonfunctional descriptive material.” (Ans. 3; see also FF 1—3.) Appellants argue that “[t]he present invention features an unexpected discovery of a unique binding site on NS5A dimers” and that “many NS5A inhibitors interact with amino acid residues located on the inside surface of NS5A dimers, with enhanced effectiveness.” (Appeal Br. 4—5.) Appellants argue further that the success of a docking program often depends on both the search algorithm and the scoring function, and that “the scoring function is based on the particularities of the inhibitor binding sites on the NS5A protein.” (Id. at 8.) Appellants further contend that the claimed SEQ ID NOs contain 163 residues and only 18 are identified by Rice as important in inhibitor binding. 4 Appeal 2015-006253 Application 12/959,941 (Id. at 9.) Appellants also contend that Rice “makes no specific mention of’ the claimed residues and that “the Examiner failed to consider the predictability of the technology or the number of species encompassed by [Rice].” (Id. at 8—10.) Moreover, according to Appellants, “the claimed amino acids transform inadequate methods of the prior art to provide effective and more efficient identification of NS 5 A inhibitors, thus serving as functional descriptive material.” (Reply Br. 3.)5 We find that the Examiner has the better position, and address Appellants’ arguments below. We address independent claim 1 as representative of claims 1, 2, 4, and 5. Identification of Amino Acid Residues Appellants argue that the identification of a group or subset of amino acid residues (37, 38, 39, and 58 in claim 1) from SEQ ID NO: 4 taught by Rice (Appellants’ claimed SEQ ID NO: 1) constituted an unexpected discovery. (Appeal Br. 4.) Like the Examiner, we recognize that there may have been some difficulty in identifying the claimed subset of residues (Ans. 4), but we do not find that any such difficulty gives rise to a patentable invention. Rather, we find such identification to be the result of using routine research methods to establish what was already suggested by Rice. (Ans. 7.) See, e.g., PharmaStem Therapeutics, Inc. v. ViaCell, Inc., 491 F.3d 1342, 1363—64 (Fed. Cir. 2007) (“Good science and useful contributions do not necessarily result in patentability.”). 5 Citations to the Reply Brief herein are to the Supplemental Reply Brief filed Dec. 1,2014. 5 Appeal 2015-006253 Application 12/959,941 Appellants’ arguments regarding the predictability of the technology and number of species encompassed by Rice are also unpersuasive. As the Examiner explains [Rice] identified several target areas of the structure for drug design and development including the groove area, the zinc binding domain, and the dimerization domain. [] Thus, it is not like what applicants want to believe selecting only 18 amino acid residues from a large number of amino acid residues. [Rice] limits the residues that define the surface of the groove area, the zinc binding domain, or the dimerization domain. The identification of these residues does not require more than building the model utilizing the atomic coordinates of the prior art, [a] commercially available computer, and visually looking at the structure, or utilizing a computer program that define [s] the amino acid residues of interest. (Ans. 7, citing Rice 111 .)6 We are also unpersuaded by Appellants’ arguments that identifying NS5 A inhibitors via docking programs, as taught by Rice, was not an efficient process, that such docking programs “provide unpredictable results,” and that docking programs at the time of filing “would not have provided an accurate identification whether the inhibitor would be a potent inhibitor of NS 5 A.” (Reply Br. 4—5.) Appellants essentially argue that a person of skill in the art would not have had a reasonable expectation of success in arriving at the claimed invention, but those contentions rely on attorney argument rather than providing evidence that a person of skill in the art would not have had a reasonable expectation of success. See In re 6 We also note that Appellants’ use of the open ended term “comprise,” in claiming the amino acid residues of the interaction site, does not limit the interaction site to only those recited residues (e.g., 37, 38, 39, and 58). See Genentech, Inc. v. Chiron Corp., 112 F.3d 495, 501 (Fed. Cir. 1997). 6 Appeal 2015-006253 Application 12/959,941 Pearson, 494 F.2d 1399, 1405 (CCPA 1974) (attorney argument in a brief cannot take the place of evidence). Moreover, “obviousness cannot be avoided simply by a showing of some degree of unpredictability in the art so long as there was a reasonable probability of success.” Pfizer, Inc. v. Apotex, Inc., 480 F.3d 1348, 1364 (Fed. Cir. 2007). Printed Matter Printed matter7 may be entitled to patentable weight if a new and nonobvious functional relationship exists between the printed matter and the substrate. See In re Lowry, 32 F.3d 1579, 1582 (Fed. Cir. 1994); see also In re Distefano, 808 F.3d at 850 (stating that printed matter may be given patentable weight “if the claimed informational content has a functional or structural relation to the substrate”). The Examiner finds that the claimed amino acid residues are nonfunctional descriptive material (Ans. 3), while Appellants contend that the amino acid residues are functional descriptive material (Reply Br. 3). The Examiner’s position is that the printed materials are the atomic coordinates for the claimed amino acids and the substrate is the computer methods (programs) for docking a small molecule into the three-dimensional structure for a protein. (Ans. 4—7, relying on MPEP § 2111.05 and Ex Parte Nehls, 88 USPQ2d 1883 (BPAI 2008) (precedential)). Moreover, the Examiner finds that “[structural coordinates are considered by the U.S. Patent and Trademark Office [as] non-functional descriptive material because they do not change the method or the algorithm used to identify inhibitors utilizing the three-dimensional structure of a protein.” (Final Act. 7 See In re Distefano, 808 F.3d 845, 848 (Fed. Cir. 2015) (“a limitation is printed matter only if it claims the content of information”). 7 Appeal 2015-006253 Application 12/959,941 4.) Appellants argue that the claimed amino acids are functional descriptive material because they transform prior art methods “to provide effective and more efficient identification of NS5A inhibitors.” (Reply Br. 2—4.) We find that the Examiner has the better position. Here, the claimed amino acid residues do not have a functional or structural relation to the computer docking program(s) because the program will operate the same way regardless of the data (amino acid coordinates) that are entered into the docking program. (Ans. 3; Final Act. 4.) See Ex Parte Nehls, 88 USPQ2d at 1888 (“The specific SEQ ID NOs recited in the claims do not affect how the method of the prior art is performed — the method is carried out the same way regardless of which specific sequences are included in the database.”). In fact, Appellants identify several of the same “suitable” docking programs for use in the claimed method that are also identified in Rice. (Compare Spec. 22,11. 5—35 and Rice 161.) Thus, while the results may differ depending on the coordinates entered, the selected computer docking program (processing steps) will work the same. See Ex Parte Nehls, 88 USPQ2d at 1888, n.5 (“Descriptive material is not functional merely because it results in different outputs when acted on by a computer program.”).8 We acknowledge, but are unpersuaded by, Appellants’ reliance on Lowry and In re Gulack, 703 F.2d 1381 (Fed. Cir. 1983), in support of their argument. (Appeal Br. 3—4.) In Lowry, the court held that the claimed data 8 We acknowledge Appellants’ position that the results are more effective and that the program is more efficient using the claimed amino acid residues, but any such improvement in effectiveness or efficiency is merely the result of changing the data entered into the program, not changing the program itself. 8 Appeal 2015-006253 Application 12/959,941 structures were not analogous to printed matter and did not merely represent underlying data in a database. In re Lowry, 32 F.3d at 1583. Rather, the court found that “Lowry’s claims dictate how application programs manage information” and thus “define functional characteristics of the memory.” Id. In Gulack, the court determined that a sequence of digits deserved patentable weight because the informational content of the sequence was functionally related to the endless-band physical structure of the substrate. In re Gulack, 703 F.2d at 1385. Unlike Lowry and Gulack, the instant claims neither define a functional characteristic nor informational content that is functionally related to the computer docking program. Accordingly, for the reasons of record and as set forth above, we affirm the rejection of claim 1. Claims 2,4, and 5 were not argued separately and fall with claim 1. Claims 6 and 7 Independent claim 6 and dependent claim 7 are similar to claim 1, but claim different amino acid residues for the interaction site. (Appeal Br. 14.) Appellants advance essentially the same arguments as set forth above in connection with claim 1, and those arguments are unpersuasive for the reasons set forth above. Claims 9 and 10 Appellants rely on “the same and similar reasons as outlined above with respect to claims 6 and 7” (Appeal Br. 12), and those arguments are unpersuasive for the reasons set forth above. 9 Appeal 2015-006253 Application 12/959,941 Claims 12, 13, 15, and 16 Appellants rely on “the same and similar reasons as outlined above with respect to claims 1, 2, 6, and 7” (Appeal Br. 12), and those arguments are unpersuasive for the reasons set forth above. Conclusion of Law A preponderance of evidence of record supports the Examiner’s rejection of claims 1, 6, 7, 9, 10, 12, 13, 15, and 16 under 35 U.S.C. § 103(a). Claims 2, 4, and 5 were not argued separately and fall with claim 1. SUMMARY We affirm the rejection of all claims on appeal. 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 10 Copy with citationCopy as parenthetical citation