Ex Parte Kronick et alDownload PDFPatent Trial and Appeal BoardNov 21, 201713116998 (P.T.A.B. Nov. 21, 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. 13/116,998 05/26/2011 Mel N. Kronick 10040532-02 6679 22878 7590 Agilent Technologies, Inc. Global IP Operations 5301 Stevens Creek Blvd Santa Clara, CA 95051 EXAMINER GROSS, CHRISTOPHER M ART UNIT PAPER NUMBER 1639 NOTIFICATION DATE DELIVERY MODE 11/24/2017 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): IPOPS .LEGAL @ agilent.com Agilentdocketing@cpaglobal.com PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE BEFORE THE PATENT TRIAL AND APPEAL BOARD Ex parte MEL N. KRONICK and ERIC M. LEPROUST Appeal 2016-004467 Application 13/116,99s1 Technology Center 1600 Before ERIC B. GRIMES, FRANCISCO C. PRATS, and JOHN E. SCHNEIDER, Administrative Patent Judges. PRATS, Administrative Patent Judge. DECISION ON APPEAL This appeal under 35 U.S.C. § 134(a) involves claims to a method of cleaving non-nucleic acid polymers immobilized to a solid support. The Examiner rejected the claims for obviousness. We have jurisdiction under 35 U.S.C. § 6(b). We reverse. STATEMENT OF THE CASE Appellants’ invention involves processes “for generating mixtures of product molecules from an initial chemical array.” Spec. 2. Specifically, “a chemical array of surface immobilized first moieties is subjected to cleavage conditions” to produce a “composition of solution phase first moieties.” Id. 1 Appellants state that the “Real Party of interest is Agilent Technologies, Inc.” Appeal Br. 1. Appeal 2016-004467 Application 13/116,998 “The resultant composition of solution phase first moieties is then contacted with one or more reactants to produce a mixture of product molecules that are different from the first moieties.” Id. The Specification discloses that the cleaved immobilized moieties are generally biopolymers, such as nucleic acids, polypeptides, and polysaccharides {id. at 3), and primarily describes the potential applications of the array-based cleavage processes in the context of nucleic acids {id. at 13-34). As to non-nucleic acid applications, the Specification explains that the array-based cleavage processes can be used to produce a population of polypeptide conjugates having differing structures: For example, an initial or precursor array having a plurality of distinct or different polypeptides immobilized on a surface thereof may be subjected to cleavage conditions to produce a plurality of solution phase polypeptides, which composition may then be contacted with a conjugation reaction system that chemically bonds a common moiety of interest to each of the members of the solution phase composition to produce a plurality of second molecules, e.g., polypeptide conjugates. Id. at 35. Relevant to our discussion below, the Specification defines “array” as follows: A chemical “array”, unless a contrary intention appears, includes any one, two or three-dimensional arrangement of addressable regions bearing a particular chemical moiety or moieties (for example, biopolymers such as polynucleotide sequences) associated with that region. For example, each region may extend into a third dimension in the case where the substrate is porous while not having any substantial third dimension measurement (thickness) in the case where the substrate is non-porous. An array is “addressable” in that it has multiple regions (sometimes referenced as “features” or “spots” of the array) of different moieties (for example, different 2 Appeal 2016-004467 Application 13/116,998 polynucleotide sequences) such that a region at a particular predetermined location (an “address”) on the array will detect a particular target or class of targets (although a feature may incidentally detect non-targets of that feature). The target for which each feature is specific is, in representative embodiments, known. An array feature is generally homogenous in composition and concentration and the features may be separated by intervening spaces (although arrays without such separation can be fabricated). Id. at 4. Claim 16 is the only independent claim on appeal, and reads as follows: 16. A method comprising: (a) subjecting an array of a plurality of non-nucleic acid polymer features comprising non-nucleic acid polymer first moieties immobilized on a surface of a solid support via a cleavable domain to conditions sufficient to cleave said cleavable domain and generate a solution phase composition of said non-nucleic acid polymer first moieties, wherein said non- nucleic acid features are arranged on the surface of said solid support in addressable regions and wherein said solution phase composition is a mixture comprising two or more of said non- nucleic acid polymer first moieties; and (b) contacting said solution phase composition of said non-nucleic acid polymer-first moieties with one or more reactants to produce a mixture of product molecules that are different from said non-nucleic acid polymer first moieties. Appeal Br. 9. The sole rejection before us for review is the Examiner’s rejection of claims 16, 17, 20, and 22-25, under 35 U.S.C. § 103(a), over Bryan,2 2 Marian C. Bryan et al.. Covalent Display of Oligosaccharide Arrays in Microtiter Plates, 126 JACS 8640—41 (2004). 3 Appeal 2016-004467 Application 13/116,998 Schleyer,3 and Fazio.4 Ans. 2-5.5 DISCUSSION In rejecting claims 16, 17, 20, and 22-25 for obviousness, the Examiner found that Bryan taught or suggested a process having all of the steps and features of the rejected claims, except that Bryan did not teach “base labile linkers such as set forth in claim 17.” Ans. 3. The Examiner also found that, “[additionally or alternatively regarding claim 16a, in scheme 3,” Schleyer taught cleaving a set of peptides (15a-d) immobilized to the same solid support, resulting in a “solution phase composition [which] is a mixture comprising the library of glycopeptides 16a-d.” Id. The Examiner found that the Bryan/Schleyer combination did not teach or suggest “enzymes as reactants per claim 22” and cited Fazio as evidence that it was known in the art that “fucosylation of sugars may be performed with the enzyme a-l,3-fucosyltransferase such as set forth in claim 22.” Id. at 4. The Examiner found that an ordinary artisan would have had motivation to, and a reasonable expectation of success in, “construct[ing] an oligosaccharide array in the manner of Bryan et al employing the cleavage chemistry of Schleyer et al and perform[ing] a fucosylation assay as 3 Axel Schleyer et al.. Direct Solid-Phase Glycosylations of Peptide Templates on a Novel PEG-Based Resin, 36 Angew. Chem. Int. Ed. 1976- 78 (1997). 4 Fabio Fazio et al., Synthesis of Sugar Arrays in Microtiter Plate, 124 JACS 14397-14402 (2002). 5 The Examiner withdrew a rejection under § 102(b) that had been entered in the office action from which the appeal was taken. Ans. 5. 4 Appeal 2016-004467 Application 13/116,998 suggested by Fazio et al for the advantages” taught in Schleyer and Fazio. Id. at 4 (citing Schleyer 1976-78; Fazio 14401^102). As stated in In re Oetiker, 977 F.2d 1443, 1445 (Fed. Cir. 1992): [T]he examiner bears the initial burden ... of presenting a prima facie case of unpatentability. . . . After evidence or argument is submitted by the applicant in response, patentability is determined on the totality of the record, by a preponderance of evidence with due consideration to persuasiveness of argument. In the present case, Appellants persuade us that the preponderance of the evidence does not support the Examiner’s prima facie case of obviousness. Appellants contend that, although Bryan describes the preparation of an oligosaccharide array on a multi-well microtiter plate, each well of Bryan’s array contains the same oligosaccharide species. Appeal Br. 5. Accordingly, Appellants contend, “[cjleavage of an oligosaccharide in a well therefore results in a solution phase containing a single oligosaccharide in, not a mixture of oligosaccharides, as required by claim 16.” Id. at 5-6. The Examiner does not dispute that Bryan’s array contains the same oligosaccharide species in each well. Rather, the Examiner contends that, given the language in the claim, the solution phase resulting from the cleavage in step (a) of claim 16 may contain “[1] different compounds, [2] two molecules of the same compound (which is consistent with claim 23) or even [3] two functional groups on the same molecule.” Ans. 6. The Examiner contends further that, “[wjhereas while Bryan et al may cleave for example saccharide 8 (in table 4) with DTT in a well of a 5 Appeal 2016-004467 Application 13/116,998 microtiter plate well in one embodiment, the reaction solution inherently includes, for example at least two released different molecules of triazole saccharide as well as oxidized DTT.” Id. We conclude that Appellants have the better position. Claim 16 recites a process involving an array composed of “non- nucleic acid polymer first moieties” immobilized to “addressable regions” of the array. Appeal Br. 9 (claim 16). The array is subjected to cleavage conditions, thereby producing a “solution phase composition [which] is a mixture comprising two or more of said non-nucleic acid polymer first moieties.” Id. (emphasis added). As noted above, the Specification’s definition of an array having addressable regions states that the array has “multiple regions (sometimes referenced as ‘features’ or ‘spots’ of the array) of different moieties.” Spec. 4 (emphasis added). Appellants persuade us, therefore, that when given its broadest reasonable interpretation in light of the Specification, claim 16 requires the solution phase composition resulting from the cleavage step to contain different species of polymer molecule cleaved from different addressable regions of the array. Accordingly, we are also persuaded that claim 16 does not encompass a process that produces a solution phase containing only multiple copies of the same molecule, which is the product that undisputedly results from Bryan’s process. Moreover, because claim 16’s cleavage results in “a mixture comprising two or more of said [previously immobilized] non- nucleic acid polymer first moieties” (Appeal Br. 9 (emphasis added)), the Examiner does not persuade us that claim 16 encompasses Bryan’s DTT 6 Appeal 2016-004467 Application 13/116,998 cleavage agent as one of the two different moieties that must be present in the cleavage product. The Examiner contends that, even interpreting claim 16 as requiring the cleaved solution phase composition to contain different species of polymer, Bryan discloses that its immobilization techniques may be used to immobilize oligosaccharides to glass slides, in addition to microtiter plates. Ans. 6-7. The disclosure cited by the Examiner appears in the concluding paragraph of Bryan, which reads as follows: In summary, this work shows a new and efficient methodology for the covalent array of saccharides on microtiter plates. The use of a cleavable linker allows characterization and quantitative analysis of the array. Moreover, binding studies have proven that this microarray is functional in biological screening and therefore applicable in ELISA-type formats. The chemistry can be applied to other surfaces such as glass slides. We believe that this new covalent array, together with the one-pot automated synthesis of complex oligosaccharides, can become useful for the high-throughput biological evaluation of carbohydrate-protein interaction. Bryan 8641 (emphasis added; citation removed). Although we, thus, acknowledge this disclosure in Bryan, we are not persuaded that it is a sufficiently specific teaching that would have suggested preparing an array having the features required by claim 16, and then cleaving that array as claim 16 requires. Nor has the Examiner explained adequately why this isolated statement about the potential applications of Bryan’s immobilization chemistry would have led an ordinary artisan to the specific process recited in claim 16. The Examiner contends in addition that Schleyer’s scheme 3 describes a process meeting claim 16’s requirement for the cleavage step to produce a population of different molecules. Ans. 7. 7 Appeal 2016-004467 Application 13/116,998 We acknowledge that in scheme 3, Schleyer describes the synthesis of a “small library of [four] glycopeptides by two consecutive, direct glycosylations of a mixture of solid phase-bound peptides.” Schleyer 1978. To confirm the expected structures, Schleyer cleaves the glycopeptides from the solid support (as required by Appellants’ claim 16), purifies them by HPLC, and analyzes them spectrometrically. Id. at 1977. As Appellants contend, however, Schleyer does not describe its immobilization process as generating an array with addressable regions, as claim 16 requires. Nor are we persuaded that the Examiner has explained adequately why, even when combined with the other cited references, Schleyer would have suggested to an ordinary artisan claim 16’s required step of subjecting an array with addressable regions to cleavage conditions that produce a population of different molecules from the different addressable regions. In sum, for the reasons discussed, Appellants persuade us that a preponderance of the evidence does not support the Examiner’s conclusion of obviousness as to claim 16. We, therefore, reverse the Examiner rejection of claim 16, and its dependents, over the cited references. REVERSED 8 Copy with citationCopy as parenthetical citation