Ex Parte Chilkoti

Patent Trial and Appeal BoardApr 22, 2016

12335235 (P.T.A.B. Apr. 22, 2016)

UNITED STA TES p A TENT AND TRADEMARK OFFICE APPLICATION NO. FILING DATE 12/335,235 12/15/2008 58249 7590 04/26/2016 COOLEYLLP ATTN: Patent Group 1299 Pennsylvania Avenue, NW Suite 700 Washington, DC 20004 FIRST NAMED INVENTOR Ashutosh CHILKOTI 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 ATTORNEY DOCKET NO. PHAS-002/02US 309646-2043 CONFIRMATION NO. 9713 EXAMINER PROUTY, REBECCA E ART UNIT PAPER NUMBER 1652 NOTIFICATION DATE DELIVERY MODE 04/26/2016 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): zpatdcdocketing@cooley.com PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE BEFORE THE PATENT TRIAL AND APPEAL BOARD Ex parte ASHUTOSH CHILKOTI1 Appeal2013-008619 Application 12/335,235 Technology Center 1600 Before ERIC B. GRIMES, JOHN G. NEW, and RICHARD J. SMITH, Administrative Patent Judges. GRIMES, Administrative Patent Judge. DECISION ON APPEAL This is an appeal under 35 U.S.C. Â§ 134 involving claims to a pharmaceutical formulation, which have been rejected as for obviousness- type double patenting. We have jurisdiction under 35 U.S.C. Â§ 6(b). We affirm. STATEMENT OF THE CASE The Specification states that "non-chromatographic, thermally- stimulated phase separation and purification of recombinant proteins can be achieved by forming fusion proteins that contain the target recombinant 1 Appellant identifies the Real Party in Interest as PhaseBio Pharmaceuticals, Inc. (Appeal Br. 2.) Appeal2013-008619 Application 12/335,235 proteins with N- or C-terminal elastin-like polypeptide (ELP) tags." (Spec. 3.) Claims 120 and 125-136 are on appeal. Claim 120 is illustrative and reads as follows (emphasis added): 120. A pharmaceutical formulation comprising a biologically active fusion protein and a pharmaceutically acceptable carrier, the fusion protein compnsmg: and Issue a biologically active protein or peptide, wherein said biologically active protein or peptide is insulin, an elastin-like peptide (ELP) of from 9 kDa to 72 kDa in size; wherein said elastin-like peptide (ELP) comprises oligomeric repeats of the pentapeptide Val-Pro-Gly-X-Gly, and wherein Xis valine, alanine, and glycine in the ratio 5:2: 3. DISCUSSION The Examiner has rejected claims 120 and 125-136 for obviousness- type double patenting on the basis that the claims on appeal are not patentably distinct from claims 1--41 of U.S. Patent 6,852,834 B2 (Feb. 8, 2005). The Examiner finds that the claims on appeal differ from the claims of the '834 patent in three ways: (1) they require a carrier, (2) they limit the biologically active protein or peptide to insulin, and (3) they require the "X" in the pentapeptide to be valine (V), alanine (A), and glycine (G) in a ratio of 5:2:3. (Ans. 3--4.) The Examiner concludes that the first two of these differences would have been obvious because use of the fusion protein of the '834 patent would require it to be in a carrier, such as water, and claim 41 of the '834 patent recites insulin as the biologically active protein or peptide. (Id. at 4.) 2 Appeal2013-008619 Application 12/335,235 The Examiner also concludes that the final difference between the sets of claims would have been obvious because "oligomeric repeats of the pentapeptide VPGXG wherein Xis V, A, and Gin a ratio of 5:2:3 as the ELP (see column 16) are preferred embodiments of the claimed fusion proteins." (Id.) That is, "it would have been obvious to one having ordinary skill in the art to modify the fusion protein of claims 1-41 of US Patent 6,852,834 by selecting a specifically disclosed embodiment that supports that claim." (Id. at 5.) Appellant contends that "the Office has used an improper analysis in which previously disclosed matter is used to form the basis of an obviousness-type double patenting rejection." (Appeal Br. 9.) Appellant also contends that, even though the claims of the '834 patent dominate the narrower claims now on appeal, that is not a basis for a double patenting rejection (id. at 10-11), and the Examiner has not shown that the disputed limitation would have been obvious in view of the "numerous 'preferred' embodiments" (id. at 12) disclosed in the '834 patent (id. at 11-13). The issue presented is whether the disclosure of a specific embodiment of the '83 4 patent's earlier-claimed genus makes a later claim to that embodiment unpatentable based on obviousness-type double patenting. Findings of Fact 1. Claim 1 of the '834 patent reads as follows: 1. A fusion protein comprising: (a) one or more biological molecules selected from the group consisting of peptides and proteins; 3 Appeal2013-008619 Application 12/335,235 (b) one or more phase transition proteins that exhibit an inverse phase transition wherein the one or more phase transition proteins are joined to the biological molecule(s) of (a); and ( c) optionally, a spacer sequence separating any of the phase transition protein(s) of (b) from any of the biological molecule(s) of (a), wherein the fusion protein retains the inverse phase transition behavior of the phase transition protein( s) of (b) and wherein said phase transition protein(s) has a molecular weight of at least 9,000 Daltons, and wherein the one or more phase transition protein( s) of (b) comprises oligomeric repeats of the pentapeptide Val-Pro-Gly-X-Gly, wherein Xis any natural or non-natural amino acid residue, and wherein X optionally varies among oligomeric repeats. ('834 patent 45:60 to 47:3.) 2. Claim 41 of the '834 patent recites a Markush group of biological molecules that includes insulin. (Id. at 50:19-28.) Appellant does not dispute that insulin would have been an obvious choice for the biologically active protein or peptide in the claims on appeal. 3. The Examiner finds that it would have been obvious to combine the fusion protein claimed in the '834 patent with a pharmaceutically acceptable carrier because using the fusion protein would require it to be present in a carrier such as water. (Ans. 4.) Appellant does not dispute this finding. 4. The '834 patent states: Previous studies by Urry and colleagues have shown that two ELP-specific variables, guest residue(s) composition (i.e., identity and mole fraction of X in the VPGXG monomer) and chain length of the ELP profoundly affect the transition temperature, and thereby provide design criteria to specify the Tt [transition temperature] for a specific application. Based on these studies, a gene was synthesized encoding an ELP sequence 4 Appeal2013-008619 Application 12/335,235 (Sequence ID No. 3) with guest residues valine, alanine, and glycine in the ratio 5:2:3. ('834 patent 16:2-10, reference citations omitted.) Analysis We agree with the Examiner that claim 120 on appeal is an obvious variant of the fusion proteins claimed in the '834 patent. Appellant does not dispute that a skilled artisan would have considered it obvious to formulate the fusion protein claimed in the '834 patent with a pharmaceutically acceptable carrier, or that insulin would have been an obvious choice for the "biological molecule" moiety of the claimed fusion protein. The issue, therefore, is whether the limitation requiring the "X" residue in the oligomeric Val-Pro-Gly-X-Gly pentapeptide to be "valine, alanine, and glycine in a ratio of 5:2:3" patentably distinguishes claim 120 from the claims of the '834 patent, which state that "X is any natural or non- natural amino acid residue, and wherein X optionally varies among oligomeric repeats." The Examiner concludes that the disputed limitation would have been obvious because the '834 patent describes a specific embodiment of the claimed fusion protein in which the X residue (or "guest residue") is "valine, alanine, and glycine in the ratio 5:2:3" (FF4). (Ans. 4--5.) The Examiner concludes that it would have been obvious to select these residues, in the recited ratio, because the '834 patent discloses a specific embodiment having those features. (Id. at 5.) Appellant argues, however, that the Examiner "has used an improper analysis in which previously disclosed matter is used to form the basis of an 5 Appeal2013-008619 Application 12/335,235 obviousness-type double patenting rejection .... The proper analysis focuses on that which is previously claimed." (Appeal Br. 9.) Appellant argues that [ n ]owhere in the claims of Chilkoti is it recited that an ELP comprises oligomeric repeats of the pentapeptide valine-proline- glycine-X-glycine wherein Xis valine, alanine, and glycine in a ratio of 5:2:3 .... Accordingly, the present claims are patentably distinct over the invention claimed in the granted parent patent. (Id. at 9-10.) We agree with the Examiner that the specific embodiment described in the '834 patent is properly considered as part of the obviousness-type double patenting analysis in this case. As previously noted, the '834 patent describes a specific embodiment of its claimed fusion protein in which the X residue in the Val-Pro-Gly-X-Gly (or VPGXG) pentapeptide is valine, alanine, and glycine in a ratio of 5:2:3 (FF4). The '834 patent also states that a "synthetic gene, which encoded 10 VPGXG pentapeptide repeats (the '10-mer'); was oligomerized up to 18 times to create a library of genes encoding ELPs with precisely-specified molecular weights (MW s) ranging from 3.9 to 70.5 kDa." ('834 patent 16:11-15.) "Thioredoxin was expressed as a N-terminal fusion with the 10-, 20-, 30-, 60-, 90-, 120-, 150-, and 180-merELP sequences." (Id. at 16:19-21.) Thus, the '834 patent describes specific embodiments of the claimed fusion protein that are identical to the fusion protein recited in claim 120 on appeal, except that they included thioredoxin rather than the insulin required by claim 120. As discussed above, however, there is no dispute that insulin would have been an obvious choice for the biological molecule of the fusion protein claimed in the '834 patent (see FF2). 6 Appeal2013-008619 Application 12/335,235 The key question, in an obviousness-type double patenting analysis, is: "Does any claim in the application define merely an obvious variation of an invention disclosed and claimed in the patent?" In re Vogel, 422 F.2d 438, 441(CCPA1970). The Vogel court stated that "[i]n considering the question, the patent disclosure may not be used as prior art." (Id.) However, the Vogel court went on to say that "[t]his does not mean that the disclosure may not be used at all." (Id.) As relevant here, the court stated that [t]he disclosure ... sets forth at least one tangible embodiment within the claim, and it is less difficult and more meaningful to judge whether that thing has been modified in an obvious manner. It must be noted that this use of the disclosure is not in contravention of the cases forbidding its use as prior art, nor is it applying the patent as a reference under 35 U.S.C. Â§ 103, since only the disclosure of the invention claimed in the patent may be examined. (Id. at 442.) The '834 patent sets forth specific examples-"tangible embodiment[s]" in the Vogel court's words---of the fusion proteins that are claimed in that patent. Thus, using that part of the '834 patent's disclosure in considering whether claim 120 defines more than an obvious variant of the '834 patent's claims is not using the disclosure of the '834 patent as prior art or applying it as a reference under 35 U.S.C. Â§ 103(a), because only the disclosure of the invention claimed in the '834 patent is being examined. The Federal Circuit has reaffirmed the use of a patent's specification, as described in Vogel, in analyzing obviousness-type double patenting. See In re Basel! Poliolefine Italia SP.A., 547 F.3d 1371, 1378-79 (Fed. Cir. 2008). The Basel! court held that "the PTO had good basis for its conclusion 7 Appeal2013-008619 Application 12/335,235 that the claims of the '987 patent rendered obvious the claims of the '687 patent and that the latter claims are invalid for obviousness-type double patenting" because "the specification of the '987 patent itself refers to ethylene, propylene, butene, and other olefins which indicates that those olefins were intended to fall within the meaning of the claims." Bas ell, 54 7 F.3d at 1378. The court held that the Board's use of the earlier patent's specification in that case was consistent with Vogel. Appellant argues, however, that this appeal is analogous to In re Kaplan, 789 F.2d 1574 (Fed. Cir. 1986), in which the court rejected the use of the earlier patent's specification in analyzing double patenting. (Reply Br. 4--9.) We disagree. In Kaplan, the claim on appeal (in an application filed by Kaplan and Walker) was directed in relevant part to a process that used a solvent mixture of tetraglyme and sulfolane. Kaplan, 789 F.2d at 1575. The claim had been rejected for obviousness-type double patenting, id. at 1576-77, based on an earlier patent to Kaplan (alone), which claimed a similar process but was generic as to the solvent used in it. Id. at 1575. More specifically, the Kaplan/Walker claim had been rejected for obviousness-type double patenting based on the earlier Kaplan patent's more generic claim, on the basis that the Kaplan specification described a mixture of tetraglyme and sulfolane in a working example. Id. at 1577. The court noted, however, that the process using a mixture of tetraglyme and sulfolane was the joint invention of Kaplan and Walker, not Kaplan alone. Id. at 1575. It was disclosed in Kaplan's (sole) application 8 Appeal2013-008619 Application 12/335,235 because he was aware of it and disclosed it as part of the best mode of practicing the claimed process. Id. The court held that [i]n effect, what the board did was to use a disclosure of appellants' own joint invention which had been incorporated in the Kaplan sole disclosure to show that their invention was but an obvious variation of Kaplan's claimed invention. That amounts to using an applicant's invention disclosure ... as prior art against him. That is impermissible. Id. at 1580. Importantly, however, the Kaplan court also cited Vogel as providing a "restatement of the law of double patenting which serves as a good starting place for deciding this case." Id. at 1579. The Kaplan court therefore saw no inconsistency between its holding and Vogel. Thus, in Kaplan, the relevant example in the disclosure of the Kaplan patent could not properly be treated as a disclosed species of the more generic process claimed by Kaplan, since Kaplan (alone) did not invent it; rather, it was the invention of Kaplan and Walker. Here, by contrast, the evidence shows that the relevant example in the '834 patent was an embodiment of Appellant's claimed invention. The '834 patent states that a gene was synthesized encoding an ELP sequence (Sequence ID No. 3) with guest residues valine, alanine, and glycine in the ratio 5:2:3. . . . The synthetic gene ... was oligomerized up to 18 times to create a library of genes. . . . To my knowledge, these are the first examples of genetically-engineered ELPs with precisely-defined chain length and amino acid sequence, which are designed to exhibit an inverse transition at a specified temperature. ('834 patent 16:8-19.) In short, Appellant disclosed a specific, tangible embodiment of the invention that was generically claimed in the '834 patent, but now seeks to 9 Appeal2013-008619 Application 12/335,235 prevent the public from practicing that embodiment of the previously claimed invention by seeking a separate patent to the previously disclosed embodiment. We agree with the Examiner that granting a patent on the instant claims, in the absence of a terminal disclaimer, would result in a unjustified timewise extension of the right to exclude others from practicing the previously disclosed, now claimed, embodiment of the '834 patent's invention. Appellant also argues that "the Office seems to reason that just because a prior patent claims a genus which dominates a later continuation application, the later application cannot claim a species of that genus without being obvious. This is improper." (Appeal Br. 10.) We do not agree with Appellant's position that the rejection is based simply on the fact that the claims on appeal are a species of the '834 patent's more generic claims. The Examiner stated that [c]laims 120 and 125-136 cannot be considered patentably distinct over claims 1-41 of US Patent 6,852,834 when there is a specifically disclosed embodiment of the fusion protein that supports claims 1-41 of that patent and falls within the scope of claims 120 and 125-136 herein because it would have been obvious to one having ordinary skill in the art to modify the fusion protein of claims 1-41 of US Patent 6,852,834 by selecting a specifically disclosed embodiment that supports that claim. (Ans. 4--5.) The Examiner therefore made clear that she was not relying simply on the genus/species relationship between the '834 patent's claims and the claims on appeal, but rather on the disclosure of a specific embodiment in the '834 patent of its generically claimed invention. Finally, Appellant argues that "Chilkoti teaches a variety of amino acids that can be X. In fact, Chilkoti discloses over fifty potential amino 10 Appeal2013-008619 Application 12/335,235 acid identities for X." (Appeal Br. 11.) "Furthermore, Chilkoti teaches numerous 'preferred' embodiments that, under the Office's rationale, would provide equally compelling selections in understanding the claims of Chilkoti." (Id. at 12.) Accordingly, Chilkoti provides numerous possibilities, including numerous "preferred" possibilities, for the identity of X and accordingly, it is incorrect to assert that a person skilled in the art would select the specific set of amino acids of valine, alanine, and glycine, let alone these amino acids in a ratio of 5:2:3. (Id. at 13.) This argument is also unpersuasive. Whether other choices for the "X" residue of the claims on appeal might also have been obvious if the '834 patent's disclosure was available as prior art is not germane to the basis of the rejection on appeal. Appellant's reasoning does not provide a basis for concluding that a skilled worker would not have considered the specifically disclosed embodiment relied on by the Examiner to be an obvious species of the '834 patent's generic claims. Conclusion of Law The disclosure of a specific embodiment of the '834 patent's earlier- claimed genus makes a later claim to that embodiment unpatentable based on obviousness-type double patenting. Claims 125-136 have not been argued separately and therefore fall with claim 120. 37 C.F.R. Â§ 41.37(c)(l)(iv). SUMMARY We affirm the rejection of claims 120 and 125-136 for obviousness- type double patenting based on claims 1--41 of U.S. Patent 6,852,834. 11 Appeal2013-008619 Application 12/335,235 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. Â§ 1.136(a). AFFIRMED 12