Trials@uspto.gov Paper 11
`Tel: 571-272-7822 Entered: August 1, 2014
`
`
`UNITED STATES PATENT AND TRADEMARK OFFICE
`_______________
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`
`_______________
`
`3D-MATRIX, LTD,
`Petitioner,
`
`v.
`
`MENICON CO., LTD,
`Patent Owner.
`_____________
`Case IPR2014-00398
`Patent 8,299,032 B2
`_______________
`Before JACQUELINE WRIGHT BONILLA, DONNA M. PRAISS, and
`BRIAN P. MURPHY, Administrative Patent Judges.
`
`MURPHY, Administrative Patent Judge.
`
`
`DECISION
`
`Denying Institution of Inter Partes Review
`37 C.F.R. § 42.108
`
`
`
`
`
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`IPR2014-00398
`Patent 8,299,032 B2
` 
`
`I.
`
`INTRODUCTION
`
`On January 31, 2014, 3D-Matrix, Ltd. (“Petitioner”) filed a Petition
`requesting inter partes review of claims 1-8 of U.S. Patent No. 8,299,032 B2
`(“the ’032 patent”). Paper 1 (“Pet.”). On May 9, 2014, Menicon Co., Ltd.
`(“Patent Owner”) filed a Preliminary Response to the Petition. Paper 9
`(“Prelim. Resp.”). We have jurisdiction under 35 U.S.C. § 314(a), which
`provides that an inter partes review may not be instituted “unless . . . there is
`a reasonable likelihood that the petitioner would prevail with respect to at
`least 1 of the claims challenged in the petition.”
`Petitioner challenges claims 1-8 of the ’032 patent as unpatentable
`under 35 U.S.C. §§ 102(b) and 103. Based on the information presented in
`the Petition, Preliminary Response, and cited exhibits, we are not persuaded
`there is a reasonable likelihood that Petitioner would prevail with respect to
`at least one of the claims challenged in the Petition. On this record, we deny
`the Petition to institute an inter partes review of claims 1-8 of the ’032
`patent.
`A. Related Proceedings
`The parties do not identify any related proceedings regarding the ’032
`patent.
`B. The ’032 Patent (Ex. 2001)
`The ’032 patent, titled “SELF-ASSEMBLING PEPTIDE AND GEL
`PRODUCED FROM THE SAME,” issued October 30, 2012, from a PCT
`application filed June 26, 2006. Ex. 2001. The self-assembling peptide
`described in the ’032 patent is comprised of polar and nonpolar amino acid
`residues, has a non-zero peptide charge at neutral pH, and forms a beta (ß)-
`sheet structure in an aqueous solution. Id. at 1:49-60. The beta (ß)-sheet has
`
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`IPR2014-00398
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`one face of only nonpolar amino acid residues. Id. at 1:57-60. Self-
`assembling peptide gels are useful, for example, as scaffolds for three
`dimensional cell cultures. Id. at 2:67-3:3. The ’032 patent recites several
`advantages resulting from the claimed peptide, including balanced
`electrostatic forces to prevent “excessive association,” transparency of
`scaffolds, ease of preparation, and beta (ß)-sheet (membrane) stability. Id. at
`2:33-67.
`The ’032 patent states that the charge of the self-assembling peptide is
`pH-dependent and can be calculated according to the method of Lehninger.
`Id. at 6:1-7. The calculation is typically executed using a computer program.
`Id. Table 8 of the ’032 patent identifies nine exemplary peptides having
`SEQ ID Nos. 1-9, and Table 9 lists the charge for each peptide at pH 7.0,
`calculated according to the method of Lehninger. 1 Id. at 17:17-18:18. The
`calculated charges for SEQ ID Nos. 1-9 are all non-zero, namely +2, +3, or -
`2. Id. at 18:1-18.
`Claim 1 of the ’032 patent, the only independent challenged claim, is
`representative and reproduced below (emphasis added).
`
`1. A self-assembling peptide comprising polar amino acid
`residues and nonpolar amino acid residues,
`wherein the self-assembling peptide consists of 12 to 32
`amino acid residues, comprises one or more acidic amino acid
`residues and one or more basic amino acid residues as the polar
`amino acid residues,
`wherein the sum of charge of the acidic amino acid
`residue(s) and charge of the basic amino acid residue(s), when
`
`                                                            
`1 Lehninger is the author of a text book titled “Principles of Biochemistry,”
`referenced in the ’032 patent as “Lehninger [Biochemie, 1979].” Ex. 2001,
`6:3.
`
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`IPR2014-00398
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`
`the self-assembling peptide is in a neutral pH environment, is
`from -3 to -2 or +2 to +3, wherein all of the amino acids in the
`self-assembling peptide form a beta (ß)-sheet structure in
`which one face consists of only nonpolar amino acid residues
`upon self-assembly in a neutral aqueous solution, and wherein
`the nonpolar amino acid residues are selected from the group
`consisting of alanine, glycine, leucine, isoleucine, methionine,
`valine, phenylalanine, and tryptophan.
`
`C. Prior Art Relied Upon in the Petition
`Petitioner relies upon the following references:
`
`Zhang II
`
`US 5,670,483
`
`Sept. 23, 1997
`
`Agelli
`
`WO 2004/007532 A2
`
`Jan. 22, 2004
`
`Altman
`
`9 PROT. SCI. 1095-1105
`
`Dado
`
`Mira
`
`Yokoi
`
`Zhang I
`
`
`115 J. AM. CHEM. Soc. 12609-
`610
`
`4 BMC STRUC. BIO. 7-21
`
`102 PNAS 8414-19
`
`90 PNAS 3334-38
`
`2000
`
`1993
`
`June 4, 2004
`
`June 14, 2005
`
`April 1993
`
`Ex. 1002
`
`Ex. 1019
`
`Ex. 1009
`
`Ex. 1004
`
`Ex. 1021
`
`Ex. 1016
`
`Ex. 1001
`
`D. Asserted Grounds of Unpatentability
`Petitioner asserts that the challenged claims are unpatentable based on
`the following grounds:
`
`
`
`
`
`
`
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`IPR2014-00398
`Patent 8,299,032 B2
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`
`Reference[s]
`
`Dado
`
`Altman
`
`Zhang II, Yokoi, and
`Agelli
`Mira and Zhang I
`
`Basis
`
`Claims challenged
`
`§ 102(b)
`
`§ 102(b)
`
`§ 103
`
`§§ 102(b)
`and 103
`
`1-8
`
`1-8
`
`1-8
`
`1-8
`
`II. ANALYSIS
`
`A. Claim Construction
`In an inter partes review, we construe claim terms according to their
`broadest reasonable interpretation in light of the patent specification.
`37 C.F.R. § 42.100(b); Office Patent Trial Practice Guide, 77 Fed. Reg.
`48,756, 48,766 (Aug. 14, 2012). Under the broadest reasonable
`interpretation standard, we assign claim terms their ordinary and customary
`meaning, as understood by one of ordinary skill in the art, in the context of
`the entire patent disclosure. In re Translogic Tech., Inc., 504 F.3d 1249,
`1257 (Fed. Cir. 2007). Any special definition for a claim term must be set
`forth in the specification with reasonable clarity, deliberateness, and
`precision. In re Paulsen, 30 F.3d 1475, 1480 (Fed. Cir. 1994).
`Petitioner does not argue that any claim term in the ’032 patent should
`take on a meaning other than its ordinary and customary meaning. Pet. 18-
`23. Patent Owner does not address claim construction. Prelim. Resp. 6-8.
`We proceed on the basis that the claim terms are given their ordinary and
`customary meaning as understood by one of ordinary skill in the art in the
`context of the ’032 patent.
`
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`
`B. Anticipation of Claims 1-8 by Dado
`Petitioner argues that the primary difference between the claimed
`peptide and the prior art generally is the claimed charge of -3 to -2 or +2 to
`+3 of the recited self-assembling peptide at neutral pH, versus a charge of
`zero (0) for prior-art self-assembling peptides at neutral pH. Pet. 20; see
`also id. at 15-17; Ex. 2001, 18:12 (describing prior art RADA16, i.e.,
`Peptide No. 10, as having a net charge of 0 at pH 7). Petitioner states that
`the charge difference of the claimed peptides results from substitution of at
`least two, possibly three, ionic amino acid residues with non-ionic polar
`amino acid residues (e.g., serine or asparagine) or alanine. Id. at 20.
`Petitioner relies on Dado as disclosing such a substituted self-assembling
`peptide and argues that Dado inherently anticipates claims 1-8 of the ’032
`patent. Id. at 23-25.
`“To establish inherency, the extrinsic evidence ‘must make clear that
`the missing descriptive matter is necessarily present in the thing described in
`the reference.’” In re Robertson, 169 F.3d 743, 745 (Fed. Cir.
`1999)(quotation omitted). Inherency is not proven “by probabilities or
`possibilities. The mere fact that a certain thing may result from a given set
`of circumstances is not sufficient.” Id. (quotation omitted). We assess the
`merits of Petitioner’s arguments and evidence in support of the asserted
`inherency, according to the aforementioned standard.
`1. Dado (Ex. 1004)
`
`Dado discloses an 18-residue peptide, Peptide 1º, that contains one
`acidic residue (glutamic acid (E)), three basic residues (lysine (K)), and
`
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`IPR2014-00398
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`nonpolar alanine (A) and leucine (L) residues.2 Ex. 1004, 12609 (left
`column and Fig. 1). Peptide 1º is capable of forming a beta (ß)-sheet
`structure having one face of only nonpolar residues upon self-assembly in an
`aqueous solution. Id. at 12610, Fig. 2. The structure of Peptide 1º is not in
`dispute. Prelim. Resp. 20-24. Petitioner recognizes that Dado does not
`disclose (i) the charge of Peptide 1º in a neutral pH environment, or (ii) the
`pH of the aqueous solution in which Peptide 1º forms a beta (ß)-sheet. Pet.
`23-25; Ex. 1004. Petitioner argues, however, that Dado inherently satisfies
`these two limitations of the ’032 patent claim 1. Patent Owner opposes.
`Prelim. Resp. 20-24.
`2. Anticipation Analysis
`a. Charge of Peptide 1º
`
`Claim 1 of the ’032 patent recites “wherein the sum of charge of the
`acidic . . . and basic amino acid residue(s), when the self-assembling peptide
`is in a neutral pH environment, is from -3 to -2 or +2 to +3.”3 Petitioner
`states the charge of Dado’s Peptide 1º is “+2 in a neutral pH environment, as
`calculated by Lehninger et al.” Pet. 23-24. Petitioner does not provide a
`declaration or other documentary evidence in support of this statement. Id.
`Petitioner relies on attorney argument to satisfy its burden of persuasion
`regarding the peptide charge limitation of claim 1. Patent Owner responds
`that, in the absence of a declaration and explanation of how the peptide
`charge calculation was performed, Petitioner cannot rely on the asserted
`
`                                                            
`2 The sequence is Ac-YLKAMºLEAMºAKLMºAKLMºA-NH2. Mº is a
`polar, non-ionic, methionine sulfoxide residue. Ex. 1004, 12609.
`3 Claims 2-8 depend from independent claim 1.
`
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`charge of +2. Prelim. Resp. 23-24 (citing 37 CFR § 42.65(b)). We agree
`with Patent Owner.
`Section 42.65 governs expert opinion testimony, tests, and data on
`which a party may rely in support of its position. 37 C.F.R. § 42.65.
`Section 42.65(a) requires an expert who gives opinion testimony in an inter
`partes review to “disclose the underlying facts or data on which the opinion
`is based,” otherwise the opinion is entitled to little or no weight. Id.
`§ 42.65(a). Section 42.65(b) provides that a party who relies on a technical
`test or data from such a test “must provide an affidavit” explaining (i) why
`the test or data is being used, (ii) how the test was performed and data
`generated, (iii) how the data is used to determine a value, (iv) how the test is
`regarded in the relevant art, and (v) any other information necessary for the
`Board to evaluate the test and data. Id. § 42.65(b). The language of §42.65
`evokes Federal Rule of Evidence 702, which permits expert testimony if
`“scientific, technical, or other specialized knowledge will assist the trier of
`fact to understand the evidence or to determine a fact in issue.”4
`The overarching subject of an inquiry under Fed. R. Evid. 702 “is
`scientific validity—and thus the evidentiary relevance and reliability—of the
`principles that underlie a proposed submission.” Daubert v. Merrell Dow
`Pharm., Inc., 509 U.S. 579, 594-95 (1993). Although a Daubert inquiry
`
`                                                            
`4 Our Rules provide that “the Federal Rules of evidence shall apply to a
`proceeding.” 37 C.F.R. § 42.62(a). The rationale is that “[t]he Federal
`Rules of Evidence provide a well-developed body of recognized case law
`that is reasonable for the Office to draw upon in administering these trial
`rules,” and our reviewing courts are familiar with those rules. Rules of
`Practice for Trials Before the Patent Trial and Appeal Board, 77 Fed. Reg.
`48,612, 48,645 (August 14, 2012).
`
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`pursuant to Fed. R. Evid. 702 is intended to relax the rigid “general
`acceptance” requirement for admission of scientific evidence under Frye,5
`the focus remains on assessing evidentiary trustworthiness, which is based
`upon scientific validity. Id. at 590 n. 9; see also Dal-Tile Corp. v. United
`States, 424 F.3d 1286, 1291-92 (Fed. Cir. 2005) (“The Court of International
`Trade, in our view, properly examined the four factors enunciated in
`Daubert to determine [test method] reliability . . . .”). The Board’s § 42.65,
`as with Fed. R. Evid. 702, is intended to ensure that a party proponent meets
`a threshold level of reliability when offering technical tests and data as
`evidence.
`The ’032 patent discloses the method of Lehninger as a preferred
`method for calculating peptide charge. Ex. 2001, 6:1-3. The patent
`indicates peptide charge is a pH-dependent calculation, and it cites an
`exemplary web page for access to a software program that, presumably,
`performs the Lehninger method of calculation. Id. at 6:1-7.6 Given that the
`peptide charge computation is pH-dependent (pH is a logarithmic scale) and
`executed via software, we determine that it is the type of technical data
`governed by § 42.65(b).
`Dado does not disclose a charge for Peptide 1º, whether or not in a
`neutral pH environment. Because Petitioner’s statement—the charge of
`Peptide 1º is +2 in a neutral pH environment as calculated by Lehninger et
`al.—is not supported by a declaration, affidavit, or any further explanation,
`we do not know how the peptide charge calculation was performed, the
`
`                                                            
`5 Frye v. United States, 293 F. 1013, 1014 (1923).
`6 The Board’s independent effort to access the cited web page resulted in a
`message that the web page could not be found.
`
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`precise method or formula used to calculate it, how the calculation method is
`regarded in the relevant art, or any other information on which we might rely
`to evaluate the scientific validity of the asserted charge for Peptide 1º. 37
`CFR § 42.65(b); see also Daubert, 509 U.S. at 594-95. Therefore, we give
`no weight to Petitioner’s unsupported statement that the charge of Peptide 1º
`is +2 in a neutral pH environment, as calculated by Lehninger et al.
`In sum, the record in this case does not contain sufficient evidence to
`support Petitioner’s assertion that the charge of Peptide 1º in a neutral pH
`environment is +2.
`b. Inherency of beta (ß)-sheet formation in a neutral
`aqueous solution
`
`
`Claim 1 of the ’032 patent recites “wherein all of the amino acids in
`the self-assembling peptide form a beta (ß)-sheet structure . . . upon self-
`assembly in a neutral aqueous solution.” Ex. 2001, 23:30-34 (emphasis
`added). The ’032 patent defines “neutral” as a pH from 6 to 8. Ex. 2001,
`6:8-9. Petitioner acknowledges that Dado does not disclose the pH of the
`aqueous solution in which beta (ß)-sheet conformation of Peptide 1º is
`observed, but argues that Dado’s Peptide 1º inherently forms a stable beta-
`sheet in a neutral aqueous solution. Pet. 24. Petitioner has chosen not to
`submit a declaration in support of the Petition and, therefore, does not cite
`any explanatory testimony in support of its inherency argument. See id. at
`23-25.
`Dado discloses that Peptide 1º forms a beta (ß)-sheet in “aqueous
`solution,” without disclosing the pH of the solution. Ex. 1004, 12609.
`Petitioner reasons that because Peptide 1º has the same structure as the
`peptide claimed in the ’032 patent, and “given the totality of the evidence
`
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`presented in the body of literature described above [Pet. 3-14], the person of
`skill in the art would conclude that Peptide 1º inherently self-assembles at
`neutral pH under the conditions explicitly taught by Zhang et al.7 for
`structurally similar peptides.” Id. at 24. This is the sum and substance of
`Petitioner’s inherency analysis.
`Petitioner’s argument is conclusory and lacks persuasive detail,
`evidentiary citations, and analysis. Petitioner does not explain or support,
`with specific citations, why Dado’s Peptide 1º necessarily would form a beta
`(ß)-sheet in a neutral aqueous solution, in view of Dado’s protein design
`strategy and any particular teaching from any one of the Zhang references.
`Pet. 23-25. For example, Dado does not disclose specific reaction
`conditions for the methionine sulfoxide side chain reaction that drives beta
`(ß)-sheet conformation of Peptide 1º. Ex. 1004; Prelim. Resp. 23.
`Petitioner, however, does not explain how any one of the Zhang references
`discloses reaction conditions for structurally similar peptides that would lead
`a person skilled in the art to conclude that Peptide 1º necessarily self-
`assembles into a beta (ß)-sheet in a neutral aqueous solution. Pet. 23-25.
`Notably, Petitioner also does not address specific similarities (or
`differences) among the peptides disclosed in the Zhang references, Peptide
`1º, and the ’032 patent peptides, particularly in terms of structure, the
`influence of pH or salt concentration, reaction conditions, charge, amino
`acid sequence, or other properties. Id.; see Prelim. Resp. 23. Petitioner,
`therefore, has not presented its inherency challenge with sufficient
`particularity by specifying “where each element of the claim is found in the
`                                                            
`7 We note that the Petition cites to sixteen different “Zhang” references. Pet.
`3-14.
`
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`prior art patents or printed publications relied upon.” Prelim. Resp. 5
`(quoting 37 CFR § 42.104(b)(4)), 21(citing 35 U.S.C. § 312(a)(3)).
`Petitioner further relies on In re Spada, 911 F.2d 705 (Fed. Cir. 1990)
`in support of its inherency argument. Pet. 24. In Spada, the Federal Circuit
`found that a claimed tackiness property of a pressure sensitive adhesive
`composition was present inherently in the prior art because the prior art
`polymer and the patent application polymer were the same, e.g., they used
`identical monomers with overlapping amounts and employed the same or
`similar polymerization techniques. Spada, 911 F.2d at 707-08. In the
`present case, unlike in Spada, Petitioner does not assert that Dado discloses
`or describes a peptide identical to any of the exemplary peptides disclosed in
`the ’032 patent. Pet. 23-24; see also Prelim. Resp. 22.8 Petitioner also does
`not assert that the reaction conditions under which Peptide 1º self-assembles
`into a beta (ß)-sheet structure (Ex. 1004) are the same as those disclosed in
`the ’032 patent (Ex. 2001, 15:45-17:7). Pet. 23-24. Thus, Spada is
`inapposite here.
`We conclude, therefore, that Petitioner’s attorney argument and
`reliance on Spada, without specific factual and evidentiary support, is
`insufficient for Petitioner to establish the asserted inherency of Peptide 1º
`forming a beta (ß)-sheet structure upon self-assembly in a neutral aqueous
`solution.
`For the reasons given above, the Petition and evidence of record are
`insufficient to persuade us of a reasonable likelihood that Petitioner would
`
`                                                            
`8 Peptide 1º is not one of the nine exemplary peptides disclosed in the ’032
`patent. See Ex. 2001, 17:20-33.
`
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`prevail in showing Dado anticipates claims 1-8 of the ’032 patent under 35
`U.S.C. §102(b).
`
`C. Anticipation of Claims 1-8 by Altman
`Petitioner asserts that claims 1-8 of the ’032 patent are inherently
`anticipated by peptide EAK12-d disclosed in Altman. Pet. 25-29. Petitioner
`asserts that EAK12-d has a -2 charge in a neutral pH environment, and
`further argues that EAK12-d inherently forms a beta (ß)-sheet “in at least
`one neutral pH environment, such as by adding salt, increasing peptide
`concentration or increasing temperature.” Pet. 26-27. Patent Owner
`opposes. Prelim. Resp. 24-28.
`
`1. Altman (Ex. 1009)
`
`Altman discloses a 12-residue peptide, EAK12-d, that contains four
`acidic residues (glutamic acid (E)), two basic residues (lysine (K)), and
`nonpolar alanine (A) residues.9 Ex. 1009, 1096 Table 1. EAK12-d is
`capable of forming a beta (ß)-sheet structure having one face of only non-
`polar residues, and “can undergo a secondary structure transformation from
`ß-sheet to α-helix with either temperature or pH [change].” Id. at 1097; see
`also, id. at 1099-1100. Altman discloses that EAK12-d “forms a ß-sheet at
`pH 1-3 with a transition at pH 4, changing to a more helical structure at pH 5
`and above.” Id. at 1100; see also, id. at 1099, Fig. 4 (“When EAK12-d is
`incubated at pH 5-10, it exhibits an α-helical spectrum with about 30%
`helical content.”). Altman does not disclose a charge for EAK12-d, whether
`or not in a neutral pH environment. Id.
`
`                                                            
`9 The sequence is Ac-AEAEAEAEAKAK-NH2.
`
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`
`2. Anticipation Analysis
`
`Petitioner asserts a charge of -2 for Altman’s EAK12-d peptide in a
`neutral environment, without citation, declaration or affidavit support, or
`further explanation of how the peptide charge was computed. Pet. 26.
`Patent Owner again objects to Petitioner’s non-compliance with § 42.65(b).
`Prelim. Resp. 27. For the same reasons discussed above, we conclude that
`the record in this case does not contain sufficient evidence to support
`Petitioner’s assertion that the charge of EAK12-d in a neutral pH
`environment is -2. See 37 C.F.R. § 42.65(b).
`Petitioner’s additional argument, that EAK12-d inherently forms a
`beta (ß)-sheet in neutral aqueous solution, refers generally to a “large body
`of art” without specific citations or analysis. Pet. 26-27. Petitioner’s
`argument also is not consistent with Altman, because Altman discloses a
`conformational change of EAK12-d from a beta (ß)-sheet at low pH to an α-
`helix structure at pH 5 and above. Ex. 1009, 1099-1100; see also Prelim.
`Resp. 26-27. Without additional evidentiary support and explanation of
`Petitioner’s argument that EAK12-d necessarily forms a beta (ß)-sheet
`structure in a neutral aqueous solution, we conclude Petitioner’s inherency
`argument regarding Altman does not satisfy the standard articulated in In re
`Robertson, 169 F.3d at 745.
`For the reasons given above, the Petition and evidence of record are
`insufficient to persuade us of a reasonable likelihood that Petitioner would
`prevail in showing Altman anticipates claims 1-8 of the ’032 patent under 35
`U.S.C. § 102(b).
`
`
`
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`
`D. Obviousness of Claims 1-8 over Zhang II, Yokoi, and Agelli
`
`Petitioner asserts that Zhang II’s EAK16 peptide (Ex. 1002, 1:30-48),
`when modified by replacing at least two glutamic acid or lysine residues
`with neutral hydrophilic or nonpolar residues, renders claims 1-8 of the ’032
`patent obvious under 35 U.S.C. § 103. Pet. 29-33. Petitioner argues that
`Agelli, reinforced by Yokoi, provides the teaching and reason for one of
`ordinary skill in the art to make the modification, with a reasonable
`expectation of successfully achieving the claim 1 peptide of the ’032 patent.
`Pet. 31-33. Patent Owner opposes. Prelim. Resp. 28-30, 32-36.
`Obviousness under 35 U.S.C. § 103 requires an assessment of (1) the
`“level of ordinary skill in the pertinent art,” (2) the “scope and content of the
`prior art,” (3) the “differences between the prior art and the claims at issue,”
`and (4) “secondary considerations” of nonobviousness such as “commercial
`success, long-felt but unsolved needs, failure of others, etc.” KSR Int’l Co.
`v. Teleflex Inc., 550 U.S. 398, 406 (2007) (quoting Graham v. John Deere
`Co., 383 U.S. 1, 17-18 (1966)). A party who petitions the Board for a
`determination of obviousness must show that “‘a skilled artisan would have
`been motivated to combine the teachings of the prior art references to
`achieve the claimed invention, and that the skilled artisan would have had a
`reasonable expectation of success from doing so.’” Proctor & Gamble Co.
`v. Teva Pharms. USA, Inc., 566 F.3d 989, 994 (Fed. Cir. 2009) (quoting
`Pfizer, Inc. v. Apotex, Inc., 480 F.3d 1348, 1361 (Fed. Cir. 2007)). We
`evaluate Petitioner’s evidence and argument according to the above-
`articulated standard for obviousness.
`
`
`
` 
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`IPR2014-00398
`Patent 8,299,032 B2
` 
`
`1. Zhang II (Ex. 1002)
`
`Zhang II discloses a 16-residue peptide, EAK16, that contains four
`acidic residues (glutamic acid (E)), four basic residues (lysine (K)), and non-
`polar alanine (A) residues.10 Ex. 1002, 3:4-11, Fig. 1. EAK16 forms a beta
`(ß)-sheet structure having alternating polar and nonpolar residues at pH 7.
`Id. at 6:25-42, 13:29-46 (“The ß-sheet structure of EAK16 was also not
`significantly affected by pH.”), Fig. 10 (pH profile confirms ß-sheet
`conformation at pH 7). Zhang II does not disclose a charge for EAK16,
`whether or not in a neutral pH environment. Id. Although the Petition does
`not contain an affidavit or declaration setting forth how Petitioner calculated
`a peptide charge of zero (0) for EAK16 (Pet. 30-31), both parties agree that a
`difference between EAK16 and the peptide of claim 1 is the peptide charge
`in a neutral pH environment. Pet. 31; Prelim. Resp. 28.
`2. Obviousness Analysis
`Petitioner contends that Zhang II teaches ionized pair formation
`between complementary hydrophilic side chains on adjacent peptides and
`the use of glutamine and asparagine (neutral residues) in place of charged
`residues in membrane-forming peptides. Pet. 31. Petitioner concludes,
`based on the teachings of Zhang II, that one of skill in the art would have
`been motivated to “replace, remove or add 2 glutamic acid or 2 lysine
`residues in the sequence of EAK16 and/or replace with neutral hydrophilic
`residues, such as asparagine or glutamine, with a reasonable expectation that
`the resulting peptide would form membranes.” Id. at 31-32. Petitioner
`argues that, because Agelli teaches a peptide having alternating hydrophobic
`
`                                                            
`10 The sequence is AEAEAKAKAEAEAKAK.
`
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`IPR2014-00398
`Patent 8,299,032 B2
` 
`and hydrophilic residues with two terminal hydrophilic residues and a
`charge of -2,11 “one of skill in the art would not be deterred from replacing,
`removing, or adding one or more ionic charges” to EAK16 and would expect
`beta (ß)-sheet formation to occur. Pet. 32 (emphasis added). Petitioner’s
`argument, however, does not satisfy the KSR/Graham standard for a
`showing of obviousness under 35 U.S.C. § 103.
`We agree with Patent Owner that, although Zhang II discloses EAK16
`as forming a beta-sheet in a neutral aqueous solution (Ex. 1002, 13:8-46),
`Petitioner does not address why one of skill in the art would have had reason
`to modify the peptide as suggested and still expect to form a beta (ß)-sheet.
`Prelim. Resp. 29. Petitioner does not explain and support, with precise
`citations and/or declaration evidence, why one of skill in the art would have
`had reason to replace two ionic charged residues in EAK16, glutamic acid or
`lysine, with two neutral hydrophilic residues such as asparagine or
`glutamine. Pet. 31-32; Prelim. Resp. 34-35. The Petition also does not
`assert, or support with an adequate explanation or declaration evidence, that
`the modified EAK16 peptide would have a charge of -3 to -2 or +2 to +3 in a
`neutral pH environment, as required by claim 1 of the ’032 patent. Pet. 31-
`33; Prelim. Resp. 30. Therefore, in the absence of supporting testimony, or
`a more in-depth analysis of the teachings of Zhang II, Agelli, and Yokoi
`supported with precise citations, we are not persuaded that Petitioner has
`made a sufficient showing of obviousness for claims 1-8 of the ’032 patent.
`For the reasons given above, the Petition and evidence of record are
`insufficient to persuade us of a reasonable likelihood that Petitioner would
`                                                            
`11 Petitioner does not support its peptide charge calculation for Agelli with
`an affidavit or declaration.
`
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`IPR2014-00398
`Patent 8,299,032 B2
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`prevail in showing Zhang II, Agelli, and Yokoi render claims 1-8 of the ’032
`patent obvious under 35 U.S.C. § 103.
`E. Anticipation of Claims 1-8 by Mira or Obviousness of Claims 1-8
`over Mira and Zhang I
`
`Petitioner argues that Mira’s Peptide-1 (Ex. 1021, 3 (Fig. 1B), 5)
`either anticipates claims 1-8 of the ’032 patent, or, when modified by
`replacing three threonine residues with three nonpolar (hydrophobic)
`residues, renders the claims obvious under 35 U.S.C. § 103. Pet. 33-36.
`Petitioner argues, in particular, that the Board should adopt “the definition of
`Zhang I,” which “clearly teaches that threonine, for purposes of self-
`assembling peptides, is hydrophobic and can be used in lieu of alanine,
`leucine, phenylalanine or the like.” Id. at 35 (emphasis added). The issue
`raised by this argument is whether threonine should be considered
`“nonpolar” for purposes of satisfying the claim limitation, “wherein all of
`the amino acids in the self-assembling peptide form a beta (ß)-sheet structure
`in which one face consists of only nonpolar amino acid residues.” Ex. 2001,
`23:30-33 (emphasis added). Patent Owner opposes. Prelim. Resp. 30-31,
`36-38.
`
`1. Mira (Ex. 1021)
`
`Mira discloses a 20-residue peptide, Peptide-1, that contains six acidic
`residues (4 glutamic acid (E) and 2 aspartic acid (D)) and four basic residues
`(lysine (K)).12 Ex. 1021, 3 (Fig. 1B). The nonpolar residues are alanine (A)
`and valine (V). Id. The hydrophobic face of Peptide-1 contains three
`threonine residues (T). Id. at 3, Fig. 1D. Threonine is defined as a polar
`
`                                                            
`12 The sequence is Ac-YKTEAETKTEAKVDAKADVE-NH2.
`
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`IPR2014-00398