`571.272.7822
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` Paper No. 46
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` Filed: Jan. 9, 2019
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`UNITED STATES PATENT AND TRADEMARK OFFICE
`____________
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`____________
`
`NUEVOLUTION A/S,
`Petitioner,
`
`v.
`
`CHEMGENE HOLDINGS APS,
`Patent Owner.
`____________
`
`Case IPR2017-01599
`Patent 8,168,381 B2
`____________
`
`
`Before SUSAN L. C. MITCHELL, ROBERT A. POLLOCK, and
`TIMOTHY G. MAJORS, Administrative Patent Judges.
`
`MAJORS, Administrative Patent Judge.
`
`
`
`
`
`
`
`
`FINAL WRITTEN DECISION
`Claims 1, 3, 5, 6, 10–15, 17, 23–26, 31, 34, 37, 44, and 45
`Shown to Be Unpatentable
`35 U.S.C. §§ 314, 318(a) and 37 C.F.R. §§ 42.4(a), 42.73
`
`ORDERS
`Denying-In-Part Petitioner’s Motion to Exclude (Paper 36)
`37 C.F.R. § 42.64(c)
`
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`IPR2017-01599
`Patent 8,168,381 B2
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` INTRODUCTION
`A. Overview
`Nuevolution A/S (“Petitioner”) filed a Corrected Petition to institute
`inter partes review of claims 1, 3, 5, 6, 10–15, 17, 23–26, 31, 34, 37, 44, and
`45 of U.S. Patent No. 8,168,381 B2 (Ex. 1001, “the ’381 patent”). Paper 8
`(“Petition” or “Pet.”). Chemgene Holdings APS (“Patent Owner”) filed a
`Preliminary Response to the Petition. Paper 10 (“Prelim. Resp.”). On
`January 11, 2018, we instituted trial to review the patentability of claims 1,
`3, 5, 6, 10–15, 17, 23–26, 31, 34, 37, 44, and 45 on four of the seven
`grounds advanced in the Petition. Paper 16 (“Inst. Dec.”).
`In light of SAS Institute, Inc. v. Iancu, 138 S. Ct. 1348 (2018), we later
`instituted trial on the remaining three grounds presented in the Petition (“the
`additional grounds”) and ordered the parties to confer to discuss whether
`changes to the schedule and/or additional briefing (beyond what was already
`filed or authorized) were necessary to address the additional grounds. Paper
`25. On May 10, 2018, the parties responded via email, informing the Board
`that no changes to the schedule were necessary, that Patent Owner requested
`its Preliminary Response (Paper 10) be considered as part of the trial
`proceedings because Patent Owner intended to rely on its arguments in that
`paper related to the additional grounds, and that Petitioner requested an
`enlargement of the word limit for its Reply Brief to Patent Owner Response
`to address the additional grounds. Paper 26, 2–3. We granted each of those
`unopposed requests. Id. We also granted the parties’ request that the Board
`consider and make part of the trial proceedings the supplemental pre-
`institution claim construction briefing that was authorized. Paper 14
`(Petitioner’s Reply to Patent Owner’s Preliminary Response) and Paper 15
`(Patent Owner’s Sur-Reply); Paper 26, 2–3.
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`Patent 8,168,381 B2
`During the trial, Patent Owner filed a Response. Paper 22 (“Resp.”).
`Petitioner filed a Reply to Patent Owner’s Response. Paper 29 (“Reply”).
`Patent Owner asked for authorization to file a motion to strike the Reply for
`alleged non-compliance with 37 C.F.R. § 42.23(b). We did not grant
`authorization, but permitted the parties to submit supplemental briefing on
`the issue. Papers 30–32. And, per Patent Owner’s request, we authorized
`argument on that issue at the oral hearing, and we indicated the Board would
`consider such briefing and oral argument in assessing whether the Reply
`exceeded the scope permitted under Rule 42.23(b). Id. Patent Owner filed a
`Contingent Motion to Amend (Paper 21), to which Petitioner filed an
`Opposition (Paper 27).1 Petitioner also filed a Motion to Exclude Evidence.
`Paper 36. Patent Owner opposed that motion, and Petitioner replied. Paper
`39; Paper 40.
`Both parties requested oral argument (Paper 37; Paper 38), which we
`scheduled for September 18, 2018 (Paper 41). On September 12, Patent
`Owner submitted an unopposed request to withdraw its Motion to Amend
`and to withdraw its request for oral argument (Paper 42 (Sept. 12, 2018
`Notice of Stipulation and Proposed Order)), which we granted (Paper 43).
`On September 14, 2018, Patent Owner responded via email to the Board’s
`Order (confirming that the September 18 Oral Argument would proceed
`(Paper 44)), and stated Patent Owner was ceding its allotted time and had
`elected not to appear at the Oral Argument. Ex. 3001; Paper 45 (“Tr.”),
`3:13–18. On September 18, 2018, we held Oral Argument (which Patent
`
`
`1 Several days before the scheduled Oral Argument, Patent Owner made an
`unopposed request to withdraw its Motion to Amend. Paper 42 (Sept. 12,
`2018 Notice of Stipulation and Proposed Order). We granted Patent
`Owner’s request. Paper 43.
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`Patent 8,168,381 B2
`Owner did not attend) and the transcript has been entered into the record.
`See Tr.
`The ’381 patent includes two independent claims (and several
`dependent claims) that recite methods of synthesizing encoded molecules,
`which are described in detail below. Petitioner’s challenges addressed in
`this Final Written Decision turn in large part on whether the asserted prior
`art discloses the synthesis of encoded molecules — via the addition of a
`molecule fragment, a linker, and an oligonucleotide identifier — in the same
`reaction well. Patent Owner agrees this is what independent claims 1 and 5
`require, but the prior art discloses only that such molecules are synthesized
`in multiple different reaction wells. See, e.g., Prelim. Resp. 3, 8–10, 16–17,
`21–26, 45–46; Paper 15, 1, 7; Resp. 11–27, 55–58. Petitioner, on the other
`hand, argues that a “well” is not limited to any specific physical container or
`vessel such that the claims embrace synthesis of particular encoded
`molecules in one container, or in many, if the desired reactions occur and the
`desired molecules are made. See, e.g., Paper 14, 3–4; Reply 1–5. Petitioner
`alternatively argues that even if the claims require synthesis of particular
`encoded molecules in the same reaction well and this means a single
`container (e.g., a well on a microtiter plate), this is disclosed in the asserted
`prior art. See, e.g., Pet. 11–13, 36–37; Reply 1, 7–26. We further address
`the arguments and evidence on these points below.
`We have jurisdiction under 35 U.S.C. § 6, and we issue this Final
`Written Decision pursuant to 35 U.S.C. § 318(a) and 37 C.F.R. § 42.73. As
`explained below, we conclude that Petitioner has established by a
`preponderance of the evidence in this trial record that claims 1, 3, 5, 6, 10–
`15, 17, 23–26, 31, 34, 37, 44, and 45 of the ’381 patent are unpatentable.
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`Related Proceedings
`B.
`Petitioner identifies no prior or pending litigation related to
`infringement or invalidity of the claims of the ’381 patent. Pet. 2.
`Petitioner, however, identifies proceedings in the United States District
`Court for the Eastern District of Virginia (Nuevolution A/S v. Pedersen, No.
`1:14-CV-00357 (E.D. Va.)) and the Maritime and Commercial High Court
`in Denmark (Nuevolution A/S v. Pedersen, T-16-12) related to correction of
`inventorship of the ’381 patent and/or Petitioner’s entitlement to rights in the
`’381 patent (or its PCT priority application). Id. at 2–3. According to
`Petitioner, the U.S. district court dismissed the proceedings in Virginia on
`the basis of forum non conveniens. Id. at 3.
`Patent Owner provides more information about those proceedings.
`Patent Owner notes that the United States Court of Appeals for the Federal
`Circuit (Nuevolution A/S v. Chemgene Holdings APS, 693 F. App’x 907
`(Fed. Cir. July 19, 2017)) affirmed the district court’s dismissal. Prelim.
`Resp. 11 Ex. 2001 (affirming under Fed. Cir. R. 36). Regarding the
`proceedings in Denmark, Patent Owner asserts that, in February 2016, the
`“Maritime and Commercial Court ruled that a 2007 Settlement Agreement
`between Nuevolution and Chemgene completely and perpetually bars
`Nuevolution from challenging Chemgene’s ownership of the PCT
`application and all related rights, including the ’381 patent.” Prelim. Resp.
`11. Nuevolution, however, appealed this ruling to the Danish Court of
`Appeal, which remanded the case to the Maritime and Commercial Court on
`December 8, 2017. Id.; Resp. 58.
`Petitioner filed another petition for inter partes review of claims in
`U.S. Patent No. 8,168,381 B2 (IPR2017-01598), as well as a petition for
`inter partes review of the sole claim in U.S. Patent No. 8,951,728 B2 (“the
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`’728 patent” (Ex. 1002)) (IPR2017-01603). Pet. 3–4. The ’728 patent
`issued from a grandchild application to the ’381 patent. Id. at 4; Exs. 1001,
`1002.
`
`The ’381 Patent
`C.
`The ’381 patent relates generally to methods for synthesizing encoded
`molecules. Ex. 1001, 1:19–20. The Specification explains that “[m]ethods
`are desired for increasing the efficiency of production and screening of
`chemical libraries with the purpose of generation and isolation of new
`compounds that can be used for applications in medicine, agriculture and
`other areas.” Id. at 1:27–30.
`According to the ’381 patent, known methods for production and
`screening of chemical libraries include the use of DNA-encoding of
`compounds. Id. at 1:51–2:3. In one approach using “DNA-encoded
`libraries, each compound in the library is attached to a unique identifier that
`‘encodes’ the chemical structure of the molecule to which it is attached.” Id.
`at 1:55–58. DNA-encoding in this way, the Specification explains, provides
`for efficient screening and selection of compounds with desired
`characteristics (e.g., binding to a target) because “the isolated compound-
`DNA complexes can be identified at the end by PCR-amplification, cloning,
`and sequencing of the DNA portion.” Id. at 1:51–55; see also id. at 1:27–50.
`In other words, “the structure of a molecule that is selected in [a] screening
`assay can easily be decoded by [an] attached unique identifier.” Id. at 1:58–
`60.
`
`As further background, the Specification discloses that DNA-encoded
`libraries have also been made with a template-based approach. Id. at 1:60–
`63. “In this approach, DNA templates direct the synthesis of the encoded
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`compounds.” Id. at 1:62–66. Recovered DNA-compound complexes can be
`amplified and used in subsequent rounds of synthesis. Id. at 1:66–2:3.
`According to the Specification, “[t]he present invention combines the
`non-templated technique . . . with the template technique . . . and thereby
`provides an improved method for the generation of oligonucleotide-encoded
`libraries.” Id. at 2:6–9; see also id. Abstract (“The present invention
`provides a method for combining the advantages of encoded molecule
`fragments made by split and mix synthesis with the advantages of template
`directed synthesis of molecules.”).
`The Specification defines several terms helpful to understanding the
`invention. Id. at 2:66–7:40. These definitions include, inter alia:
`Bi-functional molecule means a bi-functional molecule
`consisting of an encoded molecule (e.g. a low molecular weight
`organic molecule) and an oligonucleotide (e.g. a single- or
`double-stranded DNA molecule), where the oligonucleotide
`sequence uniquely identifies the identity (structure) of the
`encoded molecule. The encoded molecule and the identifier are
`physically connected through a linker moiety.
`
`Id. at 2:66–3:6. The term “[c]arrier molecule” (used interchangeably with
`carrier and bi-functional carrier molecule) “is a bi-functional molecule that
`is employed in a Stage 2 templated synthesis, and may be generated by e.g.
`stage 1 [split and mix] synthesis.” Id. at 3:14–17. The Specification also
`defines an “[e]ncoded molecule” as “[t]he portion of the bi-functional
`molecule that is encoded by the oligonucleotide identifier of the bi-
`functional molecule.” Id. at 3:28–30. And the term “[i]dentifier” is defined
`as “[a]n oligonucleotide that encodes (specifies) the identity of the molecule
`fragment or encoded molecule to which it is attached.” Id. at 3:37–39.
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`The Specification’s drawings are also helpful in understanding the
`invention. Figure 1, reproduced in part below, depicts an initial formation of
`bi-functional molecules as part of a “Stage 1” synthesis. Id. at 9:32–38.
`
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`Id. at Fig. 1 (partial). Figure 1 shows a linker molecule “L” is first added to
`wells (1 through m) in a microtiter plate. Id. at 9:44–47. This step is
`followed by addition of different amino acids (R1, 1 through m) — “one type
`of amino acid per well (i.e., a specific amino acid to each well) . . .
`operatively linked to the linker molecule.” Id. at 9:45–49. An
`oligonucleotide identifier (O1, 1 through m) is then added to each well and
`operably linked to the linker molecule, such that “[e]ach well now contains a
`bi-functional molecule that consists of a linker molecule linked to an amino
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`acid and an identifier oligonucleotide.” Id. at 9:51–55. In this way, “[t]he
`sequence of the oligo encodes the type of amino acid added to that well.” Id.
`at 9:57–58.
`After this initial process, the wells’ contents may be pooled and split
`into wells on a new plate, and a new round of synthesis applied. Id. at 9:62–
`67. For instance, by adding additional amino acids and oligonucleotide
`identifiers to the new wells, each well will contain a bi-functional molecule
`consisting of a di-peptide (two amino acids bound to each other) linked to a
`nucleotide sequence (two oligonucleotide identifiers bound to each other)
`encoding the di-peptide. Id. at 9:63–10:17, Fig. 1.
`The Specification also describes and illustrates a “Stage 2” templated
`synthesis. See, e.g., id. at 10:51–11:12, Fig. 2. This stage “essentially links
`together the bi-functional carrier molecules provided by stage 1 in different
`combinations.” Id. at 10:54–56. For example, as shown in Figure 2, the
`method uses a DNA template that is complementary to a pair of bi–
`functional molecules.
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`Id. at Fig. 2 (partial). Figure 2 shows that by hybridizing the bi-functional
`molecules’ DNA/oligo portions to a complementary template, the encoded
`molecules (e.g., di-peptide of each carrier) are brought close and allowed to
`react — transferring the encoded molecule of one bi-functional molecule to
`the other. Id. at 11:17–26. The reaction shown forms a tetrapeptide that is
`“linked . . . to a template that encodes the combination of the di-peptides and
`thus, ultimately encodes the tetrapeptide.” Id. at 11:27–40.
`
`Illustrative Claim
`D.
`Petitioner challenges claims 1, 3, 5, 6, 10–15, 17, 23–26, 31, 34, 37,
`44, and 45 of the ’381 patent. Claims 1 and 5 are the challenged
`independent claims. See Paper 9 (Appendix A to Petition, listing claims) 2–
`3, 5–6.2 Claim 1 is illustrative and reads as follows:
`1. A method for synthesizing an encoded molecule comprising
`the steps of:
`a) Adding a linker molecule L to one or more reaction
`wells;
`b) Adding a molecule fragment to each of said reaction
`wells;
`c) Adding an oligonucleotide identifier to each of said
`reaction wells;
`
`
`2 Petitioner’s Appendix A (Paper 9) does not include page numbers, but we
`treat Appendix A as though the pages were consecutively numbered 1–15.
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`d) Subjecting said wells to conditions sufficient to allow
`said molecule fragments and said oligonucleotide identifiers to
`become attached to said linker molecule, or conditions sufficient
`for said molecule fragments to bind to other molecule fragments
`and sufficient for said oligonucleotide identifiers to bind to other
`oligonucleotide identifiers, so as to form bi-functional molecules
`consisting of an encoded molecule and an oligonucleotide;
`e) Combining the contents of said one or more reaction
`wells, to produce an admixture of said bi-functional molecules;
`f) Optionally, distributing the combined product to one or
`more new reaction wells;
`g) Optionally, repeating steps b) to f) one or more times;
`
`and
`
`h) Contacting the resulting bifunctional molecule(s) of
`step e) or g) with one or more templates each capable of
`hybridizing to at least one of the oligonucleotide identifiers
`added in step c);
`wherein
`the linker molecule L contains at least one reactive group
`capable of reacting with a reactive group in the molecule
`fragment and at least one reactive group capable of reacting with
`a reactive group in the oligonucleotide;
`the molecule fragments each contain at least one reactive
`group capable of reacting with a reactive group in the linker
`molecule L or a reactive group in another molecule fragment, and
`the reactive groups of each molecule fragment may be the same
`or different;
`the oligonucleotide identifiers each contain at least one
`reactive group capable of reacting with a reactive group in the
`linker L or a reactive group in another oligonucleotide identifier,
`and the reactive groups of each oligonucleotide identifier may be
`the same or different;
`the region of the oligonucleotide identifier added to each
`well in step c) which hybridizes to said template identifies the
`molecule fragment added to the same well in step b);
`the steps a) to d) may be performed in any order;
`the steps b) to d) in step g) may also be performed in any
`order;
`the number of wells in steps a) and f) may be the same or
`different; and
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`the oligonucleotide template optionally is associated with
`a reactive group.
`
`Ex. 1001, 135:34–136:53.
`The Asserted Grounds of Unpatentability
`E.
`Petitioner contends that the challenged claims listed below are
`unpatentable under 35 U.S.C. §§ 102 and/or 103 based on the following
`grounds. Pet. 6–7.
`Ground Claims
`
`Reference(s)
`
`Basis
`
`1, 3, 5, 6, 10–15, 17, 24–26, 31,
`34, 37, 44
`1, 3, 5, 6, 10–15, 17, 24–26, 31,
`34, 37, 44
`1, 3, 5, 6, 10–15, 17, 24–26, 31,
`34, 37, 44
`1, 3, 5, 6, 10–15, 17, 24–26, 31,
`34, 37, 44
`1, 5, 23, 24, 26, 31, 45
`
`1, 5, 23, 24, 26, 31, 45
`
`Freskgård3
`
`Freskgård
`
`Freskgård and
`Pedersen4
`Freskgård and
`Franch ’9295
`Franch ’4276
`
`Franch ’427
`
`1, 3, 5, 6, 10–15, 17, 23–26, 31,
`34, 37, 44, 45
`
`Freskgård and
`Franch ’427
`
`§ 102
`
`§ 103
`
`§ 103
`
`§ 103
`
`§ 102
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`§ 103
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`§ 103
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`1
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`2
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`3
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`4
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`5
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`6
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`7
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`3 Freskgård et al., WO 2004/039825 A2, publ. May 13, 2004 (Ex. 1003).
`4 Pedersen et al., WO 02/103008 A2, publ. Dec. 27, 2002 (Ex. 1004).
`5 Franch et al., WO 2004/024929 A2, publ. Mar. 25, 2004 (Ex. 1005).
`6 Franch et al., WO 2004/083427 A2, publ. Sept. 30, 2004 (Ex. 1016);
`Petitioner contends that U.S. Application 60/434,439 (“the ’439
`Application” (Ex. 1017) is incorporated by reference in its entirety into
`Franch ’427. Pet. 100; Prelim. Resp. 50–52; see Inst. Dec. 41–43 (analyzing
`the parties’ arguments and concluding the ’439 Application is incorporated
`in its entirety into Franch ’427).
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`Petitioner also relies on, among other evidence, the Declarations of
`Nicolas Winssinger, Ph.D. Exs. 1015, 1030.
`In the initial decision on institution, the Board instituted trial only on
`those grounds asserting obviousness of the challenged claims over Freskgård
`(alone or combined with other references) — Grounds 2, 3, 4, and 7 from the
`table above. Inst. Dec. 47. Nevertheless, after the Supreme Court’s decision
`in SAS, we modified the institution decision to include the remaining
`grounds (grounds 1, 5, and 6) in the trial proceedings. Paper 25.
` ANALYSIS
`Person of Ordinary Skill in the Art
`A.
`Petitioner asserts that a person of ordinary skill in the art would have
`been one “with a Ph.D. in organic chemistry, molecular biology or a closely
`related field [, and] with a minimum of 3-5 years of additional experience in
`drug discovery.” Pet. 20; Ex. 1015 ¶¶ 30–32. Patent Owner asserts that the
`ordinarily skilled person “would have held a doctoral degree in chemistry,
`molecular biology, or a closely related discipline, and had at least three years
`of practical academic or industrial laboratory experience.” Prelim. Resp. 12.
`Although not identical, Petitioner and Patent Owner propose similar
`qualifications of the skilled artisan. We do not discern a material difference
`between the parties’ proposals and find that the parties’ proposals are
`consistent with the prior art of record. See Okajima v. Bourdeau, 261 F.3d
`1350, 1355 (Fed. Cir. 2001) (explaining that specific findings regarding
`ordinary skill level are not required “where the prior art itself reflects an
`appropriate level and a need for testimony is not shown”) (quoting Litton
`Indus. Prods., Inc. v. Solid State Sys. Corp., 755 F.2d 158, 163 (Fed. Cir.
`1985)). We apply Patent Owner’s proposal, but our conclusions in this Final
`Written Decision would be the same under either proposal.
`
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`Claim Construction
`B.
`In this inter partes review, we interpret claim terms in an unexpired
`patent based on the broadest reasonable construction in light of the
`specification of the patent in which they appear. 37 C.F.R. § 42.100(b);
`Cuozzo Speed Techs., LLC v. Lee, 136 S. Ct. 2131, 2142 (2016) (affirming
`the broadest reasonable construction standard in inter partes review
`proceedings). “Under a broadest reasonable interpretation, words of the
`claim must be given their plain meaning, unless such meaning is inconsistent
`with the specification and prosecution history.” Trivascular, Inc. v.
`Samuels, 812 F.3d 1056, 1062 (Fed. Cir. 2016). Special definitions must be
`set forth with reasonable clarity, deliberateness, and precision. In re
`Paulsen, 30 F.3d 1475, 1480 (Fed. Cir. 1994). We need only construe terms
`in controversy, and only to the extent necessary to resolve that controversy.
`Vivid Techs., Inc. v. Am. Sci. & Eng’g, Inc., 200 F.3d 795, 803 (Fed. Cir.
`1999).
`Upon review of the parties’ arguments, including the supplemental
`pre-institution claim construction briefing that we authorized (Paper 14;
`Paper 15), we interpreted two claim terms/phrases identified by the parties in
`our Decision on Institution. Inst. Dec. 21–29. Those terms/phrases are:
`(i) “template” and (ii) “one or more reaction wells . . . each of said reaction
`wells.” Id. The parties do not propose, nor do we discern, that other terms
`require further construction to resolve the patentability of the challenged
`claims in this Final Written Decision.
`Petitioner proposed an unrebutted interpretation of “template” that we
`adopted in our Decision on Institution. Id. at 28–29. As we explain further
`below, the parties disputed the interpretation of the phrase “one or more
`reaction wells . . . each of said reaction wells.” Id. at 24–28. We interpreted
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`the term “well” as “a physical containment of reagents, molecule fragments,
`etc. in a localized space,” consistent with the ’381 patent’s definition of
`“well.” Id. at 24–25. Based on, inter alia, the “each of said reaction wells”
`language in claims 1 and 5, we also agreed with Patent Owner and
`interpreted the entire phrase as requiring that synthesis of any particular bi-
`functional molecule according to steps (a) to (d) of claim 1 (and steps (a)
`and (b) of claim 5)7 be conducted within the same reaction well — the same
`physical containment in a localized space. Id. at 25–28.
`In Patent Owner’s view, this interpretation of “one or more reaction
`wells . . . each of said reaction wells” resolves the challenges raised in the
`Petition in Patent Owner’s favor. See, e.g., Prelim. Resp. 3, 8–10, 16–17,
`21–26, 45–46; Paper 15, 1, 7; Resp. 11–27, 55–58. That is because, Patent
`Owner argues, the asserted prior art discloses carrying out the synthesis
`steps (a) to (c) of claim 1, or steps (a) and (b) in claim 5, in different physical
`containers (e.g., reagent tubes, wells on a microtiter plate, etc.) for each bi-
`functional molecule. See, e.g., Prelim. Resp. 3 (“All of Nuevolution’s
`references synthesize compounds using different reaction vessels”). As we
`explained in the institution decision, however, we were not persuaded that
`was true for all the prior art references being relied upon by Petitioner and,
`in particular, we pointed to the cited teachings in Freskgård as also
`disclosing synthesis of particular bi-functional molecules in the same
`reaction well. Inst. Dec. 30–33, 35–36.
`Petitioner embraces the Board’s preliminary finding that at least
`Freskgård teaches synthesis of bi-functional molecules in the same physical
`
`
`7 The related language of claim 5 recites “each of m reaction wells . . . each
`of said m reaction wells.” Ex. 1001, 137:43–45.
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`container (i.e., a well on a microtiter plate) and, thus, in the same reaction
`well. See, e.g., Reply 1, 7–21, 26. But Petitioner also urges that a “well” is
`not limited to any specific number of reaction containers and with a “proper
`application” of the meaning of “wells,” the Board should also reconsider the
`additional grounds added post-SAS. Id. at 2–5, 34.
`We have considered the evidence and the parties’ respective
`arguments, but we find no reason sufficient to revise our construction of the
`claim terms in this Final Written Decision. Our claim construction analysis
`from the Institution Decision, which we apply here, is reproduced in
`substance below in Sections II.B.1–3. Following that analysis, we address
`Petitioner’s argument in the Reply bearing on claim construction. See infra
`Section II.B.4.
`
`1. The Parties’ Pre-Institution Claim Construction Positions
`Other than pointing to the definition of “well” in the ’381 patent, the
`Petition did not further address the meaning of “well,” and Patent Owner
`asserted in its Preliminary Response that “no claim term requires express
`construction.” Pet. 20–21; Prelim. Resp. 12. After the filing of the
`Preliminary Response, however, Petitioner requested briefing on the phrase
`“each of said reaction wells.” Paper 13, 2–3. In particular, Petitioner
`disputed Patent Owner’s assertions that the claims, by reason of the “said
`reaction wells” language, requires synthesis of at least one bi-functional
`molecule in the same reaction vessel. Id. at 2. We authorized additional
`briefing from both parties on this issue. Paper 13; Paper 14; Paper 15.
`In its additional briefing, Petitioner asserted that the ’381 patent’s
`definition of “well” disposes of Patent Owner’s arguments. Paper 14, 1–3
`(citing Ex. 1002, 4:51–5:4). According to Petitioner, although claims 1 and
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`5 “may embrace bifunctional molecule synthesis in a single container,” the
`claims are “not so limited.” Id. at 3. Rather, Petitioner argued that
`“‘reaction wells’ (as defined and claimed) can be any localized space that
`allows reaction components (e.g., the claimed linker molecules, molecule
`fragments, and oligonucleotide identifiers) to react as desired.” Id. Thus,
`Petitioner argued, the claims also read on making bi-functional molecules in
`“more than one container,” which “can constitute a ‘localized space’ (and
`thus a ‘well’)” as long as the components for making one type of
`bi-functional molecule are kept separate from the components used to make
`other bi-functional molecules. Id.
`Petitioner cited embodiments in the ’381 patent where, Petitioner
`asserted, more than one container is used to synthesize bi-functional
`molecules. See, e.g., id. at 4 (citing Example 12 as showing the addition of a
`linker molecule and oligonucleotide identifiers in several PCR tubes for
`ligation, followed by transfer of the reaction products to Eppendorf tubes for
`addition of molecule fragments). Petitioner argued claims 1 and 5 must be
`interpreted to cover those embodiments, and that Patent Owner’s assertions
`are flawed insofar as they seek to limit the claims to other embodiments in
`the ’381 patent. Id. at 4–5. And, Petitioner argued, the claims require
`neither “compatible conditions,” nor prohibit intermediate “purification” or
`“isolation” steps. Id. at 6–7.
`Patent Owner, in its additional briefing, argued that Petitioner’s
`interpretation and lexicography argument overlooks the “each of said”
`language of claims 1 and 5. Paper 15, 1–3. According to Patent Owner,
`when read in its proper context, “the construction of ‘each of said reaction
`wells’ unambiguously means that the synthesis of any particular bifunctional
`molecule according to steps (a) to (c) [of claim 1] is conducted within the
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`same reaction well.” Id. at 2 (emphasis omitted). Patent Owner argued that,
`the express definition of “well” aside, the interpretation cannot “remov[e]
`the ‘each of said’ limitations” that precede the term “well” in the claims. Id.
`at 3–4 (“[N]othing in this definition leads to a construction of ‘each of said
`reaction wells’ where reactants for each bifunctional molecule are conveyed
`to different wells for each of steps (a) to (c) . . . .”). Further, Patent Owner
`asserted, “[s]ome disclosed embodiments fall within the ‘each of said
`reaction wells’ limitations, while others do not.” Id. at 5–6.
`
`2. “one or more reaction wells . . . each of said reaction wells”
`According to the Specification, the term “well” “defines a physical
`containment of reagents, molecule fragments, etc. in a localized space.”
`Ex. 1001, 4:51–53; see also Pet. 21. The Specification explains that a “well”
`may comprise, inter alia, the well of a microtiter plate, any container, a
`reagent tube, or a bead to which the reagents and molecules to be kept
`separated are attached. Ex. 1001, 4:53–57. This separation, while not
`necessarily absolute, “should preferably ensure that the major components of
`a given well are the desired components.” Id. at 4:58–61. As a further
`example, the Specification explains that a “nanocompartment” where
`hybridization of oligonucleotide strands holds reactive groups of
`bi-functional molecules in proximity to each other may also be considered a
`“well.” Id. at 4:61–5:4.
`“[I]f the patentee acted as his own lexicographer and clearly set forth
`a definition of the disputed claim term in either the specification or
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`prosecution history,”8 we will accord the claim term that specified
`definition. See CCS Fitness, Inc. v. Brunswick Corp. 288 F.3d 1359, 1366
`(Fed. Cir. 2002); see also Paulsen, 30 F.3d at 1480 (“Although an inventor
`is indeed free to define the specific terms used to describe his or her
`invention, this must be done with reasonable clarity, deliberateness, and
`precision.”). We interpret the term “well” in the manner defined by the ’381
`patent. It means “a physical containment of reagents, molecule fragments,
`etc. in a localized space.” Ex. 1001, 4:51–53. And, as the Specification
`explains, it may be a well on a microtiter plate, a reagent tube, or the like, or
`even a nanocompartment where the desired components are physically
`contained in a localized space for a reaction to take place. Id. at 4:53–5:4.
`But the definition of “well” alone does not resolve the claim
`construction dispute here. Steps (b) and (c) of claim 1 use the phrase “each
`of said reaction wells,” and step (b) of claim 5 uses the phrase “each of said
`m reaction wells,” thus referring back to the “one or more reaction wells” in
`step (a) of claim 1 and the “each of m reaction wells” in step (a) of claim 5.
`Id. at 135:38–41 (claim 1), 137:41–48 (claim 5) (emphases added).
`We give effect to all claim terminology, including the “each of said”
`language preceding “reaction wells” in steps (b) and (c) of claim 1 and
`step (b) of claim 5. Merck & Co. v. Teva Pharm. USA, Inc., 395 F.3d 1364,
`1372 (Fed. Cir. 2005) (“A claim construction that gives meaning to all the
`terms of the claim is preferred over one that does not do so.”). The claim
`term “said” signals that there is antecedent basis in the claim for the “said”
`
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`8 The parties do not identify any relevant portions of the prosecution history
`specific to interpretation of the “each of said reaction wells” and “each of
`said m reaction wells” phras