Trials@uspto.gov
`571.272.7822
`
`
`
`
`
` Paper 47
`
` Filed: January 9, 2019
`
`
`
`
`UNITED STATES PATENT AND TRADEMARK OFFICE
`____________
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`____________
`
`NUEVOLUTION A/S,
`Petitioner,
`
`v.
`
`CHEMGENE HOLDINGS APS,
`Patent Owner.
`____________
`
`Case IPR2017-01598
`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, 2, 4, 5, 7–9, 16, 18–22, 27–30, 32, 33, 35, 36, 38–41,
`and 46 Shown to Be Unpatentable;
`Claims 23, 42, 43, and 45 Not 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)
`
`
`
`
`
`
`
`571.272.7822
`
`
`
`
`
` Paper 47
`
` Filed: January 9, 2019
`
`
`
`
`UNITED STATES PATENT AND TRADEMARK OFFICE
`____________
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`____________
`
`NUEVOLUTION A/S,
`Petitioner,
`
`v.
`
`CHEMGENE HOLDINGS APS,
`Patent Owner.
`____________
`
`Case IPR2017-01598
`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, 2, 4, 5, 7–9, 16, 18–22, 27–30, 32, 33, 35, 36, 38–41,
`and 46 Shown to Be Unpatentable;
`Claims 23, 42, 43, and 45 Not 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)
`
`
`
`
`
`
`
`
`IPR2017-01598
`Patent 8,168,381 B2
`
` INTRODUCTION
`A. Overview
`Nuevolution A/S (“Petitioner”) filed a Corrected Petition to institute
`inter partes review of claims 1, 2, 4, 5, 7–9, 16, 18–23, 27–30, 32, 33, 35,
`36, 38–43, 45, and 46 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, 2, 4, 5, 7–9, 16, 18–22, 27–30, 32, 33, 35, 36, 38–41, and 46 on
`two of the eleven 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 nine 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 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.
`
`2
`
`
`
`IPR2017-01598
`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 the 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 46 (“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.
`
`3
`
`
`
`IPR2017-01598
`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 that the prior art discloses only that such molecules are
`synthesized in multiple different reaction wells. See, e.g., Prelim. Resp. 3–4,
`8–11, 21–22, 24–25, 53–57, 63; Paper 15, 1, 7; Resp. 11–18, 43–49, 59.
`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, provided the
`desired reactions occur and the desired molecules are made. See, e.g., Paper
`14, 3–4; Reply 1, 2–5. 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, 104–114; 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, 2, 4, 5, 7–9,
`
`4
`
`
`
`IPR2017-01598
`Patent 8,168,381 B2
`16, 18–22, 27–30, 32, 33, 35, 36, 38–41, and 46 of the ’381 patent are
`unpatentable.
`
`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. 11–13; 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.
`12. 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. 60.
`
`5
`
`
`
`IPR2017-01598
`Patent 8,168,381 B2
`Petitioner filed another petition for inter partes review of claims in
`U.S. Patent No. 8,168,381 B2 (IPR2017-01599), as well as a petition for
`inter partes review of the sole claim in U.S. Patent No. 8,951,728 B2 (“the
`’728 patent” (Ex. 1002)) (IPR2017-01603). Pet. 3–4. The ’728 patent
`issued from a grandchild application to the ’381 patent. Id.; 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.
`
`6
`
`
`
`IPR2017-01598
`Patent 8,168,381 B2
`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
`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
`
`7
`
`
`
`IPR2017-01598
`Patent 8,168,381 B2
`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.
`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.
`
`
`
`
`
`
`
`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
`
`8
`
`
`
`IPR2017-01598
`Patent 8,168,381 B2
`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
`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.
`
`9
`
`
`
`IPR2017-01598
`Patent 8,168,381 B2
`
`
`
`
`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.
`
`10
`
`
`
`IPR2017-01598
`Patent 8,168,381 B2
`
`Illustrative Claim
`D.
`Petitioner challenges claims 1, 2, 4, 5, 7–9, 16, 18–23, 27–30, 32, 33,
`35, 36, 38–43, 45, and 46 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;
`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
`
`
`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.
`11
`
`
`
`IPR2017-01598
`Patent 8,168,381 B2
`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
`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. 7–8.
`Ground Claims
`
`Reference(s)
`
`Basis
`
`1, 2, 5, 16, 18–20, 22, 27, 28, 30 Gouliaev ’6273
`
`§ 102
`
`1
`
`2
`
`Pedersen4
`
`§ 102
`
`1, 2, 4, 5, 7–9, 16, 18–22, 27–30,
`32, 33, 35, 36, 38, 39, 46
`
`3 Gouliaev et al., WO 03/078627 A2, publ. Sept. 25, 2003 (Ex. 1007).
`4 Pedersen et al., WO 02/103008 A2, publ. Dec. 27, 2002 (Ex. 1004).
`12
`
`
`
`IPR2017-01598
`Patent 8,168,381 B2
`Ground Claims
`
`3
`
`4
`
`5
`
`6
`
`7
`
`8
`
`9
`
`10
`
`11
`
`1, 2, 4, 5, 7–9, 16, 18–22, 27–30,
`32, 33, 35, 36, 38, 39, 46
`1, 2, 4, 5, 7–9, 16, 18–23, 27–30,
`32, 33, 35, 36, 38, 39, 45, 46
`1, 2, 4, 5, 7–9, 16, 18–23, 27–30,
`32, 33, 35, 36, 38, 39, 45, 46
`1, 2, 4, 5, 7–9, 16, 18–22, 27–30,
`32, 33, 35, 36, 38, 39, 46
`1, 2, 4, 5, 7–9, 16, 187–22, 27–30,
`32, 33, 35, 36, 38, 39, 46
`42, 43
`
`1, 4, 5, 7–9, 16, 19–22, 27–30,
`32, 33, 35, 36, 38–419
`1, 4, 5, 7–9, 16, 19–22, 27–30,
`32, 33, 35, 36, 38–41
`1, 2, 4, 5, 7–9, 16, 18–22, 27–30,
`32, 33, 35, 36, 38–41, 46
`
`Reference(s)
`
`Pedersen
`
`Gouliaev ’9945
`
`Gouliaev ’994
`
`Franch ’9296
`
`Franch ’929
`
`Franch ’929 and
`Liu8
`Freskgård10
`
`Freskgård
`
`Freskgård and
`Pedersen
`
`Basis
`
`§ 103
`
`§ 102
`
`§ 103
`
`§ 102
`
`§ 103
`
`§ 103
`
`§ 102
`
`§ 103
`
`§ 103
`
`Petitioner also relies on, among other evidence, the Declarations of
`Nicolas Winssinger, Ph.D. Exs. 1015, 1030.
`
`
`5 Gouliaev et al., WO 2004/056994 A2, publ. July 8, 2004 (Ex. 1006).
`6 Franch et al., WO 2004/024929 A2, publ. Mar. 25, 2004 (Ex. 1005).
`7 The Petition includes claim 8 twice in its listing of claims for Ground 7,
`which we treat as a typographical error and, based on the discussion related
`to Ground 7 (Pet. 100), understand that Petitioner intended to list claim 18.
`8 Liu et al., WO 2004/016767 A2, publ. Feb. 26, 2004 (Ex. 1008).
`9 Petitioner lists various dependent claims, but does not include independent
`claims 1 and 5 in its listing of challenged claims for Grounds 9 and 10. Pet.
`7–8. The Petition does, however, address claims 1 and 5 in its discussion,
`asserting that the limitations of claims 1 and 5 are taught in Freskgård. See
`Pet. 107–118, 126; Ex. 1015 ¶¶ 425–450, 526 (Ground 10). Thus, we
`include claims 1 and 5 as being challenged under Grounds 9 and 10.
`10 Freskgård et al., WO 2004/039825 A2, publ. May 13, 2004 (Ex. 1003).
`13
`
`
`
`IPR2017-01598
`Patent 8,168,381 B2
`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 10 and 11 from the
`table above. Paper 16, 48. Nevertheless, after the Supreme Court’s decision
`in SAS, we modified the institution decision to include the remaining
`grounds (grounds 1–9) 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 having 3-5 years of additional experience in drug discovery.”
`Pet. 19; 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. 13.
`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.
`
`14
`
`
`
`IPR2017-01598
`Patent 8,168,381 B2
`
`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. 24–31. 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 express 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 31. 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 27–30. We interpreted
`
`15
`
`
`
`IPR2017-01598
`Patent 8,168,381 B2
`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 27. 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)11 be conducted within the same reaction well — the same
`physical containment in a localized space. Id. at 28–30.
`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. 3–4, 8–11, 23–25,
`53–57; 63–64; Paper 15, 1, 7; Resp. 11–18, 43–49, 59. That is because,
`Patent Owner argued, 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. 39–44.
`Petitioner embraces the Board’s preliminary finding that at least
`Freskgård teaches synthesis of bi-functional molecules in the same physical
`
`
`11 The related language of claim 5 recites “each of m reaction wells . . . each
`of said m reaction wells.” Ex. 1001, 137:43–45.
`16
`
`
`
`IPR2017-01598
`Patent 8,168,381 B2
`container (i.e., a well on a microtiter plate) and, thus, in the same reaction
`well. See, e.g., Reply 1–2, 6–21. 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. 18–19; Prelim. Resp. 13. 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;
`Ex. 1001, 4:51–5:4). According to Petitioner, although claims 1 and 5 “may
`
`17
`
`
`
`IPR2017-01598
`Patent 8,168,381 B2
`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 prohibits 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
`
`18
`
`
`
`IPR2017-01598
`Patent 8,168,381 B2
`same reaction well.” Id. at 2 (bold font 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. 19. 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
`
`19
`
`
`
`IPR2017-01598
`Patent 8,168,381 B2
`prosecution history,”12 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” al
Accessing this document will incur an additional charge of $.
After purchase, you can access this document again without charge.
Accept $ Charge
Still Working On It
This document is taking longer than usual to download. This can happen if we need to contact the court directly to obtain the document and their servers are running slowly.
Give it another minute or two to complete, and then try the refresh button.
A few More Minutes ... Still Working
It can take up to 5 minutes for us to download a document if the court servers are running slowly.
Thank you for your continued patience.
This document could not be displayed.
We could not find this document within its docket. Please go back to the docket page and check the link. If that does not work, go back to the docket and refresh it to pull the newest information.
Your account does not support viewing this document.
You need a Paid Account to view this document. Click here to change your account type.
Your account does not support viewing this document.
Set your membership
status to view this document.
With a Docket Alarm membership, you'll
get a whole lot more, including:
- Up-to-date information for this case.
- Email alerts whenever there is an update.
- Full text search for other cases.
- Get email alerts whenever a new case matches your search.
One Moment Please
The filing “” is large (MB) and is being downloaded.
Please refresh this page in a few minutes to see if the filing has been downloaded. The filing will also be emailed to you when the download completes.
Your document is on its way!
If you do not receive the document in five minutes, contact support at support@docketalarm.com.
Sealed Document
We are unable to display this document, it may be under a court ordered seal.
If you have proper credentials to access the file, you may proceed directly to the court's system using your government issued username and password.
Access Government Site
