`Patent Owner’s Preliminary Response
`
`Filed on behalf of Patent Owner Genentech, Inc. by:
`
`David L. Cavanaugh (Reg. No. 36,476)
`Owen K. Allen (Reg. No. 71,118)
`Robert J. Gunther, Jr. (Pro Hac Vice to be filed)
`Lisa J. Pirozzolo (Pro Hac Vice to be filed)
`Kevin S. Prussia (Pro Hac Vice to be filed)
`Andrew J. Danford (Pro Hac Vice to be filed)
`WILMER CUTLER PICKERING
`HALE AND DORR LLP
`1875 Pennsylvania Ave., NW
`Washington, DC 20006
`
`Adam R. Brausa (Reg. No.
`60,287)
`Daralyn J. Durie (Pro Hac
`Vice to be filed)
`DURIE TANGRI LLP
`217 Leidesdorff Street
`San Francisco, CA 94111
`
`UNITED STATES PATENT AND TRADEMARK OFFICE
`
`____________________________________________
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`
`____________________________________________
`
`PFIZER, INC.,
`Petitioner,
`
`v.
`
`GENENTECH, INC.,
`Patent Owner.
`____________________________________________
`
`Case IPR2017-01488
`Patent 6,407,213
`____________________________________________
`
`PATENT OWNER’S PRELIMINARY RESPONSE
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`
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`IPR2017-01488
`Patent Owner’s Preliminary Response
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`TABLE OF CONTENTS
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`Page
`INTRODUCTION ...........................................................................................1
`
`TECHNOLOGY BACKGROUND.................................................................4
`
`I.
`
`II.
`
`A. Antibody “Variable” And “Constant” Domains ........................................4
`
`B.
`
`“Humanized” Antibodies............................................................................6
`
`III. THE ’213 PATENT.........................................................................................8
`
`A.
`
`B.
`
`C.
`
`The Invention..............................................................................................8
`
`Advantages Of The ’213 Invention..........................................................10
`
`Prosecution History ..................................................................................11
`
`IV. PFIZER’S ASSERTED REFERENCES.......................................................12
`
`A. Kurrle........................................................................................................12
`
`B.
`
`C.
`
`D.
`
`E.
`
`F.
`
`Queen 1990...............................................................................................14
`
`Furey.........................................................................................................16
`
`Chothia & Lesk.........................................................................................16
`
`Chothia 1985.............................................................................................17
`
`Hudziak.....................................................................................................17
`
`V.
`
`PERSON OF ORDINARY SKILL ...............................................................18
`
`VI. CLAIM CONSTRUCTION ..........................................................................18
`
`VII. ARGUMENT.................................................................................................20
`
`A.
`
`The Board Should Deny All Grounds Because Neither Kurrle Nor
`Queen 1990 Is Prior Art. ..........................................................................20
`
`i
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`Patent Owner’s Preliminary Response
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`1.
`
`The inventors produced and tested humanized 4D5 antibodies
`using the ’213 invention before July 26, 1990....................................20
`
`a)
`
`b)
`
`c)
`
`Consensus sequence.......................................................................20
`
`Humanized 4D5 antibody sequences .............................................22
`
`Production and testing of humanized 4D5 antibodies ...................25
`
`(i)
`
`(ii)
`
`First humanized 4D5 variable domain fragment ......................27
`
`First humanized 4D5 full-length antibody................................29
`
`(iii) Other humanized 4D5 variants .................................................30
`
`2.
`
`The challenged claims were reduced to practice before July 26,
`1990.....................................................................................................32
`
`a)
`
`HuMAb4D5-5 and HuMAb4D5-8 embody the challenged
`claims. ............................................................................................32
`
`(i)
`
`Common limitations..................................................................32
`
`(ii) Additional limitations for certain claims ..................................37
`
`b)
`
`c)
`
`The inventors determined that HuMAb4D5-5 and
`HuMAb4D5-8 would work for the intended purpose of the
`challenged claims before July 26, 1990.........................................39
`
`Contemporaneous records from non-inventors corroborate
`the invention of the challenged claims...........................................40
`
`3.
`
`Kurrle and Queen 1990 are not prior art. ............................................40
`
`a)
`
`b)
`
`Limitations common to all claims..................................................41
`
`Additional limitations for certain claims .......................................42
`
`B.
`
`Pfizer’s Proposed Grounds Fail On The Merits.......................................43
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`ii
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`1.
`
`2.
`
`3.
`
`4.
`
`5.
`
`6.
`
`7.
`
`Grounds 1, 2, and 3: Kurrle and Queen 1990 do not anticipate
`or render obvious the “lacks immunogenicity” limitation of
`claim 63. ..............................................................................................45
`
`Grounds 2, 3, and 8: Pfizer’s asserted references do not
`anticipate or render obvious the “consensus” limitations of
`claims 4, 33, 62, 64, and 69.................................................................46
`
`Queen 1990 ....................................................................................47
`
`Kurrle .............................................................................................49
`
`Hudziak ..........................................................................................49
`
`Ground 2: Queen 1990 does not anticipate the challenged
`claims...................................................................................................49
`
`Grounds 3-7: Pfizer has failed to explain how a skilled artisan
`would combine Queen 1990 and Kurrle. ............................................52
`
`Ground 3: The Board should deny Ground 3 as duplicative of
`Grounds 1 and 2. .................................................................................52
`
`Ground 4: Claim 12 would not have been obvious over Queen
`1990 and Kurrle in view of Furey. ......................................................54
`
`Grounds 5-7: Claims 73, 74, 77, 79, and 65 would not have
`been obvious over Queen 1990 and Kurrle in view of Chothia
`& Lesk and/or Chothia 1985...............................................................55
`
`Claim 73 (Ground 5) ......................................................................55
`
`Claim 77 (Ground 5) ......................................................................56
`
`Claim 74 (Ground 6) ......................................................................57
`
`Claims 79 (Ground 7).....................................................................57
`
`Claim 65 (Ground 7) ......................................................................58
`
`a)
`
`b)
`
`c)
`
`a)
`
`b)
`
`c)
`
`d)
`
`e)
`
`iii
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`Patent Owner’s Preliminary Response
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`8.
`
`9.
`
`Ground 8: Queen 1990 would not have led a skilled artisan to
`make the substitutions required by claims 30, 31, and 33. .................59
`
`Ground 9: Claim 42 would not have been obvious over Queen
`1990 and Kurrle in view of Furey and Hudziak..................................61
`
`10. Ground 10: Claim 60 would not have been obvious over Queen
`1990 in view of Chothia & Lesk and Hudziak....................................61
`
`C.
`
`Objective Indicia Of Non-Obviousness Confirm The Patentability
`Of The Challenged Claims. ......................................................................62
`
`1.
`
`2.
`
`Unexpected results ..............................................................................62
`
`Commercial success ............................................................................64
`
`D.
`
`Inter Partes Review Proceedings Are Unconstitutional. .........................66
`
`VIII. CONCLUSION..............................................................................................66
`
`iv
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`TABLE OF AUTHORITIES
`
`Page(s)
`
`Cases
`
`Atofina v. Great Lakes Chemical Corp.,
`441 F.3d 991 (Fed. Cir. 2006) ............................................................................50
`
`Bettcher Industries, Inc. v. Bunzl USA, Inc.,
`661 F.3d 629 (Fed. Cir. 2011) ............................................................................46
`
`Brown & Williamson Tobacco Corp. v. Philip Morris Inc.,
`229 F.3d 1120 (Fed. Cir. 2000) ..........................................................................65
`
`In re Clarke,
`356 F.2d 987 (C.C.P.A. 1966)............................................................................39
`
`Cooper v. Goldfarb,
`154 F.3d 1321 (Fed. Cir. 1998) ..........................................................................40
`
`Crocs, Inc. v. International Trade Commission,
`598 F.3d 1294 (Fed. Cir. 2010) ..........................................................................62
`
`In re Cyclobenzaprine Hydrochloride Extended-Release Capsule
`Patent Litigation,
`676 F.3d 1063 (Fed. Cir. 2012) ..........................................................................60
`
`Ecolochem, Inc. v. Southern California Edison Co.,
`227 F.3d 1361 (Fed. Cir. 2000) ..........................................................................52
`
`McCormick Harvesting Machine Co. v. C. Aultman & Co.,
`169 U.S. 606 (1898)............................................................................................66
`
`Markman v. Westview Instruments, Inc.,
`517 U.S. 370 (1996)............................................................................................66
`
`In re Merchant,
`575 F.2d 865 (C.C.P.A. 1978)............................................................................61
`
`v
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`Mikus v. Wachtel,
`504 F.2d 1150 (C.C.P.A. 1974)..........................................................................36
`
`In re NTP, Inc.,
`654 F.3d 1279 (Fed. Cir. 2011) ..........................................................................32
`
`Oil States Energy Services, LLC v. Greene’s Energy Group, LLC,
`137 S. Ct. 2239 (2017)........................................................................................66
`
`Oracle Corp. v. Clouding IP, LLC,
`IPR2013-00088, Paper 13 (June 13, 2013).........................................................53
`
`In re Schaub,
`537 F.2d 509 (C.C.P.A. 1976)............................................................................37
`
`Sinorgchem Co. v. International Trade Commission,
`511 F.3d 1132 (Fed. Cir. 2007) ..........................................................................19
`
`In re Soni,
`54 F.3d 746 (Fed. Cir. 1995) ..............................................................................62
`
`In re Spiller,
`500 F.2d 1170 (C.C.P.A. 1974)..........................................................................37
`
`In re Steed,
`802 F.3d 1311 (Fed. Cir. 2015) ..........................................................................32
`
`In re Taub,
`348 F.2d 556 (C.C.P.A. 1965)............................................................................36
`
`Tokai Corp. v. Easton Enterprises, Inc.,
`632 F.3d 1358 (Fed. Cir. 2011) ..........................................................................65
`
`Statutes
`
`35 U.S.C.
`
`§ 102.........................................................................................................................40
`
`§ 120.........................................................................................................................41
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`vi
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`I.
`
`INTRODUCTION
`In the early 1990s, the field of therapeutic antibodies was still in its infancy.
`
`Although scientists had known since the 1970s how to obtain antibodies from
`
`animals (e.g., mice) that would bind to specific targets, those antibodies generally
`
`could not be used in humans because over time the body’s own immune system
`
`would attack and inactivate them (known as an “immunogenic” response).
`
`Beginning in the late 1980s, a few scientists had attempted to create “humanized”
`
`antibodies that incorporated the binding site from a non-human antibody into a
`
`human antibody framework—which they hoped might address the immunogenicity
`
`problem by reducing the amount of non-human amino acid sequences in the
`
`antibody. But those early humanized antibodies suffered from reduced binding
`
`affinity or still produced an immunogenic response. Given those challenges, which
`
`continued throughout the late 1980s, there were no humanized antibodies on the
`
`market, and some doubted it would ever be possible to develop one that could be
`
`used therapeutically.
`
`In the late 1980s, Genentech scientists began developing a new
`
`humanization approach that solved those problems. Rather than starting from an
`
`actual human antibody sequence, they created an artificial “consensus” sequence—
`
`consisting of the most frequently occurring amino acids at each location in all
`
`human antibodies of the same subclass or subunit structure. That novel consensus
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`sequence approach—which minimized the prior art immunogenicity problem and
`
`provided a broadly-applicable platform for humanizing antibodies—is protected by
`
`U.S. Patent No. 6,407,213 (“the ’213 patent”). The inventors initially applied their
`
`consensus sequence approach to humanize the murine 4D5 antibody and create the
`
`drug Herceptin®—a lifesaving therapy for an aggressive form of breast cancer.
`
`Their invention was later used to develop numerous other highly successful
`
`therapeutic antibodies for a wide range of diseases.
`
`Pfizer’s petition challenges certain claims of the ’213 patent on ten different
`
`anticipation or obviousness grounds, but fails to demonstrate a reasonable
`
`likelihood of success for any of them.
`
`As an initial matter, the primary references underlying each proposed
`
`ground—Kurrle (Ex. 1071) and Queen 1990 (Ex. 1050)—are not prior art. The
`
`’213 inventors reduced their invention to practice before the publication of Kurrle
`
`and Queen 1990 by creating and testing humanized antibodies that embody the
`
`challenged claims. That actual reduction to practice is corroborated by extensive
`
`contemporaneous records from the inventors and several non-inventors.
`
`Even if Pfizer could rely on Kurrle or Queen 1990, Pfizer has failed to
`
`demonstrate a reasonable likelihood of success for claim 63 in Ground 1 and all
`
`claims challenged in Grounds 2-10 for several additional reasons.
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`2
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`First, Pfizer has not demonstrated that certain claim limitations are disclosed
`
`or would have been obvious, including (i) “lacks immunogenicity” in claim 63
`
`(Grounds 1-3); (ii) “up to 3-fold more” binding affinity in claim 65 (Ground 7);
`
`and (iii) “consensus” sequence in claims 4, 33, 62, 64, and 69 (Grounds 2, 3, and
`
`8). Pfizer’s arguments with respect to these claims rest on speculation and are not
`
`supported by the disclosure of the asserted references.
`
`Second, for its anticipation argument in Ground 2, Pfizer has not shown that
`
`Queen 1990 teaches each limitation of any challenged claim. Pfizer does not
`
`contend that Queen 1990 discloses any antibody that reads on any challenged
`
`claim. Instead, Pfizer argues that Queen 1990 discloses general criteria that
`
`supposedly would have led a skilled artisan to arrive at the challenged claims. But
`
`Pfizer’s own arguments confirm that Queen 1990 encompasses thousands of
`
`possibilities, and Pfizer has not explained why a skilled artisan supposedly would
`
`have pursued the specific amino acid substitutions recited in the challenged claims.
`
`Third, Pfizer’s obviousness arguments (Grounds 3-10) fail for similar
`
`reasons. Pfizer presents a hindsight-driven analysis that selectively focuses on
`
`some potential amino acid substitutions without explaining why the claimed
`
`substitutions would have been chosen out of the numerous other possibilities that
`
`Pfizer admits a skilled artisan would have had to confront.
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`3
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`Finally, for Grounds 3-7, Pfizer contends the challenged claims would have
`
`been obvious over the combination of Queen 1990 and Kurrle. Pfizer, however,
`
`never identifies any claim limitation lacking from Queen 1990 that is disclosed in
`
`Kurrle, or vice versa—let alone explains how the references would be combined.
`
`Pfizer cannot cure the deficiencies in its anticipation theory with such conclusory
`
`assertions of “obviousness.”
`
`The Board should deny institution.
`
`II.
`
`TECHNOLOGY BACKGROUND
`A.
`Antibody “Variable” And “Constant” Domains
`
`The immune system defends against foreign substances, known as
`
`“antigens” (e.g., viruses or bacteria), by producing antibodies. Antibodies are
`
`proteins that recognize and bind to antigens, which facilitates their removal from
`
`the body. (Ex. 1082 at 1.) A typical antibody (sometimes called an
`
`“immunoglobulin”) consists of four amino acid chains: two identical heavy chains
`
`and two identical light chains, which join to form a “Y” shape, as shown below:
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`(Ex. 2023 at 10 (annotated); Ex. 1001, 1:17-20.) Each chain contains a “variable”
`
`domain at one end (red box above) and “constant” domains at the other (green box
`
`above). (Ex. 1001, 1:20-27.) The variable domains for the heavy chain (VH) and
`
`light chain (VL) are illustrated above in blue and pink, respectively.
`
`Variable domains directly bind to the antigen. (Id., 1:35-37.) Each variable
`
`domain contains three “complementarity determining regions,” or “CDRs,” (id.,
`
`1:35-50), shown as CDR1, CDR2, and CDR3 in the enlarged portion above.
`
`Variable domains also contain four “framework regions,” or “FRs”—one on either
`
`side of each CDR—shown as FR1, FR2, FR3, and FR4 in the same enlarged
`
`portion. The framework regions form an immunoglobulin core structure from
`
`which the CDRs extend and form a binding site for interaction with the antigen.
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`(Id., 1:47-50.) In contrast to the CDRs, which generally contain unique amino
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`acids (or “residues”) for a particular antigen, the framework regions may have
`
`more amino acid sequences in common (i.e., the same amino acids at the same
`
`positions) across other antibodies. (Id., 1:37-44.)
`
`The constant domains are not directly involved in antigen binding and
`
`typically have similar amino acid sequences across all antibodies within a subclass.
`
`(Ex. 2016, Presta Decl. ¶ 15.)
`
`B.
`
`“Humanized” Antibodies
`
`Before the ’213 patent, antibodies targeting a specific antigen could be
`
`obtained from animals, such as mice. (Ex. 1001, 1:52-58.) Although those non-
`
`human antibodies could bind to a desired target, they had limited use
`
`therapeutically because the human immune system would over time identify them
`
`as antigens and attack them—known as an “antigenic” or “immunogenic”
`
`response. (Id., 1:55-58.) An immunogenic response had adverse clinical
`
`consequences because it inactivated the antibody and resulted in its premature
`
`removal from the body. (E.g., Ex. 1028 at 3 (noting “large fall in circulating
`
`mouse immunoglobulin” due to immunogenic response and accompanying
`
`“adverse clinical reaction”).)
`
`Scientists developed several techniques trying to address that issue. One
`
`approach used “chimeric” antibodies that combined a non-human variable domain
`
`(e.g., the entire variable domain from a mouse antibody) with a human constant
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`domain. (Id., 1:59-2:19.) However, because chimeric antibodies retained a
`
`significant portion of the non-human antibody sequence, immunogenicity could
`
`still result. (Id., 2:12-19; Ex. 2022 at 2156.)
`
`Attempting to reduce immunogenicity, scientists created “humanized”
`
`antibodies that included a human variable domain substituted with the amino acid
`
`sequence of the non-human CDRs. (Ex. 1001, 2:20-52.) But that approach could
`
`reduce the antibody’s ability to bind to specific antigens. (Ex. 1034 at 5
`
`(“Unfortunately, in some cases the humanized antibody had significantly less
`
`binding affinity for antigen than did the original mouse antibody.”).)1
`
`In attempting to address these various shortcomings, scientists pursued
`
`techniques seeking to make humanized antibodies that balanced strong binding
`
`with low immunogenicity. For example, Queen 1989 (Ex. 1034) selected a human
`
`1
`
`In this proceeding, Patent Owner uses “chimeric” and “humanized” as
`
`defined in the ’213 patent. (Ex. 1001, 1:59-62 (“chimeric” antibodies have “an
`
`animal antigen-binding variable domain [that] is coupled to a human constant
`
`domain”); id., 8:11-17 (“humanized” antibodies contain a framework region
`
`“having substantially the same amino acid sequence of a human immunoglobulin
`
`and a CDR having substantially the amino acid sequence of a non-human
`
`immunoglobulin”).)
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`variable domain by comparing a mouse antibody against known human antibody
`
`sequences, and choosing a human framework that was “as homologous as possible
`
`to the original mouse antibody to reduce any deformation of the mouse CDRs.”
`
`(Ex. 1034 at 5.) The humanized sequence was then further refined using computer
`
`modeling “to identify several framework amino acids in the mouse antibody that
`
`might interact with the CDRs or directly with antigen, and these amino acids were
`
`transferred to the human framework along with the CDRs.” (Id.) That technique
`
`became known as the “best-fit” approach because it started from a human sequence
`
`with the closest match to the non-human antibody. (Ex. 2024 at 4184.)
`
`Even using the best-fit approach, however, it still was difficult to produce an
`
`antibody with both strong binding and low immunogenicity. (Ex. 1001, 3:50-52.)
`
`The best-fit approach also was inefficient because it required a new human
`
`antibody sequence as the starting point for each different humanized antibody.
`
`III. THE ’213 PATENT
`A.
`The Invention
`
`Beginning in the late 1980s, Drs. Paul Carter and Leonard Presta at
`
`Genentech developed a new approach to humanizing antibodies that solved the
`
`prior art binding and immunogenicity problems. Rather than starting from the
`
`most homologous human sequence, Drs. Carter and Presta developed a “consensus
`
`human sequence”—i.e., “an amino acid sequence which comprises the most
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`frequently occurring amino acid residues at each location in all human
`
`immunoglobulins of any particular subclass or subunit structure.” (Id., 11:32-38.)
`
`That “consensus” sequence provided a single human amino acid sequence that
`
`would be the starting point for any humanized antibody of a particular subclass or
`
`subunit structure (e.g.(cid:15)(cid:3)(cid:79)(cid:76)(cid:74)(cid:75)(cid:87)(cid:3)(cid:70)(cid:75)(cid:68)(cid:76)(cid:81)(cid:3)(cid:539)(cid:20)(cid:12). (Id., 54:66-56:57.)
`
`The ’213 inventors developed a multi-step process for their approach. First,
`
`they added the non-human CDRs to the human consensus sequence. (Id., 20:12-
`
`31.) Next, they evaluated the differences between the framework regions of the
`
`non-human antibody and the human consensus sequence to determine whether
`
`further modifications to the consensus sequence were needed. (Id., 20:32-40.)
`
`For framework positions where the non-human antibody sequence differed
`
`from the human consensus sequence, Drs. Carter and Presta used computer
`
`modeling to identify whether the different non-human amino acid (i) “non-
`
`covalently binds antigen directly”; (ii) “interacts with a CDR”; (iii) “participates in
`
`the VL-VH interface,” i.e., the interface between variable domains of the heavy and
`
`light chains, or (iv) is a glycosylation site outside the CDRs that is likely to affect
`
`“antigen binding and/or biological activity.” (Id., 20:32-21:36, 54:64-56:57.)
`
`They believed that those positions were important to maintaining binding affinity
`
`because they could influence the three-dimensional shape of the CDRs. (Id.,
`
`20:32-35.) If any of those four requirements was met, the amino acid at that
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`position in the consensus sequence could be substituted with the amino acid that
`
`appears at the same position in the non-human antibody. Otherwise, the amino
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`acid sequence of the human consensus sequence was retained. (Id., 20:66-21:8.)
`
`The ’213 challenged claims reflect the inventors’ novel consensus sequence
`
`approach. Each challenged claim requires a “humanized” antibody or variable
`
`domain that contains non-human CDRs and one or more specified framework
`
`amino acid substitutions. As explained below, the claimed framework
`
`substitutions are the amino acid positions that the inventors determined were
`
`important to antibody binding.
`
`B.
`
`Advantages Of The ’213 Invention
`
`The ’213 patent’s consensus sequence approach was a significant advance
`
`over the prior art.
`
`First, using a consensus sequence minimized the immunogenicity problems
`
`that plagued other humanization techniques. (Ex. 1002 at 3439-41, ¶¶ 2-9.) At the
`
`same time, humanized antibodies made according to the ’213 invention retain
`
`strong binding for the targeted antigen, or even have improved binding over the
`
`original non-human antibody. (Ex. 1001, 4:24-28, 51:50-53.)
`
`Second, under the best-fit approach, the most homologous human sequence
`
`itself may be a rare antibody sequence that would trigger an immunogenic
`
`response—for example, due to unique variations in individual patients. (Ex. 2016,
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`Presta Decl. ¶ 24.) The ’213 patent avoids that problem by starting from a
`
`consensus sequence comprising only the most frequently occurring amino acids at
`
`each position. (Ex. 1001, 11:32-38.)
`
`Third, unlike the prior art best-fit approach—that required identifying the
`
`most homologous human antibody sequence for each antibody to be humanized—
`
`the ’213 patent provided a single human antibody sequence as a starting point that
`
`could be applied to a wide variety of antibodies. (Ex. 1002 at 3439-41, ¶¶ 2-9.)
`
`Genentech has used the ’213 invention to develop numerous drugs for a wide
`
`variety of diseases, such as Herceptin® (breast and gastric cancer), Perjeta® (breast
`
`cancer), Avastin® (colon, lung, ovarian, cervical, kidney, and brain cancer),
`
`Lucentis® (macular degeneration), and Xolair® (asthma). (Ex. 2017, Carter Decl. ¶
`
`4; Ex. 2016, Presta Decl. ¶ 5.)
`
`C.
`
`Prosecution History
`
`The ’213 patent is a continuation-in-part of an application filed on June 14,
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`1991. (Ex. 1001, coversheet.) The challenged claims issued over hundreds of
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`references considered during prosecution, including every reference that Pfizer
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`relies upon in its proposed grounds. (Ex. 1001 at 1-6.) The examiner did not make
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`any rejection based upon any reference underlying Pfizer’s proposed grounds.
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`Pfizer asserts that Kurrle (Ex. 1071), Chothia & Lesk (Ex. 1062), and
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`Chothia 1985 (Ex. 1063) were not considered during prosecution. (Paper 1 at 14.)
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`That is incorrect. Each reference is cited on the face of the patent. (See Ex. 1001
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`at 1 (Kurrle: “EP 403156”); id. at 2 (Chothia & Lesk: right column, ninth from
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`top); id. (Chothia 1985: right column, twelfth from top).) And Chothia & Lesk
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`and Chothia 1985 are even discussed in the ’213 specification; indeed, Chothia
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`1985 is the first reference cited in the specification, and Chothia & Lesk is cited no
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`fewer than nine times. (Id., 1:27-30 (Chothia 1985); id., 3:1-3, 3:31, 7:7-8, 7:45,
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`10:38, 20:22-23, 20:29-30, 47:42-43, 48:66-67 (Chothia & Lesk).)
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`During prosecution, the applicants submitted a joint affidavit from Drs.
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`Carter and Presta to antedate U.S. Patent No. 5,693,762, which had a filing date of
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`September 28, 1990. (Ex. 1002 at 4432-33.) The examiner allowed the claims
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`after accepting that antedation evidence. (Id. at 4443.) As detailed below, the
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`record in this proceeding further confirms that the ’213 invention was also
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`conceived and reduced to practice before the publication of either Kurrle
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`(December 19, 1990) or Queen 1990 (July 26, 1990).
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`IV. PFIZER’S ASSERTED REFERENCES
`A.
`Kurrle
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`Kurrle is a European Patent Application published on December 19, 1990.
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`Because it was published after the ’213 inventors conceived and reduced their
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`invention to practice, Kurrle is not prior art. (See infra pp. 20-42.)
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`Unlike the ’213 patent’s consensus sequence approach, Kurrle used a best-fit
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`approach for antibody humanization. Starting from the murine antibody sequence,
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`Kurrle searched a database of human antibody sequences to identify “the most
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`homologous human antibody” to provide the variable domain. (Ex. 1071, 8:16-
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`18.) Kurrle incorporated the CDRs from the mouse antibody into the human
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`antibody sequence (id., 3:8-11), and then made further substitutions of murine
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`residues “in the sequence immediately before and after the CDRs” and “up to 4
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`amino acids away” (id., 8:25-29).
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`Kurrle’s technique thus involved making substitutions in any of up to 24
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`different amino acid residues per antibody chain—i.e., 4 amino acid residues on
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`either side of the 3 CDRs. Kurrle provided no guidance on which substitutions
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`may be beneficial for any given antibody. Kurrle also highlighted the
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`unpredictable and “potential[ly] adverse consequences” of modifying the human
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`antibody sequence to incorporate amino acids from the murine antibody. (Id.,
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`8:40-43 (“[E]xtreme caution must be exercised to limit the number of changes.”).)
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`Kurrle disclosed the sequence for four humanized antibodies: BMA 031-
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`EUCIV1, BMA 031-EUCIV2, BMA 031-EUCIV3, and BMA 031-EUCIV4. (Id.,
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`Tables 6A-B.)
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`B.
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`Queen 1990
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`Queen 1990 is a PCT application published July 26, 1990. It is not prior art.
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`(See infra pp. 20-42.)
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`Like Kurrle, Queen 1990 used a best-fit approach to produce a humanized
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`antibody by starting from a human sequence most homologous to the mouse
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`antibody. (Ex. 1050, 26:5-33:25.) Queen also identified four general criteria for
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`designing humanized antibodies.
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`Criterion I: As a starting point, Queen 1990 emphasized the importance of
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`choosing the human sequence most similar to the non-human antibody to reduce
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`the possibility of distorting the binding site formed by the CDRs. (Id., 12:17-35.)
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`Queen 1990 mentioned “a consensus framework” (id., 12:19-20), but included no
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`details of what that “consensus framework” might be or how it might be used to
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`make a humanized antibody.
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`Criterion II: After selecting a best-fit human framework sequence, Queen
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`1990 provided that “unusual” or “rare” amino acids could be replaced with more
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`common amino acids from the non-human sequence. (Id., 13:22-32.) This step
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`was intended to eliminate residues from the selected human framework that may
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`“disrupt the antibody structure” by replacing them with non-human residues
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`commonly found in other human antibody sequences. (Id., 13:32-37.)
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`Criterion III: Queen 1990 disclosed that non-human residues may be used
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`immediately adjacent to CDRs because “[t]hese amino acids are particularly likely
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`to interact with the amino acids in the CDR’s [sic]” or “interact directly with the
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`antigen.” (Id., 14:1-12.) Accordingly, Queen 1990 hypothesized that using non-
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`human residues at those positions may help maintain strong binding. (Id.)
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`Criterion IV: Queen 1990 used computer modeling, “typically of the
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`original donor antibody,” to identify other residues that “have a good probability of
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`interacting with amino acids in the CDR’s [sic] by hydrogen bonding, Van der
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`Waals forces, hydrophobic interactions, etc.” (Id., 14:14-19.) Non-human
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`residues