`Patent Owner’s Observations on Cross-Examination
`
`Adam R. Brausa (Reg. No. 60,287)
`Daralyn J. Durie (Pro Hac Vice)
`DURIE TANGRI LLP
`217 Leidesdorff Street
`San Francisco, CA 94111
`
`
`
`
`Filed on behalf of Patent Owner Genentech, Inc. by:
`
`David L. Cavanaugh (Reg. No. 36,476)
`Lauren V. Blakely (Reg. No. 70,247)
`Robert J. Gunther, Jr. (Pro Hac Vice)
`Lisa J. Pirozzolo (Pro Hac Vice)
`Kevin S. Prussia (Pro Hac Vice)
`Andrew J. Danford (Pro Hac Vice)
`WILMER CUTLER PICKERING
` HALE & DORR LLP
`1875 Pennsylvania Ave., NW
`Washington, DC 20006
`
`
`UNITED STATES PATENT AND TRADEMARK OFFICE
`
`
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`
`
`PFIZER, INC. and
`SAMSUNG BIOEPIS CO., LTD.,
`Petitioners,
`v.
`GENENTECH, INC.,
`Patent Owner.
`
`Case IPR2017-014881
`U.S. Patent 6,407,213
`
`PATENT OWNER’S MOTION FOR OBSERVATIONS ON CROSS-
`EXAMINATION OF JEFFERSON FOOTE, PH.D.
`
`
`
`
`
` Case IPR2017-02139 has been joined with this proceeding.
`
`
`
`
`
`
`
`
`
`
`
`
` 1
`
`
`
`
`
`IPR2017-01488
`Patent Owner’s Observations on Cross-Examination
`Pursuant to the Joint Notice of Stipulation to Revise Schedule (Paper 53),
`
`Patent Owner Genentech, Inc. (“Patent Owner”) submits the following
`
`observations on cross-examination of Jefferson Foote, Ph.D. with respect to his
`
`testimony in support of Petitioner’s reply (Paper 56). The complete transcript of
`
`this cross-examination is submitted herewith as Exhibit 2059.
`
`1.
`
`In Exhibit 2059 at 21:1-4, 22:12-23:5, and 27:11-22, Dr. Foote
`
`admitted that Ex. 1069, a paper by Dr. Lutz Riechmann et al., “is not one of the
`
`references that Pfizer relies on as grounds for invalidity in its petition.” Dr. Foote
`
`further admitted that the humanized antibodies described in Ex. 1069 include
`
`substitutions at 27H and 30H, and that the claims of the ’213 patent do not recite
`
`substitutions at either of these positions. This testimony is generally relevant to
`
`Petitioners’ argument that a person of ordinary skill in the art would create a
`
`humanized antibody with substitutions that are recited in the claims of the ’213
`
`patent. (Paper 56, Petitioner Reply at 12-14.) In particular, this testimony is
`
`relevant to Dr. Foote’s testimony in paragraph 47 of his Reply Declaration (Ex.
`
`1202) in which he asserts that both the ’213 patent and the Riechmann paper (Ex.
`
`1069) state that candidates for FR substitution include those that may interact with
`
`CDRs.
`
`2.
`
`In Exhibit 2059 at 30:13-31:2 and 31:15-32:3, Dr. Foote admitted that
`
`the experimental example in Queen 1990 (Ex. 1050) “did not mention substitutions
`
`1
`
`
`
`IPR2017-01488
`Patent Owner’s Observations on Cross-Examination
`
`that are recited in the ’213 patent claims,” and that the particular substitutions
`
`made in Queen 1990 did not “overlap with the positions substituted in – or claimed
`
`in the ’213 [patent].” This testimony is generally relevant to Petitioners’ argument
`
`that a person of ordinary skill in the art following the teachings of the prior art
`
`would arrive at a humanized antibody with substitutions that are recited in the
`
`claims of the ’213 patent. (Paper 56, Petitioner Reply at 12-14, 18-21.) In
`
`particular, this testimony is relevant to Dr. Foote’s testimony in paragraphs 130-
`
`134 of his Reply Declaration (Ex. 1202) in which he disagrees with Dr. Wilson’s
`
`assertion that the Queen 1990 criteria are far too general and vague to disclose or
`
`suggest a specific humanized antibody with substitutions recited in the ’213 patent
`
`claims.
`
`3.
`
`In Exhibit 2059 at 33:10-35:3, Dr. Foote admitted that he did not
`
`provide a specific example of how a person of ordinary skill in the art would
`
`humanize a particular antibody using the techniques of Queen 1989 (Ex. 1034),
`
`Queen 1990 (Ex. 1050), or Kurrle (Ex. 1071) to identify the substitutions recited in
`
`the ’213 patent claims. According to Dr. Foote, “[t]hat might have been a good
`
`idea, but I didn’t do that.” This testimony is generally relevant to Petitioners’
`
`argument that a person of ordinary skill in the art would create a humanized
`
`antibody with substitutions that are recited in the claims of the ’213 patent. (Paper
`
`56, Petitioner Reply at 12-14, 18-21.) In particular, this testimony is relevant to
`
`2
`
`
`
`IPR2017-01488
`Patent Owner’s Observations on Cross-Examination
`
`Dr. Foote’s testimony in paragraphs 126-134 of his Reply Declaration (Ex. 1202)
`
`in which he disagrees with Dr. Wilson’s assertion that the Kurrle and Queen 1990
`
`criteria are far too general and vague to disclose or suggest a specific humanized
`
`antibody with substitutions recited in the ’213 patent claims.
`
`4.
`
`In Exhibit 2059 at 45:4-22 and 47:6-14, Dr. Foote admitted that
`
`Queen 1990 reported that the humanized anti-TAC antibody it describes had
`
`“approximately the same affinity” as the native murine anti-TAC antibody, and
`
`that Queen 1990 “does not specifically state anywhere that the humanized anti-
`
`TAC antibody that was tested and reported in Queen 1990 had a better binding
`
`affinity than the original murine antibody.” This testimony is generally relevant to
`
`Petitioners’ argument that the “up to 3-fold more” binding affinity limitation of
`
`claim 65 would have been obvious. (Paper 56, Petitioner Reply at 21-23.) In
`
`particular, this testimony is relevant to Dr. Foote’s testimony in paragraphs 176-
`
`177 of his Reply Declaration (Ex. 1202) in which he asserts that Queen 1990’s
`
`“testing showed its humanized antibodies may have 3 to 4 fold more binding
`
`affinity than the parent, within the limits of testing.”
`
`5.
`
`In Exhibit 2059 at 52:22-53:9 and 55:7-18, Dr. Foote stated that he is
`
`not aware of the PDB database containing any information with respect to the
`
`binding affinity of any particular antibody. This testimony is generally relevant to
`
`Petitioners’ argument that the “up to 3-fold more” binding affinity limitation of
`
`3
`
`
`
`IPR2017-01488
`Patent Owner’s Observations on Cross-Examination
`
`claim 65 would have been obvious. (Paper 56, Petitioner Reply at 21-23.) In
`
`particular, this testimony is relevant to Dr. Foote’s testimony in paragraphs 176-
`
`178 of his Reply Declaration (Ex. 1202) in which he states that “a skilled artisan
`
`would expect to be able to achieve around the same binding affinity as the parent
`
`and would not have been surprised of at least a moderate improvement in affinity.”
`
`6.
`
`In Exhibit 2059 at 63:16-64:4, 76:21-77:12, and 78:2-16 Dr. Foote
`
`admitted that of the four humanized antibody constructs reported in Kurrle (Ex.
`
`1071), Kurrle reported that two constructs (CIV1 and CIV2) did not bind to the
`
`target, and that Kurrle did not include any binding data whatsoever on one
`
`construct (CIV4). Dr. Foote further admitted that Kurrle reported that the final
`
`construct (CIV3) had approximately the same binding affinity as the native murine
`
`antibody, but that there was “no clear evidence that it’s better” than the native
`
`murine antibody. This testimony is generally relevant to Petitioners’ argument that
`
`the “up to 3-fold more” binding affinity limitation of claim 65 would have been
`
`obvious. (Paper 56, Petitioner Reply at 21-23.) In particular, this testimony is
`
`relevant to Dr. Foote’s testimony in paragraphs 176-178 of his Reply Declaration
`
`(Ex. 1202) in which he states that “a skilled artisan would expect to be able to
`
`achieve around the same binding affinity as the parent and would not have been
`
`surprised of at least a moderate improvement in affinity.”
`
`7.
`
`In Exhibit 2059 at 80:19-81:13 and 82:8-20, Dr. Foote admitted that
`
`4
`
`
`
`IPR2017-01488
`Patent Owner’s Observations on Cross-Examination
`
`Kabat 1987 (Ex. 1052) does not disclose the sequence of any humanized antibody,
`
`and does not directly report on the binding affinity of any antibodies. This
`
`testimony is generally relevant to Petitioners’ argument that the “up to 3-fold
`
`more” binding affinity limitation of claim 65 would have been obvious. (Paper 56,
`
`Petitioner Reply at 21-23.) In particular, this testimony is relevant to Dr. Foote’s
`
`testimony in paragraphs 176-178 of his Reply Declaration (Ex. 1202) in which he
`
`states that “a skilled artisan would expect to be able to achieve around the same
`
`binding affinity as the parent and would not have been surprised of at least a
`
`moderate improvement in affinity.”
`
`8.
`
`In Exhibit 2059 at 83:14-22, Dr. Foote admitted that Chothia 1985
`
`(Ex. 1063) does not disclose any humanized antibodies, much less anything
`
`comparing the binding affinity of a humanized antibody with a parent antibody.
`
`This testimony is generally relevant to Petitioners’ argument that the “up to 3-fold
`
`more” binding affinity limitation of claim 65 would have been obvious. (Paper 56,
`
`Petitioner Reply at 21-23.) In particular, this testimony is relevant to Dr. Foote’s
`
`testimony in paragraphs 176-178 of his Reply Declaration (Ex. 1202) in which he
`
`states that “a skilled artisan would expect to be able to achieve around the same
`
`binding affinity as the parent and would not have been surprised of at least a
`
`moderate improvement in affinity.”
`
`9.
`
`In Exhibit 2059 at 85:11-17, Dr. Foote admitted that Chothia and Lesk
`
`5
`
`
`
`IPR2017-01488
`Patent Owner’s Observations on Cross-Examination
`
`(Ex. 1062) does not disclose any humanized antibodies, much less anything
`
`comparing the binding affinity of a humanized antibody with a parent antibody.
`
`This testimony is generally relevant to Petitioners’ argument that the “up to 3-fold
`
`more” binding affinity limitation of claim 65 would have been obvious. (Paper 56,
`
`Petitioner Reply at 21-23.) In particular, this testimony is relevant to Dr. Foote’s
`
`testimony in paragraphs 176-178 of his Reply Declaration (Ex. 1202) in which he
`
`states that “a skilled artisan would expect to be able to achieve around the same
`
`binding affinity as the parent and would not have been surprised of at least a
`
`moderate improvement in affinity.”
`
`10.
`
`In Exhibit 2059 at 88:3-13, 90:15-21, 92:7-11, 93:11-20, and 96:19-
`
`97:1, Dr. Foote admitted that Tramontano (Ex. 1051) describes three papers
`
`reporting on humanized antibodies and/or humanized heavy chains, and that none
`
`reported any experimental results in which a humanized antibody obtained better
`
`binding affinity than the parent from which it was made. This testimony is
`
`generally relevant to Petitioners’ argument that the “up to 3-fold more” binding
`
`affinity limitation of claim 65 would have been obvious. (Paper 56, Petitioner
`
`Reply at 21-23.) In particular, this testimony is relevant to Dr. Foote’s testimony
`
`in paragraphs 176-178 of his Reply Declaration (Ex. 1202) in which he states that
`
`“a skilled artisan would expect to be able to achieve around the same binding
`
`affinity as the parent and would not have been surprised of at least a moderate
`
`6
`
`
`
`
`improvement in affinity.”
`
`IPR2017-01488
`Patent Owner’s Observations on Cross-Examination
`
`11.
`
`In Exhibit 2059 at 97:19-98:4, Dr. Foote admitted that Furey (Ex.
`
`1125) does not disclose any humanized antibodies, much less anything comparing
`
`the binding affinity of a humanized antibody with a parent antibody. This
`
`testimony is generally relevant to Petitioners’ argument that the “up to 3-fold
`
`more” binding affinity limitation of claim 65 would have been obvious. (Paper 56,
`
`Petitioner Reply at 21-23.) In particular, this testimony is relevant to Dr. Foote’s
`
`testimony in paragraphs 176-178 of his Reply Declaration (Ex. 1202) in which he
`
`states that “a skilled artisan would expect to be able to achieve around the same
`
`binding affinity as the parent and would not have been surprised of at least a
`
`moderate improvement in affinity.”
`
`12.
`
`In Exhibit 2059 at 99:3-11, Dr. Foote admitted that Hudziak (Ex.
`
`1021) does not disclose any humanized antibodies, much less anything comparing
`
`the binding affinity of a humanized antibody with a parent antibody. This
`
`testimony is generally relevant to Petitioners’ argument that the “up to 3-fold
`
`more” binding affinity limitation of claim 65 would have been obvious, as well as
`
`Petitioners’ argument that the prior art would lead a person of ordinary skill in the
`
`art to make a humanized antibody that binds p185HER2 and with one or more of the
`
`substitutions recited in the ’213 patent. (Paper 56, Petitioner Reply at 21-25.) In
`
`particular, this testimony is relevant to Dr. Foote’s testimony in paragraphs 176-
`
`7
`
`
`
`IPR2017-01488
`Patent Owner’s Observations on Cross-Examination
`
`178 of his Reply Declaration (Ex. 1202) in which he states that “a skilled artisan
`
`would expect to be able to achieve around the same binding affinity as the parent
`
`and would not have been surprised of at least a moderate improvement in affinity.”
`
`It is also relevant to Dr. Foote’s testimony in paragraphs 179-181 of his Reply
`
`Declaration (Ex. 1202) in which he states that a person of ordinary skill in the art,
`
`using routine skill and based on the prior art, would make a humanized antibody
`
`that binds p185HER2 and with one or more of the substitutions recited in the ’213
`
`patent.
`
`Date: June 22, 2018
`
`
`
`
`
`Respectfully submitted,
`
`/David L. Cavanaugh/
`David L. Cavanaugh
`Reg. No. 36,476
`
`WILMER CUTLER PICKERING HALE
`AND DORR LLP
`1875 PENNSYLVANIA AVENUE NW
`WASHINGTON, DC 20006
`TEL: 650-858-6000
`FAX: 650-858-6363
`EMAIL: david.cavanaugh@wilmerhale.com
`
`8
`
`
`
`IPR2017-01488
`Patent Owner’s Observations on Cross-Examination
`
`IPR2017-01488
`Patent Owner’s Exhibit List
`
`
`Exhibit Name
`
`Genentech, Inc. Laboratory Notebook No. 10098 (Leonard
`Presta)
`PROTECTIVE ORDER MATERIAL
`Genentech, Inc. Laboratory Notebook No. 10823 (Leonard
`Presta)
`PROTECTIVE ORDER MATERIAL
`Genentech, Inc. Laboratory Notebook No. 11268 (Paul Carter)
`PROTECTIVE ORDER MATERIAL
`Genentech, Inc. Laboratory Notebook No. 11643 (Paul Carter)
`PROTECTIVE ORDER MATERIAL
`Genentech, Inc. Laboratory Notebook No. 10840 (John Brady)
`PROTECTIVE ORDER MATERIAL
`Genentech, Inc. Laboratory Notebook No. 11162 (John Brady)
`PROTECTIVE ORDER MATERIAL
`Excerpts from Genentech, Inc. Laboratory Notebook No. 11008
`(Ann Rowland)
`PROTECTIVE ORDER MATERIAL
`Excerpts from Genentech, Inc. Laboratory Notebook No. 11297
`(Tim Hotaling)
`PROTECTIVE ORDER MATERIAL
`Excerpts from Genentech, Inc. Laboratory Notebook No. 11568
`(Monique Carver)
`PROTECTIVE ORDER MATERIAL
`Genentech, Inc. Interoffice Memorandum from Paul Carter to
`Leonard Presta and Dennis Henner
`PROTECTIVE ORDER MATERIAL
`Genentech, Inc. Interoffice Memorandum from Paul Carter to
`Leonard Presta
`PROTECTIVE ORDER MATERIAL
`Genentech, Inc. Synthetic DNA Requests
`PROTECTIVE ORDER MATERIAL
`Genentech, Inc. Synthetic DNA Requests
`PROTECTIVE ORDER MATERIAL
`
`Patent Owner’s
`Exhibit Number
`2001
`
`
`2002
`
`2003
`
`2004
`
`2005
`
`2006
`
`2007
`
`2008
`
`2009
`
`2010
`
`2011
`
`2012
`
`2013
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`Patent Owner’s
`Exhibit Number
`2014
`
`
`2015
`
`2016
`
`2017
`
`2018
`
`2019
`2020
`
`2021
`
`2022
`
`2023
`
`2024
`
`2025
`
`2026
`
`2027
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`IPR2017-01488
`Patent Owner’s Observations on Cross-Examination
`
`Exhibit Name
`
`Genentech, Inc. Protein Engineering of 4D5 Status Report
`PROTECTIVE ORDER MATERIAL
`Genentech, Inc. Interoffice Memorandum re: RCC Minutes and
`Recommendations
`PROTECTIVE ORDER MATERIAL
`Declaration of Dr. Leonard G. Presta
`PROTECTIVE ORDER MATERIAL
`Declaration of Dr. Paul J. Carter
`PROTECTIVE ORDER MATERIAL
`Declaration of John Ridgway Brady
`PROTECTIVE ORDER MATERIAL
`Declaration of Irene Loeffler
`Paul Carter, et al., Humanization of the Anti-p185 Antibody for
`Human Cancer Therapy, 89 PROC. NATL. ACAD. SCI. 4285-
`4289 (1992)
`Leonard Presta, et al., Humanization of an Anti-Vascular
`Endothelial Growth Factor Monoclonal Antibody for the
`Therapy of Solid Tumors and Other Disorders, 57 CANCER
`RESEARCH 4593-4599 (1997)
`Marianne Brüggerman, et al., The Immunogenicity of Chimeric
`Antibodies, 170 J. EXP. MED. 2153-2157 (1989)
`Jatinderpal Kalsi, et al., Structure-function Analysis and the
`Molecular Origins of Anti-DNA Antibodies in Systemic Lupus
`Erythematosus, EXPERT REVIEWS IN MOLECULAR MEDICINE 1-
`28 (1999)
`Scott Gorman, et al., Reshaping a Therapeutic CD4 Antibody,
`88 PROC. NATL. ACAD. SCI. 4181-4185 (1991)
`John Isaacs, et al., Humanised Monoclonal Antibody Therapy
`for Rheumatoid Arthritis, 340 THE LANCET 748-752 (1992)
`Elvin Kabat, et al., Sequences of Proteins of Immunological
`Interest 1-23 (4th ed. 1987)
`Anna Tramontano, et al., Framework Residue 71 Is a Major
`Determinant of the Position and Conformation of the Second
`Hypervariable Region in the VH Domains of Immunoglobulins,
`215 J. MOL. BIOL. 175-182 (1990)
`
`
`
`
`
`
`
`
`IPR2017-01488
`Patent Owner’s Observations on Cross-Examination
`
`Exhibit Name
`
`H.M. Shepard, et al., Herceptin, in THERAPEUTIC ANTIBODIES.
`HANDBOOK OF EXPERIMENTAL PHARMACOLOGY 183-219 (Y.
`Chernajovsky & A. Nissim, eds. 2008)
`Excerpt from Roche Finance Report 2016
`Modified Default Standing Protective Order and Patent
`Owner’s Certification of Agreement to Terms
`Modified Default Standing Protective Order – Redline
`File History for U.S. Patent Application No. 07/715,272
`Immunoglobulin Variants (filed June 14, 1991).
`Shearman, et al. Construction, expression and characterization
`of humanized antibodies directed against the human a/b T cell
`receptor. J. Immunol. 147(12):4366-4373, (December 15,
`1991)
`Declaration of Robert J. Gunther, Jr. in support of Motion for
`Admission Pro Hac Vice
`Declaration of Daralyn J. Durie in support of Motion for
`Admission Pro Hac Vice
`Declaration of Lisa J. Pirozzolo in support of Motion for
`Admission Pro Hac Vice
`Declaration of Kevin S. Prussia in support of Motion for
`Admission Pro Hac Vice
`Declaration of Andrew J. Danford in support of Motion for
`Admission Pro Hac Vice
`Deposition Transcript of Jefferson Foote, Pfizer, Inc. v.
`Genentech, Inc. (PTAB), Feb. 4, 2018
`Deposition Transcript of Timothy Buss, Pfizer, Inc. v.
`Genentech, Inc. (PTAB), Feb. 8, 2018
`Expert Declaration of Dr. Ian A. Wilson
`U.S. Patent No. 7,375,193
`U.S. Patent No. 7,560,111
`Leonard Presta, et al., Humanization of an Antibody Directed
`Against IgE, 151 J. IMMUNOLOGY 2623-2632 (1993)
`A. Bondi, van de Waals Volumes and Radii, 68 J. PHYSICAL
`CHEMISTRY 441-451 (1964)
`Reserved
`Reserved
`Reserved
`
`Patent Owner’s
`Exhibit Number
`2028
`
`
`2029
`2030
`
`2031
`2032
`
`2033
`
`2034
`
`2035
`
`2036
`
`2037
`
`2038
`
`2039
`
`2040
`
`2041
`2042
`2043
`2044
`
`2045
`
`2046
`2047
`2048
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`Patent Owner’s
`Exhibit Number
`2049
`
`2050
`
`2051
`
`
`2052
`
`2053
`
`2054
`
`2055
`
`2056
`
`2057
`
`2058
`
`2059
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`IPR2017-01488
`Patent Owner’s Observations on Cross-Examination
`
`Exhibit Name
`
`Reserved
`Reserved
`Man Sung Co, et al., Chimeric and Humanized Antibodies with
`Specificity for The CD33 Antigen, 148 J. IMMUNOLOGY 1149-
`1154 (1992)
`Trial Transcript – Vol. II, Sinomab Bioscience Ltd. v.
`Immunomedics, Inc., No. 2417-VCS (Del. Ch. Nov. 13, 2008)
`(Excerpted)
`Ole Brekke, et al., Therapeutic Antibodies for Human Diseases
`at the Dawn of the Twenty-First Century, 2 NATURE REVIEWS |
`DRUG DISCOVERY 52- 62 (2003)
`Thomas A. Waldmann, Monoclonal Antibodies in Diagnosis
`and Therapy, 252 SCIENCE 1657-1662 (1991)
`Greg Winter, et al., Antibody-Based Therapy: Humanized
`Antibodies, 14 TIPS 139-143 (1993)
`IPR2016-01694 Expert Declaration of Edward Ball, M.D. In
`Support of Petition for Inter Partes Review of Patent No.
`6,407,213
`About HNCs and HNDs, SCOTTISH QUALIFICATIONS AUTH.,
`https://www.sqa.org.uk/sqa/168.2432.html (last visited Feb. 6,
`2018)
`Redline of IPR2016-01694 Expert Declaration of Edward Ball,
`M.D. in Support of Petition for Inter Partes Review of Patent
`No. 6,407,213 and IPR2017-01488 Declaration of Timothy
`Buss
`Deposition Transcript of Jefferson Foote, Pfizer, Inc. v.
`Genentech, Inc. (PTAB), June 14, 2018
`
`
`
`
`
`
`
`
`
`
`