Case 1:18-cv-00924-CFC Document 399 Filed 10/07/19 Page 1 of 30 PageID #: 30385
`
`
`
`
`IN THE UNITED STATES DISTRICT COURT
`FOR THE DISTRICT OF DELAWARE
`
`
`GENENTECH, INC. and CITY OF HOPE, )
`
`
`
`
`
`
`
`)
`Plaintiffs and Counterclaim Defendants,
`
`)
`
`
`
`
`
`
`
`)
`
`
`
`v.
`
`
`
`)
`
`
`
`
`
`
`
`)
`AMGEN INC.,
`
`
`
`
`)
`
`
`
`
`
`
`
`)
`Defendant and Counterclaim Plaintiff.
`
`)
`
`
`
`
`
`
`
`)
`GENENTECH, INC. and CITY OF HOPE, )
`
`
`
`
`
`
`
`)
`Plaintiffs and Counterclaim Defendants,
`
`)
`
`
`
`
`
`
`
`)
`
`
`
`v.
`
`
`
`)
`
`)
`
`
`
`
`
`
`AMGEN INC.,
`
`
`
`
`)
`
`
`
`
`
`
`
`)
`Defendant and Counterclaim Plaintiff.
`
`)
`
`
`
`
`
`
`
`)
`
`
`
`
`C.A. No. 17-cv-1407-CFC (Consol.)
`
`C.A. No. 18-cv-924-CFC
`
`DECLARATION OF MICHAEL GLACKEN, Sc.D. REGARDING INDEFINITENESS
`OF “FOLLOWING FERMENTATION”
`
`
`
`
`
`
`
`
`
`
`

`

`Case 1:18-cv-00924-CFC Document 399 Filed 10/07/19 Page 2 of 30 PageID #: 30386
`
`Table of Contents
`
`
`Page
`
`BACKGROUND AND QUALIFICATIONS ................................................................... 1
`NATURE OF ASSIGNMENT .......................................................................................... 4
`LEGAL FRAMEWORK ................................................................................................... 5
`A.
`Person of Ordinary Skill in the Art (POSA) .......................................................... 5
`B.
`Claim Construction ................................................................................................ 6
`C.
`Indefiniteness ......................................................................................................... 7
`TECHNOLOGY BACKGROUND ................................................................................... 7
`A.
`Proteins and Antibodies ......................................................................................... 7
`B.
`Disulfide Bonds and the Role of Oxygen in Disulfide Bonds ............................. 10
`C.
`Protein and Antibody Manufacturing .................................................................. 12
`INVALIDITY OF THE ASSERTED CLAIMS OF THE ’869 PATENT FOR
`INDEFINITENESS OF “FOLLOWING FERMENTATION” ....................................... 15
`A.
`The Scope of “following fermentation” Differs Depending on Context and
`is Subjective ......................................................................................................... 16
`The '869 Patent Does Not Provide Reasonable Certainty on the Scope of
`“following fermentation” Within the Context of the Claimed Invention ............ 21
`Indefiniteness of “following fermentation” in View of Proposed Claim
`Constructions ....................................................................................................... 22
`1.
`Under Genentech's proposed construction, “following
`fermentation” is indefinite ....................................................................... 22
`Under Amgen's proposed construction, “following fermentation”
`would be definite...................................................................................... 25
`
`B.
`
`C.
`
`2.
`
`-i-
`
`
`
`
`I.
`II.
`III.
`
`IV.
`
`V.
`
`
`
`
`
`
`
`
`

`

`Case 1:18-cv-00924-CFC Document 399 Filed 10/07/19 Page 3 of 30 PageID #: 30387
`
`
`
`I, Dr. Michael Glacken, declare as follows:
`
`I.
`
`BACKGROUND AND QUALIFICATIONS
`
`1.
`
`I have been working with cell culture bioreactor processes and purification for
`
`biopharmaceutical manufacturing for more than 35 years and have a considerable amount of
`
`academic and industry experience on this subject matter.
`
`2.
`
`My mammalian cell culture bioreactor research career started in 1981 as a
`
`doctoral candidate at Massachusetts Institute of Technology. There, I completed my doctoral
`
`thesis in 1986 entitled “Development of mathematical descriptions of mammalian cell culture
`
`kinetics for the optimization of fed-batch bioreactors.” This work focused on characterizing
`
`those factors impacting the production of a monoclonal antibody in a fed-batch bioreactor of
`
`hybridoma cells. This thesis work included:
`
`3.
`
`Exploring the optimal levels of typical medium components, such as glucose and
`
`glutamine, in the basal and feed media (Glacken, M.W., E. Adema, and A.J. Sinskey,
`
`“Mathematical descriptions of hybridoma culture kinetics I:
`
` Initial metabolic rates.”
`
`Biotechnology and Bioengineering 32: 491-506, 1988; Glacken, M.W., R.J. Fleischaker, and
`
`A.J. Sinskey, “Reduction of waste product excretion via nutrient control: possible strategies for
`
`maximizing product and cell yields on serum in cultures of mammalian cells.” Biotechnology
`
`and Bioengineering 28: 1376-1389, 1986);
`
`4.
`
`Characterizing the stimulatory effect of thiol containing compounds, like
`
`glutathione and the amino acid cysteine, in low cell density and low serum level cultures
`
`(Glacken, M.W., E. Adema, and A.J. Sinskey, “Mathematical description of hybridoma culture
`
`kinetics II: The relationship between thiol chemistry and the degradation of serum activity,”
`
`Biotechnology and Bioengineering 33: 440-450, 1989); and
`
`
`
`- 1 -
`
`

`

`Case 1:18-cv-00924-CFC Document 399 Filed 10/07/19 Page 4 of 30 PageID #: 30388
`
`
`5.
`
`Developing optimal algorithms for feeding glutamine to fed-batch hybridoma
`
`bioreactors so as to minimize ammonia formation and maximize antibody production (Glacken,
`
`M.W., C. Huang, and A.J. Sinskey, “Mathematical descriptions of hybridoma culture kinetics III:
`
`Simulation of fed-batch bioreactors.” Journal of Biotechnology 10: 39-66, 1989).
`
`6.
`
`The publications stemming from this thesis work were very well received in the
`
`field, as they have been cited by at least 529 scientific journal articles since their publications.
`
`More than 40 of these journal articles that have cited my thesis work have been published in the
`
`last five years, indicating that my thesis work is still very relevant.
`
`7.
`
`After graduation, I became a member of the Chemical Engineering faculty at Rice
`
`University in Houston for 3 years. During this time, I gave five presentations at conferences and
`
`published a review article based in part on my research (Glacken, M.W., Catabolic control of
`
`mammalian cell culture. Biotechnology 6: 1041-1045 (1988).) This article was very well
`
`received in the field as it has been cited by at least 194 scientific journal articles since
`
`publication.
`
`8.
`
`After spending three years at Rice University, in 1990, I took a position as Senior
`
`Scientist at SmithKline Beecham (“SKB”) where I was responsible for developing large scale
`
`serum-free mammalian cell culture bioreactor processes producing recombinant proteins for
`
`human clinical trials. My group developed the first serum-free media feeding strategy for
`
`mammalian bioreactor processes at SKB, resulting in a several-fold increase in bioreactor
`
`product titer. Later during my tenure at SKB, I was given responsibility for the cell banking and
`
`cell culture media development group.
`
`9.
`
`In 1993, I joined Bristol Myers Squibb (“BMS”) to lead the bioreactor
`
`optimization group and eventually also became responsible for cell line development. Part of the
`
`
`
`- 2 -
`
`

`

`Case 1:18-cv-00924-CFC Document 399 Filed 10/07/19 Page 5 of 30 PageID #: 30389
`
`
`responsibilities for this group was to develop serum-free fed-batch bioreactor strategies. Due to
`
`resource and time constraints, BMS did not develop its own serum-free medium but instead
`
`worked with media vendors to customize its formulations to its cell lines and processes. This
`
`strategy for working with vendors to develop customized serum-free media was presented at a
`
`conference and published in the proceedings to that conference (Newell, A.H., E.G. Sutton, and
`
`M.W. Glacken, “Optimizing vendor proprietary serum-free media, in Animal Cell Technology:
`
`Developments Towards the 21st century, E.C. Beuvery, J.B. Griffiths, and W.P. Zeijlemaker
`
`(Eds), Kluwer Academic Publishers, Dordrecht, pp. 277-281, 1995.) One of the projects that
`
`employed this strategy was for a recombinant protein that eventually became the commercial
`
`product, Orencia® (abatacept).
`
`10.
`
`As part of my role in leading the bioreactor optimization group, I also developed
`
`control methods for bioreactors, including the control of dissolved oxygen concentration in the
`
`bioreactor. This strategy was published in Glacken, M.W. Instrumentation and Control Methods
`
`for Mammalian Cell Bioreactors. Genetic Engineering News 16: Sept (1995).
`
`11.
`
`Following my employment at BMS, I started my own private consulting
`
`company, Michael W. Glacken Consulting, where I consulted for various biotechnology and
`
`pharmaceutical clients.
`
`12.
`
`After private consulting, I joined Millennium Pharmaceuticals as Director of
`
`Process Development Technologies. Part of my responsibilities was to develop high-throughput
`
`serum-free media development technologies. These technologies were eventually spun out to a
`
`company called Xcellerex.
`
`13. While I was Vice President of Process Development Technologies and Services at
`
`Xcellerex, I gave a presentation at the 2004 BIO Conference describing the application of this
`
`
`
`- 3 -
`
`

`

`Case 1:18-cv-00924-CFC Document 399 Filed 10/07/19 Page 6 of 30 PageID #: 30390
`
`
`technology. (Glacken, M.W., “High Throughput Biopharmaceutical Process Development” BIO
`
`2004 Annual International Convention, San Francisco, CA, June 8, 2004).)
`
`14.
`
`In 2004, I returned to Millennium Pharmaceuticals and eventually led the
`
`Biologics Process Development group including cell culture process development and
`
`purification process development. In addition, I became the CMC (Chemistry, Manufacturing
`
`and Controls) lead for the project that would eventually become the commercial product
`
`Entyvio® (vedolizumab). Part of my group’s achievement was to develop a commercial
`
`mammalian cell fed-batch process using a serum-free medium formulation that my group
`
`developed in-house. Since Entyvio®’s launch in 2014, more than 1.5 billion dollars in sales has
`
`been achieved by Entyvio® produced by this serum-free medium process.
`
`15.
`
`I have also served as a peer reviewer for the journal Biotechnology and
`
`Bioprocess Engineering from 1988 to 1994.
`
`16.
`
`Betweeen 1992 – 2007, I served as an Industrial Course Instructor at the annual
`
`Bioprocess Technology Seminar Series sponsored by the American Society of Mechanical
`
`Engineers. I taught a session on “Instrumentation and Control of Animal Cell Culture Reactors”.
`
`17.
`
`A copy of my curriculum vitae, which describes in greater detail my professional
`
`experience, publications, and qualifications, is attached to this declaration as Exhibit 1.
`
`18.
`
`In the past four years, I have testified by deposition in Janssen Biotech, Inc. v.
`
`Celltrion Healthcare Co., Ltd. et al., C.A. No. 17-11008-MLW (D. Mass).
`
`19.
`
`The consulting company at which I am employed, the Bioprocess Technology
`
`Group (BTG) of the company BDO, is being compensated at the customary rate of $750 per hour
`
`of my consulting time. My compensation is not dependent on the outcome of this litigation.
`
`II.
`
`NATURE OF ASSIGNMENT
`
`20.
`
`I have been asked to opine regarding the indefiniteness of the claim term
`- 4 -
`
`
`
`

`

`Case 1:18-cv-00924-CFC Document 399 Filed 10/07/19 Page 7 of 30 PageID #: 30391
`
`
`“following fermentation” in U.S. Patent No. 8,574,869 (Ex. 2, the “’869 patent”).
`
`21.
`
`I have based my opinion regarding indefiniteness of “following fermentation” on
`
`the specification and file history of the ’869 patent, over 35 years of experience in the field, and
`
`on the other materials cited in this declaration.
`
`III. LEGAL FRAMEWORK
`Attorneys for Amgen have described to me the relevant law as it relates to the
`22.
`
`subject matter of this declaration. This section summarizes my understandings of the relevant
`
`legal standards.
`
`A.
`23.
`
`Person of Ordinary Skill in the Art (POSA)
`
`I understand that claim terms are interpreted from the perspective of a POSA at
`
`the time of the invention. I understand that a POSA is a hypothetical person who is presumed to
`
`have known the relevant art at the time of the alleged invention. I have been asked to assume
`
`that the relevant time of invention is July 9, 2007, which is the filing date of the earliest
`
`application listed on the first page of the ’869 Patent (Provisional Application No. 60/948,677)
`
`and the date Genentech has identified as the date of invention. In preparing my opinion, I have
`
`applied the POSA perspective as of the time of the alleged invention.
`
`24.
`
`I have been informed that the following factors may be considered in determining
`
`the level of ordinary skill: (A) type of problems encountered in the art; (B) prior art solutions to
`
`those problems; (C) rapidity with which innovations are made; (D) sophistication of the
`
`technology; and (E) educational level of active workers in the field.
`
`25.
`
`Based upon my review of the ’869 patent, I have concluded that the relevant art is
`
`the art of protein and/or antibody production.
`
`26.
`
`A person of ordinary skill in the art would have had a Ph.D. or Sc.D. in chemical
`
`engineering, molecular biology, or a closely related field, and at least 2-3 years of experience
`
`
`
`- 5 -
`
`

`

`Case 1:18-cv-00924-CFC Document 399 Filed 10/07/19 Page 8 of 30 PageID #: 30392
`
`
`related to protein and/or antibody production. A person of ordinary skill may have less formal
`
`education and more direct experience. Based on my review of the issues, if a person of ordinary
`
`skill in the art is considered to have greater skill or less skill than what I have defined, I do not
`
`think it would be likely to impact the analysis.
`
`B.
`27.
`
`Claim Construction
`
`I am informed that claim construction is the process of interpreting certain terms
`
`in the patent claims. Patent claims define the scope of the patented invention, and they must be
`
`definite in that they must particularly point out and distinctly claim the invention.
`
`28.
`
`I am informed that words in a claim are generally given their ordinary and
`
`customary meaning to a POSA, in view of the context of the claim language in which the term
`
`appears, other claims, the specification and figures of the patent, and the prosecution history. I
`
`understand that these sources are collectively called the “intrinsic” evidence and that claim terms
`
`must be interpreted in light of the “intrinsic” record because a POSA would read the term in the
`
`context of that evidence.
`
`29.
`
`I am also informed that a patentee may define a term in the specification and act
`
`as a lexicographer. I am informed by counsel that to act as a lexicographer, the patentee must
`
`clearly set forth a definition of the term that is different from its plain and ordinary meaning,
`
`doing so in a manner that expresses a clear intent to redefine the term.
`
`30.
`
`I am informed by counsel that the prosecution history, as part of the “intrinsic”
`
`record as noted above, can be informative for understanding the meaning of a claim term. I am
`
`informed that if the patentee makes clear and unambiguous disavowals of claim scope during
`
`prosecution, that a claim term should be interpreted to exclude the disclaimed or disavowed
`
`scope.
`
`
`
`31.
`
`I am informed by counsel that “extrinsic evidence” refers to evidence outside of
`- 6 -
`
`

`

`Case 1:18-cv-00924-CFC Document 399 Filed 10/07/19 Page 9 of 30 PageID #: 30393
`
`
`the intrinsic evidence, such as expert testimony, scientific articles not cited in the patent or
`
`prosecution history, and dictionary definitions. I am informed that extrinsic evidence can also be
`
`considered and may be useful in understanding the meaning of claim terms in view of the
`
`intrinsic evidence to one of ordinary skill in the art at the time of the alleged invention, but that
`
`extrinsic evidence is generally considered less significant than intrinsic evidence.
`
`C.
`32.
`
`Indefiniteness
`
`I understand that a patent claim must particularly point out and distinctly claim
`
`the subject matter that the patentee regards as his invention, see 35 U.S.C. § 112, ¶ 2, such that a
`
`POSA would understand the scope of the claim when it is read in light of the specification. I
`
`understand that a claim is invalid as “indefinite” if it includes terms that, when read in light of
`
`the specification and prosecution history, fail to inform a POSA about the scope of the invention
`
`with reasonable certainty.
`
`IV.
`
`TECHNOLOGY BACKGROUND
`
`33.
`
`34.
`
`This section provides selected points of the background of the technology.
`
`In preparing this background, I reviewed the Background Section in the
`
`“Declaration of Jeffrey Chalmers, Ph.D. in Support of Defendants’ Claim Construction Brief.”
`
`Based on my review, I agree with the general scientific principles in the Background Section of
`
`Dr. Chalmers’s declaration, and have accordingly used portions of that section in preparing the
`
`background description below.
`
`A.
`35.
`
`Proteins and Antibodies
`
`Proteins are biological molecules composed of amino acids. (See Ex. 2, ’869
`
`patent at APPX 0048:61-63 (p. 8:61-63).) A protein functions, in part, through its structure – a
`
`protein that acts by binding to another molecule does so because it has a particular three-
`
`dimensional shape. (See id. (’869 patent) at APPX 0045:33-37 (p, 1:33-37.)) Protein structure
`
`
`
`- 7 -
`
`

`

`Case 1:18-cv-00924-CFC Document 399 Filed 10/07/19 Page 10 of 30 PageID #: 30394
`
`
`classically involves four hierarchical levels: primary structure, secondary structure, tertiary
`
`structure, and quaternary structure. All structural levels contribute to a protein’s overall shape.
`
`(See Ex. 3, Alberts, Bruce, et al., Molecular Biology of the Cell, Fourth Edition, Garland Science
`
`Taylor & Francis Group, 2002 (“Alberts 2002”) at APPX 0112 (p. 140).)
`
`36.
`
`A protein’s primary structure is the most important contributor to its three-
`
`dimensional shape. (See Ex. 3 (Alberts 2002) at APPX 0101, 0112 (pp. 129, 140).) Primary
`
`structure refers to a protein’s amino acid sequence, with individual amino acids referred to as
`
`residues. (See Ex. 3 (Alberts 2002) at APPX 0112 (p. 140).) In proteins, amino acids chemically
`
`bind, one to another, to form amino acid chains of variable length. (See Ex. 2 (’869 patent) at
`
`APPX 0048:61-63 (p. 8:61-63); see Ex. 3 (Alberts 2002) at APPX 0101, 0112 (pp. 129, 148).)
`
`There are twenty amino acids, each with distinct chemical properties that can influence the other
`
`hierarchical levels of structure. (See Ex. 3 (Alberts 2002) at APPX 0101 (p. 129).)
`
`37.
`
`Secondary structure refers to distinct, local substructures that exist throughout a
`
`protein’s three-dimensional shape. The form of a substructure depends on the amino acid
`
`content (i.e., the primary structure) of a particular portion of an amino acid chain. For example,
`
`some amino acids are more stable when they interact with water whereas other amino acids
`
`benefit from being shielded from water. Amino acid chains containing both of these types of
`
`amino acids may form local substructures, such as helical or sheet-like substructures, that
`
`optimize the amino acids’ interactions with water. Amino acid chains often comprise a
`
`combination of both local substructures and relatively unstructured regions. (See Ex. 3 (Alberts
`
`2002) at APPX 0112, 0130 (pp. 140, 158).)
`
`38.
`
`Tertiary structure refers to the three-dimensional shape of a protein. The local
`
`substructures and other unstructured regions of an amino acid chain interact with each other to
`
`
`
`- 8 -
`
`

`

`Case 1:18-cv-00924-CFC Document 399 Filed 10/07/19 Page 11 of 30 PageID #: 30395
`
`
`form distinct three-dimensional conformations. (See Ex, 3 (Alberts 2002) at APPX 0112 (p.
`
`140).) Again, the amino acid content of the protein dictates how it will fold – for example,
`
`positively-charged amino acids may interact with negatively-charged amino acids, thus bringing
`
`two portions of the amino acid chain into close proximity. (See Ex. 3 (Alberts 2002) at APPX
`
`0130 (p. 158).) The tertiary structure is the highest-order structure for proteins with only a single
`
`amino acid chain. (See Ex. 3 (Alberts 2002) at APPX 01112 (p. 140).)
`
`39.
`
`For proteins composed of multiple amino acid chains, the highest-order structural
`
`level is the quaternary structure, which refers to how multiple amino acid chains interact with
`
`each other. (See Ex. 3 (Alberts 2002) at APPX 0112 (p. 140).) The same principles apply here
`
`as for secondary and tertiary structures: water-repelling amino acids may be shielded from water
`
`in the interior of the protein whereas amino acids that favorably interact with water may be
`
`moved to the exterior of the three-dimensional structure, and positively-charged and negatively-
`
`charged amino acids may interact, thus strongly linking two or more amino acid chains together.
`
`(See Ex. 3 (Alberts 2002) at APPX 0112, 0130 (pp. 140, 158).)
`
`40.
`
`Antibodies are a type of protein that specifically binds to other molecules. (See
`
`Ex. 2 (’869 patent) at APPX 0049:4-6 (p. 10:4-6).) They are composed of four amino acid
`
`chains, and thus four primary structures: two “heavy chains” and two “light chains,” described as
`
`such due to differences in their relative lengths. (See Ex. 3 (Alberts 2002) at APPX 0133 (p.
`
`161).) Antibodies are held together by all four levels of hierarchical structure, with the primary
`
`structure linking amino acids together in the heavy and light chains, secondary structure creating
`
`localized substructures that further stabilize the chains, tertiary structure establishing the three-
`
`dimensional structure of each chain, and the quaternary structure linking the chains together to
`
`form the antibody’s three-dimensional shape. (See Ex. 3 (Alberts 2002) at APPX 0112, 0114,
`
`
`
`- 9 -
`
`

`

`Case 1:18-cv-00924-CFC Document 399 Filed 10/07/19 Page 12 of 30 PageID #: 30396
`
`
`0133 (pp. 140, 142, 161).) Higher organisms produce antibodies as a component of their
`
`immune system. (See, e.g., Ex. 3 (Alberts 2002) at APPX 0136 (p. 164).) Because antibodies
`
`can bind specifically to other molecules, they have both therapeutic and non-therapeutic uses
`
`(e.g., as a research reagent). (See Ex. 2 (’869 patent) at APPX 0049:21-25, 0049:44-51 (pp,
`
`9:21-25, 9:44-51).)
`
`B.
`41.
`
`Disulfide Bonds and the Role of Oxygen in Disulfide Bonds
`
`One aspect of protein (and antibody) structure is disulfide bonds. Some proteins
`
`contain the amino acid cysteine interspersed throughout their primary structure. Cysteine
`
`residues contain chemical groups known as sulfhydryl groups, which are comprised of a sulfur
`
`atom and a hydrogen atom and often are referred to by the following designation: “—SH.” (See
`
`Ex. 3 (Alberts 2002) at APPX 0105, 0123-24 (pp. 133, 151-152).)
`
`42.
`
`For proteins, such as antibodies, a disulfide bond can be understood as a cross-
`
`linkage between the thiol groups of two cysteine amino acids. As shown in the figure below
`
`from Defendants' Claim Construction materials, the bond itself can be understood as a bridge or
`
`connection between the sulfur atoms in the cysteine residues:
`
`43.
`
`In what are known as “reducing” environments, sulfhydryl groups can maintain
`
`
`
`- 10 -
`
`
`
`
`
`

`

`Case 1:18-cv-00924-CFC Document 399 Filed 10/07/19 Page 13 of 30 PageID #: 30397
`
`
`their sulfur and hydrogen components. In “oxidizing” environments, sulfhydryl groups can lose
`
`their hydrogen atom, and the remaining sulfur atoms on two different cysteine residues can bind
`
`together, thereby linking the cysteine residues and forming a disulfide bond, often denoted as “—
`
`S—S—.” (See Ex. 3 (Alberts 2002) at APPX 0105, 0123-24 (pp. at 133, 151-152).) Disulfide
`
`bonds have been “reduced” if they have been broken due to exposure to a reducing environment.
`
`(See Ex. 2 (’869 patent) at APPX 0048:47-60 (p. 8:47-60).) Notably, “[d]isulfide bonds do not
`
`change the conformation of a protein but instead act as atomic staples to reinforce its most
`
`favored conformation.” (See Ex. 3 (Alberts 2002) at APPX 0123-24 (pp. 151-152).)
`
`44.
`
`Disulfide bonds
`
`in antibodies vary
`
`in
`
`their susceptibility
`
`to reducing
`
`environments. (See Ex. 2 (’869 patent) at APPX 0056:36-42 (p. 23:36-42).) These outcomes
`
`rely both on the overall structure of the antibody, including all levels of its hierarchical structure,
`
`as well as the chemical strength of the reducing environment. (See Ex. 3 (Alberts 2002) at
`
`APPX 0112, 0123-24 (pp. 140, 151-152).)
`
`45.
`
`In general, disulfide bonds are formed through oxidation of the sulfhydryl groups
`
`from two separate cysteine structures. Inversely, the reduction of disulfide bonds refers to when
`
`the connection between the sulfur atoms breaks apart as depicted generally below:
`
`
`
`- 11 -
`
`

`

`Case 1:18-cv-00924-CFC Document 399 Filed 10/07/19 Page 14 of 30 PageID #: 30398
`
`
`
`
`
`
`46.
`
`Proteins may have multiple disulfide bonds, each of which could be formed
`
`improperly and/or reduced and reformed improperly.
`
`C.
`47.
`
`Protein and Antibody Manufacturing
`
`Antibody manufacturers produce an antibody-of-interest by cultivating cells that
`
`have been genetically programmed to produce the antibody in a process known as cell culture.
`
`(See Ex. 2 (’869 patent) at APPX 0045 (p. 1:52-54).) Commercial cell culture operations are
`
`massive, with antibody manufacturers utilizing large tanks known as bioreactors to cultivate
`
`culture volumes on the order of thousands of liters. (See Ex. 2 (’869 patent) at APPX 0049:9-20
`
`(p. 9:9-20).) When producing an antibody-of-interest, commercial manufacturers include in the
`
`bioreactor, among other things, the cells programmed to generate the antibody, as well as culture
`
`medium. (See Ex. 2 (’869 patent) at APPX 0057 (p. 25:43-49).)
`
`48.
`
`Culture medium is a nutrient-rich liquid in which antibody-producing cells are
`
`
`
`- 12 -
`
`

`

`Case 1:18-cv-00924-CFC Document 399 Filed 10/07/19 Page 15 of 30 PageID #: 30399
`
`
`suspended during the culturing process. Culture medium provides, among other things, the
`
`nutrients that cells need to survive and produce the antibody-of-interest. (See Ex. 4, Butler,
`
`Michael, Animal cell cultures: recent achievements and perspectives in the production of
`
`biopharmaceuticals, Appl Microbial Biotechnology (2005) 68: 283-291 (“Butler 2005”) at APPX
`
`0223 (p. 286).) Antibody manufacturers understand the needs of a particular antibody-producing
`
`cell prior to using that cell for producing commercial amounts of the antibody-of-interest. (See
`
`Ex. 2 (’869 patent) at APPX 0057 (p. 25:36-39), APPX 0057 (p. 26:12-24), APPX 0068 (p.
`
`48:39-41); see also Ex. 5, Wurm, Florian, Production of recombinant protein therapeutics in
`
`cultivated mammalian cells, Nature Biotechnology, Vol. 22, No. 11 (November 2004) (“Wurm
`
`2004”) at APPX 0233 (p. 1397) (“Most high-yielding processes today are extended batch
`
`cultures . . . [t]he development of these extended batch processes requires a good understanding
`
`of the cell line and the product, and is usually only applied to processes that supply material for
`
`phase 3 clinical trials and for the market”).)
`
`49.
`
`Oxygen can be consumed during the manufacturing process and as a result,
`
`antibody manufacturers supplement the culture medium by “sparging,” or bubbling, oxygen-
`
`containing gas directly into the culture medium. (See Ex. 2 (’869 patent) at APPX 0056 (p.
`
`23:22-26), APPX 0070 (p. 51:18-21).) A “sparger” is a device incorporated into bioreactors as a
`
`standard component. A sparger is submerged below the surface of the culture medium and
`
`serves to bubble a desired gas into the culture medium. (See, e.g., Ex. 6, Bailey, James,
`
`Biochemical Engineering Fundamentals, McGraw-Hill, Inc. (1986) (“Bailey 1986”) at APPX
`
`0246 (p. 475).) When a sparger introduces, for example, pure oxygen into a bioreactor’s culture
`
`medium, a portion of that oxygen dissolves into the culture medium. (See, e.g., Ex. 6 (Bailey
`
`1986) at APPX 0238-39 (pp. 459-60).) The culture medium thus has a dissolved oxygen (“DO”)
`
`
`
`- 13 -
`
`

`

`Case 1:18-cv-00924-CFC Document 399 Filed 10/07/19 Page 16 of 30 PageID #: 30400
`
`
`content, and if that value drops below a certain level (again, determined through process
`
`development), the productivity of the culture could be impacted, including increased cell death.
`
`(See, e.g., Ex, 6 (Bailey 1986) at APPX 0329 (p. 639).)
`
`50.
`
`However, a bioreactor can be outfitted with means for monitoring and controlling
`
`its internal environment, including probes for measuring the dissolved oxygen (“DO”) content of
`
`the culture medium contained within. Therefore, if the culture medium’s DO content dips below
`
`a predetermined threshold, the DO probe will send a signal to a monitoring system (usually
`
`computer software) that will then cause oxygen, or an oxygen-containing gaseous mixture, to be
`
`supplemented into the culture medium via the sparger. (See Ex. 2 (’869 patent) at APPX 0068
`
`(p. 48:37-39); see also Ex. 6 (Bailey 1986) at APPX 0340-42 (pp. 661-64) and APPX 0345 (pp.
`
`700-01).)
`
`51.
`
`It is worth noting that antibody manufacturers introduce numerous gases into
`
`bioreactor-contained culture medium. For example, while antibody manufacturers may
`
`introduce pure oxygen into the culture medium to boost the culture medium’s DO content, they
`
`also may introduce carbon dioxide to modify the culture medium’s pH in response to a signal
`
`from a pH probe. (See Ex. 2 (’869 patent) at APPX 0070 (p. 51:15-18).) Antibody
`
`manufacturers may also sparge air into bioreactor-contained culture medium. (See Ex. 2 (’869
`
`patent) at APPX 0056 (p. 23:22-26:42), APPX 0070 (p. 51:10-26).)
`
`52.
`
`The ’869 patent presents a typical antibody production process using cells
`
`genetically engineered to produce an antibody-of-interest. The patent provides that “[o]nce the
`
`cells have undergone several rounds of replication, they are transferred to a larger container
`
`where they are prepared to undergo fermentation.” (Ex. 2 (’869 patent) at APPX 0045 (p. 1:54-
`
`57).) The ’869 patent does not state what “fermentation” is or when “fermentation” ends. The
`
`
`
`- 14 -
`
`

`

`Case 1:18-cv-00924-CFC Document 399 Filed 10/07/19 Page 17 of 30 PageID #: 30401
`Case 1:18-cv-00924-CFC Document 399 Filed 10/07/19 Page 17 of 30 PageID #: 30401
`
`patent does state that “[flollowing fermentation proteins are purified.” (Id. at APPX 0057 (p.
`
`26:41).)
`
`53.
`
`Sparging has been a well-known option for introducing air into a culture fluid for
`
`decades. Those of skill in the art treated sparging as a standard option for introducing air (and
`
`oxygen) to a fluid at all stages of the protein/antibody manufacturing process. As discussed in
`
`more detail below, the ’869 patent claims relate to the use of sparging with air “following
`
`ferementation” to purportedly prevent disulfide bond reduction.
`
`V.
`
`INVALIDITY or THE ASSER'I'ED CLAIMS OF THE ’869 PATENT FOR INDEFINITENESS 0F
`
`“FOLLOWING FERMENTATION”
`
`54.
`
`The claim term “following fermentation” appears in claim 1 of the ’869 patent,
`
`which is reproduced below with underlining to indicate the claim language at issue. I understand
`
`that Plaintiffs have asserted claims 5 and 8 in this case. Claims 5 and 8 depend from
`
`independent claim 1 either directly or indirectly.
`
`I have included below all of the claims in the
`
`chain of dependency.
`
`Claim
`
`Asserted
`
`.
`
`A method for the prevention of the reduction of a
`disulfide bond in an antibody expressed in a recombinant
`host cell, comprising, following fermentation, sparging
`the pre-harvest or harvested culture
`fluid of said
`recombinant host cell with air, wherein the amount of
`dissolved oxygen (d02) in the pre-harvest or harvested
`culture fluid is at least 10%.
`
`5
`
`7
`
`The method of claim 1 wherein the host cell is eukaryotic
`
`55.
`
`Based on my review of the claim language,
`
`the patent specification,
`
`the
`
`-15-
`
`
`
`Asserted
`
`The method of claim 1 wherein the antibody is a
`
`-- therapeutic antibody.
`-_—
`“-—a mammalian host cell.
`
`

`

`Case 1:18-cv-00924-CFC Document 399 Filed 10/07/19 Page 18 of 30 PageID #: 30402
`
`
`prosecution history, and the extrinsic evidence, in my opinion a POSA would not understand
`
`with reasonable certainty the scope of “following fermentation” as it appears in the ’869 patent
`
`claims.
`
`A.
`
`The Scope of “following fermentation” Differs Depending on