IN THE UNITED STATES PATENT AND TRADEMARK OFFICE
`_______________
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`_______________
`
`ARGENTUM PHARMACEUTICALS LLC,
`Petitioner,
`
`v.
`
`RESEARCH CORPORATION TECHNOLOGIES, INC.,
`Patent Owner.
`
`Case No. IPR2016-00204
`Patent No. RE38551
`
`DECLARATION OF WILLIAM R. ROUSH, PH.D.,
`IN SUPPORT OF PATENT OWNER RESPONSE
`PURSUANT TO 37 C.F.R. § 42.120
`
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`IPR2016-00204
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`TABLE OF CONTENTS
`
`I.
`
`II.
`
`PRELIMINARY STATEMENT .................................................................... 1
`
`BACKGROUND AND QUALIFICATIONS ................................................ 2
`
`III.
`
`SUMMARY OF OPINIONS ........................................................................ 10
`
`IV. TECHNICAL BACKGROUND .................................................................. 11
`
`A. Key Organic Chemistry Principles ..................................................... 11
`1.
`Aromatic and Aliphatic Carbon Molecules ............................. 13
`2.
`Substituted Carbon Molecules ................................................. 14
`3.
`Stereochemistry—Racemic Compounds and Enantiomers ..... 16
`4.
`Amino Acids ............................................................................ 26
`The Unpredictable Art of Drug Development ................................... 27
`1.
`Biological and Physical Considerations in Drug
`Development. ........................................................................... 30
`Lead Compound Identification ................................................ 36
`The Difficulty of Predicting Effects of Structural
`Changes .................................................................................... 37
`
`2.
`3.
`
`B.
`
`V.
`
`THE ’551 PATENT ...................................................................................... 46
`
`A. Overview ............................................................................................ 46
`B.
`Claims of the ’551 Patent ................................................................... 50
`1.
`Claims 1-9 ................................................................................ 50
`2.
`Claim 10 ................................................................................... 51
`3.
`Claims 11-13 ............................................................................ 51
`Level of Ordinary Skill in the Art ...................................................... 52
`The Board’s Claim Construction........................................................ 54
`
`C.
`D.
`
`VI. STATE OF THE PRIOR ART ..................................................................... 54
`
`A.
`
`Judith D. Conley & Harold Kohn, Functionalized DL-Amino
`Acid Derivatives. Potent New Agents for the Treatment of
`Epilepsy, 30 J. Med. Chem. 567 (1987) (Exhibit 2004)
`(“Conley 1987”) ................................................................................. 55
`1.
`The results of modifications at the α-carbon. .......................... 59
`2.
`The results of modifications at the N-benzylamide. ................ 62
`3.
`The results of modifications at the N-acetyl. ........................... 64
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`B.
`
`C.
`
`E.
`F.
`
`Harold Kohn et al., Marked Stereospecificity in a New Class of
`Anticonvulsants, 457 Brain Res. 371 (1988) (Exhibit 2053)
`(“Kohn 1988”) .................................................................................... 65
`Harold Kohn et al., Preparation and Anticonvulsant Activity of
`a Series of Functionalized α-Aromatic and α-Heteroaromatic
`Amino Acids, 33 J. Med. Chem. 919 (1990) (Exhibit 1018)
`(“Kohn 1990”) .................................................................................... 67
`D. Harold Kohn et al., Preparation and Anticonvulsant Activity of
`a Series of Functionalized α-Heteroatom-Substituted Amino
`Acids, 34 J. Med. Chem. 2444 (1991) (Exhibit 1012) (“Kohn
`1991”) ................................................................................................. 71
`U.S. Patent No. 5,378,729 (Exhibit 1009) (“the ’729 patent”) .......... 77
`Harold Kohn et al., Synthesis and Anticonvulsant Activities of
`α-Heterocyclic α-Acetamido-N-Benzylacetamide Derivatives,
`36 J. Med. Chem. 3350 (1993) (Exhibit 1017) (“Kohn 1993”) ......... 80
`G. Harold Kohn et al., Anticonvulsant Properties of N-Substituted
`α,α-Diamino Acid Derivatives, 83 J. Pharmaceutical Sci. 689
`(May 1994) (Exhibit 2055) (“Kohn 1994”) ....................................... 88
`Patrick Bardel et al., Synthesis and Anticonvulsant Activities of
`α-Acetamido-N Benzylacetamide Derivatives Containing an
`Electron-Deficient α-Heteroaromatic Substituent, 37 J. Med.
`Chem. 4567 (1994) (Exhibit 2056) (“Bardel 1994”) ......................... 90
`Silverman, R. B., The Organic Chemistry of Drug Design and
`Drug Action, Academic Press (1992) (Exhibit 1013)
`(“Silverman”) ..................................................................................... 93
`
`H.
`
`I.
`
`VII. A POSA WOULD NOT HAVE SELECTED A FUNCTIONALIZED
`AMINO ACID AS A LEAD COMPOUND WHEN SEARCHING
`FOR A NEW ANTI-EPILEPTIC DRUG ..................................................... 96
`
`A. No FAA Compound Had Been Approved by the FDA. .................... 96
`B.
`No FAA Compound Was Included in Cumulative Reviews of
`Potentially Promising AEDs. ........................................................... 101
`The Mode of Action and Target of FAAs in Preventing
`Seizures Was Not Understood.......................................................... 102
`There Was Not Yet Enough Data for a POSA to Have a
`Reasonable Understanding of FAA Properties, Let Alone SAR. .... 103
`
`D.
`
`C.
`
`VIII. A POSA WOULD NOT HAVE SELECTED THE
`METHOXYAMINO COMPOUND 31 AS A LEAD COMPOUND. ....... 107
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`A.
`
`B.
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`2.
`
`The State of the Art as of March 1996. ............................................ 107
`1.
`Identifying potential AED candidates was challenging
`and highly unpredictable. ....................................................... 107
`The state of the art demonstrated that the SAR of the
`numerous areas for modification on the FAA backbone
`was not sufficiently advanced to draw reasonable
`expectations about each modification’s biological impact. ... 108
`Even Assuming a POSA Would Select an FAA as a Lead
`Compound, a POSA Would Not Have Selected the
`Methoxyamino Compound (Kohn 1991 Compound 3l) as a
`Lead Compound. .............................................................................. 130
`
`IX. EVEN ASSUMING, ARGUENDO, THAT A POSA WOULD
`SELECT AN FAA AS A LEAD COMPOUND, AND WOULD
`HAVE SELECTED THE METHOXYAMINO COMPOUND
`(KOHN 1991 COMPOUND 3L) AS A LEAD COMPOUND, A
`POSA WOULD NOT HAVE MODIFIED COMPOUND 3L INTO
`THE COMPOUNDS OF CLAIMS 1-9 WITH A REASONABLE
`EXPECTATION OF SUCCESS. ............................................................... 135
`
`X.
`
`CLAIMS 10-13 ........................................................................................... 154
`
`XI. UNEXPECTED RESULTS ........................................................................ 156
`
`XII. LONG FELT NEED/FAILURE OF OTHERS .......................................... 160
`
`XIII. SKEPTICISM ............................................................................................. 163
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`XIV. CONCLUSION ........................................................................................... 164
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`I.
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`PRELIMINARY STATEMENT
`
`I, WILLIAM R. ROUSH, Ph.D., hereby state as follows:
`
`1.
`
`I have been retained as a consultant on behalf of Research
`
`Corporation Technologies, Inc. (“RCT”), the patent owner in the present
`
`proceeding. I understand that the petition names Argentum Pharmaceuticals LLC
`
`(“Argentum”) as the petitioner, and that Intelligent Pharma Research LLC, APS
`
`GP LLC, and APS GP Investors LLC have been identified as real parties-in-
`
`interest. I further understand that KVK-TECH, Inc. has also been identified as a
`
`potential real party-in-interest. I have no financial interest in, or affiliation with,
`
`the petitioner, the identified actual or potential real parties-in-interest, or the patent
`
`owner. I am being compensated for my work at my usual and customary
`
`consulting rate, and my compensation is not dependent upon the outcome of, or my
`
`testimony in, the present inter partes review or any litigation proceedings.
`
`2.
`
`I have reviewed the Petition for Inter Partes Review of Patent
`
`No. RE38,551 (“the ’551 Patent”) filed by Argentum Pharmaceuticals LLC,
`
`including Dr. Wang’s Declaration, as well as the exhibits and articles cited in those
`
`documents. I have also reviewed the articles and documents cited in this
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`declaration.
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`3.
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`I am aware of information generally available to, and relied
`
`upon by, persons of ordinary skill in the art at the relevant times. Some statements
`
`below are expressly based on such awareness.
`
`II. BACKGROUND AND QUALIFICATIONS
`I am Professor of Chemistry and Executive Director of
`4.
`
`Medicinal Chemistry of the Scripps Research Institute in Jupiter, Florida (“Scripps
`
`Florida”). Until July 1, 2016, I was also the Associate Dean of the graduate school
`
`at Scripps Florida. A copy of my curriculum vitae is attached as Exhibit 2037.
`
`My educational background and my professional experience are summarized
`
`below.
`
`5.
`
`I obtained a Bachelor of Science degree in Chemistry from the
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`University of California, Los Angeles in 1974, graduating summa cum laude. I
`
`obtained my Ph.D. in Chemistry from Harvard University in 1977. My Ph.D.
`
`thesis concerned the synthesis of a natural product known as dendrobine.
`
`Synthesis is the process by which a molecule is constructed from available
`
`precursors. Syntheses of natural products (e.g., dendrobine) or of drug substances
`
`frequently involve multi-step sequences.
`
`6.
`
`After a year of post-doctoral work at Harvard (1977-78), I
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`joined the faculty at the Massachusetts Institute of Technology (MIT) as an
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`Assistant Professor of Chemistry. I taught chemistry courses and performed
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`research at MIT from 1978 to 1987. My research interests included the total
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`synthesis of natural products and the development of new synthetic methods.
`
`7.
`
`In 1987, I moved to Indiana University, where I ultimately
`
`became Distinguished Professor of Chemistry. At Indiana University, I initiated a
`
`research program on the design and synthesis of inhibitors of cysteine proteases.
`
`These inhibitors, designed to combat certain tropical parasitic diseases, are
`
`chemical compounds which prevent (i.e., inhibit) an enzyme, specifically a
`
`cysteine protease, from performing an essential chemical reaction in the parasite,
`
`resulting in the death of the microorganism. The majority of these inhibitors are
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`dipeptide derivatives and are synthesized starting from amino acids.
`
`8.
`
`In 1997, I was appointed the Warner-Lambert/Parke-Davis
`
`Professor of Chemistry at the University of Michigan. This is an endowed chair
`
`established by a gift from Parke-Davis to the University of Michigan. I
`
`subsequently served as the Chairman of the Department of Chemistry at the
`
`University of Michigan from 2002–2004. While at the University of Michigan, I
`
`served as Co-Director of the Life Sciences Initiative Commission, which conceived
`
`the Life Sciences Institute (LSI), and laid out the blueprint for its creation and
`
`development to stimulate interdisciplinary research in the biomedical sciences. I
`
`also continued to develop my research program focusing on the synthesis of
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`biologically active natural products, the development of new synthetic
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`methodology, and the design and development of inhibitors of cysteine proteases.
`
`9.
`
`In 2004, I was recruited to join the Scripps Research Institute at
`
`its new campus in Florida. I assumed three positions—Executive Director of
`
`Medicinal Chemistry, Professor of Chemistry, and Associate Dean of the Kellogg
`
`School of Science and Technology—in 2005. Scripps Florida is a branch of the
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`well-known Scripps Research Institute, which is headquartered in La Jolla,
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`California. The Scripps Research Institute is one of the leading biomedical
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`research institutes in the world and is internationally recognized for its
`
`commitment to, and its basic research in, the fields of immunology, biology,
`
`chemistry, neurosciences, virology, autoimmune and cardiovascular diseases, and
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`synthetic vaccine development. Particularly significant is the Scripps Research
`
`Institute’s study of the basic structure and design of biological molecules.
`
`10. As Associate Dean of the graduate program at Scripps Florida, I
`
`developed and led the graduate program on the Jupiter campus, until July 1, 2016.
`
`11.
`
`I currently serve as Executive Director of Medicinal Chemistry
`
`in the Drug Discovery Division of Scripps’ Translational Research Institute at
`
`Scripps Florida. In this position, I direct the research of twelve to sixteen (12–16)
`
`staff medicinal chemists who are charged with performing structure-activity
`
`relationship (“SAR”) studies to optimize drug candidates for several drug
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`discovery projects internal to Scripps. Projects at Scripps Florida that have been
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`performed under my directorship, or are still active, include the development and
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`optimization of enzyme inhibitors for cancer targets, central nervous system
`
`diseases (e.g., Parkinson’s disease), and metabolic diseases, among others. In
`
`addition, I personally direct an academic research program with twelve (12)
`
`graduate students and postdoctoral associates that is funded primarily by the
`
`National Institutes of Health (“NIH”). This program includes medicinal chemistry
`
`research projects focusing on development of agonists and antagonists of nuclear
`
`receptors, development of inhibitors of enzyme targets (including kinases, cysteine
`
`proteases, metallomatrix proteinases, histone deacetylates, and cytochrome P51,
`
`among others) and development of inhibitors of transporters responsible for active
`
`transport of molecules into and out of cells. In addition to the latter work, we are
`
`also actively pursuing strategies to utilize amino acid transporters to deliver drugs
`
`to the brain.
`
`12.
`
`I am currently engaged in an NIH funded project to develop a
`
`novel class of prodrugs—antibody-drug conjugates—in which the antibody targets
`
`specific cells, and the drug is cleaved by enzymes within the cell after the
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`conjugate is internalized. Specific cleavage mechanisms being pursued include use
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`of peptide linkers (to connect the drug to the antibody) that are specifically targeted
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`by enzymes inside the cancer cell.
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`13.
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`In addition to the research on Parkinson’s disease, see ¶11, I am
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`currently leading efforts to develop a brain penetrant kinase inhibitor targeting
`
`glioblastoma (brain cancer). Through my work as a consultant with
`
`pharmaceutical companies, I have provided advise on multiple projects focusing on
`
`brain penetrant CNS active drugs.
`
`14.
`
`I am well-known for my research on the synthesis of natural
`
`products, development of new synthetic methodology(with a focus on new
`
`methods for enantioselective synthesis), and medicinal chemistry. While at MIT,
`
`Indiana University, the University of Michigan, and now at Scripps Florida, I have
`
`synthesized more than twenty-five (25) stereochemically complex, optically active
`
`natural products and more than six hundred (600) cysteine protease inhibitors, two
`
`of which have undergone detailed preclinical evaluation. The vast majority of the
`
`cysteine protease inhibitors are optically active molecules synthesized from amino
`
`acid precursors.
`
`15. An important aspect of my work is understanding the
`
`biochemistry of the biological drug targets. I frequently work with biologists and
`
`pharmacologists on projects, and I regularly review and assess the results of
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`biological experiments and use those results to make decisions about how to
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`further improve the compounds that are the subjects of these medicinal chemistry
`
`research projects.
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`16. From 2007 through 2014 I served as the Chairman of the
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`Chemistry Coordination Committee of the Scripps Molecular Screening Center,
`
`which was one of four centers forming the Molecular Libraries Production Centers
`
`Network (MLPCN), an NIH-funded program which screened potential drug targets
`
`and performed SAR studies to optimize potential drug candidates.
`
`17.
`
`I have served a five-year term on the NIH Medicinal Chemistry
`
`Study Section, including two years as Chair. The Medicinal Chemistry Study
`
`Section reviewed research proposals in medicinal chemistry submitted to the NIH,
`
`and ranked these applications in terms of their scientific merit.
`
`18.
`
`I have presented my research in more than two hundred (200)
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`invited lectures at universities and pharmaceutical companies. In addition, I have
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`been invited to deliver more than one hundred (~115) named, keynote, or plenary
`
`lectures at universities national and international symposia, and conferences. All
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`of the invited, named, keynote, and plenary lectures that I have presented during
`
`my career have been based on my research on compound synthesis and/or the
`
`biological evaluation of specific compounds that I have synthesized. A significant
`
`number of these lectures have focused on the synthesis of optically active,
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`stereochemically complex molecules.
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`19. Over the course of my academic career, I have taught many
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`undergraduate and graduate courses in organic chemistry. The graduate courses
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`have focused mainly on asymmetric synthesis, which is the making of
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`stereochemically complex, optically active molecules.
`
`20.
`
`I have also repeatedly taught a two-and-a-half day short course
`
`entitled “Recent Advances in Organic Synthesis Methodology: Stereocontrolled
`
`Synthesis of Acyclic Organic Compounds” to members of the pharmaceutical
`
`industry in the United States, Canada, and Europe. The typical participants in this
`
`course are medicinal chemists with B.S., M.S., or Ph.D. backgrounds.
`
`21.
`
`I have published extensively in the scientific literature and have
`
`authored or co-authored over three hundred forty (340) papers relating to organic
`
`synthesis and medicinal chemistry. This includes more than fifty (50) scientific
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`articles dealing specifically with the synthesis and biochemical and/or biological
`
`evaluation of small molecule inhibitors of protein targets as well as more than one
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`hundred ninety-five (195) scientific articles dealing specifically with the synthesis
`
`and evaluation of optically active compounds.
`
`22.
`
`I have received a number of awards for my research, including
`
`the Arthur C. Cope Scholar Award (1994) from the American Chemical Society,
`
`the Paul G. Gassmann Distinguished Service Award from the American Chemical
`
`Society Division of Organic Chemistry (2002), and the Ernest Guenther Award in
`
`the Chemistry of Natural Products from the American Chemical Society (2004). In
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`2006, I was elected a Fellow of the American Association for the Advancement of
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`Science, and in 2009, I was elected a Fellow of the American Chemical Society.
`
`23.
`
`I was an Associate Editor of the Journal of the American
`
`Chemical Society from 1999-2016. In addition, I am on the editorial board of
`
`Organic Letters and previously served on the editorial advisory board of Chemical
`
`Biology and Drug Design. I am also a member of the Boards of Directors of
`
`Organic Syntheses, Inc. and Organic Reactions, Inc., which publish the Organic
`
`Syntheses and Organic Reactions monographs.
`
`24.
`
`In my position as Associate Editor of the Journal of the
`
`American Chemical Society, I was regularly called on to make editorial decisions
`
`to accept or to reject manuscripts relating to general medicinal chemistry topics,
`
`many of which deal with compound synthesis.
`
`25.
`
`I also regularly consult with pharmaceutical and biotechnology
`
`companies. These consultations focus, in general, on aspects of medicinal
`
`chemistry, synthetic chemistry, and process chemistry for companies engaged in
`
`drug discovery and development. I also participate, as a consultant, in strategic
`
`planning exercises. The companies I currently consult with are Eli Lilly and
`
`Company and IFM Therapeutics. In the past I have also consulted with Pfizer Inc.,
`
`Genzyme Corporation, ArQule Inc., NeXstar Pharmaceuticals Inc., Lycera
`
`Corporation, and GMP Immunotherapeutics, among others.
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`26.
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`I consider myself to be an expert in organic chemistry,
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`including one in the field of medicinal chemistry.
`
`III. SUMMARY OF OPINIONS
`In my opinion, a POSA would not have selected an
`27.
`
`Functionalized Amino Acid (“FAA”) as a lead compound, as explained more fully
`
`below. See ¶¶195-219. No FAA had been FDA-approved as an antiepileptic drug
`
`(AED) or was recognized in the review literature as a promising compound. A
`
`POSA would have had very little data on FAAs as potential AEDs. Thus, for these
`
`and other reasons, a POSA would not have reasonably expected the compound of
`
`claims 1-9 to be a successful AED.
`
`28. Even if a POSA would have considered selecting an FAA as a
`
`lead compound, such a person would not have selected Kohn 1991 Compound 3l,
`
`as explained more fully below. See ¶¶220-273. It is clear that Dr. Wang has made
`
`his lead compound selection based on hindsight. A POSA would have understood,
`
`among other things, that as of March 1996, the limited data showed that the most
`
`promising FAAs were compounds that contained heteroaromatic substituents at the
`
`α-carbon and substituted benzylamide substituents.
`
`29. Even if a POSA would have selected Kohn 1991 Compound 3l
`
`as a “lead compound,” she would not have modified the compound to arrive at the
`
`compounds of claims 1-9, and in particular, the compound of claims 1-9, let alone
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`reasonably expected that such modification would create a successful AED, as
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`explained more fully below. See, e.g., ¶¶274-300.
`
`30. Claims 10 and 11-13 claim therapeutic compositions containing
`
`the compound of claims 1-9 and methods of using the compound of claims 1-9. In
`
`my opinion, because a POSA would not reasonably expect that claims 1-9 would
`
`be successful AEDs, a POSA would similarly not reasonably expect that such
`
`compounds could be used in 1) therapeutic compositions or 2) methods of treating
`
`central nervous system disorders. See, e.g., ¶¶301-303.
`
`31. Lacosamide, as an embodiment of claims 1-5 and 7-13
`
`exhibited unexpected results. See, e.g., ¶¶304-309. There was a long-felt need for
`
`new AEDs in March of 1996, which many others had tried and failed to achieve.
`
`See, e.g., ¶¶310-314. Finally, there is evidence of skepticism in the field, as
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`evidenced by Eli Lilly’s determination to terminate its FAA program, despite
`
`knowing about, for example, Compound 3l. See, e.g., ¶¶315-317.
`
`IV. TECHNICAL BACKGROUND
`A. Key Organic Chemistry Principles
`In general, organic molecules are carbon-based molecules.
`32.
`
`However, organic molecules normally also contain hydrogen, as well as other
`
`types of atoms such as nitrogen, oxygen, sulfur, chlorine, fluorine, and phosphorus.
`
`These other types of atoms are often referred to as “heteroatoms.”
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`33. Compounds for pharmaceutical use developed by medicinal
`
`chemists are typically organic compounds. In the chemical arts, specific
`
`nomenclature is used from which a compound may be transcribed, typically into a
`
`two-dimensional pictorial illustration. The transcription of a compound from name
`
`to two-dimensional illustration itself can be cumbersome, complex, and time-
`
`consuming, depending on the complexity of the underlying chemical name. There
`
`are also ways to name and depict in a two-dimensional illustration certain three-
`
`dimensional characteristics of a molecule, most particularly stereochemistry, which
`
`I will discuss in more detail below. The actual three-dimensional configuration of
`
`a molecule, however, may be very complex, and the recitation of a chemical name
`
`or a two-dimensional illustration would not generally capture that three-
`
`dimensional configuration. I have included below an overview of the
`
`nomenclature used in this report to facilitate an understanding of the various
`
`compound names.
`
`34. When drawing chemical structures, chemists generally omit the
`
`“C,” which denotes a carbon atom. Instead, organic and medicinal chemists
`
`represent carbon through the terminus or apex of the straight-line drawing. The
`
`hydrogen atoms attached to these carbons are also omitted. Because carbon forms
`
`four bonds, each terminus is assumed to contain the appropriate number of bonded
`
`hydrogens to satisfy each carbon’s four-bond requirement.
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`H2
`C
`
`CH3
`
`H3C
`
`Carbon atoms
`
`
`
`35. Another shorthand used by chemists is to depict single, double,
`
`and triple chemical bonds by single, double, and triple lines, respectively. These
`
`conventions have been adopted for representing the chemical structures discussed
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`below, and for the chemical structures throughout this report.
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`Aromatic and Aliphatic Carbon Molecules
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`1.
`36. Carbon containing molecules are divided roughly into two
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`types: aromatic molecules and aliphatic molecules. Aromatic molecules are
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`unusually stable—meaning the carbon-carbon bonds of an aromatic molecule are
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`difficult to break—and usually have a flat three-dimensional orientation. These
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`properties are due to the unique electronic configuration of aromatic molecules. In
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`contrast, aliphatic molecules lack these unique electronic properties. The most
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`common aliphatic molecules are straight and branched carbon chains, and saturated
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`and unsaturated rings.1 The carbon atoms can all be bound only to hydrogen atoms
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`and other carbon atoms (“unsubstituted”), or other atoms may be bonded to the
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`carbon atoms (“substituted”).
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`1 A compound is “unsaturated” when the carbon is doubly or triply bonded to
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`another carbon, or if rings are present.
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`Substituted Carbon Molecules
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`2.
`37. Organic molecules often include “substituents” as part of their
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`overall structure. A substituent is an atom, or group of atoms, that is substituted in
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`place of a hydrogen atom on the carbon backbone of an organic molecule. The
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`total structure of the organic molecule—which consists of the carbon backbone,
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`the substituents, and the orientation of these components in space (referred to as
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`molecular conformation)—determines how the molecule will act in a biological
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`system. The substituents are therefore a critical element of the organic molecule,
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`particularly in medicinal chemistry applications. At issue in this case are
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`substituents such as alkyl groups (e.g., –CH3, –CH2CH3), alkoxy groups (e.g.,
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`methoxy groups, abbreviated as “OMe” or “OCH3”), and halogens (e.g., fluorine,
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`or “F”).
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`38. One way a substituent affects the overall biological properties
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`of a molecule is by modulating the electronic properties of the carbon atom to
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`which the substituent is attached. Although the ultimate effect of a particular
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`substituent on a particular carbon atom requires analysis of the cumulative effects
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`of the surrounding atoms on that carbon atom, it is well known that certain
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`substituent groups tend to cause certain electron donating or electron withdrawing
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`effects. These effects depend on the identity of the particular substituent as well as
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`the electronic configuration of the particular carbon to which the substituent is
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`attached. These differences are caused by the electronic properties of resonance
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`and induction. For example, a particular substituent, like a methoxy group, will
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`affect the electronic properties of a carbon in aromatic compounds differently than
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`a carbon in an aliphatic group. It is well known that an alkoxy group, like
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`methoxy, will be electron donating when attached to an aromatic carbon, but will
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`be electron withdrawing when attached to an aliphatic carbon. See, e.g., Exhibit
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`2040 J. March, Advanced Organic Chemistry, John Wiley& Sons, New York, N.Y.
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`(1985) at 17 and 238 (hereinafter, “March Textbook”).
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`39. Several of these points are illustrated by the structures below.
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`An unsubstituted benzene ring (called a “phenyl group” when used as a
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`substituent), for example, is a six-carbon ring with single- and double-bonds
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`resonating between adjacent carbon atoms and one hydrogen atom bonded to each
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`carbon atom (to make a total of four bonds per carbon atom):
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`
`“Benzene”
`(unsubstituted)
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`40. A substituted phenyl group discussed in this case is a
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`fluorobenzyl group; that is, a phenyl group attached as a substituent to a one
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`carbon unit, that also contains a fluorine substituent on the phenyl ring. Fluorine is
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`an electron withdrawing group, regardless of whether it is attached to an aromatic
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`carbon or an aliphatic carbon. The structure of p-fluorobenzyl is depicted below;
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`the wavy line denotes the point of attachment to the rest of the molecule:
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`
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`“a fluorobenzyl group”
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`3.
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`Stereochemistry—Racemic Compounds and
`Enantiomers
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`41.
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`“Stereochemistry” is a branch of organic chemistry dealing with
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`the configuration of molecules in three-dimensional space.
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`42. Organic chemists use the following terms to describe the gross
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`structural characteristics of compounds. For example:
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`(a) “Isomers” are chemical compounds that have the same molecular
`formula but different structures (i.e., the number and type of atoms are
`the same, but the way the atoms are connected to each other is different).
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`(b) “Stereoisomers” are chemical compounds that have the same number
`and type of atoms and identical atomic connectivity; stereoisomers differ
`in the way in which the atoms are oriented in three-dimensional space;
`
`(d) “Enantiomers” are pairs of stereoisomers that are non-
`superimposable mirror image isomers of each other. Enantiomers occur
`if a molecule contains an asymmetric carbon atom. An asymmetric
`carbon atom (which is also referred to in the literature as a “stereogenic
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`center,” as a “center of chirality,” or as a “chiral” carbon atom) has four
`different atoms or groups of atoms attached to it.
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`(e) “Diastereomers” are stereoisomers with two or more asymmetric
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`carbon atoms that are not mirror image isomers. The term “epimer” is
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`often used to refer to a specific asymmetric carbon atom in a molecule
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`that is different from the same center in a second diastereomer. This case
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`involves several examples of diastereomers.
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`(f) “Racemates” or “racemic mixtures