IN THE UNITED STATES PATENT AND TRADEMARK OFFICE
`_________________
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`_________________
`
`LUPIN LTD. and LUPIN PHARMACEUTICALS INC.
`
`Petitioners,
`
`v.
`
`HORIZON THERAPEUTICS, INC.
`
`Patent Owner.
`_________________
`
`IPR2016-00829
`
`DECLARATION OF KEITH VAUX, M.D.
`
`
`
`
`
`1 of 57
`
`

`
`
`
`Table of Contents
`
`I. QUALIFICATIONS ................................................................................................................ 1
`II.
`INFORMATION CONSIDERED ....................................................................................... 3
`III.
`SUMMARY OF OPINIONS AND EXPECTED TESTIMONY ........................................ 6
`IV. LEGAL STANDARDS ....................................................................................................... 6
`(i)
`Law of Obviousness ......................................................................................................... 6
`(ii)
`Person of Ordinary Skill in the Art .................................................................................. 9
`(iii) Claim Construction .......................................................................................................... 9
`V.
`BACKGROUND ............................................................................................................... 12
`(i)
`The ʼ559 Patent .............................................................................................................. 12
`(ii)
`The Urea Cycle and Nitrogen Scavenging Drugs .......................................................... 18
`VI. CLAIMS 1, 2, 4, 5, 7–10, 12, AND 13 OF THE ’859 PATENT WOULD HAVE BEEN
`OBVIOUS OVER BLAU, SIMELL, AND THE ’859 PUBLICATION ..................................... 25
`(i)
`Overview of Applied Prior Art ....................................................................................... 25
`(ii) Combining Applied Prior Art ......................................................................................... 28
`(iii)
`Independent Claims 1 and 2 ........................................................................................... 31
`(iv) Dependent Claim 4 ......................................................................................................... 38
`(v) Dependent Claim 5 ......................................................................................................... 39
`(vi) Dependent Claim 7 ......................................................................................................... 40
`(vii) Dependent Claim 8 ......................................................................................................... 40
`(viii) Dependent Claim 9 ..................................................................................................... 41
`(ix) Dependent Claim 10 ....................................................................................................... 42
`(x) Dependent Claims 12 and 13 ......................................................................................... 43
`(xi) Summary of Claims 1, 2, 4, 5, 7-10, 12 and 13.............................................................. 43
`VII. CLAIMS 3, 6, 11, 14, AND 15 OF THE ’859 PATENT WOULD HAVE BEEN
`OBVIOUS OVER BLAU, SIMELL, THE ’859 PUBLICATION, AND BRUSILOW ’84 ........ 44
`(i)
`Overview of Applied Prior Art ....................................................................................... 44
`(ii) Combining Applied Prior Art ......................................................................................... 45
`(iii)
`Independent Claim 3 ...................................................................................................... 46
`(iv) Dependent Claim 6 ......................................................................................................... 51
`(v) Dependent Claim 11 ....................................................................................................... 52
`(vi) Dependent Claims 14 and 15 ......................................................................................... 53
`(vii) Summary of Claims 3, 6, 11, 14 and 15 ......................................................................... 54
`
`
`
`
`
`2 of 57
`
`

`
`
`
`I, Keith Vaux, M.D., declare and state as follows:
`
`I. QUALIFICATIONS
`1.
`I am a medical doctor with specialty training in Pediatrics and
`
`Clinical Genetics. I am currently Professor and Clinical Chief of the Division of
`
`Medical Genetics in the Department of Medicine at UC San Diego. I also have an
`
`appointment as Professor of Neurosciences at UC San Diego, and I am a physician
`
`at Point Loma Pediatrics. Since 1994, I have regularly diagnosed and treated
`
`patients with urea cycle disorders (“UCD”), and continue to do so today. In
`
`treating UCD patients, I regularly prescribe nitrogen scavenging drugs and treat
`
`patients who are maintained on therapy with nitrogen scavenging drugs.
`
`2.
`
`I received a B.A. in History, Philosophy and Social Studies of
`
`Science and Medicine from the University of Chicago in 1987, and an M.D. from
`
`the University of Chicago in 1994. I have an unrestricted license to practice
`
`medicine in the State of California.
`
`3.
`
`After medical school, I completed a three year residency in
`
`pediatrics including a year as Chief Resident from 1994-1997, and a three year
`
`fellowship in dysmorphology and medical genetics with an additional certificate in
`
`teratology (environmentally induced birth defects) at UC San Diego from 2001 to
`
`2004. I am Board Certified by the American Board of Pediatrics (received in 1997
`
`and recertified in 2007 and 2015), am a Fellow of the American Academy of
`
`
`
`3 of 57
`
`

`
`
`
`Pediatrics and serve on the AAP National Council on Children with Disabilities
`
`and Society on Genetics and Birth Defects. I am a member of the California
`
`Department of Public Health, Genetic Diseases Screening Program Biobank
`
`Committee which address policy issues surrounding metabolic screening in
`
`newborns.
`
`4.
`
`I teach Medical Students, Medical and Pediatric Residents and
`
`Specialty Fellows in Genetics, Complex Care Pediatrics and Metabolic Diseases. I
`
`have published in peer reviewed Journals on metabolic disorders. I regularly speak
`
`at national and international conferences on a variety of genetic, metabolic and
`
`genomic medicine topics.
`
`5.
`
`A copy of my curriculum vitae, which sets forth my education and
`
`experience in further detail, is provided herewith as Exhibit 1003.
`
`6.
`
`I have been engaged as an expert on behalf of Petitioners Lupin, Ltd.
`
`and Lupin Pharmaceuticals, Inc. I am being compensated for my time at my
`
`standard consulting rate of $670/hour. My compensation in no way depends on the
`
`outcome of this proceeding or the content of my opinions.
`
`7.
`
`In the previous four years, I have testified by trial or deposition in
`
`the following matters:
`
` Montgomery v. USS/Clicker; mediation; July 2012;
`
` Fields v. Eli Lilly and Company; October 2014;
`
`
`
`
`2
`
`4 of 57
`
`

`
` Schomake v. Eli Lilly and Company; November 2014;
`
` Brookes Issue; February 2015.
`
`INFORMATION CONSIDERED
`8.
`
`In forming the opinions set forth herein, I have relied on my own
`
`
`
`II.
`
`experiences and knowledge. I have also considered the documents discussed
`
`herein, which include the following:
`
`a. U.S. Patent No. 9,059,559 (the “ʼ559 Patent) (Ex. 1001);
`
`b. Brusilow, et al., Treatment of Episodic Hyperammonemia in Children
`
`with Inborn Errors of Urea Synthesis, 310 The New England Journal
`
`of Medicine, 1630-1634 (1984) (“Brusilow’84”) (Ex. 1004);
`
`c. Simell, et al., Waste Nitrogen Excretion Via Amino Acid Acylation:
`
`Benzoate and Phenylacetate in Lysinuric Protein Intolerance, 20
`
`Pediatric Research, 1117-1121 (1986) (“Simell”) (Ex. 1005);
`
`d. Blau, Duran, Blaskovics, Gibson (editors), Physician’s Guide to the
`
`Laboratory Diagnosis of Metabolic Diseases, 261-276 (2d ed. 1996)
`
`(“Blau”) (Ex. 1006);
`
`e. U.S. Patent Publication No. 2010/0008859, filed January 7, 2009,
`
`published January 14, 2010 (the “’859 Publication”) (Ex. 1007);
`
`f. Scientific Discussion for Ammonaps, EMEA 2005, available at
`
`http://www.ema.europa.eu/docs/en_GB/document_library/EPAR_-
`
`
`
`
`3
`
`5 of 57
`
`

`
`_Scientific_Discussion/human/000219/WC500024748.pdf (“Scientific
`
`Discussion”) (Ex. 1008);
`
`g. Dixon, et al., Intercurrent Illness in Inborn Errors of Intermediary
`
`Metabolism, 67 Archives of Disease in Childhood, 1387-1391 (1992)
`
`(“Dixon”) (Ex. 1009);
`
`h. UMass Memorial Laboratories, Lab Updates, February 2007,
`
`Measurement of Ammonia in Blood (Ex. 1010);
`
`i. Brusilow, Phenylacetylglutamine May Replace Urea as a Vehicle for
`
`Waste Nitrogen Excretion, 29 Pediatric Research, 147-150 (1991)
`
`(“Brusilow ’91”) (Ex. 1011);
`
`j. Yajima, et al. Diurnal Fluctuations of Blood Ammonia Levels in
`
`Adult-Type Citrullinemia, 137 Tokohu J. Ex/ Med, 213-220 (1982)
`
`(“Yajima”) (Ex. 1012);
`
`k. Batshaw, et al., Treatment of Carbamyl Phosphate Synthetase
`
`Deficiency with Keto Analogues of Essential Amino Acids, 292 The
`
`New England J. Medicine, 1085-90 (1975) (“Batshaw”) (Ex. 1013);
`
`l. Kasumov, et al., New Secondary Metabolites of Phenylbutyrate in
`
`Humans and Rats, 32 Drug Metabolism and Disposition, 10-19 (2004)
`
`(“Kasumov”) (Ex. 1014);
`
`4
`
`
`
`
`
`
`6 of 57
`
`

`
`m. Barsotti, Measurement of Ammonia in Blood, 138 J. Pediatrics, S11-
`
`S20 (2001) (“Barsotti”) (Ex. 1015);
`
`n. Berry, et al., Long-term management of patients with urea cycle
`
`disorders, Journal of Pediatrics, Vol. 138, No. 1, S56–S61 (2001) (Ex.
`
`1016);
`
`o. Levin, et al., Hyperammonaemia A Variant Type of Deficiency of
`
`Liver Ornithine Transcarbamylas, Arch. Dis. Childh. 1969, 44, 162
`
`(1968) (“Levin”) (Ex. 1017);
`
`p. Prosecution History of U.S. Patent No. 8,404,215 (Ex. 1018);
`
`q. Excerpt from Stedman’s Medical Dictionary (Lippincott Williams &
`
`Wilkins 2006) (Ex. 1019);
`
`r. BUPHENYL® label, Physician’s Desk Reference, 60th ed. (2006), at
`
`3327–28 (Ex. 1020);
`
`s. AMMONUL® label, Physician’s Desk Reference, 60th ed. (2006), at
`
`3323–25 (Ex. 1021);
`
`t. Prosecution History of U.S. Patent No. 9,095,559 (Ex. 1022) (part 1
`
`of 2); and
`
`u. Prosecution History of U.S. Patent No. 9,095,559 (Ex. 1023) (part 2
`
`of 2).
`
`5
`
`
`
`
`
`
`7 of 57
`
`

`
`
`
`III. SUMMARY OF OPINIONS AND EXPECTED TESTIMONY
`9.
`I have reviewed the documents referenced above, in view of my own
`
`knowledge and experience concerning the treatment of UCD patients with nitrogen
`
`scavenging drugs. As explained in detail herein, it is my opinion that at the time of
`
`the alleged invention (September 2011), that a person of ordinary skill in the art
`
`would have been aware of and motivated to carry out methods of using a patient’s
`
`fasting plasma ammonia levels to guide treatment decisions with nitrogen
`
`scavenging drugs (including glyceryl tri-[4-phenylbutyrate]), including in patients
`
`who have a plasma ammonia level between half the upper limit of normal and the
`
`upper limit of normal for plasma ammonia.
`
`10. As of September 2011, it was also known that one could calculate an
`
`effective dosage glyceryl tri-[4-phenylbutyrate]) based on a mean conversion of
`
`glyceryl tri-[4-phenylbutyrate]) to urinary PAGN of 60 to 75%.
`
`IV. LEGAL STANDARDS
`(i)
`Law of Obviousness
`11. I have been informed that if the differences between the subject matter
`
`claimed in a patent and the prior art are such that the claimed subject matter as a
`
`whole would have been obvious to a person of ordinary skill at the time of the
`
`alleged invention, then the patent claim is unpatentable as obvious. I understand
`
`that the following factors must be evaluated in determining whether the claimed
`
`
`
`
`6
`
`8 of 57
`
`

`
`
`
`subject matter is obvious: (1) the scope and content of the prior art; (2) the
`
`differences between the claim and the prior art; (3) the level of ordinary skill in the
`
`art at the time the patent was filed; and (4) any “secondary considerations” of
`
`nonobviousness.
`
`12. I have been informed that “secondary considerations” of non-
`
`obviousness include: (i) any long-felt and unmet need in the art that was satisfied
`
`by the invention of the patent; (ii) failure of others to achieve the results of the
`
`invention; (iii) commercial success of products and processes covered by the
`
`invention; (iii) unexpected results achieved by the claimed invention; (iv)
`
`deliberate copying of the invention by others in the field; (v) taking of licenses
`
`under the patent by others; (vi) expressions of disbelief or skepticism by those
`
`skilled in the art upon learning of the invention; (vii) praise of the invention by
`
`others skilled in the art; and (viii) lack of contemporaneous and independent
`
`invention by others. I understand that evidence of potential secondary
`
`considerations must have a nexus to the claimed invention.
`
`13. I have been informed that at this time, Patent Owner has not identified
`
`any secondary considerations of nonobviousness. I reserve the right to respond to
`
`any secondary considerations that Patent Owner may raise.
`
`
`
`
`7
`
`9 of 57
`
`

`
`14. I have been informed that in the context of this proceeding, a claim will
`
`
`
`be found unpatentable as obvious if the preponderance of the evidence indicates
`
`that the claim would have been obvious.
`
`15. I have been informed that a claim can be obvious in light of multiple
`
`prior art references. I have been informed, however, that a patent claim is not
`
`obvious merely by demonstrating that each of its elements was, independently,
`
`known in the prior art. To be obvious in light of a combination of prior art
`
`references, there must have been a reason, at the time of the alleged invention, for
`
`a person of ordinary skill in the art to have combined the teachings of two or more
`
`references in order to achieve the claimed invention. This reason may come from a
`
`teaching, suggestion, or motivation to combine, or may come from the reference or
`
`references themselves, the knowledge or “common sense” of one skilled in the art,
`
`or from the nature of the problem to be solved, and may be explicit or implicit
`
`from the prior art as a whole.
`
`16. I have been informed that the combination of familiar elements
`
`according to known methods is likely to be obvious when it does no more than
`
`yield predictable results. I also understand it is improper to rely on hindsight in
`
`making the obviousness determination.
`
`
`
`
`8
`
`10 of 57
`
`

`
`(ii)
`Person of Ordinary Skill in the Art
`17. I have been informed that a patent is not written for the general public,
`
`
`
`but instead is directed to a “person of ordinary skill” in the field of the patent. I
`
`have been informed that factors such as the education level of those working in the
`
`field, the sophistication of the technology, the types of problems encountered in the
`
`art, the prior art solutions to those problems, and the speed at which innovations
`
`are made, help establish the level of skill in the art.
`
`18. For purposes of this declaration, I have been asked to assume that the
`
`date of the invention for the ’559 Patent is September 30, 2011.
`
`19. In my opinion, a person of ordinary skill in the art as of September 30,
`
`2011 would have been a physician with a M.D. degree with a residency in
`
`pediatrics or internal medicine, and would have had specialized training in the
`
`diagnosis or treatment of inherited metabolic disorders, such as UCDs and other
`
`nitrogen retention disorders.
`
`(iii)
`Claim Construction
`20. I have been informed that in the context of the current proceedings,
`
`each of the terms in the patent claims is given its broadest reasonable interpretation
`
`in light of the patent specification. I have reviewed the specification of the ʼ559
`
`patent, and I interpret the below claim terms under the “broadest reasonable”
`
`standard, as follows.
`
`
`
`
`9
`
`11 of 57
`
`

`
`21. According to the specification, “upper limit of normal” (“ULN”), which
`
`
`
`appears in each of the challenged claims, means “the highest level in the range of
`
`normal values.” (Ex. 1001 at 12:11–12.)
`
`22. Each of independent claims 1, 2, and 3, as well as dependent claims 5,
`
`6, and 8, recite a “fasting” plasma ammonia level. The plain and ordinary meaning
`
`of the term “fast” in the medical context means abstaining from at least food. See,
`
`e.g., Stedman’s Medical Dictionary (Lippincott Williams & Wilkins 2006) (Ex.
`
`1019). The specification of the ’559 patent makes clear that fasting means
`
`abstaining from at least food for a minimum of four hours:
`
`In certain embodiments of the methods disclosed
`
`herein, the fasting period for obtaining a fasting blood
`
`ammonia level is overnight. In certain embodiments,
`
`the fasting period is 4 hours or more, 5 hours or more,
`
`6 hours or more, 7 hours or more, 8 hours or more, 9
`
`hours or more, 10 hours or more, 11 hours or more, or
`
`12 hours or more, and in certain embodiments the
`
`fasting period is 4-8 hours, 6-8 hours, or 8-12 hours.
`
`(Ex. 1001, 10:23–29.) The specification also makes clear that fasting means that
`
`the subject preferably does not ingest any food, and in certain embodiments, some
`
`non-food substances (such as certain supplements, beverages, etc.):
`
`
`
`
`10
`
`12 of 57
`
`

`
`During the fasting period, the subject preferably does
`
`not ingest any food. In certain embodiments, the
`
`subject may also refrain from ingesting certain non-
`
`food substances during the fasting period. For
`
`example, in certain embodiments the subject does not
`
`ingest any supplements and/or nitrogen scavenging
`
`drugs during the fasting period. In certain of these
`
`embodiments, the subject may nonetheless ingest one
`
`or more drugs other than nitrogen scavenging drugs
`
`during the fasting period. In certain embodiments, the
`
`subject does not ingest any high calorie liquids during
`
`the fasting period. In certain of these embodiments, the
`
`subject does not ingest any liquids other than water
`
`during the fasting period. In other embodiments, the
`
`subject may ingest small amounts of low calorie
`
`beverages, such as tea, coffee, or diluted juices.
`
`
`
`(Id. at 10:30–44.) In view of specification and the plain and ordinary meaning of
`
`the term fasting, “fasting” plasma ammonia level means the plasma ammonia level
`
`in a person who has not eaten food for at least four hours.
`
`
`
`
`11
`
`13 of 57
`
`

`
`23. Claims 1, 2, and 6 require that the “adjusted dosage” is “greater than the
`
`
`
`initial dosage.” With regard to an adjusted dosage of glyceryl tri-[4-
`
`phenylbutyrate] that is greater than the initial dosage, the specification states:
`
`“Increasing the dosage of a nitrogen scavenging drug may refer to increasing the
`
`amount of drug per administration (e.g., an increase from a 3 mL dosage to a 6 mL
`
`dosage), increasing the number of administrations of the drug (e.g., an increase
`
`from once-a-day dosing to twice- or three-times-a-day), or any combination
`
`thereof.” (Id. at 10:20–25.) In view of this disclosure, an adjusted dosage that is
`
`“greater than the initial dosage” means a dosage that increases the amount of drug
`
`per administration, an increased number of administrations of the drug, or any
`
`combination thereof.
`
`24. In addition, I understand that each of the challenged claims contains the
`
`transition term “comprising.” I am informed that in the patent context, this term
`
`signals that the claims require the claimed method steps, but do not exclude
`
`additional steps.
`
`V. BACKGROUND
`(i) The ʼ559 Patent
`25. The ʼ559 Patent, titled “Methods of Therapeutic Monitoring of
`
`Nitrogen Scavenging Drugs,” provides a method for evaluating daily ammonia
`
`exposure based on a single fasting ammonia blood level measurement, as well as
`
`
`
`
`12
`
`14 of 57
`
`

`
`
`
`methods that utilize this technique to adjust the dosage of a nitrogen scavenging
`
`drug, determine whether to administer a nitrogen scavenging drug, and treat
`
`nitrogen retention disorders. (Ex. 1001 at Abstract.) I understand that the ’559
`
`Patent claims a filing date back to September 30, 2011 (“the priority date”), which
`
`is when Provisional Application No. 61/542,100 was filed.
`
`26. Specifically, the ’559 Patent claims a method for adjusting the dosage
`
`of the nitrogen scavenging drug glyceryl tri-[4-phenylbutyrate] in a patient who
`
`has a fasting plasma ammonia level less than the ULN for plasma ammonia, which
`
`involves measuring the patient’s fasting plasma ammonia level, comparing it to the
`
`ULN, and administering more drug if the fasting plasma ammonia level is greater
`
`than half the ULN. (Ex. 1001 at claim 1.)
`
`27. The ’559 Patent also claims a method of administering glyceryl tri-[4-
`
`phenylbutyrate] to a UCD patient, which involves measuring a first fasting plasma
`
`ammonia level, comparing it to the ULN, and administering drug if the fasting
`
`plasma ammonia level is greater than half the ULN and less than the ULN. (Ex.
`
`1001 at claim 3.)
`
`28. The ’559 Patent claims read:
`
`1. A method for adjusting the dosage of glyceryl tri-[4-
`phenylbutyrate] in a subject being treated for a urea cycle
`disorder who has previously been administered an initial
`dosage of glyceryl tri-[4-phenylbutyrate] and who has a
`
`
`
`
`13
`
`15 of 57
`
`

`
`fasting plasma ammonia level less than the upper limit of
`normal for plasma ammonia level, the method
`comprising:
`
`(a) measuring a fasting plasma ammonia level for
`the subject;
`
`(b) comparing the fasting plasma ammonia level to
`the upper limit of normal for plasma ammonia
`level; and
`
`(c) administering an adjusted dosage of glyceryl
`tri-[4-phenylbutyrate], wherein the adjusted dosage
`is greater than the initial dosage if the fasting
`plasma ammonia level is greater than half the
`upper limit of normal for plasma ammonia level.
`
`2. A method of treating a subject with a urea cycle
`disorder who has previously been administered an initial
`dosage of glyceryl tri-[4-phenylbutyrate] and who has a
`fasting plasma ammonia level less than the upper limit of
`normal for plasma ammonia level, the method
`comprising:
`
`(a) measuring a fasting plasma ammonia level for
`the subject;
`
`14
`
`
`
`
`
`
`16 of 57
`
`

`
`(b) comparing the fasting plasma ammonia level to
`the upper limit of normal for plasma ammonia
`level; and
`
`(c) administering an adjusted dosage of glyceryl
`tri-[4-phenylbutyrate] that is greater than the initial
`dosage if the fasting plasma ammonia level is
`greater than half the upper limit of normal for
`plasma ammonia level.
`
`3. A method of administering glyceryl tri-[4-
`phenylbutyrate] to a subject having a urea cycle disorder,
`the method comprising:
`
`(a) measuring a first fasting plasma ammonia level
`for the subject;
`
`(b) comparing the first fasting plasma ammonia
`level to the upper limit of normal for plasma
`ammonia level; and
`
`(c) administering an initial dosage of glyceryl tri-
`[4-phenylbutyrate] to the subject if the fasting
`plasma ammonia level is greater than half the
`upper limit of normal for plasma ammonia level
`and less than the upper limit of normal for plasma
`ammonia level.
`
`15
`
`
`
`
`
`
`17 of 57
`
`

`
`4. The method of claim 1 or 2, wherein administering the
`adjusted dosage of glyceryl tri[4-phenylbutyrate]
`produces a normal average daily ammonia level in the
`subject.
`
`5. The method of claim 4, further comprising repeating
`steps (a) to (c) until the subject exhibits a fasting plasma
`ammonia level at or below half the upper limit of normal
`for plasma ammonia level.
`
`6. The method of claim 3, further comprising:
`
`(d) measuring a second fasting plasma ammonia
`level for the subject;
`
`(e) comparing the second fasting plasma ammonia
`level to the upper limit of normal for plasma
`ammonia level; and
`
`(f) administering an adjusted dosage of glyceryl
`tri-[4-phenylbutyrate] that is greater than the initial
`dosage if the second fasting plasma ammonia level
`is greater than half the upper limit of normal for
`plasma ammonia level and less than the upper limit
`of normal for plasma ammonia level.
`
`7. The method of any of claims 1-3, wherein the upper
`limit of normal for plasma ammonia level is 35 µmol/L.
`8. The method of any of claims 1-3, wherein the upper
`
`16
`
`
`
`
`
`
`18 of 57
`
`

`
`limit of normal is specific to the laboratory in which the
`fasting plasma ammonia level is measured.
`
`9. The method of any of claims 1-3, further comprising
`the step of determining an upper limit of normal for
`plasma ammonia level for the subject prior to step (b).
`
`10. The method of claim 1 or 2, wherein the adjusted
`dosage is calculated by: (i) measuring urinary
`phenylacetyl glutamine (P AGN) output; and (ii)
`calculating an effective adjusted dosage of glyceryl tri-
`[4-phenylbutyrate] based on the urinary P AGN output,
`wherein the effective adjusted dosage is calculated based
`on a mean conversion of glyceryl tri-[4-phenylbutyrate]
`to urinary PAGN of 60 to 75%.
`
`11. The method of claim 3, wherein the initial dosage is
`calculated by: (i) determining a target urinary
`phenylacetyl glutamine (P AGN) output; and (ii)
`calculating an effective initial dosage of glyceryl tri-[4-
`phenylbutyrate] based on a mean conversion of glyceryl
`tri-[4-phenylbutyrate] to urinary PAGN of 60 to 75%.
`12. The method of claim 1, wherein the adjusted dosage
`of glyceryl tri-[4-phenylbutyrate] is administered orally.
`
`13. The method of claim 2, wherein the adjusted dosage
`of glyceryl tri-[4-phenylbutyrate] is administered orally.
`
`17
`
`
`
`
`
`
`19 of 57
`
`

`
`14. The method of claim 3, wherein the initial dosage of
`glyceryl tri-[4-phenylbutyrate] is administered orally.
`
`15. The method of claim 6, wherein the adjusted dosage
`of glyceryl tri-[4-phenylbutyrate] is administered orally.
`
`
`
`(ii) The Urea Cycle and Nitrogen Scavenging Drugs
`29. Prior to September 2011, using nitrogen scavenging drugs to treat
`
`nitrogen retention disorders was well known. (See, e.g., Ex. 1004 at 1631; Ex.
`
`1005 at 1118.) These drugs included phenylbutyrate, phenylacetate, sodium
`
`phenylbutyrate (sold as BUPHENYL®), sodium benzoate, glyceryl tri-[4-
`
`phenylbutyrate] (“HPN-100”), or a combination of two or more of HPN-100,
`
`phenylbutyrate, and sodium phenylbutyrate. (See, e.g., Ex. 1004 at 1631; Ex.
`
`1014 at 10–19; Ex. 1020; Ex. 1021.)
`
`30. Nitrogen retention disorders that may be treated with these nitrogen
`
`scavenging drugs include hepatic encephalopathy and UCDs. In the human body,
`
`the urea cycle is the major pathway for the excretion of waste nitrogen. Enzymes
`
`and transporters within the urea cycle synthesize urea from ammonia, which is then
`
`excreted in urine to remove excess nitrogen. In a patient with a UCD, an enzyme
`
`or transporter in the urea cycle is deficient, and, therefore, the patient is not able to
`
`remove excess nitrogen. The inability to remove excess nitrogen in these patients
`
`
`
`
`18
`
`20 of 57
`
`

`
`
`
`can lead to elevated plasma ammonia levels and hyperammonemia, which in turn
`
`can lead to lethargy, coma, brain damage, and death.
`
`31. In the human body, the urea cycle is the major pathway for the
`
`metabolism and excretion of waste nitrogen. Nitrogen enters the body as
`
`constituents of the amino acids in dietary protein. Amino acids that are not used
`
`for endogenous protein synthesis are broken down, forming pools of free amino
`
`acids, including glutamine and glycine. Ammonia is liberated during the
`
`breakdown of free amino acids and through the sequential actions of carbamoyl
`
`phosphate synthetase and the enzymes of the urea cycle, wherein two moles (a unit
`
`of measurement) of amino acid nitrogen (from free ammonia and aspartate) are
`
`converted into the two moles of nitrogen in urea. Urea is then excreted in urine,
`
`removing the excess nitrogen from the body. Each urea molecule removes two
`
`nitrogen molecules. The urea cycle works as follows:
`
`
`
`
`19
`
`21 of 57
`
`

`
`
`
`32. In UCD patients, enzymes or transporters in the urea cycle are deficient.
`
`This can cause excess dietary amino acids to be converted into ammonia that
`
`
`
`
`
`
`20
`
`22 of 57
`
`

`
`
`
`accumulates rather than get excreted, causing toxicity. It was well known prior to
`
`September 2011 that treating patients with UCDs involved achieving a balance
`
`between diet, amino acid supplementation, and use of nitrogen scavenging drugs.
`
`(Ex. 1016 at S56.) Nitrogen scavenging drugs that are metabolized to
`
`phenylacetate (including sodium phenylbutyrate and glyceryl tri-[4-
`
`phenylbutyrate] or HPN-100) provide an alternative mechanism for the clearance
`
`of glutamine in the form of phenylacetylglutamine (“PAGN”), which like urea,
`
`carries two nitrogen out of the body. Similarly, hippurate can be formed from the
`
`conjugation of glycine and benzoate to excrete one mole of nitrogen per mole of
`
`hippurate.
`
`33. Nitrogen scavenging drugs provide an alternative pathway to the urea
`
`cycle for waste nitrogen excretion. These drugs were known to remove waste
`
`nitrogen in both normal individuals and UCD patients. Known nitrogen
`
`scavenging drugs as of September 2011 included sodium benzoate, phenylacetic
`
`acid (“PAA”), and PAA prodrugs phenylbutyrate (“PBA”), sodium phenylbutyrate
`
`(“NaPBA,” sold as BUPHENYL®), and glycerl tri-[4-phenylbutyrate] (also known
`
`as “HPN-100”). (See, e.g., Ex. 1011 at 147–48; Ex. 1014 at 10–11, 13; Ex. 1020;
`
`Ex. 1021.)
`
`34. It was known that PAA prodrugs rapidly metabolize to PAA, and that
`
`PAA in turn metabolizes to PAGN. PAGN, like urea, removes two nitrogen
`
`
`
`
`21
`
`23 of 57
`
`

`
`
`
`molecules from the body. (Ex. 1011 at 147; Ex. 1015 at S13, S16; Ex. 1020; Ex.
`
`1021.) The removal of nitrogen by a PAA prodrug works as follows:
`
` 
`
`β‐oxidation 
`
`
`
`PAA prodrug 
`
`
`
`  
`
`Glutamine
`(2 moles N) 
`
`
`
` PAA 
`
` 
`
`PAGN 
`(2 moles of N) 
`
` 
`
`35. Nitrogen scavenging drugs greatly simplify the process of balancing
`
` 
`
`dietary intake of nitrogen with bodily demand in patients with UCDs. These
`
`medications act prior to the release of free ammonia, providing a shunt away from
`
`its formation. The inability to remove excess ammonia in these patients can lead to
`
`elevated plasma ammonia levels and hyperammonemia,1 which in turn can lead to
`
`lethargy, coma, brain damage, and death.
`
`36. Nitrogen scavenging drugs remove excess nitrogen to bring the plasma
`
`ammonia value back to a normal range. Further, it was taught in the prior art that
`
`
`1 Hyperammonemia is a metabolic disturbance that is characterized by an excess of
`
`ammonia in the blood.
`
`
`
`
`22
`
`24 of 57
`
`

`
`
`
`the conversion rate of PAA prodrugs into PAGN is 60%–75% in the body, and that
`
`this conversion rate can also be used to determine an effective dose of PAA
`
`prodrug to administer to a UCD patient. (Ex. 1007 at [0020], [0043], [0223].)
`
`37. Prior to September 2011, it was well known that the goal of treating
`
`UCD patients is to maintain plasma ammonia levels within normal ranges. (See,
`
`e.g., Ex. 1004 at 1631; Ex. 1008 at 10; Ex. 1020 at 3327 (“Laboratory Tests”
`
`section); Ex. 1007 at [0083], [0094]; Ex. 1016 at S58.) This involved regularly
`
`measuring a patient’s plasma ammonia levels and comparing them to the ULN.
`
`(See, e.g., Ex. 1004 at 1631; Ex. 1007 at [0083], [0094]; Ex. 1008 at 10.) It was
`
`also well known that the ULN of plasma ammonia levels will vary depending
`
`exactly on how it was measured, but that some clinical tests showed a normal
`
`range of less than 35 μM, which would place the ULN at 35 μM (See, e.g., Ex.
`
`1004 at 1632 (Fig. 1); Ex. 1007 at [0063], Fig. 13, [0094], [0201].)
`
`38. In practice, when measuring a patient’s plasma ammonia levels to
`
`compare it to the ULN, it was recommended to measure a fasting plasma ammonia
`
`level. (Ex. 1005 at 1118; Ex. 1006 at Table 11.9; Ex. 1015 at S11.) This fasting
`
`plasma ammonia level is important, as a person’s daily ammonia level will vary
`
`throughout the day, and in response to protein intake during meals. (Ex. 1006 at
`
`268, Table 11.5; Ex. 1012 at 213; Ex. 1015 at S19.) However, it was known that a
`
`fasting plasma ammonia level will typically be lower than the daily average plasma
`
`
`
`
`23
`
`25 of 57
`
`

`
`
`
`ammonia level in the patient and would show a smaller fluctuation within an
`
`individual. (Ex. 1012 at 214.)
`
`39. In practice, it was also well known prior to September 2011 that
`
`ammonia levels may be markedly influenced by the manner in which the sample
`
`was obtained (phlebotomy with and without a tourniquet, for example