`
`
`
`
`
`UNITED STATES PATENT AND TRADEMARK OFFICE
`___________
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`___________
`
`
`INITIATIVE FOR MEDICINES, ACCESS & KNOWLEDGE (I-MAK), INC.
`Petitioner
`
`v.
`
`GILEAD PHARMASSET LLC
`Patent Owner
`
`___________
`
`Case No. IPR2018-00123
`U.S. Patent No. 8,735,372
`
`
`
`
`
`
`PETITION FOR INTER PARTES REVIEW
`
`

`

`TABLE OF CONTENTS
`
`I.
`
`INTRODUCTION ........................................................................................... 1
`
`II. MANDATORY NOTICES ............................................................................. 1
`
`A. Real Parties-in-Interest (37 C.F.R. § 42.8(b)(1)) .................................. 1
`
`B.
`
`C.
`
`D.
`
`Related Matters (37 C.F.R. § 42.8(b)(2)) .............................................. 2
`
`Lead and Back-Up Counsel (37 C.F.R. § 42.8(b)(3)) ........................... 2
`
`Service Information (37 C.F.R. § 42.8(b)(4)) ....................................... 2
`
`III. REQUIREMENTS FOR REVIEW ................................................................. 3
`
`A. Grounds For Standing ........................................................................... 3
`
`B.
`
`Identification of Challenge .................................................................... 3
`
`IV. OVERVIEW OF THE ‘372 PATENT ............................................................ 4
`
`V.
`
`FILE HISTORY OF THE ‘372 PATENT ....................................................... 5
`
`VI. PERSON OF ORDINARY SKILL IN THE ART .......................................... 5
`
`VII. CLAIM CONSTRUCTION ............................................................................ 6
`
`VIII. BACKGROUND KNOWLEDGE IN THE ART ........................................... 6
`
`A.
`
`The Use of Nucleoside Analogs As Antiviral Agents And Their
`Mechanism of Action Were Known...................................................... 7
`
`B. Anti-Viral Nucleosides Must Be Converted Into Their Triphosphates
`To Be Active, Monophosphorylation Was The Rate-Limiting Step In
`Such Conversion, and 5’-Phosphate Prodrugs – in Particular
`Phosphoramidates - Enabled Nucleosides To Overcome This
`Limitation ............................................................................................ 11
`
`C.
`
`The Means Were Available To Determine Which Nucleosides Were
`Kinase Dependent................................................................................ 15
`
`i
`
`

`

`D. Narrowing The Selections For The Phosphoramidate Prodrug .......... 15
`
`E.
`
`F.
`
`Phosphoramidates Improved Nucleosides .......................................... 24
`
`The ‘372 Patent Acknowledges This Common Knowledge ............... 25
`
`G. Nucleoside NS5B Inhibitors Were Combined With Other Antiviral
`Agents, Including NS5A Inhibitors, To Treat HCV ........................... 27
`
`IX. SCOPE AND CONTENT OF THE PRIOR ART ......................................... 31
`
`A.
`
`B.
`
`C.
`
`Sofia ..................................................................................................... 31
`
`Congiatu .............................................................................................. 33
`
`Serrano-Wu ......................................................................................... 35
`
`X. CLAIMS 1 AND 2 ARE UNPATENTABLE ............................................... 36
`
`A. Ground 1: Claims 1-2 Were Obvious Over Sofia, Congiatu and
`Serrano-Wu ......................................................................................... 36
`
`XI. CONCLUSION .............................................................................................. 47
`
`XII. APPENDIX – LIST OF EXHIBITS .............................................................. 48
`
`XIII. CERTIFICATE OF COMPLIANCE ............................................................ 49
`
`XIV. CERTIFICATE OF SERVICE ...................................................................... 50
`
`
`
`
`
`ii
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`

`

`I.
`
`
`
`INTRODUCTION
`
`Initiative for Medicines, Access & Knowledge (I-MAK), Inc. (“Petitioner”)
`
`requests inter partes review (“IPR”) of claims 1 and 2 of United States Patent No.
`
`8,735,372 to Du et al. (“the ‘372 patent”; EX1001) under the provisions of 35
`
`U.S.C. § 311, § 6 of the Leahy-Smith America Invents Act (“AIA”), and 37 C.F.R.
`
`§ 42.100 et seq. The ’372 patent issued on May 27, 2014, and is currently assigned
`
`to Gilead Pharmasset LLC (“Patent Owner”). This petition demonstrates that
`
`claims 1 and 2 are unpatentable.
`
`
`
`The ‘372 patent claims methods that were obvious in light of the prior art.
`
`Specifically, the ‘372 claims a method of treating hepatitis C virus (“HCV”) with a
`
`combination of two nucleoside compounds, but both nucleoside compounds were
`
`known as a result of being previously published and combining the two classes of
`
`compounds was also known as a preferred method for treating HCV.
`
`
`
`Thus, claims 1 and 2 of the ‘372 patent are unpatentable and should be
`
`cancelled.
`
`II. MANDATORY NOTICES
`
`A. Real Parties-in-Interest (37 C.F.R. § 42.8(b)(1))
`
`
`
`The real parties-in-interest for this petition are Initiative for Medicines,
`
`Access & Knowledge (I-MAK), Inc., and the Laura and John Arnold Foundation.
`
`-1-
`
`

`

`B. Related Matters (37 C.F.R. § 42.8(b)(2))
`
`
`
`Petitioner recently filed two petitions for Inter Partes Review of U.S. Patent
`
`No. 7,964,580 and two petitions for Inter Partes Review of U.S. Patent No.
`
`8,333,270, both of which relate to the ‘372 patent. Case Nos. IPR2018-
`
`00119, -00120, -00121 and -00122. Petitioner is not aware of any other matter that
`
`would affect, or be affected by, a decision in this proceeding.
`
`C. Lead and Back-Up Counsel (37 C.F.R. § 42.8(b)(3))
`
`
`
`Petitioner designates Daniel B. Ravicher (Reg. No. 47,015) as lead counsel.
`
`Petitioner is a not-for-profit public charity of limited resources and has been unable
`
`to retain back-up counsel. Petitioner respectfully requests that the Board exercise
`
`its authority under 37 C.F.R. § 42.5(b) to waive or suspend the requirement under
`
`37 C.F.R. § 42.10 that Petitioner designate at least one back-up counsel.
`
`D.
`
`Service Information (37 C.F.R. § 42.8(b)(4))
`
`
`
`Papers concerning this matter should be served on the following:
`
`
`
`
`
`
`
`
`Address: Daniel B. Ravicher
`
`
`Ravicher Law Firm PLLC
`
`
`2000 Ponce De Leon Blvd Ste 600
`
`
`Coral Gables, FL 33134
`Email:
`dan@ravicher.com
`Telephone: 786-505-1205
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`
`Petitioner consents to service by email to dan@ravicher.com.
`
`-2-
`
`

`

`III. REQUIREMENTS FOR REVIEW
`
`A. Grounds for Standing
`
`
`
`Petitioner certifies that the ’372 patent is available for inter partes review
`
`and that Petitioner is not barred or estopped from requesting the inter partes review
`
`sought herein. The required fee is being paid through the Patent Trial and Appeal
`
`Board End to End System. The Office is authorized to charge fee deficiencies and
`
`credit overpayments to Deposit Account No. 601986.
`
`B.
`
`Identification of challenge
`
`
`
`Petitioner respectfully requests cancellation of claims 1 and 2 of the ’372
`
`patent based on the following ground:
`
`# Claims
`1
`1 and 2
`
`35 U.S.C. § Prior Art
`103(a)
`Sofia, Congiatu and Serrano-Wu
`
`
`This Petition is supported by the declaration of Joseph M. Fortunak, Ph.D.
`
`EX1002. Dr. Fortunak is well qualified as an expert, possessing the necessary
`
`scientific, technical, and other specialized knowledge and training to assist in an
`
`understanding of the evidence presented herein, as well as possessing the expertise
`
`necessary to determine and explain the level of ordinary skill in the art as of the
`
`relevant timeframe.
`
`
`
`The Petition and its supporting materials, which are listed in the Appendix,
`
`establish a reasonable likelihood that Petitioner will prevail with respect to
`
`-3-
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`

`

`cancellation of the challenged claims. See 35 U.S.C. § 314(a).
`
`IV. OVERVIEW OF THE ‘372 PATENT
`
`The ‘372 patent relates to phosphoramidate prodrugs of nucleoside
`
`derivatives for the treatment of viral infections of the following general formula:
`
`
`EX1001 at 5:4 – 7:45. In defining the structure’s various components, the ‘372
`
`patent states that the Base is “a naturally occurring or modified purine or
`
`pyrimidine base.” EX1001 at 6:36 – 7:10. The ‘372 patent further provides a long
`
`list of substituents for each of R1, R2, R3a, R3b, R4, R5, R6, X and Y. EX1001 at 5:15
`
`– 6:37.
`
`The following chart describes the ‘372 patent’s 2 claims:
`
`Recite
`
`Methods of treating hepatitis C virus by administering an NS5a
`inhibitor and a compound within the general formula.
`
`Claim(s)
`
`1, 2
`
`
`
`-4-
`
`

`

`V.
`
`FILE HISTORY OF THE ‘580 PATENT
`
`U.S. Patent Application No. 14/057,675 (“the ‘675 application”), filed on
`
`October 18, 2013, issued as the ‘372 patent on May 27, 2014. The ‘675 application
`
`claimed the benefit of U.S. Patent Application No. 13/609,614 (“the ‘614
`
`application”), filed on September 11, 2012, U.S. Patent Application No.
`
`13/099,671 (“the ‘671 application”), filed on May 3, 2011, U.S. Patent Application
`
`No. 12/053,015 (“the ‘015 application”), filed on March 21, 2008, and two
`
`provisional applications, Provisional Application No. 60/909,315 filed on March
`
`30, 2007 (“the ‘315 provisional application”), and Provisional Application No.
`
`60/982,309 filed on October 24, 2007 (“the ‘309 provisional application”).
`
`During prosecution of the ‘675 application, the Examiner allowed the claims
`
`without making any substantive prior-art based rejections. EX1002 ¶27.
`
`VI. PERSON OF ORDINARY SKILL IN THE ART
`
`Because the ‘372 patent pertains to nucleoside compounds, a POSA would
`
`have either (1) a Ph.D. in chemistry or a closely related field with some experience
`
`in an academic or industrial laboratory focusing on drug discovery or development,
`
`and would also have some familiarity with antiviral drugs and their design and
`
`mechanism of action, or (2) a Bachelor’s or Master’s degree in chemistry or a
`
`closely related field with significant experience in an academic or industrial
`
`laboratory focusing on drug discovery and/or development for the treatment of
`
`-5-
`
`

`

`viral diseases. EX1002 ¶33.
`
`VII. CLAIM CONSTRUCTION
`
`
`
`In an inter partes review, a claim in an unexpired patent is given its broadest
`
`reasonable construction in light of the specification. 37 C.F.R. § 42.100(b). Claim
`
`terms are also “generally given their ordinary and customary meaning,” which is
`
`the meaning that the term would have to a person of ordinary skill in the art at the
`
`time of the invention in view of the specification. In re Translogic Tech., Inc., 504
`
`F.3d 1249, 1257 (Fed. Cir. 2007). Under either standard, there is a reasonable
`
`likelihood that Petitioner will prevail with respect to the challenged claims.
`
`The ‘372 patent provides definitions for certain claim terms, but these
`
`definitions are conventional. EX1002 ¶35. Thus, there is no reason to give any of
`
`the terms of the claims of the ‘372 a meaning other than their ordinary and
`
`accustomed meaning. Id.
`
`VIII. BACKGROUND KNOWLEDGE IN THE ART
`
`
`
`The background discussed below reflects knowledge skilled artisans would
`
`bring to bear in reading the prior art at the time of the invention and thereby assists
`
`in understanding how one would have inherently understood the references and
`
`why one would have been motivated to combine the references as asserted in this
`
`Petition. Ariosa Diagnostics v. Verinata Health, Inc., No. 15-1215, slip op. 1, 11-
`
`12 (Fed. Cir. 2015). This knowledge of a skilled artisan is part of the store of
`
`-6-
`
`

`

`public knowledge that must be consulted when considering whether a claimed
`
`invention would have been obvious. KSR Int'l Co. v. Teleflex Inc., 550 U.S. 398,
`
`406 (2007); Randall Mfg. v. Rea, 733 F.3d 1355, 1362-63 (Fed. Cir. 2013).
`
`Below is a description of some of the relevant aspects of what was generally
`
`known in the art as of either March 30, 2007, or March 21, 2008.
`
`A. The Use of Nucleoside Analogs As Antiviral Agents And Their
`Mechanism of Action Were Known
`
`It was generally known to persons skilled in the art that viruses replicate
`
`their genetic materials in their host cell through one of two mechanisms. EX1002
`
`¶37. RNA viruses and reverse-transcribing (RT) viruses rely on their special
`
`DNA/RNA polymerases to synthesize viral DNA/RNA chains in the host cell,
`
`while DNA viruses use host-cell DNA polymerases to synthesize their viral DNA
`
`chains. Id.
`
`The basic building blocks that DNA/RNA polymerases recognize and use to
`
`synthesize viral DNA/RNA are 5’-triphosphate nucleosides (NTP, where N=A,
`
`U/T, G, C). EX1002 ¶38. Nucleoside (N), after entering the cell, is converted into
`
`its 5’-monophosphate (NMP) by intracellular host or viral nucleoside kinases. Id.
`
`NMP is then further converted into the 5’-triphosphate form (NTP), and finally
`
`NTP is recognized by host or viral RNA/DNA polymerases and added to the tail of
`
`the viral DNA/RNA chain being synthesized. Id. The below figure exemplifies the
`
`known mechanism for phosphorylation of nucleosides for incorporation into RNA.
`
`-7-
`
`

`

`
`
`Id.
`
`The incorporation of modified nucleosides, however, into lengthening RNA
`
`chains can result in viral inhibition, when the modified nucleoside will inhibit
`
`further incorporation of subsequent nucleoside units. EX1002 ¶39. This inhibition
`
`is known as “chain termination.” Id. Based on this mechanism, people in the art
`
`-8-
`
`

`

`have long used nucleoside analogs (N’) that are recognizable by viral DNA/RNA
`
`polymerases or viral nucleoside kinases to inhibit viral DNA/RNA replication. Id.
`
`Specifically, such nucleoside analogs (N’) are recognized by host or viral
`
`nucleoside kinases and converted sequentially into their 5’-triphosphate (NTP),
`
`which is then recognized by a corresponding host or viral DNA/RNA polymerase
`
`in the cell so as to compete with natural 5’-triphosphate nucleosides (NTP) for
`
`incorporation into the viral DNA/RNA chain being synthesized. EX1002 ¶40. The
`
`extension of the viral DNA/RNA chain is terminated because of the difference
`
`between the analog and natural nucleosides, which results in suppression of viral
`
`replication. Id.
`
`Several references recognized this general knowledge. EX1002 ¶41. First,
`
`Wagner et al. “Pronucleotides: Toward the In Vivo Delivery of Antiviral and
`
`Anticancer Nucleotides,” Medical Research Reviews, 2000, 20(6), 417-451
`
`(“Wagner”; EX1003), described the use of nucleoside analogs for inhibition of
`
`various viruses. Id. Second, WO 2005/003147 to Clark (“Clark ‘147”; EX1004)
`
`described research and results about use of various nucleoside analogs for
`
`treatment of Flaviviridae infections from 1994 to 2004. Id.; EX1004 at 12:11 –
`
`13:4.
`
`The first commercially available antiviral nucleoside was the anti-herpes
`
`virus uridine analog Idoxuridine. EX1002 ¶42; Prusoff, WH, "Synthesis and
`
`-9-
`
`

`

`biological activities of iododeoxyuridine, an analog of thymidine," Biochim
`
`Biophys Acta. 32(1):295-6 (1959) (“Prusoff”; EX1005).
`
`Since then many nucleoside analogs have been discovered and used as
`
`inhibitors of viral enzymes involved in viral DNA/RNA synthesis, including those
`
`listed in the table below. EX1002 ¶43.
`
`Anti-viral nucleoside
`analog
`
`9-β-D-
`arabinofuranosyladeni
`ne (Vidarabine)
`
`Acycloguanosine
`(ACV, Aciclovir)
`
`Target for inhibition
`
`DNA polymerase of
`multiple viruses
`
`herpes simplex virus
`thymidine kinase;
`varicella herpes zoster
`virus thymidine kinase
`
`Analogous
`to
`
`Publication
`time
`
`adenosine
`
`1964
`
`guanosine
`
`1970s
`
`Ribavirin
`
`Hepatitis C virus (HCV)
`RNA polymerase
`
`guanosine
`/adenosine
`
`1972
`
`2′,3′-dideoxy-3′-
`thiacytidine (3TC,
`Lamivudine)
`
`Hepatitis B virus (HBV)
`reverse transcriptase;
`HIV reverse transcriptase
`
`cytidine
`
`1980s
`
`Stavudine (d4T)
`
`HIV reverse transcriptase
`
`thymidine
`
`1980s
`
`Azidothymidine
`(AZT, Zidovudine)
`
`HTLV-III/LAV reverse
`transcriptase
`
`thymidine
`
`1985
`
`HIV reverse transcriptase
`
`thymidine
`
`1986
`
`HIV reverse transcriptase
`
`adenosine
`
`1988
`
`2′,3′-dideoxyinosine
`(ddI, Didanosine)
`
`-10-
`
`

`

`2′,3′-dideoxycytidine
`(ddC, Zalcitabine)
`
`dideoxy uridine (ddU)
`5’-phosphates
`
`HIV reverse transcriptase
`
`cytidine
`
`1988
`
`HIV reverse transcriptase
`
`uridine
`
`1994
`
`Emtricitabine (FTC)
`
`HIV reverse transcriptase
`
`cytidine
`
`1996
`
`Abacavir (ABC)
`
`HIV reverse transcriptase
`
`guanosine
`
`Before 1998
`
`DHPG (Ganciclovir)
`
`Cytomegalovirus
`guanosine kinase
`
`guanosine
`
`1998
`
`Entecavir (ETV)
`
`HBV reverse transcriptase guanosine
`
`1990s
`
`(2’R)-2’-dO-2’-F-2’-
`C-methyluridine 5’-
`phosphate
`
`HCV RNA polymerase
`
`uridine
`
`2005
`
`Telbivudine
`
`HBV reverse transcriptase
`
`thymidine
`
`2005
`
`4’-azido-uridine 5’-
`phosphoramidate
`
`HCV RNA polymerase
`
`uridine
`
`Feb 2007
`
`
`
`Thus, it was generally known that nucleoside analogs suppress viral
`
`replication, particularly by incorporation into viral DNA/RNA chains.
`
`EX1002 ¶44.
`
`B. Anti-Viral Nucleosides Must Be Converted Into Their
`Triphosphates To Be Active, Monophosphorylation Was The
`Rate-Limiting Step In Such Conversion, and 5’-Phosphate
`Prodrugs – in Particular Phosphoramidates - Enabled
`Nucleosides To Overcome This Limitation
`
`It was well known that, to interact with HCV NS5B polymerase, anti-viral
`
`nucleosides must generally first be converted into their triphosphate form. EX1002
`
`-11-
`
`

`

`¶45. This was described, for example, in Ma et al. “Characterization of the
`
`Metabolic Activation of Hepatitis C Virus Nucleoside Inhibitor β-D-2'-Deoxy-2-
`
`Fluro-2'-C -Methylcytidine (PSI-6130) and Identification of a Novel Active 5'-
`
`Triphosphate Species,” J. Biol. Chem., 2007, 282(41), 29812-29820 (“Ma”;
`
`EX1006), which recognized this general knowledge, saying, “[c]onversion to the
`
`active 5’-triphosphate form by cellular kinases is an important part of the
`
`mechanism of action for nucleoside analogs.” EX1002 ¶45; EX1006 at 2.
`
`Perrone et al. “Application of the Phosphoramidate ProTide Approach to 4’-
`
`Azidouridine Confers Sub-micromolar Potency versus Hepatitis C Virus on an
`
`Inactive Nucleoside,” J. Med. Chem. 2007, 50(8), 1840-1849 (“Perrone”; EX1007)
`
`also recognized this general knowledge, saying, “[a]ll antiviral agents acting via a
`
`nucleoside analogue mode of action need to be phosphorylated, most of them to
`
`their corresponding 5'-triphosphates.” EX1002 ¶46; EX1007 at 1.
`
`It was also well known that, for incorporation of a nucleoside analog into the
`
`viral DNA/RNA chain, kinase-mediated 5’-monophosphorylation of the nucleoside
`
`analog (N’→NMP) is generally the rate-limiting step in the course of its
`
`trisphosphorylation. EX1002 ¶47. Several references recognized this general
`
`knowledge. Id.
`
`First, Perrone recognized that, “the first phosphorylation step to produce the
`
`5’-monophosphate has often been found to be the rate-limiting step in the pathway
`
`-12-
`
`

`

`to intracellular nucleotide triphosphate formation.” EX1007 at 1. Second, Wagner
`
`recited that ddNs’ activation is hindered at the first phosphorylation step. EX1003
`
`at 2. Third, McGuigan, et al. “Application of Phosphoramidate ProTide
`
`Technology Significantly Improves Antiviral Potency of Carbocyclic Adenosine
`
`Derivatives,” J. Med. Chem., 2006, 49, 7215-7726 (“McGuigan 2006”; EX1008),
`
`recognized that, “in most cases the first phosphorylation to the 5’-monophosphate
`
`is the rate-limiting step.” EX1008 at 1.
`
`Perrone (EX1007), Wagner (EX1003), and McGuigan 2006 (EX1008) also
`
`evinced the general knowledge that, although 5’-triphosphates of some nucleoside
`
`analogs (NTP) are potent viral inhibitors, these nucleoside analogs (N’) themselves
`
`showed little or no activity in inhibition assays, generally because of the host cell’s
`
`lack of corresponding kinase activity which renders the 5’-monophosphorylation of
`
`these analogs extremely slow. EX1002 ¶49.
`
`Several other references recognized this general knowledge. EX1002 ¶50.
`
`First, McGuigan et al. “Certain phosphoramidate derivatives of dideoxy uridine
`
`(ddU) are active against HIV and successfully by-pass thymidine kinase” FEBS
`
`Letters, 1994, 351, 11-14 (“McGuigan 1994”; EX1009), recognized that
`
`nucleoside analogs have limitations because they depend on kinase-mediated
`
`activation to generate the bioactive (tri)phosphate forms. EX1009 at 1. McGuigan
`
`1994 also recognized that dideoxythymidine and 3’-O-methylthymidine are
`
`-13-
`
`

`

`nucleoside analogs which are inactive against HIV, while their triphosphates are
`
`exceptionally potent inhibitors of HIV reverse transcriptase, and the inactivity of
`
`these nucleoside analogs is attributed to poor phosphorylation by host cells. Id.
`
`McGuigan 2006 also recognized that poor phosphorylation can be a major
`
`cause of poor activity, with several examples known where nucleoside analogs are
`
`inactive, but the corresponding triphosphates are inhibitors at their enzyme target.
`
`EX1008 at 1.
`
`To address this widely known issue, it was contemplated in the art to use the
`
`5’-phosphate of nucleoside analogs as prodrugs to “bypass” the kinase-mediated
`
`monophosphorylation step of generating the active triphosphate form. EX1002
`
`¶52. Since 1990 or earlier, stable 5’-phosphate-based prodrugs of nucleoside
`
`analogs have been designed and employed to improve the intracellular delivery and
`
`activation of the nucleoside analogs, and such prodrugs could readily be
`
`hydrolyzed into 5’-monophosphates of the nucleoside analogs (NMP) by enzymes
`
`inside the cell. EX1009 (McGuigan 1994). The 5’-monophosphate is then rapidly
`
`converted into the triphosphate form to be fully activated. Such a technique has
`
`been called “Pronucleotide” or simply “ProTide”. EX1002 ¶52.
`
`First, Wagner, recognized that various prodrug or “pronucleotide”
`
`approaches have been devised and investigated, with the general goal of promoting
`
`passive diffusion through cell membranes and increasing the bioavailability of
`
`-14-
`
`

`

`nucleosides or phosphorylated nucleosides. EX1002 ¶53; EX1003 at 3 and 8. This
`
`approach of derivatization had been applied using various protecting groups for the
`
`phosphate moiety. Id.
`
`Second, Cahard et al. “Aryloxy phosphoramidate triesters as pro-tides,”
`
`2004, 4(4), 371-81 (“Cahard”; EX1010) recognized that aryloxy phosphoramidate
`
`triesters are an effective pro-tide motif for the intracellular delivery of (otherwise)
`
`charged antiviral nucleoside monophosphates and that the phenyl alanyl
`
`phosphoramidate approach was successful on a range of nucleosides by many
`
`research groups. EX1002 ¶54; EX1010 at 1, 4.
`
`Third, Perrone recognized that unmodified nucleoside monophosphates are
`
`unstable in biological media and also show poor membrane permeation because of
`
`the associated negative charges at physiological pH. EX1002 ¶55; EX1007 at 1.
`
`Perrone also recognized that the known aryloxy phosphoramidate ProTide
`
`approach allows bypass of the initial kinase dependence by intracellular delivery of
`
`the mono-phosphorylated nucleoside analog as a membrane-permeable ProTide
`
`form. Id. The technology greatly increased the lipophilicity of the nucleoside
`
`monophosphate analog with a consequent increase of membrane permeation and
`
`intracellular availability. Id.
`
`The “ProTide” technology was known to show great success in the
`
`intracellular delivery and activation of many nucleoside analogs. EX1002 ¶56. A
`
`-15-
`
`

`

`large number of thus-modified nucleosides showed a boost in the inhibition
`
`activity on virus replication by tens, hundreds, or even thousands of times, in
`
`comparison with the parent nucleoside analogs. Id.
`
`McGuigan 1994 recognized that the aryloxy phosphoramidate (3c) of a ddU
`
`increases its potency by approximately 50 times. EX1002 ¶57; EX1009 at 3 (Fig.
`
`1).
`
`Cahard recognized that the aryloxy phosphoramidate prodrug (21) for d4A
`
`boosts the activity of the parent nucleoside analog d4A by 1000 – 4000 fold and
`
`the aryloxy phosphoramidate prodrug (22) for ddA boosts the activity of the parent
`
`nucleoside analog ddA by >100 fold. EX1002 ¶58; EX1010 at 2-3 (Fig. 1).
`
`McGuigan 2006 recognized that the ProTide approach was highly successful
`
`when applied to L-Cd4A with potency improvements in vitro as high as 9000-fold
`
`against HIV. EX1002 ¶59; EX1008 at 1. McGuigan 2006 also recognized that
`
`several aryloxy phosphoramidate prodrugs achieve an anti-HIV activity (IC50) at
`
`the concentration of about 10 nM. EX1002 ¶59; EX1008 at 4 (Table 1).
`
`Congiatu et al., "Novel Potential Anticancer Naphthyl Phosphoramidates of
`
`BVdU: Separation of Diastereomers and Assignment of the Absolute Configuration
`
`of the Phosphorous Center," J. Med Chem. 2006, 49(2), 452-455 (“Congiatu”;
`
`EX1011) illustrated the well-known fact that the phosphorous atom of ProTide
`
`prodrugs constitutes a center of chirality. EX1002 ¶60; EX1011 at 2-3. Thus, a
`
`-16-
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`

`

`phosphoramidate prodrug may exist as a mixture of stereochemical centers at the
`
`phosphorous. EX1002 ¶60. In the case of molecules with multiple centers of
`
`chirality (as is the case with nucleosides), these phosphorous stereoisomers are
`
`referred to as “diastereomers.” Id. Congiatu also taught that the individual
`
`diastereomers at the phosphorous might likely possess different biological activity.
`
`Id. Congiatu further taught that separation of the phosphorous diastereomers gave
`
`rise to an approximately 15:1 difference in biological activity between such
`
`diastereomers. Id. Thus, Congiatu taught a POSA that the ProTide strategy must
`
`include testing of the individual phosphorous diastereomers to understand their
`
`differences in biologic activity. Id.
`
`Therefore, the “Pronucleotide” or “ProTide” strategy, including the testing
`
`of the individual phosphorous diastereomers therein, had been a conventional
`
`technical means in the art. EX1002 ¶61.
`
`In summary, it was generally known that, for antiviral 5’-phosphate
`
`prodrugs, the antiviral activity lies in the nucleoside itself. EX1002 ¶62. It was also
`
`generally known that the intracellular delivery (cell membrane permeation) could
`
`be improved because of the lipophilicity rendered by the modified phosphate
`
`group. Id. It was also generally known that intracellular hydrolysis of nucleoside
`
`monophosphate prodrugs into the monophosphate form is mainly attributed to the
`
`structural nature of the modified phosphate group and the corresponding enzymes
`
`-17-
`
`

`

`in the host-cell. Id. It was also known that the ProTide monophosphate prodrugs
`
`were capable of overcoming the need for kinases in the first phosphorylation step
`
`of nucleosides. Id. It was further known that the phosphorous diastereomers of
`
`ProTide prodrugs likely exhibited different biologic activity with one diastereomer
`
`being very significantly more active than the other. Id.
`
`C. The Means Were Available To Determine Which Nucleosides
`Were Kinase Dependent
`
`The general knowledge that many nucleosides were kinase-dependent in
`
`activation to their triphosphates was reflected in an early reference in the field.
`
`EX1002 ¶63; EX1009 (McGuigan 1994) at 1-3. The means existed to assess the
`
`cellular uptake and subsequent phosphorylation of nucleosides. EX1002 ¶63;
`
`EX1006 (Ma) at 4-8. Thus, it was generally known that the identification of
`
`nucleoside analogs whose activity was kinase-dependent was readily available.
`
`EX1002 ¶63.
`
`D. Narrowing The Selections For The Phosphoramidate Prodrug
`
`Phosphoramidate prodrugs have substitutions to be selected at the: 1) amino
`
`acid; 2) ester group on the amino acid; 3) ester group on phosphorous; and 4)
`
`optional substitution on nitrogen of the amino acid. EX1002 ¶64. Of these
`
`possibilities, the range of realistic options is reasonably limited. EX1002 ¶64.
`
`Perrone and Congiatu demonstrated how the amino acid moiety is most often
`
`glycine, alanine or valine, and how the ester group on the amino acid is most often
`
`-18-
`
`

`

`methyl, ethyl, isopropyl, butyl, or benzyl. EX1002 ¶64; EX1007; EX1011. The
`
`useful ester groups on phosphorous are aryl (typically phenyl but occasionally
`
`naphthyl). EX1002 ¶64. Among these aryloxy phosphoramidate prodrugs, Perrone
`
`particularly taught that, “the isopropyl ester (15) showed high potency and
`
`represented one of the most active phosphoramidates prepared.” EX1002 ¶64;
`
`EX1007 at 3.
`
`It was readily known to a POSA that designing an appropriate ProTide
`
`involves a selection process that is limited in scope and adaptable to a nucleoside
`
`that is the promising drug candidate. EX1002 ¶65. As such, the selection of a
`
`phosphoramidate prodrug moiety would require labor, but with a limited selection
`
`of options and a high degree of probable success. Id.
`
`More specifically, Perrone taught the activity of a series of 22
`
`phosphoramidate nucleoside ProTide derivatives of 4'-azidouridine for antiviral
`
`hepatitis C activity, the choice of 1) alanine for the amino acid; 2) 2-butyl, benzyl,
`
`and isopropyl for the amino acid ester; 3) phenoxy for the ester on phosphorous;
`
`and 4) no substitution (i.e., a free N-H) on the amino acid nitrogen provided a very
`
`short list of three (Table 1 below) very active compounds. EX1002 ¶66.
`
`-19-
`
`

`

`
`
`EX1007 at 4.
`
`Perrone concluded that, although quite a number of active ProTide
`
`derivatives could readily be synthesized, a distinctive Structure-Activity-
`
`Relationship (SAR) was observed. EX1002 ¶67. Specifically, Perrone taught:
`
`In conclusion, ester variation was widely tolerated except for
`
`the tert-butyl, which gave a slight reduction in potency in the L-
`alanine series (16) and the benzyl in the case of the L-phenylalanine
`derivative (23). L-Alanine remained the most effective amino acid,
`
`-20-
`
`

`

`with glycine and D-alanine showing only slightly reduced potency.
`Dimethylglycine, L-leucine, and L-proline also provided compounds
`with antiviral potencies in a low micromolar range. It therefore
`appears that the amino acid core could be considerably varied to give
`antiviral agents with potencies within a 10-fold range in replicon cells.
`Importantly, potency optimization requires consideration of both
`amino acid and ester moieties as most clearly shown for the ethyl and
`benzyl esters of the L-phenylalanine analogues. Moreover, quite
`distinct SARs emerged from this family versus HCV as compared to
`our prior studies in other families. (emphasis added)
`We also explored the possibility to replace the phenyl
`substituent on the phosphate with a more hydrophobic moiety, 1-
`naphthyl. Previously, we noted an increase in the in vitro potency of
`1-naphthyl phosphoramidates compared to the corresponding phenyl
`phosphoramidates when investigating BVdU phosphoramidates in an
`anticancer assay.
`
`EX1007 at 4.
`
`Perrone also indicated (as shown in Table 3, reproduced below) that the 1-
`
`naphthyl(oxy) phosphate ester diastereomers displayed little or no difference in
`
`anti-HCV activity. EX1002 ¶68.
`
`-21-
`
`

`

`
`
`EX1007 at 4. These diastereomers were separated and displayed modestly better
`
`potency than the mixture of diastereomers for the direct phenoxy ester analog.
`
`EX1002 ¶68. While Perrone did not separate the diastereomers of the phenoxy
`
`ProTides, Congiatu taught that these diastereomers very often showed a marked
`
`difference in anti-HCV activity. EX1002 ¶68; EX1011.
`
`Thus, Perrone taught that many phosphoramidate analogs can provide
`
`excellent activation of nucleosides for antiviral activity against HCV. EX1002 ¶69.
`
`Perrone also taught that the range of amino acids that were useful (out of 13
`
`examined) was limited, with L-alanine being the best option. EX1002 ¶69.
`
`Only 6 highly active phosphoramidate groups were particularly identified in
`
`Perrone (i.e. No.14, 15, 17, and 33-35) with compounds 34-35 being two separate
`
`diastereomers of compound 33. EX1002 ¶70; EX1007 at 4 (Tables 1 and 3). A
`
`POSA would have been motivated to try to attach each to the 5’-position of (2’R)-
`
`2’-deoxy-2’-fluoro-2’-C-methyluridine resulting in compounds within claims 1 and
`
`2 of ‘372. EX1002 ¶70. This would have required synthesizing only 4 different
`
`-22-
`
`

`

`ProTide phosphoramidates. Id. Given that Congiatu found significant difference
`
`between the activity of phosphorous diastereomers, EX1011 at 2-3, a POSA would
`
`then have separated and tested the diastereomers of each of these 4 referred
`
`analogs. EX1002 ¶70.
`
`Perrone described a uridine analog (4'-azidouridne), which like PSI-6206,
`
`was inactive in the HCV replicon assay although its triphosphate form (4'-
`
`azidouridine-TP) was a potent inhibitor of HCV NS5B polymerase. EX1007 at 1,
`
`2-3,