UNITED STATES PATENT AND TRADEMARK OFFICE
`________________________
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`________________________
`
`AGILA SPECIALTIES INC. AND
`MYLAN PHARMACEUTICALS INC.,
`Petitioner,
`v.
`
`CUBIST PHARMACEUTICALS, INC.
`Patent Owner
`
`U.S. Patent No. 8,129,342
`
`________________________
`
`Case IPR2015: Unassigned
`________________________
`
`EXPERT DECLARATION OF CATHERINE MULLIGAN, PH.D
`
`PETITIONERS
`
`EXHIBIT NO. 1006 Page 1 of 155
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`

`

`TABLE OF CONTENTS
`
`I.
`
`Qualifications and Background ............................................................................1
`
`A.
`B.
`C.
`
`Education and Experience; Prior Testimony..............................................1
`Bases for Opinions and Materials Considered...........................................4
`Scope of Work ............................................................................................5
`
`Summary of Opinions...........................................................................................5
`
`Legal Standards ....................................................................................................8
`
`Person of Ordinary Skill in the Art.....................................................................10
`
`The ‘342 Patent...................................................................................................11
`
`II.
`
`III.
`
`IV.
`
`V.
`
`VI. Background.........................................................................................................16
`
`A.
`B.
`
`Use of Surfactants and Biosurfactants .....................................................16
`Biosurfactant Purification and State of the Art in 2000...........................20
`
`VII. Scope and Content of the Prior Art References..................................................29
`
`U.S. Patent No. 4,874,843 (‘843 Patent) [Ex. 1007]................................29
`A.
`U.S. Patent No. 4,331,594 (‘594 Patent) [Ex.1009].................................30
`B.
`U.S. Patent No. 5,912,226 (‘226 Patent) [Ex.1010].................................31
`C.
`D. Mulligan and Gibbs, “Recovery of Biosurfactants by
`Ultrafiltration,” Journal of Chemical Technology & Biotechnology,
`47:23-9 (1990) (Mulligan) [Ex.1013] ......................................................33
`Lin and Jiang, “Recovery and Purification of the Lipopeptide
`Biosurfactant Bacillus subtilis by Ultrafiltration,” Biotechnology
`Techniques, 11:413-6 (June 1997) (Lin I) [Ex. 1014] .............................35
`
`E.
`
`PETITIONERS
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`EXHIBIT NO. 1006 Page 2 of 155
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`

`

`F.
`
`G.
`H.
`
`Lin et al., “General Approach for the Development of High-
`Performance Liquid Chromatography Methods for Biosurfactant
`Analysis and Purification,” Journal of Chromatography, 825:149-
`59 (1998) (Lin II) [Ex.1015] ....................................................................37
`U.S. Patent No. 5,227,294 (‘294 Patent) [Ex. 1016]................................40
`Tally et al., “Daptomycin: A Novel Agent for Gram-positive
`Infections,” Expert Opin. Invest. Drugs 8:1223-38 (1999) [Ex.
`1018].........................................................................................................41
`
`VIII. INVALIDITY OF THE ‘342 PATENT .............................................................42
`
`B.
`
`A.
`
`The Challenged Claims of the ‘342 Patent are Anticipated and/or
`Obvious Over the ‘226 Patent ..................................................................42
`Claims 1-4, 7-18, 21, 30-34 and 40-43 of the ‘342 Patent are
`Obvious Over the ‘843 Patent or ‘594 Patent In View of Mulligan,
`Lin II and the ‘226 Patent.........................................................................57
`(a)
`Claims 1-4 and 7-16 of the ‘342 Patent are Invalid as Obvious Over
`the ‘843 Patent in View of Mulligan, Lin II and the ‘226 Patent ..........................58
`(b)
`Claims 17-18 and 21 of the ‘342 Patent are Invalid as Obvious Over
`the ‘843 Patent in View of Mulligan and Lin II.....................................................64
`(c)
`Claims 30-34 of the ‘342 Patent are Invalid as Obvious Over the
`‘843 Patent in View of Mulligan and Lin II ..........................................................68
`(d)
`Claims 40-43 of the ‘342 Patent are Invalid as Obvious Over the
`‘843 Patent in View of Mulligan and Lin II ..........................................................71
`C.
`Claims 5-6 and 50 of the ‘342 Patent are Obvious Over the ‘843
`Patent or the ‘594 Patent In View of Mulligan, Lin I and/or Lin II
`and the ‘226 Patent...................................................................................75
`
`EXPERT DECLARATION OF CATHERINE N. MULLIGAN, PH.D.
`
`PETITIONERS
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`EXHIBIT NO. 1006 Page 3 of 155
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`

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`Claim 50 of the ‘342 Patent is Invalid as Obvious Over the ‘843
`(a)
`Patent or the ‘594 Patent in View of Mulligan, Lin I, Lin II and the ‘226 Patent.75
`(b)
`Claims 5-6 of the ‘342 Patent are Invalid as Obvious Over the ‘843
`Patent or ‘594 Patent in View of Mulligan, Lin I, Lin II and the ‘226 Patent.......79
`D.
`Claims 19-20, 25-29, 35-39 and 44-49 of the ‘342 Patent are
`Obvious Over the ‘843 Patent or the ‘594 Patent In View of
`Mulligan, Lin II, the ‘226 Patent and/or Tally.........................................82
`(a)
`Claims 19-20 and 25-29 of the ‘342 Patent are Invalid as Obvious
`Over the ‘843 Patent or ‘594 Patent in View of Mulligan, Lin II, the ‘226 Patent
`and Tally
`82
`(b)
`Claims 25-29, 35-39 and 44-49 of the ‘342 Patent are Invalid as
`Obvious Over the ‘843 Patent or ‘594 Patent in View of Mulligan and Lin II.....84
`E.
`Claims 22-24 and 51-54 of the ‘342 Patent are Obvious Over the
`‘843 Patent or ‘594 Patent In View of Mulligan, Lin II, the ‘226
`Patent ........................................................................................................86
`(a)
`Claims 22-24 of the ‘342 Patent are Invalid as Obvious Over the
`‘843 Patent in View of Mulligan, Lin II and the ‘226 Patent, and Lin I, and
`Further in View of ‘594 Patent...............................................................................87
`(b)
`Claims 51-54 of the ‘342 Patent are Invalid as Obvious Over the
`‘843 Patent in View of Mulligan, Lin II and the ‘226 Patent and the ‘594 Patent 90
`
`IX. CONCLUSION...................................................................................................95
`
`EXPERT DECLARATION OF CATHERINE N. MULLIGAN, PH.D.
`
`PETITIONERS
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`EXHIBIT NO. 1006 Page 4 of 155
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`1
`
`1.
`
`My name is Catherine N. Mulligan, Ph.D. I have been retained by
`
`counsel for Mylan Inc. (Mylan). I understand that Mylan intends to petition for
`
`inter partes review of U.S. Patent No. 8,129,342 (the ‘342 patent) [Ex. 1002],
`
`which is assigned to Cubist Pharmaceuticals, Inc. I also understand that Mylan
`
`intends to petition for inter partes review of U.S. Patent No. 8,058,238 (the ‘238
`
`patent) [Ex. 1001], which is also assigned to Cubist Pharmaceuticals, Inc. I further
`
`understand that Mylan will request that the United States Patent and Trademark
`
`Office cancel certain claims of the ‘342 patent and the ‘238 patent as unpatentable
`
`in the Inter Partes Review petitions. I submit this expert declaration, which
`
`addresses and supports Mylan’s Inter Partes Review petition for the ‘342 patent. I
`
`have prepared and submitted a separate declaration which addresses and supports
`
`Mylan’s Inter Partes Review petition for the ‘238 patent.
`
`I.
`
`Qualifications and Background
`
`A.
`
`2.
`
`Education and Experience; Prior Testimony
`
`I received my Bachelors of Engineering and Masters of Engineering
`
`in Chemical Engineering in 1983 and 1985, respectively, from McGill University.
`
`My Masters thesis was under the supervision of Professor David Cooper, an expert
`
`in biosurfactants. I went on to obtain my Ph.D in Geoenvironmental Engineering
`
`from McGill University in 1998 with Professor Raymond N. Yong. My thesis
`
`EXPERT DECLARATION OF CATHERINE N. MULLIGAN, PH.D.
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`2
`
`project centered around the purification and use of biosurfactants, including
`
`surfactin, a cyclic lipopetide produced as a secondary metabolite during
`
`fermentation of Bacillus subtilis, for the removal of heavy metals from soils and
`
`sediments.
`
`3.
`
`Between obtaining my Masters in Chemical Engineering and entering
`
`the doctoral program at McGill University, I worked at several industrial biological
`
`and chemical engineering facilities, including as a Research Associate in
`
`Fermentation Engineering from 1985-1989 at the Biotechnology Research Institute
`
`(NRCC) in Montreal, Canada, and a Research Engineer from 1989-1999 at SNC
`
`Research Corporation, also in Montreal, Canada. At the Biotechnology Research
`
`Institute, I studied factors that influenced the production of biosurfactants by
`
`Bacillus and Pseudomonas species during fermentation. My work resulted in the
`
`publication of a research article in the Journal of Chemical Technology and
`
`Biotechnology in 1990 related to the use of ultrafiltration technology to purify
`
`biosurfactants, including surfactin and rhamnolipids, from culture supernatant
`
`fluids. See Mulligan, C.N. and Gibbs, B.F., “Recovery of biosurfactants by
`
`ultrafiltration,” J. Chem. Technol. Biotechnol. 47:23-9 (1990) [Ex.1013]. My 1990
`
`research article took advantage of the ability of biosurfactant molecules to form
`
`micelles at concentrations above the critical micelle concentration. This allowed
`
`EXPERT DECLARATION OF CATHERINE N. MULLIGAN, PH.D.
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`PETITIONERS
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`3
`
`the surfactant aggregates to be retained by relatively high molecular weight cut-off
`
`membranes, demonstrating a simple technique to purify biosurfactants, including
`
`removing low molecular weight impurities, such as salts, free amino acids,
`
`peptides and small proteins, to be easily removed.
`
`4.
`
`I am currently a Professor of Civil and Environmental Engineering at
`
`Concordia University, Montreal, Canada, and have held this position since 1999. I
`
`am also the Associate Dean in the Faculty of Engineering and Computer Science of
`
`Research and Graduate Studies, and Research Chair in Geoenvironmental
`
`Sustainability at Concordia University. I teach graduate level courses in
`
`Environmental Engineering at Concordia University, including engineering aspects
`
`of bioremediation, such as the industrial production, purification and use of
`
`biosurfactants.
`
`5.
`
`In all, I have more than 25 years of experience in fermentation
`
`engineering and purification of secondary metabolites from microbial cultures,
`
`such as biosurfactants, including cyclic lipopeptides.
`
`6.
`
`My research has resulted in the publication of over 220 refereed
`
`articles, conference proceedings and abstracts. I have also contributed or served as
`
`editor of 14 book chapters and books. I recently served as a co-editor of the
`
`reference book “Biosurfactants: Research Trends & Applications,” CRC Press
`
`EXPERT DECLARATION OF CATHERINE N. MULLIGAN, PH.D.
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`PETITIONERS
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`4
`
`2014 [Ex. 1019]. I authored several chapters, including a chapter entitled
`
`“Characterization, Production and Application of Lipopeptides.” The chapter
`
`reflects work in the field from the early 1980s to the present, and discusses in
`
`detail the production and purification of biosurfactant lipopeptides, including
`
`cyclic lipopeptides.
`
`7.
`
`In addition, I have held or currently hold various editorial positions
`
`for a number of scientific publications related to environmental engineering and
`
`biosurfactants, and have chaired, co-chaired and organized various meetings and
`
`conferences for the field.
`
`8.
`
`I am a member of the American Chemical Society, the American
`
`Institute of Chemical Engineering, the Canadian Society of Chemical Engineering
`
`and other professional and scientific society memberships.
`
`9.
`
`I am an inventor or co-inventor of at least three U.S. patents and
`
`international applications.
`
`10.
`
`I have not testified previously as an expert witness.
`
`11. My curriculum vitae is attached here as Exhibit A.
`
`B.
`
`12.
`
`Bases for Opinions and Materials Considered
`
`Exhibit B includes a list of the materials I considered, in addition to
`
`my experience, education, and training, in providing the opinions contained herein.
`
`EXPERT DECLARATION OF CATHERINE N. MULLIGAN, PH.D.
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`PETITIONERS
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`5
`
`Scope of Work
`
`I have been retained by Mylan as a technical expert in this matter to
`
`C.
`
`13.
`
`provide various opinions regarding the ‘342 patent. I receive $325.00 per hour for
`
`my services. No part of my compensation is dependent upon my opinions given or
`
`the outcome of this case. I do not have any other current or past affiliation as an
`
`expert witness or consultant with Mylan. I do not have any current or past
`
`affiliation with Cubist Pharmaceuticals, Inc., or any of the named inventors on the
`
`‘342 patent.
`
`II.
`
`Summary of Opinions
`
`14.
`
`To summarize, for the reasons set forth below, it is my opinion that
`
`each claim of the ‘342 patent is anticipated and/or obvious in view of the prior art,
`
`including the use of micelles and ultrafiltration to purify lipopeptide preparations.
`
`15.
`
`I understand that the challenged claims are “product by process”
`
`claims, which are composition claims that list manufacturing process steps. I have
`
`been told that as a result of the claims being classified as “product by process”
`
`claims, the claims should be analyzed through the claimed composition only, and
`
`not through the methods that are recited in the claims. I have reviewed the
`
`daptomycin prior art, and find that one of ordinary skill in the art would have
`
`understood that U.S. Patent No. 5,912,226 (‘226 patent) [Ex. 1010] to Eli Lilly and
`
`EXPERT DECLARATION OF CATHERINE N. MULLIGAN, PH.D.
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`PETITIONERS
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`6
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`Company anticipate and/or render obvious all claims of the ‘342 patent. The ‘226
`
`patent disclosed a daptomycin composition that one of ordinary skill in the art
`
`would have understood approached homogeneity through the combination of a
`
`variety of chromatography and adsorption process steps, combined with
`
`preparative HPLC (high-performance or high pressure liquid chromatography)
`
`purification. The ‘226 patent also disclosed pharmaceutical formulations
`
`comprising the purified daptomycin composition, as well as administration of the
`
`formulations to humans. In my opinion, the ‘226 patent anticipates, and at the very
`
`least renders obvious, all of the challenged claims of the ‘342 patent.
`
`16. Moreover, the processes (if considered as part of the claim language)
`
`were all well-known and used by those of ordinary skill in the art. In 1990, ten
`
`years before the earliest filing of the ‘342 patent, my laboratory demonstrated that
`
`the propensity for biosurfactants such as lipopeptides (including the cyclic
`
`lipopeptide surfactin) to form micelles could be exploited to purify lipopeptide
`
`preparations when used in conjunction with high molecular weight ultrafiltration
`
`cells. Our results showed that this one-step process, which required only a fraction
`
`(approximately 2%) of the time as compared to conventional chemical extraction
`
`processes and required no organic solvents, retained in excess of 96% of surfactin
`
`in the crude fermentation preparation while simultaneously removing smaller
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`EXPERT DECLARATION OF CATHERINE N. MULLIGAN, PH.D.
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`PETITIONERS
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`7
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`molecular weight impurities in the process. This led to purification of the surfactin
`
`preparation by almost 10-fold. Because of the simplicity, time- and cost-savings, as
`
`well as the efficiency of the micelle/ultrafiltration process for purifying lipopeptide
`
`preparations, others in the field began to incorporate this technique into their
`
`biosurfactant purification protocols to obtain highly purified surfactin preparations.
`
`It would have thus been obvious by January 2000, as others were doing for cyclic
`
`lipopeptides, to employ a micelle formation and ultrafiltration step in the
`
`purification of daptomycin.
`
`17.
`
`In addition, the combination of a micelle formation and ultrafiltration
`
`step with other purification processes, such as anion-exchange chromatography,
`
`hydrophobic interaction chromatography, HPLC preparative and other column
`
`chromatography techniques to reach certain purity levels and to further remove
`
`impurities in the preparation would have also been obvious to employ for cyclic
`
`lipopeptides, such as daptomycin, prior to January 2000. These techniques were
`
`standard to biochemists and chemists for the purification of lipopeptides; those of
`
`ordinary skill in the art, including my laboratory and others in the biosurfactant
`
`field, routinely employed these purification techniques to obtain biosurfactant
`
`preparations approaching homogeneity. Well before the filing of the ‘342 patent,
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`8
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`biosurfactant preparations were routinely purified to greater than 98%, and greater
`
`than 99% purity levels.
`
`18. Moreover, the use of HPLC to identify and analyze impurities in
`
`lipopeptide preparations was also well known to those of ordinary skill in the art
`
`by January 2000. Chromatography and other mass- and charge-based analysis
`
`techniques, including mass spectrometry and HPLC, were routinely employed by
`
`those of ordinary skill in the art. It would have thus been obvious to use HPLC to
`
`identify and analyze impurities in lipopeptide preparations, such as daptomycin.
`
`III.
`
`Legal Standards
`
`19.
`
`In preparation for forming the opinions set forth in this declaration, I
`
`have been informed regarding the relevant legal principles. I have used my
`
`understanding of those principles in forming my opinions. My understanding of
`
`those principles is summarized below.
`
`20.
`
`I have been told that Mylan bears the burden of proving invalidity by
`
`a preponderance of the evidence. I am informed that this preponderance of the
`
`evidence standard means that Mylan must show invalidity is more probable than
`
`not. I have taken these principles into account when forming my opinions in this
`
`case.
`
`EXPERT DECLARATION OF CATHERINE N. MULLIGAN, PH.D.
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`9
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`21.
`
`I have also been told that claims should be construed given their
`
`broadest reasonable interpretation in light of the specification from the perspective
`
`of a person of ordinary skill in the art.
`
`22.
`
`I am told that the concept of anticipation requires that each element of
`
`a claim be found in a single prior art reference as understood in the context of the
`
`skill and knowledge of one of ordinary skill in the art. I have also been told that
`
`the claims in the ‘342 patent are “product by process claims,” where a composition
`
`is claimed in terms of recited process steps.
`
`23.
`
`I am told that the concept of patent obviousness involves four factual
`
`inquiries: (1) the scope and content of the prior art; (2) the differences between the
`
`claimed invention and the prior art; (3) the level of ordinary skill in the art; and (4)
`
`secondary considerations of non-obviousness.
`
`24.
`
`I am also informed that when there is some recognized reason to solve
`
`a problem, and there are a finite number of identified, predictable and known
`
`solutions, a person of ordinary skill in the art has good reason to pursue the known
`
`options within his or her technical grasp. If such an approach leads to the expected
`
`success, it is likely not the product of innovation but of ordinary skill and common
`
`sense. In such a circumstance, when a patent simply arranges old elements with
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`each performing its known function and yields no more than one would expect
`
`10
`
`from such an arrangement, the combination is obvious.
`
`IV.
`
`Person of Ordinary Skill in the Art
`
`25.
`
`I have been informed by counsel that the obviousness analysis is to be
`
`conducted from the perspective of a person of ordinary skill in the art (a “person of
`
`ordinary skill”) at the time of the invention.
`
`26.
`
`I have also been informed by counsel that in defining a person of
`
`ordinary skill in the art the following factors may be considered: (1) the
`
`educational level of the inventor; (2) the type of problems encountered in the art;
`
`(3) prior art solutions to those problems; (4) rapidity with which innovations are
`
`made; and (5) sophistication of the technology and educational level of active
`
`workers in the field.
`
`27. A person of ordinary skill in the art related to the ‘342 patent typically
`
`would have held a Masters or Ph.D. in Chemistry, Biochemistry or Chemical
`
`Engineering with experience in microbial fermentation and product purification. A
`
`person of ordinary skill in the art would have had the necessary skill set for
`
`purifying, for example, secondary metabolites from microbial fermentation,
`
`including but not limited to filtration and adsorption techniques, chemical
`
`extractions and analysis, including chromatography, such as anion exchange
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`11
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`chromatography, hydrophobic interaction chromatography, thin layer
`
`chromatography (TLC), high-performance (high-pressure) liquid chromatography
`
`(HPLC) and gel filtration analysis. Moreover, a person of ordinary skill in the art
`
`for the ‘342 patent would have had the requisite skill set to analyze biosurfactant
`
`products obtained, including the use of chromatography and mass- or charge-based
`
`analytical techniques, such as mass spectrometry and HPLC. One of the first
`
`pieces of equipment obtained for my laboratory when I started at the
`
`Biotechnology Research Institute in Montreal, Canada in 1985 was an HPLC,
`
`specifically for the purpose of analyzing biosurfactant preparations, as well as
`
`preparing highly purified preparations of surfactin. In my experience, an HPLC is
`
`standard for biochemistry and chemistry laboratories.
`
`V.
`
`The ‘342 Patent
`
`28.
`
`I have read the ‘342 patent and the issued claims, which is entitled
`
`“High Purity Lipopeptides.” The ‘342 patent was filed September 22, 2010, and is
`
`a continuation of US Patent Application No. 11/739,180 (‘342 patent) filed April
`
`24, 2007, which is a continuation of US Patent Application No. 10/747,485, which
`
`was filed on December 29, 2003, now abandoned, which is a divisional application
`
`of US Patent Application No. 09/735,191, which was filed on November 28, 2000,
`
`now U.S. Patent No. 6,696,412. The ‘342 patent also claims priority to U.S.
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`12
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`Provisional Application No. 60/177,190, filed on January 20, 2000. The ‘342
`
`patent issued March 6, 2012, and names Thomas Kelleher, Jan-Ji Lai, Joseph P.
`
`DeCourcey, Paul Lynch, Maurizio Zenoni and Auro Tagliani as inventors.
`
`29.
`
`I understand that Mylan is challenging claims 1-54 of the ‘342 patent.
`
`Claims 1, 17, 30, 40, 50 and 41 are independent claims.
`
`30. Claim 1 recites “[a] composition obtained by a process comprising the
`
`step of forming a daptomycin aggregate, the composition comprising daptomycin
`
`of greater than or about 93% purity relative to impurities 1-14 defined by peaks 1-
`
`14 shown in FIG. 12 and having less than 4% of anhydro-daptomycin and having
`
`less than 4% of β-isomer of daptomycin.”
`
`31.
`
`FIG. 12 is a chromatogram from an HPLC assay, which shows several
`
`peaks numbers 1-14 in the margins:
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`13
`
`32.
`
`Independent claim 17 of the ‘342 patent recites “[a] pharmaceutical
`
`composition compatible with a pharmaceutically acceptable carrier for the
`
`treatment of an infection of the blood, skin or soft tissue, the composition
`
`comprising daptomycin obtained by a process comprising the step of forming a
`
`daptomycin aggregate, the composition having daptomycin with greater than or
`
`about 93% purity relative to impurities 1-14 defined by peaks 1-14 shown in FIG.
`
`12.”
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`14
`
`33.
`
`Independent claim 30 recites “[a] pharmaceutical composition for the
`
`treatment of an infection, the composition comprising daptomycin having greater
`
`than 93% purity relative to impurities 1-14 defined by peaks 1-14 shown in FIG.
`
`12, the daptomycin purified by a process comprising the formation of micelles
`
`comprising daptomycin.”
`
`34.
`
`Independent claim 40 recites “[a] A pharmaceutical composition for
`
`the treatment of an infection of the blood, skin or soft tissue, the pharmaceutical
`
`composition comprising a solution of a pharmaceutically acceptable carrier for
`
`intravenous administration and daptomycin, the daptomycin having greater than
`
`93% purity relative to impurities 1-14 defined by peaks 1-14 shown in FIG. 12,
`
`and the daptomycin obtained from a purification process comprising the formation
`
`of a daptomycin micelle.”
`
`35.
`
`Independent claim 50 recites “[a] A vial containing a lyophilized
`
`powder pharmaceutical composition compatible with a pharmaceutically
`
`acceptable carrier for the treatment of an infection by a daily intravenous dose of
`
`the lyophilized powder reconstituted in the pharmaceutically acceptable carrier, the
`
`composition a) having daptomycin with greater than or about 93% purity relative
`
`to impurities 1-14 defined by peaks 1-14 shown in FIG. 12; and b) the composition
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`comprising daptomycin purified by a process including the steps of forming a
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`daptomycin aggregate, converting the daptomycin aggregate to monomers and
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`obtaining the daptomycin in the composition from the monomers by a process
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`including one or more steps selected from the group consisting of anion exchange
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`chromatography and hydrophobic interaction chromatography. “
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`36.
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`Independent claim 51 recites “[a] A vial containing a lyophilized
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`powder pharmaceutical composition compatible with a pharmaceutically
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`acceptable carrier for the treatment of an infection by a daily intravenous dose of
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`the lyophilized powder reconstituted in the pharmaceutically acceptable carrier, the
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`composition a) having daptomycin with greater than or about 93% purity relative
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`to impurities 1-14 defined by peaks 1-14 shown in FIG. 12; and b) the composition
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`comprising daptomycin purified by a process including the steps of forming a
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`daptomycin aggregate, converting the daptomycin aggregate to monomers and
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`obtaining the daptomycin in the composition from the monomers by a process
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`including one or more steps selected from the group consisting of anion exchange
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`chromatography and hydrophobic interaction chromatography.”
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`37. Dependent claims 2-16, 18-29, 31-39, 41-49 and 52-54 relate to
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`various purity levels of the claimed daptomycin compositions and measurement of
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`the purity levels with HPLC analysis (claims 2-4, 7-16, 18, 32-34, 41-43 and 52)
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`pharmaceutical compositions and doses comprising excipients for intravenous
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`administration, including physiological saline (claims 19, 21, 49 and 53-54), use of
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`the pharmaceutical compositions in the treatment of infections (claims 20, 25-29,
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`35-39, 44-48), and additional processing steps, including the lyophilization of the
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`claimed daptomycin compositions as well as the use of anion exchange
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`chromatography and hydrophobic ion chromatography (claims 5-6, 22-24, 31).
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`VI.
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`Background
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`A.
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`38.
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`Use of Surfactants and Biosurfactants
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`Surfactants are amphiphilic compounds that can reduce the free
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`energy of a system by replacing bulk molecules of higher energy at an interface.
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`Surfactant molecules contain two physically separate regions: a hydrophobic
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`portion with little affinity for a hydrophilic bulk medium (e.g., water), and a
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`hydrophilic portion that is attracted to a hydrophilic bulk medium. As amphiphiles,
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`surfactants are able to reduce interfacial/surface tension at liquid-liquid and liquid-
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`gas interfaces, making these compounds invaluable for a variety of industrial and
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`therapeutic applications, including solubility enhancement and surface tension
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`reduction in food, as well as in the pharmaceutical, cosmetic and environmental
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`industries.
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`39. Biosurfactants are biologically produced surfactants, usually by fungi,
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`yeast or bacteria from various substrates, including sugars, oils, alkanes and wastes.
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`See, e.g., Lin SC, “Biosurfactant: Recent Advances,” J. Chem. Tech. Biotechnol.
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`66:109-20 (1996) [Ex. 1020]. Biosurfactants are made up of a hydrophilic moiety,
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`comprising an acid, peptide cations, or anions, mono-, di- or polysaccharides, and a
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`hydrophobic moiety of unsaturated or saturated hydrocarbon chains or fatty acids.
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`Like surfactants, biosurfactants are able to lower surface tension and enhance
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`solubility. Biosurfactants also form micelles (structured aggregates of
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`biosurfactants that form with the hydrophilic “head” region in contact with a
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`hydrophilic bulk medium, and the hydrophobic tail sequestered in the micelle
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`center) readily due to low critical micelle concentration (CMC) values for these
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`compounds. Id. The CMC value represents the concentration at which micelle
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`structures will form. Biosurfactants are typically grouped into several categories,
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`including glycopeptides, lipopeptides, phospholipids, fatty acids, neutral lipids and
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`polymeric and particulate compounds.
`
`40.
`
`Lipopeptides, one of the most studied biosurfactant category, are
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`produced by a variety of microorganisms, including Bacillus, Lactobacillus,
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`Streptomyces, Pseudomonas, and Serratia. The lipopeptides produced by these
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`microorganisms are typically cyclic lipopeptides with a fatty acyl chain. These
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`cyclic lipopeptides vary in terms of the amino acid content, as well as in the chain
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`length and structure of the fatty acid component. They all, however, possess the
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`same desirable characteristics of solubility enhancement, surface tension reduction
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`and low CMC values, amongst other attributes, that make them valued in industrial
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`and therapeutic applications.
`
`41.
`
`Surfactin, which was first discovered in 1968 by Arima, is the most
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`studied biosurfactant lipopeptide. See Arima et al., “Surfactin, a crystalline peptide
`
`lipid surfactant produced by Bacillus subtilis: Isolation, characterization and its
`
`inhibition of fibrin clot formation,” Biochem. Biophys. Res. Comm. 31:488-94
`
`(1968) [Ex. 1021]. Surfactin, also known as subtilysin, consists of a seven-amino
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`acid sequence in a cyclical structure with a 13-16 carbon fatty acid tail. Kakinuma
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`et al., “Confirmation of the structure of surfactin by mass spectrometry,” Ag. Biol.
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`Chem. 33:1669-72 (1969) [Ex. 1022].
`
`42.
`
`The capabilities of surfactin have been well explored, and its potency
`
`and efficacy documented for a variety of biomedical and bioengineering
`
`applications. For example, lipopeptides, including surfactin, were exploited for
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`their bioremediation properties, including use in environmental disasters such as
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`oil or toxic spills, or other environmental disaster. Lipopeptides were also valued
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`prior to January 2000 for their ability to disrupt membranes, which leads to cell
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`lysis. Surfactin was shown to be a potent antimicrobial, disrupting bacterial
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`spheroplasts and protoplasts. See, e.g., Bernheimer et al. “Nature and properties of
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`a cytolytic agent produced by Bacillus subtilis,” J. Gen. Microbiol. 61:361-69
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`(1970) [Ex. 1023]. Surfactin was also shown to inhibit blood coagulation and
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`protein denaturation, to accelerate fibrinolysis, and to have antimyoplasmic
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`properties. See Vollenbroich et al. “Antimycoplasma properties and application on
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`cell surface of surfactin, a lipopeptide antibiotic from Bacillus subtilis,” Appl.
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`Environ. Microbiol. 63:44-69 (1997) [Ex. 1025].
`
`43. Other antimicrobial lipopeptides with pharmaceutical properties
`
`include fengycin, iturin, bacillomysins, mycosubtilins, as well as the cyclic
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`lipopeptide daptomycin. See Mulligan, “Characterization, Production, and
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`Applications of Lipopeptides” in BIOSURFACTANTS: RESEARCH TRENDS AND
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`APPLICATIONS (C. Mulligan, S. Sharma and A. Mudhoo eds., 2014) [Ex. 1019].
`
`These antimicrobial lipopeptides share a common amphiphilic structure, forming a
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`hydrophil