United States Patent
`
`(12)
`(10) Patent No.:
`US 9,643,997 B2
`
`Shultz et a].
`(45) Date of Patent:
`*May 9, 2017
`
`US009643997B2
`
`(54) CAPTURE PURIFICATION PROCESSES FOR
`PROTEINS EXPRESSED IN A
`
`NON-MAMMALIAN SYSTEM
`(71) Applicant: AMGEN INC., Thousand Oaks, CA
`(US)
`Inventors: Joseph Edward Shultz, Binningen
`(CH); Roger Hart, Loveland, CO (US)
`
`(72)
`
`( * ) Notice:
`
`.
`.
`(73) A551gnee. AMGEN INC., Thousand Oaks, CA
`(US)
`Subject to any disclaimer, the term of this
`patent is extended or adjusted under 35
`USC 15403) by 0 days
`.
`.
`.
`.
`.
`This patent is subject to a terminal dis-
`C1a1mer~
`
`10/2006 Brady et a1.
`2006/0228329 A1
`10/2007 Schlegl
`2007/0238860 A1
`9/2008 Ramanan et a1.
`2008/0214795 A1
`10/2008 Dietrich et a1.
`2008/0260684 A1
`10/2010 Treuheit et al.
`2010/0267936 A1
`FOREIGN PATENT DOCUMENTS
`
`DE
`EP
`EP
`EP
`W0
`$8
`WO
`W0
`WO
`WO
`WO
`
`10—2005-033250 A1
`0 657 466 Al
`1 845 103 A1
`1845103 A1
`92/04382 A1
`332%; :1
`01/07477 A1
`02/020762 A3
`2004/058988 A3
`2009/023270 A1
`W02011/005488 Al
`
`1/2007
`6/1995
`10/2007
`5/2015
`3/1992
`$33;
`2/2001
`8/2002
`11/2007
`2/2009
`1/2011
`
`(21) Appl. No.: 14/599,336
`
`OTHER PUBLICATIONS
`
`(22)
`
`(65)
`
`(62)
`
`(60)
`
`Filed:
`
`Jan. 16, 2015
`_
`_
`_
`Prior Publication Data
`US 2015/0361130 A1
`Dec. 17, 2015
`
`Related US. Application Data
`
`Division of application No. 12/822,990, filed on Jun.
`24, 2010, now Pat. No. 8,940,878.
`
`Provisional application No. 61/220,477, filed on Jun.
`25, 2009.
`
`(51)
`
`2006.01
`E20061”;
`(2006.01)
`(200601)
`(2006.01)
`
`Int. Cl-
`C07K 1/14
`C07K 1/22
`C07K 1/18
`C07K 1/32
`C07K 16/00
`(52) US' CL
`CPC ................ C07K 1/22 (2013.01); C07K 1/145
`(2013.01); C07K 1/18 (2013.01); C07K 1/32
`(201301); C07K 16/00 (201301)
`(58) Field of Classification Search
`None
`
`See application file for complete search history.
`
`(56)
`
`References Cited
`
`U.S. PATENT DOCUMENTS
`
`452375224 A
`4,468,464 A
`4 740 470 A
`5’466’377 A
`5,663,304 A
`5,922,846 A
`2,283,333 3%
`.
`.
`6,972,327 B1
`7,138,370 B2
`7,442,738! 3%
`7’511’012 B2
`7’723’490 B2
`8,906648 B2
`8:940:878 B2
`8,952,138 132
`9,090,684 B2
`9,200,030 B2
`
`12/1980 Cohen et 31.
`8/1984 Cohen et 31.
`4/ 1988 C h
`t
`1.
`“/1995 (,3;ng g, 31.
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`7/ 1999 Cerletti et a1.
`i338?! 56036131 et 31~
`1
`reuelteta~
`12/2005 Madani et a1.
`11/2006 Oliner et a1.
`igggg: Eordyutmlet 31'
`3/2009 HZEgef: 313'
`5/2010 Treuheit a al
`”/2014 Butler et a1.
`1/2015 Shultz et 31.
`2/2015 Shultz et 31.
`7/2015 Borras et a1.
`12/2015 Pizarro et a1.
`
`'
`
`30 Claims, 5 Drawing Sheets
`
`Page 1
`
`KASHIV EXHIBIT 1001
`
`|PR2019-00797
`
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`$63377, (2393611
`'
`'
`f DC SIGN/R '
`'
`'th
`HY er et
`. “
`“acterlzafilon 0
`'
`Interaction W1
`Huwflmmugweficle“? ““15 Type 11‘3" 12° and ICAM M°1'
`ecu es avors
`e receptor s role as an antigen-capturing rather than
`an adhesion receptor,” J. Virology 79(8):4589-4598, Apr. 2005.
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`A Sepharose CL-4B. p. 1-8, Mar. 2006 (Cited in JP Office action as
`D5 http://eclubbiomart.cn/sites/eclub.biomart.cn/themes/aktac1ub/
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`Mar. 2006).
`GE Healthcare Instructions 71-5002-60 AE: Ion exchange chroma-
`tography; Q Sepharose XL, XL virus licensed. SP Sepharose XL,
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`gelifesciences.com/gehc1siimages/GELS/Related%20C0ntent/
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`Feb~ 2006)
`.
`(Continued)
`Primary Examiner 7 Brian J Gangle
`74 An
`A
`t
`F' 7R
`(
`)
`omey’
`gen ’ or
`”m
`aymon
`(57)
`ABSTRACT
`Methods ofpurifying proteins expressed in non-mammalian
`expression systems in a non-native soluble form directly
`from cell lysate are disclosed. Methods of purifying proteins
`expressed in non-mammalian expression systems in a non-
`native limited solubility form directly from a refold solution
`are also disclosed. Resin regeneration methods are also
`prOVIded.
`
`dM.D
`
`055
`
`KASHIV EXHIBIT 1001
`IPR2019-00797
`
`Page 1
`
`

`

`US 9,643,997 B2
`Page 2
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`

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`
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`OTHER PUBLICATIONS
`
`Document 35: Answer and Affirmative Defenses to Complaint,
`Counterclaim against All Plaintiifs by Apotex Corp., Apotex Inc.
`(Brier, Simeon) (Entered: Oct. 5, 2015), pp. 1-41.
`Document 42: Plaintiffs Motion for Preliminary Injunction and
`Incorporated Memorandum of Law by Amgen Inc., Amgen Manu-
`facturing Limited, pp. 1-25. Attachments: #1 Aifidavit Declaration
`of Robert Azelby, pp. 1-4. # 2, Affidavit Declaration of Nicholas
`Groombridge, pp. 1-4. # 3 Exhibit AiApr. 17, 2015 Letter to
`GroombridgeiPegfilgrastim, pp. 1-2. # 4 Exhibit BiMay 8, 2015
`Ltr. Groombridge to Coblentz re pegfilgrastim (1)(8)(A) notice, pp.
`1-3. # 5 Exhibit CiJul. 29, 2015 N Groombridge letter to B
`Coblentz, pp. 1-3. # 6 Exhibit DiAug. 24, 2015 Letter to
`Groombridge, pp. 1-2. # 7 Exhibit EiMay 5, 2015 Order Granting
`Motion for an Injunction Pending Appeal, pp. 1-3. # 8 Exhibit
`FiJoint Stip Re Amgens Motion for Preliminary Injunction Jan.
`10, 2015, pp. 1-5. # 9 Exhibit GiFDA Website Printout, pp.
`1-3. # 10 Exhibit HiJorge Mestre-Ferrandiz, et al., The R&D Cost
`ofa New Medicine (2012), pp. 1-101. # 11 Exhibit 140d. 16,2015
`Order Denying Petition for En Banc Rehearing, pp. 1-3. # 12 Text
`of Proposed Order Proposed Order)(O’Sullivan, John) (Entered:
`Oct. 16, 2015), pp. 1-2.
`Document 47: Apotex’s Corrected Answer, Affirmative Defenses &
`Counterclaims to Amgen’s Complaint, Oct. 23, 2015, pp. 1-42.
`Document 64: Defendants Apotex’s Answer, Affirmative Defenses
`and Counterclaims to Plaintiffs’ Complaint, Dec. 1, 2015, pp. 1-45.
`Document 76: Apotex’s Opening Claim Construction Brief, Dec.
`11, 2015, pp. 1-26.
`Document 77: Amgen’s Opening Claims Construction Brief, Dec.
`11, 2015, pp. 1-23; Document 77-1 to Exhibit 1, US. Pat. No.
`8,952,138, document entered on Dec. 11, 2015, pp. 1-19; Document
`77-2 to Exhibit 2, US. Pat. No. 6,162,427, document entered Dec.
`11, 2015, pp. 1-7; Document 77-3 to Exhibit 3, US. Pat. No.
`5,824,784, document entered Dec. 11, 2015, pp. 1-31; Document
`77-4 to Exhibit 4, Declaration of Ricth C. Willson, Ph. D.
`Regarding Claim Constructions of Shultz et al., document entered
`Dec. 11, 2015, pp. 1-16, Document 77-5 to Exhibit A, Ricth
`Willson CV, document entered Dec. 11, 2015, pp. 1-21; Document
`77-6 to Exhibit B, Effective renaturation of denatured and reduced
`immunoglobulin G in vitro without assistance of chaperone, docu-
`ment entered on Dec. 11, 2015, pp. 1-7; Document 77-7 to Exhibit
`C, Eifective renaturation of reduced lysosome by gentle removal of
`urea, document entered on Dec. 11, 2015, pp. 1-6; Document 77-8
`to Exhibit D, Perspectives in Biochemistry, Biochemistry, document
`entered on Dec. 11, 2015, pp. 1-10; Document 77-9 to Exhibit E,
`Structural Stability of Covalently Linked GroES Heptamer: Advan-
`tages in the Formulation of Oligomeric Structure, Science Direct,
`document entered on Dec. 11, 2015, pp. 1-16.
`Document 82: Brief in response to Plaintiffs’ Opening Claim
`Construction Brief by Apotex Corp., Apotex Inc. re 77 Trial Brief,
`documents entered on Jan. 8, 2016, pp. 1-25. Attachments: # 1
`Declaration ofW. Blake Coblentz in Support of Defendants Respon-
`sive Claim Construction Brief, pp. 1-2. # 2 Exhibit AiDeclaration
`ofAnne S. Robinson, Ph.D., pp. 1-17. # 3 Exhibit BiR. Rudolph
`and H. Lilie, In vitro folding of inclusion body proteins). Entered:
`Jan. 8, 2016, pp. 1-9.
`Document 83: Responsive Claim Construction Briefby Amgen Inc.,
`Amgen Manufacturing Limited. Documents entered on Jan. 8, 2016.
`pp. 1-25. Attachments: # 1 Aifidavit Exh. liRebuttal Declaration
`of Ricth C. Willson, pp. 1-19. # 2 Exhibit AiFeb. 23, 2012
`Office Action Response, pp. 1-6. # 3 Exhibit B7’370 Patent, pp.
`1-167. # 4 Exhibit CiJan. 29, 2014 Office Action, pp. 1-8. # 5
`Exhibit DiApr. 28, 2014 Office Action Response, # 6 Affidavit
`Exh. 27Rebuttal Declaration of Louis M. Pelus, pp. 1-22. # 7
`Exhibit AiPelus CV, pp. 1-49. # 8 Exhibit BiRichman, pp. 1-11.
`# 9 Exhibit Cishirota, pp. 1-8. # 10 Exhibit DiNeben, pp. 1-10.
`Document 89: Apotex’s Reply to Plaintiffs’ Responsive Claim
`Construction Brief. Notice by Apotex Corp., Apotex Inc. re 83 Trial
`Brief,, Defendants Apotex Inc. and Apotex Corp.’s Reply to
`Plantiffs’ Responsive Claim Construction Brief. Documents entered
`
`on Jan. 27, 2016, pp. 1-16. Attachments: # 1 Declaration of W.
`Blake Coblentz in Support of Defendants’ Reply to Plaintiffs’
`Responsive Claim Construction Brief, pp. 1-2 # 2 Exhibit AiEx-
`cerpts of deposition transcript of Ricth C. Willson, III, Ph.D., pp.
`1-47 # ’3 Exhibit BiExcerpts of deposition transcript of Anne
`Robinson, Ph.D., pp. 1-5 # 4 Exhibit CiExcerpts of deposition
`transcript of Louis M. Pelus, Ph.D. pp. 1-16.
`Document 90: Amgen’s Reply Claim Construction Brief. Document
`entered on Jan. 27, 2016, pp. 1-15. Attachments: Exhibit 1; Video-
`taped Deposition of Ricth C. Willson, Ph. D. Jan. 18, 2016; pp.
`1-109 Exhibit 2: Videotaped Deposition of Louis M. Pelus, Ph.D.
`Jan. 19, 2016; pp. 1-33. Exhibit 3: Transcript of the Testimony of
`Videotaped Deposition of Anne Robinson, Ph. D., Jan. 20, 2016; pp.
`1-60. Exhibit 4: Videotaped Deposition of David T. Scadden, M.D.
`Jan. 22, 2016; pp. 1-43.
`Document 184: Brief Plaintiffs Supplemental Claim Construction
`Brief Regarding the Meaning of “Protein” in Claim 1 of the ’138
`Patent by Amgen Inc., Amgen Manufacturing Limited. Documents
`Entered: Jun. 22, 2016), pp. 1-15. Attachments: #1 Exhibit Ex.
`liUS Pat. No. 8,952,138, pp. 1-19. # 2 Exhibit Ex. 57Jan. 18,
`2016 Willson Dep. Tr. (Excerpt), pp. 1-12. # 3 Exhibit Ex. 67Jun.
`22, 2012 Response to Office Action from File History of US. Pat.
`No. 8,952,138)(O’Sullivan, John), pp. 1-6.
`Document 186: Trial Brief Apotex’s Supplemental Claim Construc-
`tion Brief in Support of Their Construction for the Term ‘protein’ As
`Used in Claim 1 of US. Pat. No. 8,952,138 by Apotex Corp.,
`Apotex Inc.pp. 1-18 (Attachments: #1 Exhibit
`1 US. Pat. No.
`8,952,138; pp. 1-19; # 2 Exhibit 67Response to Office Action dated
`Jun. 22, 2012)(Brier, Simeon) (Entered: Jun. 22, 2016); pp. 1-6.
`Document 244: Motion for Judgment on Partial Findings Pursuant
`to Fed. R. Civ. P. 52(c) by Apotex Corp., Apotex Inc. pp. 1-12,
`Entered: Jul. 18, 2016: Attachments #1 Exhibit AiPages from Trial
`Transcript Day 1 (Jul. 11, 2016) (Willson), pp. 1-6 # 2 Exhibit
`BiPages from Trial Transcript Day 2 (Jul. 12, 2016) (Willson), pp.
`1-9 # 3 Exhibit CiPages from Trial Transcript Day 3 (Jul. 13,
`2016) (Dowd), pp. 1-13 # 4 Text of Proposed Order, pp. 1.
`Document 247:Transcript of Bench Trial held on Jul. 11, 2016
`before Judge James I. Cohn, 1-245 pages, Court Reporter: Karl
`Shires, 954-769-5496 / Karl,Shires@flsd.uscourts.gov. Transcript
`may be viewed at
`the court public terminal or purchased by
`contacting the Court Reporter/Transcriber before the deadline for
`Release of Transcript Restriction. After that date it may be obtained
`through PACER. Redaction Request due Aug. 11, 2016. Redacted
`Transcript Deadline set for Aug. 22, 2016. Release of Transcript
`Restriction set for Oct. 20, 2016. (Shires, Karl) (Entered: Jul. 18,
`2016).
`Document 248: Transcript of Bench Trial held on Jul. 12, 2016
`before Judge James I. Cohn, 1-171 pages, Court Reporter: Karl
`Shires, 954-769-5496 / Karl,Shires@flsd.uscourts.gov. Transcript
`may be viewed at
`the court public terminal or purchased by
`contacting the Court Reporter/Transcriber before the deadline for
`Release of Transcript Restriction. After that date it may be obtained
`through PACER. Redaction Request due Aug. 11, 2016. Redacted
`Transcript Deadline set for Aug. 22, 2016. Release of Transcript
`Restriction set for Oct. 20, 2016. (Shires, Karl) (Entered: Jul. 18,
`2016).
`Document 249: Transcript of Bench Trial held on Jul. 13, 2016
`before Judge James I. Cohn, 1-61 pages, Court Reporter: Karl
`Shires, 954-769-5496 / Karl,Shires@flsd.uscourts.gov. Transcript
`may be viewed at
`the court public terminal or purchased by
`contacting the Court Reporter/Transcriber before the deadline for
`Release of Transcript Restriction. After that date it may be obtained
`through PACER. Redaction Request due Aug. 11, 2016. Redacted
`Transcript Deadline set for Aug. 22, 2016. Release of Transcript
`Restriction set for Oct. 20, 2016. (Shires, Karl) (Entered: Jul. 18,
`2016).
`Document 250: Transcript of Bench Trial held on Jul. 14, 2016
`before Judge James I. Cohn, 1-242 pages, Court Reporter: Karl
`Shires, 954-769-5496 / Karl,Shires@flsd.uscourts.gov. Transcript
`may be viewed at
`the court public terminal or purchased by
`contacting the Court Reporter/Transcriber before the deadline for
`Release of Transcript Restriction. After that date it may be obtained
`through PACER. Redaction Request due Aug. 11, 2016. Redacted
`
`Page 4
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`US 9,643,997 B2
`Page 5
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`(56)
`
`References Cited
`OTHER PUBLICATIONS
`
`Transcript Deadline set for Aug. 22, 2016. Release of Transcript
`Restriction set for Oct. 20, 2016. (Shires, Karl) (Entered: Jul. 18,
`2016).
`Document 254: Response in Opposition re 244 Motion for Judg-
`ment on Partial Findings Pursuant to Fed. R. CiV. P. 52(c) filed by
`Amgen Inc., Amgen Manufacturing Limited. Replies due by Aug.
`15, 2016; pp. 1-20.
`Document 259: Mandate of US Federal Circuit (certified copy)
`Affirm Judgment/ Order of the district court with courts opinion re
`72 Notice of Appeal, filed by Apotex Corp., Apotex Inc.
`; Date
`Issued: Aug. 11, 2016 ; US Federal Circuit Case Number: 16-1308
`(amb) (Entered: Aug. 11, 2016); pp. 1-26.
`Document 260: Reply to Response to Motion re 244 Motion for
`Judgment on Partial Findings Pursuant to Fed. R. CiV. P 52(c) filed
`by Apotex Corp., Apotex Inc. pp. 1-11; Attachments: # 1 Exhibit
`liTrial Transcript Day 2 (Jul. 12, 2016) (Willson), pp. 1-7. # 2
`Exhibit 27Trial Transcript Day 3 (Jul. 13, 2016) (Dowd), pp. 1-4.
`# 3 Exhibit 37Trial Transcript Day 4 (Jul. 14, 2016) (Robinson),
`pp. 1-4. # 4 Exhibit 47Tria1 Transcript Day 5 (Jul. 18, 2016), pp.
`1-3.
`Document 268: Final Judgment Signed by Judge James I. Cohn on
`Sep. 6, 2016. (tpl) Notice: If there are sealed documents in this case,
`they may be unsealed after 1 year or as directed by Court Order,
`unless they have been designated to be permanently sealed. See
`Local Rule 5.4 and Administrative Order 2014-69. (Entered: Sep. 6,
`2016); pp. 1-5.
`
`Page 5
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`U.S. Patent
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`May 9, 2017
`
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`US 9,643,997 B2
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`U.S. Patent
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`May 9, 2017
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`U.S. Patent
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`May 9, 2017
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`U.S. Patent
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