Pfenex Inc. vs GlaxoSmithKline Biologicals SA

Termination Decision Document

Amended Joint Motion to Terminate

Order Denying Joint Motion To Terminate, Granting Leave To File Amended Motion To Terminate, And Granting Joint Request That Settlement Agreement Be Treated As Business Confidential Information And Be Kept Separate

Exhibit 3005

Joint Motion to Terminate

Joint Request to File Settlement Materials as Business Confidential Information and to Maintain Said Materials Separate from the Public File

Confidential Settlement Agreement

Patent Owner's Updated Exhibit List as of October 30, 2020

Ex. 3004

Hearing Transcript

Patent Owner's Updated Mandatory Notices

LEAP Practitioner Request and Verification Form

Petitioner's Reply to Patent Owner's Opposition to Petitioner's Motion to Exclude Evidence

Petitioner's Sur-Reply in Opposition to Patent Owner's Revised Contingent Motion to Amend

Petitioner's Updated Exhibit List

EX1080 ¿¿¿ Petitioner's Demonstrative Exhibit

GSK Trial Demonstratives

Patent Owner's Reply to Petitioner's Opposition to Patent Owner's Motion to Exclude

Patent Owner's Updated Exhibit List as of September 2, 2020

Petitioner's Opposition to Patent Owner's Motion to Exclude

Petitioner's Updated Exhibit List

Declaration National Library Netherlands

Declaration of Dr. Hilary Pioro re EMA document

Declaration of Dr. Hilary Pioro re Signal Peptide Database

Patent Owner's Opposition to Petitioner's Motion to Exclude

Petitioner's Motion to Exclude

Patent Owner's Motion to Exclude

Patent Owner's Reply to Petitioner's Opp. to Patent Owner's Revised Contingent Motion to Amend

Oral Hearing 37 C.F.R. sec 42.70

Patent Owner's Request for Oral Hearing

Petitioner's Request for Oral Argument

Petitioner's Opposition to Patent Owner¿¿¿s Revised Contingent Motion to Amend

Petitioner's Updated Exhibit List

EX1078 - Georgiou Dec ISO Opposition to Revised Contingent MTA

EX1079 - Chen (2004)

Petitioner's Objections

REVISED SCHEDULING ORDER

Petitioner's Notice of Deposition of James E. Galen, Ph.D

Patent Owner's Sur-Reply

Patent Owner's Revised Contingent Motion to Amend

Patent Owner's Updated Exhibit List

Galen Declaration

Chen 2006

Preliminary Guidance - Patent Owner's Motion to Amend

Petitioner¿¿¿s Updated Exhibit List

Patent Owner's Objections to Petitioner's Evidence

Deposition of James E. Galen

Reply Declaration of George Georgiou

Definition of Capable

MTA Declaration of George Georgiou

Kaczorek (1983)

Petitioner¿¿¿s Opposition to Patent Owner¿¿¿s Contingent Motion to Amend

Petitioner's Reply to Patent Owner Response

Kaczorek (1985)

Williams (1987)

Movva (1980)

Updated Exhibit List

Exhibit 3002

ORDER Conduct of the Proceeding 37 C.F.R. ¿¿ 42.5

Exhibit 3003

Petitioner's Notice of Rescheduled Deposition of James E. Galen, Ph.D

Joint Stipulation to Modify the Scheduling Order

Petitioner Notice of Deposition of James E. Galen, Ph.D

Pfenex Inc. Objections

Patent Owner's Contingent Motion to Amend Under 37 C.F.R. 42.121 and Request for Preliminary Guidance Under Pilot Program

Bowden 1990

Gentz 1988

Desvaux 2009

Patent Owner Response

Patent Owner's Updated Exhibit List

Georgiou 1986

Baneyx 1992

Sarvas 2004

Schlegel 2013

Rippmann 1998

Halfmann 1993

Pratap 1998

Chung 1998

Castineiras 2018

Park 2018

Murphy 2000

Galen Declaration

Georgiou Depo Transcript of Jan 30, 2020

Markrides 1996

Latifi 2015

Stefan 2011

Yamaizumi 1982

Rappuoli 1983

Definition of Signal Sequence

Teintze 1985

Cui 2018

Patent Owner's Notice of Deposition of Dr. George Georgiou

Joint Stipulation to Modify the Scheduling Order

Patent Owner's Objections to Petitioner's Evidence

IPR2019-01028 Petitioner's Objections

Trial Instituted Document

Ex. 3001

SCHEDULING ORDER

Patent Owner's Response to Petitioner's Explanation of Multiple Petitions Challenging Patent No. 9,422,345 and Ranking Petitions

Petitioner's Explanation of Multiple Petitions Challenging Patent No. 9,422,345 and Ranking of Petitions

Patent Owner Preliminary Response

Patent Owner Exhibit List

Galen Declaration

Madigan 2000, Part 1 of 2

van Wely 2001

Mergulhao 2004

Orr 1999

Hemila 1989

Bishai II 1987

Madigan 2000, Part 2 of 2

Choi 2004

Hegde 2006

Pappenheimer 1977

Perentesis 1988

Bashai I 1987

Zettlmeissl 1986

Terpe 2006

Natale 2008

Papanikou 2007

Mogensen 2005

Uchida 1971

Cabiaux 1988

Petitioner Power of Attorney

Petitioner's Mandatory Change-of-Information Notices

Patent Owner's Power of Attorney

Patent Owner's Mandatory Notices

Notice of Accord Filing Date

File History of U.S. Patent No.: 9,422,345

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D. O¿¿¿Keefe and R. Collier, ¿¿¿Cloned diphtheria toxin within the periplasm of Escherichia coli causes lethal membrane damage at low pH,¿¿¿ Proceedings of the National Academy of Sciences USA 86;343-346 (1989)

S. Choe et al., ¿¿¿The crystal structure of diphtheria toxin,¿¿¿ Nature 357:216-222 (1992)

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U.S. Patent No.: 9,422,345, N. Blais et al., Issued: August 23, 2016

U.S. Patent Application Publication No.: 2009/0010966, C. Davis et al., Published: January 8, 2009

S. Inouye and M. Inouye, ¿¿¿Up-promoter mutations in the lpp gene of Escherichia coli,¿¿¿ Nucleic Acids Research 13:3101-3110 (1985) (¿¿¿Inouye¿¿¿)

H. Ikemura et al., ¿¿¿Requirement of pro-sequence for the production of active subtilisin E in Escherichia coli,¿¿¿ Journal of Biological Chemistry 262(16):7859-7864 (1987)

U.S. Patent No. 5,264,365, G. Georgiou et al., Issued: November 23, 1993

U.S. Patent No. 5,508,192, G. Georgiou et al., Issued: April 16, 1996

U.S. Patent No. 7,083,945, G. Chen et al., Issued: August 1, 2006

S. Dittmann, ¿¿¿Epidemic diphtheria in the newly independent states of the former USSR¿¿¿situation and lessons learned,¿¿¿ Biologicals 25:179-186 (1997)

M. Eaton, ¿¿¿The purification and concentration of diphtheria toxin,¿¿¿ Journal of Bacteriology 31:347-383 (1936)

A. Glenny and B. Hopkins, ¿¿¿Diphtheria toxoid as an immunising agent,¿¿¿ British Journal of Experimental Pathology 4:283-288 (1923)

B. Metz Dissertation Thesis ¿¿¿Structural characterisation of diphtheria toxoid,¿¿¿ (Universitat Utrecht) (2005)

R. Collier, ¿¿¿Understanding the mode of action of diphtheria toxin: a perspective on progress during the 20th century,¿¿¿ Toxicon 39:1793-1803 (2001)

T. Uchida et al., ¿¿¿Reconstitution of diphtheria toxin from two nontoxic cross-reacting mutant proteins,¿¿¿ Science 175:901-903 (1972)

P. Braun et al., ¿¿¿Improving protein secretion by engineering components of the bacterial translocation machinery,¿¿¿ Current Opinion in Biotechnology 10:376-381 (1999)

A. Rietsch and J. Beckwith, ¿¿¿The genetics of disulfide bond metabolism,¿¿¿ Annual Review of Genetics 32:163-184 (1998)

F. Katzen and J. Beckwith, ¿¿¿Disulfide bond formation in periplasm of Escherichia coli,¿¿¿ Methods in Enzymology 348:54-66 (2002).

J. Ghrayeb et al. ¿¿¿Secretion cloning vectors in Escherichia coli,¿¿¿ The EMBO Journal 10:2437-2442 (1984)

M. Baeshen et al., ¿¿¿Production of biopharmaceuticals in E. coli: current scenario and future perspectives,¿¿¿ Journal of Microbiology and Biotechnology 25:953-962 (2015)

C. French et al., ¿¿¿Development of a simple method for the recovery of recombinant proteins from the Escherichia coli periplasm,¿¿¿ Enzyme and Microbial Technology 19:332-338 (1996)

A. Skerra and A. Pluckthun, ¿¿¿Assembly of a functional immunoglobulin Fv fragment in Escherichia coli,¿¿¿ Science 240:1038-1041 (1988)

K. Talmadge et al., ¿¿¿Eukaryotic signal sequence transports insulin antigen in Escherichia coli,¿¿¿ Proceedings of the National Academy of Sciences USA 77:3369-3373 (1980)

K. Talmadge et al., ¿¿¿Bacteria mature preproinsulin to proinsulin,¿¿¿ Proceedings of the National Academy of Sciences USA 77:3988-3992 (1980) (¿¿¿Talmadge II¿¿¿)

G. Georgiou and L. Segatori, ¿¿¿Preparative expression of secreted proteins in bacteria: status report and future prospects,¿¿¿ Current Opinion in Biotechnology 16:538-545 (2005)

G. Georgiou and L. Segatori, ¿¿¿Preparative expression of secreted proteins in bacteria: status report and future prospects,¿¿¿ Current Opinion in Biotechnology 16:538-545 (2005)

pET Vector Cloning/Expression Regions (https://web.archive.org/web/19971119174110/http:/www.novagen.com/append/append1.pdf)

S. Dilsen et al., ¿¿¿Fed-batch production of recombinant human calcitonin precursor fusion protein using Staphylococcus carnosus as ...,¿¿¿ Applied Microbiology and Biotechnology 54:361-369 (2000)

G. Duffaud et al., ¿¿¿Expression and secretion of foreign proteins in Escherichia coli,¿¿¿ Methods in Enzymology 153:492-507 (1987)

F. Mergulhao et al., ¿¿¿Recombinant protein secretion in Escherichia coli,¿¿¿ Biotechnology Advances 23:177-202 (2005)

S. Chan et al., ¿¿¿Biosynthesis and periplasmic segregation of human proinsulin in Escherichia coli,¿¿¿ Proceedings of the National Academy of Sciences USA 78:5401-5405 (1981)

H. Hsiung et al., ¿¿¿High-level expression, efficient secretion and folding of human growth hormone in Escherchia coli,¿¿¿ Nature Biotechnology 4:991-995 (1986)

A. Ghorpade and L. Garg, ¿¿¿Efficient processing and export of human growth hormone by heat labile enterotoxin chain B signal sequence,¿¿¿ FEBS Letters 330:61-65 (1993)

J. Choi and S. Lee, ¿¿¿Secretory and extracellular production of recombinant proteins using Escherichia coli.,¿¿¿ Applied Microbiology and Biotechnology 64(5):625-635 (2004)

U.S. Patent No. 5,917,017, R. Collier et al., Issued: June 29, 1999

H. Thie et al., ¿¿¿SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli,¿¿¿ New Biotechnology 25:49-54 (June 2008)

S. Cantrell, ¿¿¿Vectors for the expression of recombinant proteins in E. coli,¿¿¿ Methods in Molecular Biology 235:257-275 (2003)

Patent Owner Preliminary Response in IPR2019-00241, filed February 14, 2019.

Indian Patent Application No. 9745/DELNP/2007, E. Mekada et al., Published: June 20, 2008

B. Zuber et al., ¿¿¿Granular layer in the periplasmic space of gram-positive bacteria and fine structures of Enterococcus gallinarum and Streptococcus gordonii septa...,¿¿¿ Journal of Bacteriology 188:6652-6660 (2006)

European Medicines Agency, ¿¿¿Refusal Assessment Report for Cimzia, Procedure No. EMEA/H/C/740,¿¿¿ Document Reference EMEA/176303/2008 (2008)

Patent Owner Preliminary Response in IPR2019-00230, filed February 14, 2019.

Definition of ¿¿¿capable,¿¿¿ in THE MERRIAM-WEBSTER DICTIONARY, Home and Office ed., p. 75 (Merriam-Webster, Springfield, Massachusetts) (1998)

Curriculum Vitae of George Georgiou, Ph.D.

pET-26b(+) Vector Map (https://web.archive.org/web/20030620093207/http://www.novagen.com/SharedImages/TechnicalLiterature/7_TB071.pdf) [with higher resolution image appended from www.synthesisgene.com/vector/pet-26b.pdf]

pET System Tutorial (https://web.archive.org/web/20030408091617/http://novagen.com/SharedImages/TechnicalLiterature/7_pETExp.pdf) (accessed April 15, 2019)

pET-22b(+) Vector Map (https://web.archive.org/web/20030819085202/http://www.novagen.com/docs/NDIS/69744-000.pdf) [with higher resolution image appended from https://plasmid.med.harvard.edu/PlasmidRepository/file/map/pET22b(+).pdf]

pET-25b(+) Vector Map (https://web.archive.org/web/20030516011318/http://novagen.com/SharedImages/TechnicalLiterature/7_TB065.pdf) [with higher resolution image appended from www.synthesisgene.com/vector/pET-25b.pdf]

pET-27b(+) Vector Map (https://web.archive.org/web/20030622190457/http://www.novagen.com/SharedImages/TechnicalLiterature/7_TB073.pdf) [with higher resolution image appended from http://www.emdmillipore.com/US/en/product...

PCT Priority Document JP 2005-181314, E. Mekada et al., retrieved from ¿¿¿Related Documents¿¿¿ section at https://patentscope.wipo.int/search/en/detail.jsf?docId=WO2006137398&tab=PCTDOCUMENTS (2006) (accessed April 26, 2019)

PCT Publication No.: WO 2006/137398, E. Mekada et al., Published: December 28, 2006, with sequence listing retrieved from ¿¿¿Published International Application¿¿¿ section at https://patentscope.wipo.int/search/en/detail.jsf?docId=WO2006137398

TolB entry in the Signal Peptide Database at http://signalpeptide.de/index.php?sess=&m=listspdb_bacteria&s=details&id=29110&listname=, creation date July 11, 2003 (accessed May 3, 2019)

Parathyroid Hormone entry in the DrugBank database at https://www.drugbank.ca/drugs/DB05829, creation date November 18, 2007 (accessed May 3, 2019)

Z. Lin et al., ¿¿¿Functional expression of horseradish peroxidase in E. coli by directed evolution,¿¿¿ Biotechnology Progress 15:467-471 (1999)

Declaration of George Georgiou, Ph.D. in Support of Petition for Inter Partes Review of U.S. Patent No. 9,422,345

Petitioner's Power of Attorney

Petition for Inter Partes Review