Merck Sharp & Dohme LLC v. Halozyme, Inc. et al. - PGR2025-00050

Ex. 3001 Attorney Correspondence

Order: Conduct of Proceeding

Order: Granting Motion to Seal

Petitioner's Opposition to Patent Owner's Motion for Additional Discovery

MERCK_PGR00355 - PTAB-PGR2021-00036-1 Merck- Genentech PGR

MERCK_PGR00458 - PTAB-PGR2021-00036-16 Merck- Genentech PGR

MERCK_PGR00462 - RE_ 2_25-cv-03179-ES-JRA_ HALOZYME, INC. v. MERCK SHARP & DOHME CORP.

MERCK_PGR00094 - DNJ-2-25-cv-03179 Stipulation to Substitute Parties

MERCK_PGR00090 - DNJ-2-25-cv-03179 2025-07-14 [019] Corporate Disclosure Statement

EX2068 - Simpson Declaration

EX2069 - Simpson CV

EX2071 - Petsko CV

EX2076 - Hecht Deposition Transcript

EX2077 - Park Deposition Transcript 2025-08-07

EX2078 - Park Deposition Transcript 2025-08-21

EX2079 - Koehl 1999

EX2080 - Pommié 2004

EX2082 - Kyte and Doolittle 1982

EX2083 - Assay Guidance Manual (Part 1 of 6)

EX2083 - Assay Guidance Manual (Part 2 of 6)

EX2083 - Assay Guidance Manual (Part 3 of 6)

EX2083 - Assay Guidance Manual (Part 4 of 6)

EX2083 - Assay Guidance Manual (Part 5 of 6)

EX2083 - Assay Guidance Manual (Part 6 of 6)

EX2084 - The Central Role of Enzymes as Biological Catalysts

EX2085 - French 1983

EX2086 - El-Safory 2010

EX2087 - Lu 2025

EX2088 - Stern & Cóska 2000

EX2089 - Gmachl 1993

EX2090 - Gmachl-Kreil 1993

EX2091 - Davies 1995

EX2092 - Marković-Housley 2000

EX2093 - Baker (US8343487B2)

EX2094 - MULTIDROP 384 Liquid Handling Device Manual 2008

EX2096 - Frost 1997

EX2097 - Bookbinder (US20050260186A1)

EX2098 - Delpech 1995

EX2099 - Takahashi 2003

EX2174 - Park 2068

EX2175 - Park 2069

EX2176 - Park 2070

EX2177 - E-mail

EX2178 - 1LOH pdb file

EX2179 - 1FCV pdb file

EX2180 - 2PE4 pdb file

EX2181 - 8SMN pdb file

EX2163 - Gregory Petsko - National Science and Technology Medals Foundation

EX2164 - Protein Structure and Function (Part 1 of 4)

EX2164 - Protein Structure and Function (Part 2 of 4)

EX2164 - Protein Structure and Function (Part 3 of 4)

EX2164 - Protein Structure and Function (Part 4 of 4)

EX2165 - Wei (US20100143457A1)

EX2166 - Petsko Patent Analysis Data

EX2168 - Gregory A. Petsko - American Academy of Arts and Sciences

EX2169 - Query Input and database selection - BlastTopics 0.1.1 documentation

EX2170 - Chain and Duthie 1940

EX2070 - Petsko Declaration

EX2182 - I309L Swiss Model

EX2183 - I309N Swiss Model

EX2184 - I309E Swiss Model

EX2185 - I309G Swiss Model

EX2186 - I309H Swiss Model

EX2187 - I309M Swiss Model

EX2188 - I309Q Swiss Model

EX2189 - I309R Swiss Model

EX2190 - I309S Swiss Model

EX2191 - PH20

EX2193 - I309N, N47A, N219A Swiss Model

EX2194 - I309N, N47A, N131A Swiss Model

EX2195 - I309N, N47A, N131A, N219A Swiss Model

EX2196 - I309N, N131A, N219A Swiss Model

EX2197 - Orangutan I309N Swiss Model

EX2198 - Chimpanzee I309N Swiss Model

EX2199 - Gibbon I309N Swiss Model

EX2200 - I309T Swiss Model

Patent Owner's Response

EX2400 - Merck Co - 10Q - 11-05-2025

EX2402 - MERCK_PGR00006 - Sidley MSA (CONFIDENTIAL - PROTECTIVE ORDER MATERIAL)

EX2403 - MERCK_PGR00056 - Dechert MSA (CONFIDENTIAL - PROTECTIVE ORDER MATERIAL)

EX2404 - MERCK_PGR00467 - Mark Stewart Offer Letter (CONFIDENTIAL - PROTECTIVE ORDER MA

EX2405 - MERCK_PGR00052 - Hecht Engagement Letter (CONFIDENTIAL - PROTECTIVE ORDER MATE

EX2406 - MERCK_PGR00086 - Park Engagement Letter (CONFIDENTIAL - PROTECTIVE ORDER MATER

EX2407 - Executive Team - MSD

EX2408 - Executive Team - Merck

EX2409 - Board of Directors - MSD

EX2410 - Board of Directors - Merck

EX2411 - Contact Us - MSD

EX2412 - Contact Us - Merck

EX2413 - Who We Are - MSD

EX2414 - Who We Are - Merck

EX2415 - Merck Co - 10k - year 2024

EX2416 - USPTO OED Practitioner Search - Mark Stewart registration

EX2417 - IPR2024-00240 Petition

EX2418 - IPR2024-00622 Petition

EX2419 - IPR2024-00623 Petition

EX2420 - IPR2024-00624 Petition

EX2421 - IPR2024-00625 Petition

EX2422 - IPR2024-00647 Petition

EX2423 - IPR2024-00648 Petition

EX2424 - IPR2024-00649 Petition

EX2425 - IPR2024-00650 Petition

EX2426 - MERCK_PGR00035 - 20250813 Payment Remittance (CONFIDENTIAL - PROTECTIVE ORDER MATERIAL)

EX2427 - MERCK_PGR00042 - Dechert T360 Halozyme (CONFIDENTIAL - PROTECTIVE ORDER MATERIAL)

EX2428 - MERCK_PGR00045 - FW_ Attn_ Accounts Receivable Dept (CONFIDENTIAL - PROTECTIVE ORDER MATERIAL)

EX2429 - MERCK_PGR00049 - Halozyme - 202000447 - Invoices (CONFIDENTIAL - PROTECTIVE ORDER MATERIAL)

EX2430 - MERCK_PGR00465 - Mark Stewart Payroll Statement (CONFIDENTIAL - PROTECTIVE ORDER MATERIAL)

EX2431 - MERCK_PGR00001 - Ginkel Organization Screen Shot (CONFIDENTIAL - PROTECTIVE ORDER MATERIAL)

EX2432 - MERCK_PGR00002 - Lally Organization Screen Shot (CONFIDENTIAL - PROTECTIVE ORDER MATERIAL)

EX2433 - MERCK_PGR00003 - Majchrzak Organization Screen Shot (CONFIDENTIAL - PROTECTIVE ORDER MATERIAL)

EX2434 - MERCK_PGR00004 - Stewart Organization Screen Shot (CONFIDENTIAL - PROTECTIVE ORDER MATERIAL)

EX2435 - MERCK_PGR00005 - Su Organization Screen Shot (CONFIDENTIAL - PROTECTIVE ORDER MATERIAL)

EX2436 - MERCK_PGR00036 - 20250903 Payment Remittance_Redacted (CONFIDENTIAL - PROTECTIVE ORDER MATERIAL)

EX2437 - MERCK_PGR00037 - 20251001 Payment Remittance_Redacted (CONFIDENTIAL - PROTECTIVE ORDER MATERIAL)

EX2438 - MERCK_PGR00038 - 20251203 Payment Remittance_Redacted (CONFIDENTIAL - PROTECTIVE ORDER MATERIAL)

EX2439 - MERCK_PGR00040 - 20251215 Payment Remittance_Redacted (CONFIDENTIAL - PROTECTIVE ORDER MATERIAL)

EX2440 - MERCK_PGR00046 - PAYMENT REMITTANCE DETAIL (Oct 2025) (CONFIDENTIAL - PROTECTIVE ORDER MATERIAL)

EX2441 - MERCK_PGR00047 - PAYMENT REMITTANCE DETAIL (Sep 2025) (CONFIDENTIAL - PROTECTIVE ORDER MATERIAL)

EX2442 - MERCK_PGR00048 - Invoice IN00125072310 Review History (CONFIDENTIAL - PROTECTIVE ORDER MATERIAL)

EX2443 - MERCK_PGR00050 - Invoices 5_1_2024-12_22_2025_2 of 3 (CONFIDENTIAL - PROTECTIVE ORDER MATERIAL)

EX2444 - MERCK_PGR00051 - Invoices 5_1_2024-12_22_2025_3 of 3 (CONFIDENTIAL - PROTECTIVE ORDER MATERIAL)

EX2445 - Merck Co - Bylaws

EX2401 - E-mail (CONFIDENTIAL - PROTECTIVE ORDER MATERIAL)

Patent Owner's Motion to Seal

Patent Owner's Motion for Additional Discovery (CONFIDENTIAL - PROTECTIVE ORDER MATERIAL)

Patent Owner's Motion for Additional Discovery (PUBLIC - REDACTED)

Notice of Joint Stipulation to Modify Due Dates

Petitioner's Objections to Evidence

Patent Owner's Objections to Evidence

SCHEDULING ORDER

DECISION Granting Institution of Post-Grant Review 35 U.S.C. § 324

Patent Owner's Updated Mandatory Notices

Notice of Intent to Designate Leif Peterson as Backup Counsel

Declaration of Leif Peterson

Notice of Intent to Designate Sue Wang as Backup Counsel

Declaration of Sue Wang

Notice of Intent to Designate Brian Goldberg as Backup Counsel

Declaration of Brian Goldberg

Notice of Intent to Designate Katherine Helm as Backup Counsel

Declaration of Katherine Helm

Petitioner's Updated Exhibit List

Petitioner's Updated Mandatory Notice

Petitioner's Updated Power of Attorney

Director Discretionary Decision: Refer

Petitioner's Reply to Patent Owner's Discretionary Denial Brief

News Release, "Halozyme Raises 2025 Financial Guidance Ranges and Reports Strong First Quarter 2025 Results"

News Release, "Merck Breaks Ground on New $1 Billion Biologics Center of Excellence in Wilmington, Delaware”

Halozyme Therapeutics, Inc. Q1 2025 Earnings Call Transcript (May 6, 2025)

Halozyme Therapeutics, Inc., Form 10-K (Feb. 18, 2025)

I-MAK Drug Patent Book (June 2025)

Halozyme Therapeutics, Inc., Morgan Stanley Global Healthcare Conference: Question and Answer Section (Sept. 8, 2025)

Second Declaration of Jeffrey P. Kushan

Patent Owner's Waiver of Patent Owner Preliminary Response

Patent Owner's Discretionary Denial Brief

EX2001 - Triggs-Raine Declaration

EX2002 - Triggs-Raine CV

EX2003 - Disclaimer

EX2004 - Sequence Listing

EX2005 - 2023 Pharma 50

EX2006 - Merck Financial Results

EX2007 - Merck Market Cap Nasdaq

EX2008 - Halozyme Market Cap Nasdaq

EX2009 - Halozyme News Revenue

EX2010 - Halozyme - Commercial Products

EX2011 - Halozyme - About Us

EX2012 - District Court Complaint

EX2013 - Alteogen announces amendment to license agreement with MSD

EX2014 - Big Pharma Business Model Report

EX2015 - CNN Medicare Article

EX2016 - White House Fact Sheet

EX2017 - Big Pharma Earnings Watch

Patent Owner's Updated Power of Attorney

Patent Owner's Updated Mandatory Notices

Patent Owner's Updated Mandatory Notices

Petitioner's Updated Mandatory Notices

Patent Owner's Updated Power of Attorney

Patent Owner's Updated Mandatory Notices

Notice: Notice filing date accorded

Patent Owner's Power of Attorney

Patent Owner's Mandatory Notices

U.S. Patent No. 12,077,791

File History of US Patent No. 12,077,791 Part 1

File History of US Patent No. 12,077,791 Part 2

File History of US Patent No. 12,077,791 Part 3

U.S. Patent No. 7,767,429

Chao, Structure of Human Hyaluronidase-1 (2007)

WO/2010/077297, published July 8, 2010

Stern, The Hyaluronidases: Their Genomics, Structures, & Mechanisms (2006)

Jedzrejas, Structures of Vertebrate Hyaluronidases (2005)

Zhang, Hyaluronidase Activity of Human Hyal1 (2009)

Arming, In vitro Mutagenesis of PH-20 Hyaluronidase from Human Sperm (1997)

Bordoli, Protein Structure Homology Modeling Using SWISSMODEL (2008)

Frost, Recombinant Human Hyaluronidase (rHuPH20) (2007)

Branden & Tooze, Introduction to Protein Structure (1999) Part 1

Branden & Tooze, Introduction to Protein Structure (1999) Part 2

Table Associating ’791 Patent to Corresponding ’731 Application

Steipe, Consensus-Based Engineering of Protein Stability (2004)

Green, Computer Graphics, Homology Modeling, and Bioinformatics (2010)

Chica, Semi-rational Approaches to Engineering Enzyme Activity (2005)

Hardy, Assessment of Contraceptive Vaccines Based on Recombinant Mouse

Pomering, Restricted Entry of IgG (2002)

Baba, Mouse Sperm Lacking Cell Surface Hyaluronidase PH-20 (2002)

Primakoff, Reversible Contraceptive Effect of PH-20 Immunization (1997)

Tung, Mechanism of Infertility in Male Guinea Pigs Immunized with Sperm

Rosengren, Recombinant Human PH20 (2018)

U.S. Patent No. 9,447,401

U.S. Patent Application No. 13/694,731

2024 Chemistry Nobel Prize Background

Gmachl, The Human Sperm Protein PH-20 Has Hyaluronidase Activity (1993)

Sills, "Retraction," Science, 319:569 (2008)

Yue, Loss of Protein Structure Stability as a Major Causative Factor (2005)

Wang & Moult, SNPs, Protein Structure, and Disease (2001)

Marković-Housley, Crystal Structure of Hyaluronidase (2000)

"Negative Results," Nature: Editorials, 453:258 (2008)

Lins, Analysis of Accessible Surface of Residues in Proteins (2003)

Hayden, Chemistry: Designer Debacle (2008)

Benkert, Toward the Estimation of the Absolute Quality (2010)

Schwede, SWISS-MODEL: An Automated Protein Homology-Modeling Server (2003)

Alberts, Molecular Biology of the Cell, Chapter 3 (2007)

He, NMR Structures of Two Designed Proteins with High Sequence Identity

Alexander, A Minimal Sequence Code for Switching Protein Structure (2009)

Ruan, Design & Characterization of a Protein Fold Switching Network (2023)

Sievers, Fast, Scalable Generation of High-Quality Protein (2011)

Mihel, PSAIA – Protein Structure and Interaction Analyzer (2008)

Redline Comparison of the ’731 and ’791 Specifications

Beasley & Hecht, Protein Design: The Choice of de Novo Sequences (1997)

Xiong, Periodicity of Polar and Nonpolar Amino Acids (1995)

Hayden, Key Protein-Design Papers Challenged (2009)

KEGG, DRUG: Hyaluronidase (human recombinant)

Pace & Scholtz, A Helix Propensity Scale (1998)

U.S. Patent Application No. 61/631,313

U.S. Patent Application No. 61/796,208

Hom_pre2011

Hom_pre2011_header

Hom_pre2011_header_clean

Hom_pre2011.fasta

Ph20_pre2011.aln-clustal_num

Ph20_pre2011 Alignment html

Leisola & Turunen, Protein Engineering: Opportunities and Challenges (2007)

Hecht, De Novo Proteins from Designed Combinatorial Libraries (2004)

Rosengren, Clinical Immunogenicity of rHuPH20 (2015)

Collection of BLAST Webpages from the Internet Archive

Collection of Clustal Omega Webpages from the Internet Archive

Collection of SWISS-MODEL Webpages from the Internet Archive

Collection of PyMol Webpages from the Internet Archive

Swiss Model Printout of PH20 Model

Swiss Model Printout of PH20 Model with I309N Mutation

Swiss Model Printout of PH20 Model with I309L Mutation

Swiss Model Printout of PH20 Model with I309M Mutation

Hunnicutt, Sperm Surface Protein PH-20 Is Bifunctional (1996)

Bookbinder, A Recombinant Human Enzyme for Enhanced Interstitial...(2006)

Goldberg, “Protein degradation and protection of against misfolded...(2003)

Declaration of Jeffrey P. Kushan

Declaration of Dr. Michael Hecht

Declaration of Dr. Sheldon Park

Petition for Post Grant Review of U.S. Patent No. 12,077,791

Petitioner's Power of Attorney