(rJ GI LEAi) Galapagos CLINICAL STUDY PROTOCOL Study Title: A Phase 2, Double-Blind, Randomized, Placebo-Controlled Study Evaluating the Efficacy and Safety of Filgotinib in the Treatment of Small Bowel Crohn’s Disease (SBCD) Sponsor: Gilead Sciences, Inc. 333 Lakeside Drive Foster City, CA 94404, USA IND Number: 129646 EudraCT Number: 2016-003179-23 Clinical Trials.gov NCT03046056 Identifier: Indication: Small Bowel Crohn’s Disease Protocol ID: GS-US-419-4015 Contact Information: The medical monitor name and contact information will be provided on the Key Study Team Contact List. Protocol Original: 12 September 2016 Version/Date: Amendment 1: 16 December 2016 Amendment 2: 26 June 2017 Amendment 3: 04 February 2020 CONFIDENTIALITY STATEMENT The information contained in this document, particularly unpublished data, is the property or under control of Gilead Sciences, Inc., and is provided to you in confidence as an investigator, potential investigator, or consultant, for review by you, your staff, and an applicable Institutional Review Board or Independent Ethics Committee. The information is only to be used by you in connection with authorized clinical studies of the investigational drug described in the protocol. You will not disclose any of the information to others without written authorization from Gilead Sciences, Inc., except to the extent necessary to obtain informed consent from those persons to whom the drug may be administered. Filgotinib Protocol GS-US-419-4015 Final Gilead Sciences, lnc. Amendment3 TABLE OF CONTENTS TABLE O F CONTENTS .............................................................................................................................................. 2 LIST OF IN-TEXTTABLES ........................................................................................................................................ 5 LIST OF IN-TEXT FIG URES ...................................................................................................................................... 5 PROTOCOL SYNOPSIS .............................................................................................................................................. 6 GLOSSARY O F ABBREVIATIONS AND DEFINITION OF TERMS .................................................................... 16 DEFI NITION OF TERMS .......................................................................................................................................... 20 I. INTRODUCTION .............................................................................................................................................. 2 1 1.1. Background ............................................................................................................................................ 2 1 1.2. Filgotinib (GS-6034) .............................................................................................................................. 23 1.2.1. General Information ............................................................................................................. 23 1.2.2. Preclinical Pharmacology and Toxicology ........................................................................... 24 1.2.3. Clinical Trials of Filgotini b .................................................................................................. 26 1.3. Rationale for This Study ........................................................................................................................ 27 1.4. Rationale for Dose .................................................................................................................................. 29 1.5. Ri sk/Benefit Assessment for the Study .................................................................................................. 29 1.6. Compliance ............................................................................................................................................ 30 2. OBJECTIVES ..................................................................................................................................................... 3 1 3. STUDY DESIGN ................................................................................................................................................ 33 3.1. Endpoints ............................................................................................................................................... 33 3.2. Study Design .......................................................................................................................................... 34 3.3. Study Treatments ................................................................................................................................... 35 3.4. Duration of Treatment ............................................................................................................................ 36 3.5. Criteria for Study Drug lntenu ption or Discontinuation ........................................................................ 36 3 .5.1. Study Dmg Interruption Considerations ............................................................................... 36 3.5.2. Study Dmg Discontinuation Considerations ........................................................................ 37 3.6. Non-Responding Subjects ...................................................................................................................... 39 3.7. Disease Worsening Cri teria .................................................................................................................... 39 3.8. End of Study ........................................................................................................................................... 39 -3.9. Post Stud Care ...................................................................................................................................... 39 4. SUBJECT PO PULATION .................................................................................................................................. 42 4.1. Number of Subjects and Subject Selection ............................................................................................ 42 4.2. Inclusion Criteria .................................................................................................................................... 42 4.3. Exclusion Criteria ................................................................................................................................... 46 5. INVESTIGATIONAL MEDICINAL PRODUCTS ........................................................................................... 49 5.1. Randomization, Blinding and Treatment Codes .................................................................................... 49 5.1.1. Procedures for Breaking Treatment Codes ........................................................................... 49 5.1.2. Blinding ................................................................................................................................ 49 5.2. Description and Handling of Fil gotini b and Placebo to Match (PTM) Fil gotini b .................................. 50 5.2.1. Formulation .......................................................................................................................... 50 5.2.2. Packaging and Labeling ....................................................................................................... 50 CONFIDENTIAL Page 2 04 February 2020 Filgotinib Protocol GS-US-419-4015 Final Gilead Sciences, lnc. Amendment3 5.2.3. Storage and Handling ........................................................................................................... 50 5.3. Dosage and Administration of Study Drug ............................................................................................ 51 5.4. Prior and Concomitant Medications ....................................................................................................... 51 5.4.1. Allowed Concomitant Medications ...................................................................................... 52 5.4.2. Prohibited Concomitant Medications ................................................................................... 53 5.4.3. Corticosteroid Tapering ........................................................................................................ 53 5.5. Vaccine Guidelines ................................................................................................................................ 54 5.6. Accountability for Study Drug ............................................................................................................... 54 5.6.1. lnvestigational Medicinal Product Return or Disposal ......................................................... 54 6. STUDY PROCEDURES .................................................................................................................................... 55 6.1. Subject Enrollment and Treatment Assignment ..................................................................................... 55 6.2. Sequence of Assessments ....................................................................................................................... 55 6.3. COAi Score and e-Diary ........................................................................................................................ 55 6.4. Randomization and Study Dmg Administration ...................................................................................