Conditions: Alzheimer Disease
Allocation: RANDOMIZED | Intervention model: PARALLEL
Enrollment: 95
Healthy volunteers: no

Brief summary:
The study is a 24-week, randomized, double-blind, multi-site, placebo-controlled study in participants with mild cognitive impairment (MCI) or early dementia due to Alzheimer's disease (AD).

Detailed description:
The study is a 24-week, randomized, double-blind, multi-site, placebo-controlled study in participants with mild cognitive impairment (MCI) or early dementia due to Alzheimer's disease (AD). The study is designed to evaluate the safety, tolerability, drug target engagement and neurobiological effects of treatment with AMX0035 over 24 weeks. The study is designed to yield deep phenotyping insight for the purposes of demonstrating the effects of AMX0035 on mechanistic targets of engagement and disease biology. The study will evaluate diverse disease-relevant markers and produce an informative dataset that will allow for evaluation and correlation of imaging-based markers, neurobiological changes, functional measures, and cognitive outcomes. Participants receive orally administered study drug twice daily for a treatment duration of approximately 24 weeks and attend clinic visits at Screening, Baseline, Week 6, Week 12, Week 18, and Week 24.

Arms:
arm 1: AMX0035 twice daily--a combination of Sodium Phenylbutyrate (3g) and Taurursodiol (1g) arm 2: Taste-matched Placebo

Interventions: intervention 1: AMX0035 intervention 2: Placebo
Intervention descriptions: intervention 1: Combination Therapy of PB and TURSO intervention 2: Placebo

Protocol document:
Prot_000.pdf: 
Page 1 of 92 
Phase II Study to Assess the Safety, Tolerability, and Target Engagement of AMX0035, a 
Fixed Combination of Sodium Phenylbutyrate and Tauroursodeoxycholic Acid for the 
Treatment of Alzheimer’s Disease 
Regulatory Sponsor: 
Amylyx Pharmaceuticals Inc. 
Funding Sponsor: 
Amylyx Pharmaceuticals Inc. 
Alzheimer’s Association 
Alzheimer’s Drug Discovery Foundation 
Cure Alzheimer’s Fund 
Study Product: 
AMX0035 
Protocol Number: 
AMX8000 
IND Number: 
125935 
Draft or Version Number: 
4.0 
10 April 2020 
The information contained herein is confidential and proprietary in nature, and will not be 
disclosed to any third party without written approval of authorized designee. 
This document may be disclosed to the appropriate institutional review boards or to duly 
authorized representatives of the US Food and Drug Administration or a national 
regulatory authority under the condition that they maintain confidentiality.  


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 2 of 92 
STATEMENT OF COMPLIANCE 
 
This study will be conducted in compliance with the protocol, International Conference on 
Harmonization of Technical Requirements for Registration of Pharmaceuticals for Human Use 
(ICH), Good Clinical Practice (GCP), and the applicable regulatory requirements, United States 
Code of Federal Regulations (CFR) Title 45 CFR Part 46 and Title 21 CFR Parts 50, 56, and 312. 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 3 of 92 
SIGNATURE PAGE 
 
I have read the attached protocol entitled, Phase II Study to Assess the Safety, Tolerability, and 
Target Engagement of AMX0035, a Fixed Combination of Sodium Phenylbutyrate and 
Tauroursodeoxycholic Acid for the Treatment of Alzheimer’s Disease, dated April 10, 2020 
(Version 4.0) and agree to abide by all described protocol procedures. I agree to comply with the 
International Conference on Harmonization Tripartite Guideline on Good Clinical Practice, 
applicable FDA regulations and guidelines identified in 21 CFR Parts 11, 50, 56, and 312, local 
Institutional Review Board (IRB) guidelines and policies, and the Health Insurance Portability and 
Accountability Act (HIPAA). 
 
 
Site Investigator: _________________________________________ 
 
Name Printed: ___________________________________________ 
 
Signed: 
 
Date: 
 
 
 
 
 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 4 of 92 
TABLE OF CONTENTS 
 
STATEMENT OF COMPLIANCE 
2 
SIGNATURE PAGE 
3 
TABLE OF CONTENTS 
4 
LIST OF ABBREVIATIONS 
9 
SCHEDULE OF ACTIVITIES 
11 
STUDY WORKFLOW 
14 
1 
Ethics/Protection of Human Subjects 
15 
1.1 
Institutional Review Board (IRB) 
15 
1.2 
Ethical Conduct of Study 
15 
1.3 
Subject Information and Consent 
15 
2 
Introduction: Background Information and Scientific Rationale 
16 
2.1 
Background Information 
16 
2.1.1 
Alzheimer’s Disease (AD) Overview 
16 
2.1.2 
AMX0035 Rationale 
16 
2.1.3 
Prior Clinical Use of PB and TUDCA in Subjects with Neurodegenerative 
Disease 18 
2.1.4 
Additional Previous Clinical Experience with Phenylbutyrate 
21 
2.1.5 
Additional Previous Clinical Experience with TUDCA 
22 
2.2 
Potential Risks and Benefits 
23 
2.2.1 
Potential Risks 
23 
2.2.2 
Known Potential Benefits 
25 
3 
Objectives 
26 
3.1 
Study Objectives 
26 
3.2 
Study Outcome Measures 
26 
3.2.1 
Primary Outcome Measures 
26 
3.2.2 
Secondary Outcome Measures 
26 
 
 
 
4 
Study Design 
29 
4.1 
Overall Study Design and Plan 
29 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 5 of 92 
4.1.1 
Response to Coronavirus Disease 2019 (COVID-19) 
29 
4.2 
Study Centers 
30 
4.3 
Study Duration 
30 
4.4 
Protocol Adherence 
31 
5 
Study Enrollment and Withdrawal 
32 
5.1 
Number of Study Subjects 
32 
5.2 
Inclusion and Exclusion Criteria 
32 
5.2.1 
Inclusion Criteria 
32 
5.2.2 
Exclusion Criteria 
32 
5.3 
Treatment Assignment Procedures 
33 
5.3.1 
Randomization Procedures 
34 
5.3.2 
Reasons for Withdrawal 
34 
5.3.3 
Handling of Withdrawals 
34 
5.3.4 
Termination of Study 
35 
6 
Treatments Administered 
36 
6.1 
Treatments 
36 
6.1.1 
Study Product Description 
36 
6.1.2 
Placebo 
37 
6.2 
Acquisition 
37 
6.2.1 
Formulation, Packaging, and Labeling 
37 
6.2.2 
Product Storage and Stability 
38 
6.3 
Dosage, Preparation and Administration of Study Intervention/Investigational Product
 
38 
6.4 
Modification of Study Intervention/Investigational Product for a Subject 
38 
6.4.1 
Dosage Discontinuation 
39 
6.5 
Accountability Procedures for AMX0035 
39 
6.6 
Assessment of Subject Compliance with AMX0035 
39 
6.7 
Prior and Concomitant Therapy 
39 
6.7.1 
Prohibited Medications and Contraindications 
40 
7 
Study Schedule 
42 
7.1 
Screening Visit 
43 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 6 of 92 
7.1.1 
Screen Failures 
43 
7.2 
Baseline Visit 
43 
7.3 
Week 1 Phone Call 
44 
7.4 
Week 6 Visit 
44 
7.5 
Week 12 Visit 
44 
7.6 
Week 18 Visit 
45 
7.7 
Week 24 Final Study Visit/Early Discontinuation Visit 
46 
7.7.1 
Final Follow-up Telephone Call 
47 
7.8 
Protocol Deviations 
47 
7.9 
Missed Visits and Procedures 
47 
Details and specific instructions regarding protocol deviations, including any exceptions to 
this standard procedure, are found in the study operations manual. 
47 
8 
Clinical Assessments and Outcome Measures 
48 
8.1 
Clinical Variables 
48 
8.1.1 
Vital Signs, Height, & Weight 
48 
8.1.2 
Clinical Laboratory Assessments 
48 
8.1.3 
Blood Draw and Urine Sample 
49 
8.1.4 
12-Lead Electrocardiogram (ECG) 
49 
8.1.5 
Physical and Neurological Examination 
49 
8.1.6 
Geriatric Depression Scale (GDS) 
49 
8.1.7 
Columbia Suicide Severity Rating Scale (C-SSRS) 
50 
8.1.8 
Adverse Events 
50 
8.2 
Outcome Measures 
50 
8.2.1 
Functional Activities Questionnaire (FAQ) 
50 
8.2.2 
Dementia Severity Rating Scale (DSRS) 
51 
8.2.3 
Cognitive Evaluations 
51 
8.2.4 
Neuropsychiatric Inventory Questionnaire (NPI-Q) 
52 
8.2.5 
Lumbar Puncture for CSF Biomarker 
52 
8.2.6 
Neuroimaging 
53 
8.2.7  
Pharmacokinetics 
53 
8.2.8 
Training and Validation 
53 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 7 of 92 
9 
Safety and Adverse Events 
54 
9.1 
Definitions of AEs, Suspected Adverse Drug Reactions & SAEs 
54 
9.1.1 
Adverse Event and Suspected Adverse Drug Reactions 
54 
9.1.2 
Serious Adverse Events 
55 
9.2 
Assessment and Recording of Adverse Events 
56 
9.2.1 
Assessment of Adverse Events 
56 
9.2.2 
Relatedness of Adverse Event to Investigational Product 
57 
9.2.3 
Adverse Events in Prior Human Experience with Each Individual Component 58 
9.2.4 
Recording of Adverse Events 
58 
9.3 
Adverse Events and Serious Adverse Events - Reportable Events 
58 
10 
Data Safety Monitoring and Statistical Analysis Plan 
59 
10.1 
Medical Monitoring 
59 
10.2 
Protocol Steering Committee 
59 
10.3 
Statistical Methods 
59 
10.3.1 
Sample-Size Determination 
59 
10.3.2 
Study Unblinding 
62 
10.3.3 
Safety Endpoints 
62 
10.3.3.1 Safety Endpoints 
62 
10.3.3.2 Primary Efficacy Endpoints 
62 
10.3.3.3 Secondary Efficacy Endpoints 
62 
10.3.3.4 Volumetric MRI 
63 
10.3.3.5 CSF 
63 
10.3.4 
Analysis Populations 
63 
10.3.5 
Analysis for Safety 
63 
10.3.5.1 Adverse Events 
64 
10.3.5.2 Laboratory Parameters 
64 
10.3.5.3 Other Safety Parameters 
64 
10.3.6 
Analysis for Efficacy 
65 
10.4 
Missing Data 
66 
10.5 
Stopping Rules 
66 
10.6 
Interim Analysis 
66 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 8 of 92 
11 
Data Collection, Management and Monitoring 
66 
11.1 
Role of Data Management 
66 
11.1.1 
Data Entry and Checks 
67 
11.1.2 
Data Lock Process 
67 
11.1.3 
Quality Assurance 
67 
11.2 
Clinical Monitoring 
67 
11.3 
Data Handling and Record Keeping 
68 
11.3.1 
Confidentiality 
68 
11.3.2 
Study Discontinuation 
68 
11.3.3 
Retention of Records 
69 
11.3.4 
Publications 
69 
12 
Literature References 
70 
13 
APPENDICES 
74 
13.1 
Appendix I: Columbia-Suicide Severity Rating Scale (C-SSRS) Screening Version 74 
13.2 
Appendix II: Columbia-Suicide Severity Rating Scale (C-SSRS) Since Last Visit 
Version 79 
C-SSRS (Columbia – Suicide Severity Rating Scale – Since Last Visit) 
79 
13.3 
Appendix III: Montreal Cognitive Assessment (MOCA) 
85 
13.4 
Appendix IV: Dementia Severity Rating Scale (DSRS) 
86 
13.5 
Appendix V: Functional Activities Questionnaire 
90 
13.6 
Appendix VI: Geriatric Depression Scale 
91 
13.7 
Appendix VII: Instructions to subjects 
92 
 
 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 9 of 92 
LIST OF ABBREVIATIONS 
 
 
 
ADR 
Adverse Drug Reaction 
AE 
Adverse Event/Adverse Experience 
AD 
Alzheimer’s disease 
ADAS-Cog 
Alzheimer’s disease Assessment Scale – Cognitive Subscale 
ALS 
Amyotrophic Lateral Sclerosis 
b.i.d 
Twice a Day 
BOLD 
Blood Oxygen-Level Dependent Imaging 
C-CASA 
Columbia Classification Algorithm for Suicide Assessment 
CFR 
Code of Federal Regulations 
CIB 
Clinical Investigator’s Brochure 
CNS 
Central Nervous System 
CRF 
Case Report Form 
CSF 
Cerebrospinal Fluid 
C-SSRS 
Columbia Suicide Severity Rating Scale 
DM 
Data Management 
DSRS 
Dementia Severity Rating Scale 
eCRF 
Electronic Case Report Form 
ER 
Endoplasmic Reticulum 
FAQ 
Functional Activities Questionnaire 
FDA 
Food and Drug Administration 
FWA 
G 
Federal-wide Assurance 
Gram 
GDS 
Geriatric Depression Scale 
GCP 
Good Clinical Practice 
HDAC 
Histone Deacetylase 
HIPAA 
Health Insurance Portability and Accountability Act 
ICF 
Informed Consent Form 
ICH 
International Conference on Harmonisation 
IDE 
Investigational Device Exemption 
IEC 
Independent Ethics Committee 
IND 
Investigational New Drug Application 
IRB 
ITT 
Institutional Review Board 
Intention to Treat 
LP 
Lumbar Puncture 
MCI 
Mild Cognitive Impairment 
MedDRA 
Medical Dictionary for Regulatory Activities 
MoCA 
Montreal – Cognitive Assessment 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 10 of 92 
MOP 
MRI 
Manual of Procedures 
Magnetic Resonance Imaging 
N 
Number (typically refers to subjects) 
NDA 
New Drug Application 
NIH 
National Institutes of Health 
NfL 
Neurofilament Light Chain 
Ng 
Neurogranin 
NPI 
Neuropsychiatric Inventory 
NPI-Q 
Neuropsychiatric Inventory Questionnaire 
OHRP 
Office for Human Research Protections 
OHSR 
Office of Human Subjects Research 
PAA 
Phenylacetate (metabolite of PB) 
PB 
Sodium Phenylbutyrate 
pCASL 
Pseudo-Continuous Arterial Spin Labeling 
PET 
Positron Emission Tomography 
PHI 
Protected Health Information 
PI 
Principal Investigator 
PK 
Pharmacokinetics 
PSC 
Protocol Steering Committee 
QA 
Quality Assurance 
QC 
ROI 
Quality Control 
Region of Interest 
SAE 
SAP 
SI 
Serious Adverse Event/Serious Adverse Experience 
Statistical Analysis Plan 
Site Investigator 
SDT 
Source Document Templates 
SOP 
Standard Operating Procedure 
t.i.d 
Three Times a Day 
TUDCA 
UDCA 
Tauroursodeoxycholic Acid 
Ursodeoxycholic Acid 
US 
United States 
vMRI 
Volumetric Magnetic Resonance Imaging 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 11 of 92 
SCHEDULE OF ACTIVITIES 
Study table 
 
 
Screening 
Baseline1 
Week 1 
Phone 
Call 
Week 615 
Week 1216 
Week 1815 
Week 2417/Early 
Discontinuation18 
Final Follow-Up 
Call14 
-28 Days 
Day 0 
+5 Days 
Day 7  
±1 Days  
Day 42  
±14 Days 
Day 84 
±28 Days 
Day 126  
±14 Days 
Day 168  
±28 Days 
Last Dose of IP 
+14 ±5 Days 
Written Informed consent 
X 
 
 
 
 
 
 
 
Inclusion/Exclusion Review 
X 
X 
 
 
 
 
 
 
Randomization2 
 
X 
 
 
 
 
 
 
Medical History/Demographics 
X 
 
 
 
 
 
 
 
AD Diagnosis History 
X 
 
 
 
 
 
 
 
Montreal - Cognitive Assessment (MoCA) 
X 
 
 
X 
 
X 
X 
 
DSRS 
 
X 
 
 
X 
 
X 
 
Geriatric Depression Scale 
X 
 
 
 
 
 
 
 
Vital Signs3 
X 
X 
 
 
X 
 
X 
 
FAQ 
 
X 
 
 
X 
 
X 
 
Physical Exam including Height and 
Weight4 
X 
 
 
 
 
 
X 
 
Neurology Exam5 
X 
 
 
 
 
 
X 
 
Safety labs6 
X 
 
 
 
X 
 
X 
 
12-Lead ECG (Electrocardiogram) 
X 
 
 
 
X 
 
X 
 
Neuropsychiatric Inventory Questionnaire 
(NPI-Q)  
X7 
 
 
X 
 
X 
 
ADAS-Cog 
 
X 
 
 
X 
 
X 
 
MRI Assessment8 
X 
 
 
 
 
X 
 
Adverse Events  
X 
X 
X 
X 
X 
X 
X 
X 
Concomitant Medications 
X 
X 
 
X 
X 
X 
X 
X 
Dispense Study Drug9 
 
X 
 
X 
X 
X 
 
 
Drug Accountability/Compliance 
 
 
X10 
X 
X 
X 
X 
 
Suicide Rating Scale (C-SSRS)11 
X 
X 
 
X 
X 
X 
X 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 12 of 92 
 
Screening 
Baseline1 
Week 1 
Phone 
Call 
Week 615 
Week 1216 
Week 1815 
Week 2417/Early 
Discontinuation18 
Final Follow-Up 
Call14 
-28 Days 
Day 0 
+5 Days 
Day 7  
±1 Days  
Day 42  
±14 Days 
Day 84 
±28 Days 
Day 126  
±14 Days 
Day 168  
±28 Days 
Last Dose of IP 
+14 ±5 Days 
Blood draw for biomarker analysis 
 
X 
 
 
X 
 
X 
 
Lumbar puncture/CSF draw for 
biomarkers12 
 
X 
 
 
 
 
X 
 
Blood draw for pharmacokinetics13 
 
 
 
 
X 
 
X 
 
Blood draw for genetic analysis 
 
X 
 
 
 
 
 
 
 
1The Baseline Visit can be completed any time after the screening so long as all eligibility criteria are met and occur no more than 28 
+5 days after the Screening Visit. 
2Randomization should occur at the Baseline Visit. Randomization will entail entering a subject’s kit number into the electronic data 
capture system. 
3Vital signs include systolic and diastolic pressure in mmHg, respiratory rate/minute, heart rate/minute and temperature.  
4Height is only recorded once at the Screening Visit. 
5The standard Neurological Exam will be used for all subjects. 
6Safety labs include Hematology (CBC with differential), Complete Chemistry Panel, Liver Function Tests, B12 and TSH (at Screening 
Visit only) and Urinalysis.  
7 The NPI-Q Test can be performed either at the screening or baseline visit 
8The MRI assessment can be completed anytime between the Screening and up to 7 days prior to the Baseline Visit and will have a 
clinical read done locally. 
9First dose of study drug will be administered in clinic after ALL Baseline Visit procedures are completed. 
10Notify subjects of increase from one sachet per day to two sachets per day 
11C-SSRS Screening Version to be completed at Screening Visit only. C-SSRS Since Last Visit version to be completed at all other 
visits.  
12The first LP can be completed anytime between the Screening and up to 7 days prior to the Baseline Visit. 
13Take a single PK plasma sample on Visits 12 and 24 (same time as lumbar puncture). A PK sample will not be taken on subjects 
completing the Early Discontinuation Visit if the subject discontinued study drug more than 48 hours before the visit. 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 13 of 92 
14The Final Follow-Up Call is to occur 14 ± 5 days after the participant’s last dose of study drug. For participants who discontinue 
treatment early, the Final Follow-Up Call is not required if the Early Discontinuation visit occurs 14 ± 5 days after the last dose of 
study drug. 
15To the extent possible, the Week 6 and Week 18 visits may be done remotely. If the visit is done remotely, Drug 
Accountability/Compliance will occur at the next in-person clinic visit. 
16It is preferred that the Week 12 visit be conducted at the site with the participant physically present. If it is not possible to complete an 
in-person Week 12 visit at the site, the safety assessments below must be completed by Week 16/Day 112 for the subject to remain on 
study drug. Sites may make alternative arrangements to complete these assessments per institutional and IRB policy. 
• ECG 
• Safety Labs: Hematology (Complete Blood Count with Differential), Complete Chemistry Panel, Liver Function Tests, and 
Urinalysis 
• Vital Signs 
• C-SSRS 
17 The window for the Week 24 visit is Day 168 ± 28 days. However, if COVID-19 related restrictions (e.g., site closure, travel 
restrictions) make it impossible to conduct an in-person clinic visit during the specified window, then any assessment that can be 
performed remotely should be completed as an unscheduled visit during the Week 24 window. The actual Week 24 visit, with all of 
the assessments indicated on the SOA, may be postponed for up to 12 weeks and treatment extended. The maximum duration a subject 
may be on IP is 40 weeks. Safety checks (i.e., ECG, safety labs, vital signs, and C-SSRS) must be completed, at minimum, every 16 
weeks/112 days. If safety assessments are performed so that the Week 24 visit may be postponed, the assessments should be 
documented as an unscheduled visit. 
18If possible, an Early Discontinuation visit should be done within 14 days of the last dose of IP (i.e., last dose of IP + 14 days). The 
MRI and lumbar puncture may be done as soon as is practical and, if possible, within 60 days of the last dose of IP (i.e., last dose of IP 
+ 60 days). 
 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 14 of 92 
STUDY WORKFLOW  
 
 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 15 of 92 
1 
ETHICS/PROTECTION OF HUMAN SUBJECTS 
 
1.1 
Institutional Review Board (IRB) 
This study will be conducted in compliance with current Good Clinical Practices (GCP) and 
Title 21 Part 56 of the United States of America Code of Federal Regulations (CFR) relating to 
IRBs. 
 
1.2 
Ethical Conduct of Study 
The study will be conducted in accordance with GCP defined by the International Conference on 
Harmonization (ICH) and the ethical principles of the Declaration of Helsinki. 
 
1.3 
Subject Information and Consent 
This study will be conducted in compliance with Title 21 Part 50 of the United States of America 
CFR, Federal Regulations and ICH Guidance Documents pertaining to informed consent.  At the 
first visit, prior to initiation of any study-related procedures, subjects will be informed about the 
nature and purpose of the study, participation/termination conditions, and risks and benefits. 
Subjects will be given adequate time to ask questions and become familiar with the study prior to 
providing consent to participate. Subjects will give their written consent to participate in the study 
and will be provided with a copy of the fully executed consent form for their records. 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 16 of 92 
2 
INTRODUCTION: BACKGROUND INFORMATION AND SCIENTIFIC RATIONALE 
 
2.1 
Background Information 
 
2.1.1 Alzheimer’s Disease (AD) Overview 
Alzheimer’s disease (AD) is the most prevalent form of dementia affecting more than 5,000,000 
subjects in the US and an estimated 20,000,000 people worldwide, according to the Alzheimer’s 
Association. AD causes progressive neuronal degeneration, resulting in progressive memory loss 
and dementia. AD has no available cure; however, treatments exist that can temporarily slow 
dementia symptoms. There are five FDA-approved medications for the treatment of Alzheimer’s 
disease. These drugs fall into two categories; acetylcholinesterase inhibitors and NMDA receptor 
antagonists. Approved acetylcholinesterase inhibitors include tacrine (Cognex®), rivastigmine 
(Exelon®), galantamine (Nivalin® and Razadyne®), and donepezil (Aricept®). The only 
approved NMDA receptor antagonist for the treatment of AD is memantine (Namenda®). 
 
Alzheimer’s disease is characterized by the loss of neurons and synapses in the cerebral cortex and 
atrophy in the temporal and parietal lobes. Abnormal aggregates of amyloid plaques and 
neurofibrillary tangles are two of the primary histopathological findings of AD and have been the 
target of many recent clinical trials. However, recent studies suggest that amyloid reduction is less 
able to halt pathology after AD progresses beyond the stage of mild cognitive impairment (MCI). 
By this point, parallel neuronal death and inflammatory pathways may contribute to disease 
progression greater than either amyloid or tau. This suggests that there is a significant patient group 
that may not respond to amyloid-targeted therapies alone, yet may benefit from therapies targeting 
cell death and inflammation. 
 
2.1.2 AMX0035 Rationale 
AMX0035 is a combination of two compounds, Sodium Phenylbutyrate (PB) and 
Tauroursodeoxycholic Acid (TUDCA), that target the cellular unfolded protein response (UPR) 
and bioenergetics stress, respectively. Both compounds, at our selected doses are expected to cross 
the blood-brain-barrier at therapeutic levels based on observed CNS target engagement observed 
in previous in vivo studies3,4,7,11,14 and are hypothesized to prevent neuronal death through distinct 
pathways. 
 
Each compound has exhibited strong efficacy in several cellular and animal models of AD, as well 
as models of endoplasmic reticulum (ER) stress and mitochondrial dysfunction. Amylyx has 
demonstrated robust synergy when PB and TUDCA are dosed simultaneously and found the 
combination to be efficacious in many preclinical models. 
 
PB is a class I and class II HDAC inhibitor that ameliorates ER stress through upregulation of DJ-
1, a master chaperone regulator1, and other chaperone proteins2. The epigenetic and cellular stress 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 17 of 92 
response activities of PB have been demonstrated to modify the AD phenotype in the Tg2576 
mouse model of AD, through a prevention of neuronal loss in the hippocampus and increased 
clearance of Aβ deposits3,4. PB has been shown to reduce cortical and hippocampal amyloid plaque 
burden in the APP/PS1 double-transgenic model of AD, resulting in increased cognitive 
performance of the mice in spatial memory tasks5. PB was shown to reduce tau 
hyperphosphorylation in in vivo studies of AD through reduction of ER-stress dependent kinase 
activity6. PB has been tested in many other in vivo models of neurodegenerative diseases and has 
been demonstrated to increase survival in the G93A SOD1 mouse model of ALS7 and the N171-
82Q mouse model of Huntington’s disease8 through chaperone mediated mechanisms. Finally, as 
expected by its HDAC inhibition properties, PB has been reported to increase astrocyte BDNF and 
NT-3 production and secretion in culture and in vivo and improve synaptic protein expression and 
spatial memory in the 5XFAD mouse9. 
 
TUDCA has been shown to recover mitochondrial bioenergetic deficits through incorporation into 
the mitochondrial membrane, reducing Bax translocation to the mitochondrial membrane, 
reducing mitochondrial permeability, and increasing the apoptotic threshold of the cell10. TUDCA, 
through these anti-apoptotic pathways, prevents cognitive decline in the APP/PS1 mouse model 
of AD, reduces hippocampal and frontal cortex amyloid deposits11,12 and reduces glial activation13. 
TUDCA has shown efficacy in many oxidative injury models, including mouse models of 
ischemia14, the MPTP mouse model of Parkinson’s15, and ALS models of poly(GA)-induced 
toxicity16. 
 
ER and mitochondrial stress can both cause neuronal death and a subsequent cytotoxic immune 
response. Therefore, we combined PB and TUDCA and have since demonstrated that they have 
synergistic efficacy when dosed at particular ratios. Specifically, the combination of agents 
resulted in a synergistic increase in neuronal viability in an H2O2-mediated insult model. In the 
assay, H2O2 was dosed at 40μM for one hour, a dose causing approximately 50% neuronal death. 
Administration of TUDCA or PB individually resulted in a modest increase in viability, while the 
combination returned cell viability nearly to control (>90% viability). To demonstrate the 
reproducibility of these results, as well as to determine optimal ratios of AMX0035, we repeated 
the experiment with 20 different combinations of TUDCA and PB. These experiments replicated 
our previous results and revealed the optimal efficacious concentrations in vitro. PB demonstrated 
optimal efficacy at concentrations between 150µM-500µM and TUDCA at concentrations 
between 50µM-200µM. These correspond to the clinical dose we are evaluating in a clinical trial 
in ALS. The combination dose that demonstrated optimal efficacy in the H2O2-mediated insult 
model was evaluated in an acute, pre-plaque Tg2576 mouse model. AMX0035 treatment 
significantly reduced soluble amyloid beta, preferentially Aβ42 (Figure 1). 
 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 18 of 92 
 
Figure 1: Treatment with AMX0035 at a dose of 200µM TUDCA and 200µM PB reduced 
levels of Aβ42 relative to control in the Tg2576 mouse model of Alzheimer’s disease. 
 
2.1.3 Prior Clinical Use of PB and TUDCA in Subjects with Neurodegenerative Disease 
Neither PB or TUDCA have been evaluated in subjects with AD or MCI likely related to AD, 
however, both PB and TUDCA have been evaluated, individually, in subjects with 
neurodegenerative diseases and were found to be safe, well-tolerated, and exhibited preliminary 
signs of efficacy. PB was evaluated in a 20-week safety and biomarker study in ALS subjects17. 
This study was a Phase I dose-escalation trial and each subject was scheduled to receive PB at 
increasing dose from 9 to 21 g/day. A total of 40 subjects were recruited at 8 trial sites in the United 
States. Twenty-six subjects completed the 20-week treatment phase. Histone acetylation was 
decreased by approximately 50% in blood buffy-coat specimens at screening and was significantly 
increased following PB treatment (Figure 2). Blood levels of PB and the primary metabolite, 
phenylacetate, increased with dosage (Figure 3) with a plateau between the 3 and 6g t.i.d. regimen. 
While the majority of subjects tolerated higher dosages of PB, the lowest dose (9 g/day, 3g t.i.d) 
was the most effective at increasing histone acetylation levels in blood (Figure 3). Treatment with 
PB did not alter blood riluzole levels. Adverse events in subjects taking riluzole and PB together 
did not occur more frequently. 
 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 19 of 92 
 
Figure 2: Histone acetylation levels with PB dose. Blood histone acetylation levels are shown 
compared with dose taken prior to blood draw. The error bars represent standard error. (Doses are 
repeated t.i.d in this study). 
 
Figure 3: Plasma levels of phenylbutyrate and its metabolite, phenylacetate. Plasma 
phenylbutyrate and phenylacetate levels are shown compared with dose taken prior to blood draw. 
The error bars represent standard error (Dosing was t.i.d in this study). 
 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 20 of 92 
It is not clear why acetylation levels were highest at 9g/day, however the authors noted that in a 
study of PB in Huntington’s disease (HD)18, the effects of PB on mRNA expression levels of a 12-
gene biomarker set were greatest at lowest evaluated dosage (12g/day), indicative of an inverse 
dose response. Furthermore, in the clinical study of PB in Huntington’s disease, the maximum 
tolerated dose was determined to be 15g/day, with PB at 12-15g/day appearing to be safe and well-
tolerated.19 
 
TUDCA, dosed at 1g b.i.d., demonstrated a statistically significant slowing of ALSFRS-R 
progression rate in a 54-week, multi-site, placebo-controlled clinical trial of ALS209.  In this proof-
of-principle trial, 34 ALS subjects under concomitant treatment with riluzole were randomized to 
receive placebo or TUDCA (1g b.i.d.) for 54 weeks. The proportion of responders (defined as 
subjects with >15% improvement in ALSFRS-R scale) was higher under TUDCA (87%) than 
under placebo (43%; P=0.021). At study end, baseline-adjusted ALSFRS-R was signiﬁcantly 
higher (P=0.007) in TUDCA than in placebo group. Comparison of the slopes of regression 
analysis showed slower progression in the TUDCA than in the placebo group (P<0.01) (Figure 4). 
 
 
Figure 4: Linear regression analysis of ALSFFRS-R mean scores over time for the TUDCA 
(circles, slope -0.388) and placebo groups (triangles, slope -0.262). 
 
 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 21 of 92 
In this Phase II trial, subject with AD or MCI related to AD will receive 3g PB and lg TUDCA 
twice a day orally.  AMX0035 will be presented as a roughly 10-gram sachet to be suspended in 
water and taken prior to a meal. Treatment of single agent TUDCA or PB in subjects with other 
neurodegenerative diseases was very well tolerated. In a study of TUDCA in subjects with ALS 
subjects20, the AE profile and laboratory anomalies were not different between the TUDCA and 
placebo cohort. In the small group of 15 subjects treated with TUDCA, the AEs were limited to 
diarrhea. In the PB ALS clinical study17, tolerability was similar to that reported in trials of PB in 
other indications. There were no changes in safety laboratory tests, ECG or vital signs. The most 
common AEs were those previously reported with PB, including falls, dizziness, diarrhea, edema, 
dry mouth, headache, nausea and rash. A single subject interrupted treatment with PB at the 9g per 
day dose (i.e. a dose higher than that planned in the proposed Phase II) for the occurrence of edema 
on the feet and under the eyes. 
 
2.1.4 Additional Previous Clinical Experience with Phenylbutyrate 
Sodium phenylbutyrate (PB) is generally well tolerated. It is FDA approved for subjects with urea 
cycle 
disorders, 
including 
deficiencies 
of 
carbamylphosphate 
synthetase, 
ornithine 
transcarbamylase, or argininosuccinic acid synthetase. It is indicated in subjects with either 
neonatal-onset deficiency or late-onset disease. The typical daily dose is 450-600 mg/kg in subjects 
weighing less than 20kg, or 9.9-13.0 g/day in larger subjects. Detailed information can be found 
on the package insert for PB22 
 
PB is also under development as an anticancer agent. In a dose-escalation study in subjects with 
refractory solid tumor malignancies, doses of up to 45g/day PB were administered23. Due to dose-
limiting toxicities, the study concluded that 27g/day was the maximum tolerated dose. Nausea, 
vomiting, hypocalcemia and fatigue occurred at the 36g/day and 45g/day doses. Gastrointestinal 
upset (nausea, dyspepsia and vomiting) occurred at the lowest dose of 9g/day and was seen within 
30 minutes of drug ingestion. However, 82% of subjects completed the study despite these side 
effects. Other frequently reported side effects include a "sweat"-like odor, usually noticeable only 
to the caregiver. Mild neurotoxicity (confusion, lethargy) has been noted at higher doses of close 
to 30g/day but resolved with dose reduction. 
 
A dose-escalation study of intravenous PB in subjects with myelodysplastic syndromes and acute 
myelogenous leukemia found a maximally tolerated dose at 375 mg/kg/day (26.3g/day for a 70kg 
individual) with no serious toxicities detected in subjects receiving doses between 125 and 375 
mg/kg/day (8.8 and 26.3g/day for a 70kg individual)24. Dose-limiting toxicities (lethargy, 
confusion, slurred speech) were detected at 440 and 500 mg/kg/day PB (30.8 and 35g/day 
respectively, for a 70kg individual). Reports of edema have been blamed on the high sodium load 
associated with the drug. Phase I/II studies in subjects with sickle cell anemia and beta thalassemia 
report similar side effects. 
 
Another phase I study in subjects with refractory solid tumors tested IV PB doses between 150 to 
515 mg/kg/day (up to 36g/day for a 70kg individual) with dose-limiting toxicities (excessive 
somnolence, confusion) and electrolyte abnormalities resulting at a dose of 515 mg/kg/day (36.0 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 22 of 92 
g/day for a 70kg individual). The maximally tolerated dose of PB was determined to be 410 
mg/kg/day (28.7 grams/day for a 70kg individual) as there were no dose-limiting toxicities at this 
dose and no subjects required dose reductions or escalations. 
 
The most common side effects of PB include: menstrual irregularities, decreased appetite, sweat-
like body odor, and bad taste. Less common side effects include: nausea, vomiting, stomach upset, 
stomach pain, gastritis, headache, and skin rash. Rarely, cases of peptic ulcers, rectal bleeding, 
constipation, pancreatitis and renal tubular acidosis have been reported. Hypoalbuminemia, 
metabolic acidosis, alkalosis, hyperchloremia, hyperuricemia, hypokalemia, hypophosphatemia, 
hyperphosphatemia and hypernatremia have been observed. At higher doses, some subjects 
experienced confusion and fatigue, both of which resolved with dose reductions. Rarely, the 
following may occur, but have not been directly linked to sodium phenylbutyrate therapy: anemia, 
leukopenia, leukocytosis, thrombocytopenia, thrombocytosis, arrhythmia, syncope and 
depression. 
 
2.1.5 Additional Previous Clinical Experience with TUDCA 
Tauroursodeoxycholic acid (TUDCA) is currently marketed in Italy under the brand name 
Tudcabil® (
). It is exported to China and Turkey under the brand name 
Taurolite®. It is used clinically for the indications of treatment of cholesterol gallstones. TUDCA 
has been used for the treatment of cholestatic liver diseases including primary cirrhosis, pediatric 
familial intrahepatic cholestasis, and primary sclerosing cholangitis and cholestasis due to cystic 
fibrosis. To our knowledge there are no other off-label uses of TUDCA.  
 
Ursodeoxycholic acid, which is widely used in the United States under the trade name Ursodiol®, 
is an endogenous secretion of the liver, most often as a taurine (TUDCA) or glycine (GUDCA) 
conjugate. Taurine conjugation increases the solubility of UDCA by increasing its hydrophicity. 
TUDCA is taken up in the distal ileum under active transport and therefore likely has a slightly a 
longer dwell time within the intestine than UDCA which is more proximally absorbed in the ileum 
(IND 
).  
 
TUDCA is used in some countries internationally for the dissolution of cholesterol gallstones. This 
generally requires long periods of treatment often 1 to 2 years to obtain complete dissolution (IND 
).  
 
Between 1997 and 2007, 898,000 Tudcabil® tablets were sold in Italy (Product profile contained 
in referenced IND 
). There were no reported cases of toxicity related to Tudcabil® 
capsules. There were no reports of overdose or drug abuse during this period. There were no reports 
related to its use in pregnancy (all pregnant subjects, and those planning to become pregnant, are 
excluded from this trial).  Common adverse events included mild abdominal pain and diarrhea. 
There are some cases of pruritus and a very limited number of cases of elevated liver enzymes. It 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 23 of 92 
should be noted that most of the referenced studies were conducted in subjects with chronic liver 
disease. 
 
TUDCA is contraindicated in subjects with biliary tree infections, frequent biliary colic, or in 
subjects who have trouble absorbing bile acids (e.g. ileal disease or resection). The only known or 
theoretical drug interactions are with substances that inhibit the absorption of bile acids such as 
cholestyramine and with drugs that increase the elimination of cholesterol in the bile (TUDCA 
reduces biliary cholesterol content) (Please refer to section 6.7.1). Based on similar 
physicochemical characteristics, it is likely that drug toxicity/interactions are very similar to those 
of UDCA which are summarized below.  
 
TUDCA has been and is being evaluated in multiple other studies as well. A study at Columbia 
University of 20 subjects with new onset type 1 diabetes in which subjects are administered 1.75g 
TUDCA daily for 12 months is ongoing. A study at Washington University in St. Louis assessing 
the effect of TUDCA on lipid markers and ER stress has been completed in 101 subjects at 1.75g 
daily for 4 weeks; an additional study arm in this study assessed PB at 20g/day. A study at 
Washington University assessing subjects with HIV receiving 1.75g daily TUDCA for 30 days is 
ongoing. 
 
2.2 
Potential Risks and Benefits 
 
2.2.1 Potential Risks 
The safety profile with PB administration is in large part derived from studies of subjects with 
urea cycle disorders. Refer to the phenylbutyrate tablet label (Buphenyl®). 
In female subjects, the most common clinic adverse event report was amenorrhea/menstrual 
dysfunction (irregular menstrual cycles), which occurred in 23% of the menstruating subjects. 
Decreased appetite occurred in 4% of all subjects. Body odor, likely caused by the metabolite, 
phenylacetate [PAA]) and bad taste or taste aversion were each reported in 3% of subjects. 
 
Other adverse events reported in 2% of fewer subjects were: 
● Gastrointestinal: abdominal pain, gastritis, nausea and vomiting; constipation rectal 
bleeding, peptic ulcer disease, and pancreatitis each occurred in one subject. 
● Hematologic: aplastic anemia and ecchymoses each occurred in one subject. 
● Cardiovascular: arrhythmia and edema occurred in one subject 
● Renal: renal tubular acidosis 
● Psychiatric: depression 
● Skin: rash 
● Miscellaneous: headache, syncope, and weight gain 
  


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 24 of 92 
As previously described (Sections 2.1.3 and 2.1.4), PB has been evaluated in a dose-escalating 
study in subjects with neurodegenerative diseases and was found to be generally safe and tolerable 
at significantly higher doses than will be assessed in this study17,19. Specifically, the most common 
AEs included falls or other accidental injury, dizziness, diarrhea, edema, dry mouth, headache, 
nausea, and rash. Apart from the emergence of headaches in subjects, these AEs occurred at a 
higher rate compared to the placebo cohort. These events are expected side effects from PB. No 
clinically significant changes in laboratory values, ECGs, or vital signs were observed. No deaths 
or unexpected and related serious adverse events occurred. Importantly, these studies evaluated 
daily dosages of PB between 9-21g and 12-18g while our study will use 6 grams daily17,19. 
 
Neurotoxicity was reported in cancer subjects receiving intravenous phenylacetate at dosages of 
250-300mg/kg/day for 14 days, repeated at 4-week intervals. Manifestations were predominately 
somnolence, fatigue, and lightheadedness; with less frequent headache, dysgeusia, and hypoacusis, 
disorientation, impaired memory, and exacerbation of a pre-existing neuropathy. The majority of 
these adverse events were mild in severity. The acute onset and reversibility following 
discontinuation of phenylacetate infusion suggest a possible treatment-related effect. 
 
TUDCA is generally well-tolerated. A derivative, UDCA, is approved for subjects with primary 
biliary cirrhosis. Common adverse events with TUDCA include mild abdominal pain and diarrhea. 
There are some cases of pruritus and a very limited number of cases of elevated liver enzymes. 
The most common adverse reactions reported with the use of TUDCA are abdominal discomfort, 
abdominal pain, diarrhea, nausea, pruritus, and rash. 
 
As previously described (Section 2.1.3) TUDCA was recently evaluated in a 54-week, placebo-
controlled study in ALS subjects at 1g b.i.d20. The population for safety analysis consisted of 15 
subjects who took TUDCA and 14 placebo subjects. Treatment was well tolerated in all subjects. 
Laboratory parameters did not change in either treatment group during the study. Except for the 
expected complications related to ALS, no changes in vital signs and laboratory values that could 
possibly be attributed to the study drug or placebo were recorded. Overall, five AEs were 
considered by the Site Investigators to be study-related based on the subjects’ descriptions. Two 
events were reported in the 15 TUDCA-treated subjects (13.3%); three events occurred in the 14 
placebo-treated subjects (21.4%). Mild diarrhea occurred in two subjects treated with TUDCA and 
in two treated with placebo. Anorexia was reported in a placebo-treated subject. Four subjects died 
during the study period, one in the TUDCA group and three in the placebo group. The one death 
in the treated group was not considered drug related—TUDCA trended towards a survival benefit. 
 
There are potential risks and side effects of lumbar punctures, commonly called a spinal tap. We 
will draw cerebrospinal fluid (CSF) using a needle inserted in the lower back for analysis of 
biomarkers and pharmacokinetic analysis. Lumbar punctures will be performed under local 
anesthesia to numb the area. Collected CSF will be analyzed to assess biomarkers 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 25 of 92 
. Lumbar 
punctures will occur at the Screening or Baseline Visit and again at the Week 24 Visit.  
 
2.2.2 Known Potential Benefits 
TUDCA and PB have both been tested individually in clinical trials in patients with 
neurodegenerative diseases and have met their primary endpoints of safety and tolerability. If 
successful, this trial will allow further clinical development of AMX0035 for the treatment of 
Alzheimer’s disease. The trial is also assessing multiple biomarkers in concert with clinical 
outcomes, which will provide a detailed understanding of drug activity and provide a well-curated 
data set for the Alzheimer’s research community to improve our understanding of Alzheimer’s 
disease. 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 26 of 92 
3 
OBJECTIVES 
 
3.1 
Study Objectives 
The primary objectives of the study will be: 
1. To compare the safety and tolerability of a fixed-dose combination of AMX0035 (a 
TUDCA/PB combination) versus placebo in subjects with MCI (high or intermediate 
likelihood due to AD) or dementia due to AD over an approximate 24-week treatment 
period; 
 
The secondary objectives of the study will be:  
1. To determine the effects of AMX0035 treatment on whole brain and regional brain atrophy, 
as assessed by volumetric Magnetic Resonance Imaging (vMRI); 
2. To measure the effects of treatment on functional MRI measures including connectivity 
with resting state BOLD; 
3. To assess the impact of AMX0035 on clinical symptoms as measured by ADAS-Cog, 
DSRS, and FAQ; 
4. To assess the effect of AMX0035 on measures of neuropsychiatric symptoms, as assessed 
by the Neuropsychiatric Inventory Questionnaire (NPI-Q) 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
3.2 
Study Outcome Measures 
 
3.2.1 Primary Outcome Measures 
The primary outcome measures for the study will include safety and tolerability of AMX0035 in 
Alzheimer’s disease. 
 
Adverse events (AE), symptomatic, physical exam, neurological exam, and laboratory parameters 
will be collected prospectively to monitor the safety and tolerability of study drugs. Safety and 
tolerability will be assessed by the procedures outlined in section 9. 
 
3.2.2 Secondary Outcome Measures 
The secondary outcome measures will include neurophysiological biomarker assessments and 
cognitive and symptom-based measures. The effect of AMX0035 on the rate of cognition (ADAS-
Cog and MoCA), functioning (DSRS and FAQ), and neuropsychiatric symptoms (NPI-Q) will be 
evaluated. Additionally, effects of AMX0035 will be assessed by multi-sequence MRI to evaluate 
treatment-related changes and will consist of T1 for regional volumetric analyses (especially 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 27 of 92 
hippocampus as primary vMRI outcome), T2 FLAIR for assessment of lesions and white matter 
hyperintensities, and resting state BOLD to measure posterior and anterior default mode network 
functional connectivity. Safety outcomes, specifically ARIA-E and ARIA-H, will be monitored by 
T2 FLAIR and susceptibility-weighted imaging (SWI). 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 28 of 92 
 
 
 
 
 
 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 29 of 92 
4 
STUDY DESIGN 
 
4.1 
Overall Study Design and Plan 
During the enrollment period, approximately 140 subjects will be screened and around 100 of 
those subjects will be randomized from approximately 10 AD specialty clinical centers in the US.  
These subjects will be randomly assigned in a 3:2 ratio to oral twice daily sachet of active 
combination TUDCA/PB or matching placebo. Treatment duration will be approximately 24 
weeks. Subjects will be administered study drug or matching placebo twice daily.  Visits will occur 
at Screening, Baseline, Week 6, Week 12, Week 18, and Week 24. Subjects who dropout of the 
study will be asked to return for an Early Discontinuation Visit approximately 14 days after last 
dose of study drug. 
 
If allowable by the local IRB and local regulations, Week 6 and Week 18 visits can take place at 
the subjects’ residence. 
 
All visit windows are consecutive calendar days and are calculated from the day the participant 
starts study treatment (Day 0 is the day of the Baseline Visit and first day of therapy) except the 
Final Follow-Up Call. The target date for the Final Follow-Up Call is calculated from the last dose 
of study drug. 
 
4.1.1 Response to Coronavirus Disease 2019 (COVID-19) 
Week 6 and Week 18 may be completed remotely as needed. 
 
It is preferred that the Week 12 visit be conducted at the site with the participant physically present. 
If it is not possible to complete an in-person Week 12 visit at the site, the safety assessments below 
must be completed by Week 16/Day 112 for the subject to remain on study drug. Sites may make 
alternative arrangements to complete these assessments per institutional and IRB policy. 
 
• ECG 
• Safety Labs: Hematology (Complete Blood Count with Differential), Complete Chemistry 
Panel, Liver Function Tests, and Urinalysis 
• Vital Signs 
• C-SSRS 
 
All reasonable efforts should be made to complete the Week 24 or Early Discontinuation visit at 
the site with the participant physically present. However, if COVID-19 related restrictions (e.g., 
site closure, travel restrictions) make it impossible to conduct an in-person clinic visit during the 
specified window, then any assessment that can be performed remotely should be completed as 
an unscheduled visit during the Week 24 window. The actual Week 24 visit, with all of the 
assessments indicated on the SOA, may be postponed for up to 12 weeks and treatment 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 30 of 92 
extended. The maximum duration a subject may be on IP is 40 weeks. Safety checks (i.e., ECG, 
safety labs, vital signs, and C-SSRS) must be completed, at minimum, every 16 weeks/112 days. 
If safety assessments are performed so that the Week 24 visit may be postponed, the assessments 
should be documented as an unscheduled visit. 
 
If possible, an Early Discontinuation visit should be done within 14 days of the last dose of IP (i.e., 
last dose of IP + 14 days). The MRI and lumbar puncture may be done as soon as is practical and, 
if possible, within 60 days of the last dose of IP (i.e., last dose of IP + 60 days). 
 
Ideally, remote visits will be conducted using a HIPAA-compliant video conferencing platform. If 
video conferencing is not available or not feasible, remote visits may be conducted by phone. The 
Montreal Cognitive Assessment (MoCA) is to be completed to the extent possible given the 
available technology, and drug accountability/compliance will be performed at the subject’s next 
in-person visit. 
 
Sites may send study drug to participants’ residences. When transferring study drug to a 
participant, all reasonable efforts should be made to maintain the correct temperature. If possible, 
sites should use the Sponsor-selected vendor who will manage the shipments from the site to the 
subject using a certified shipping container and temperature monitor. Study drug is to be provided 
to subjects only after reviewing and documenting concomitant medications and therapies, and 
Adverse Events. Each subject will be instructed to use study drug from the new kit after receipt 
and verification of condition, regardless of the amount of study drug remaining from any previous 
kit in the subject’s possession. 
 
The longest period a subject may continue taking study drug without having completed the safety 
assessments listed below is 16 weeks/112 days. 
• ECG 
• Safety Labs: Hematology (Complete Blood Count with Differential), Complete Chemistry 
Panel, Liver Function Tests, and Urinalysis 
• Vital Signs 
• C-SSRS 
 
4.2 
Study Centers 
This study will be conducted at approximately 10 specialty AD clinical research centers located in 
the United States.  Sites will be selected based on recruitment record from prior trials, compliance 
with prior study protocols, clinical research expertise, availability of necessary resources, and 
enthusiasm for the study design and objectives. 
 
4.3 
Study Duration 
Subjects will remain on randomized, placebo-controlled, double-blind treatment until the Week 
24 Visit. Including the screening and follow-up visits, each subject will be in the study for 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 31 of 92 
approximately 8 months. However, the Week 24 visit may be delayed, and study treatment 
extended, up to Week 40/Day 280 if COVID-19 restrictions make it impossible to complete the 
Week 24 visit in window.  Therefore, a subject’s participation in the study may be up to 
approximately 11 months. 
 
4.4 
Protocol Adherence 
Each Site Investigator (SI) must adhere to the protocol detailed in this document and agree that 
any changes to the protocol must be approved by the NCRI Coordination Center (CC) or their 
representative prior to seeking approval from the site Internal Review Board (IRB).  Each SI will 
be responsible for enrolling only those study subjects who have met protocol eligibility criteria. 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 32 of 92 
5 
STUDY ENROLLMENT AND WITHDRAWAL 
 
5.1 
Number of Study Subjects 
Approximately 100 subjects will be randomized 3:2 to AMX0035 or matching placebo. 
 
5.2 
Inclusion and Exclusion Criteria 
 
5.2.1 Inclusion Criteria 
Study subjects should meet all the inclusion criteria during screening evaluations to be 
entered into the study: 
1) Ages 55-89, inclusive, male or female 
2) Must have a diagnosis of "Probable Alzheimer's Disease" or “Mild Cognitive 
Impairment” with a primarily amnestic presentation (deficit in learning and recall of 
recently learned information) that is accompanied by the presence of documented 
biomarkers (amyloid PET, CSF AD biomarkers, FDG-PET, or vMRI) supporting that the 
syndrome is likely due to AD pathology 
3) MoCA score ≥8 
4) Able to read and write in English sufficiently to complete all study procedures 
5) Geriatric Depression Scale <7 
6) Willing and able to complete all assessments and study procedures 
7) Not pregnant, lactating or of child-bearing potential (women must be >2 years post-
menopausal or surgically sterile) 
8) Study partner with at least two days per week with contact with the subject willing to 
accompany patient to visits and complete partner study forms 
9) No known hypersensitivity to Tauroursodeoxycholic acid or Phenylbutyrate 
10) If on a cholinesterase inhibitor and/or memantine, treatment must have started for no 
less than 3 months (84 days) prior to baseline and the dosing regimen must have 
remained stable for 6 weeks (42 days) prior to baseline.  The Investigator anticipates that 
the dosing regimen at baseline will remain unchanged throughout participation in the 
study.  
 
5.2.2 Exclusion Criteria  
Study subjects should not meet any exclusion criteria during screening evaluations or they 
will be excluded from entry into the study: 
1) Any CNS disease other than suspected AD, such as clinical stroke, brain tumor, normal 
pressure hydrocephalus, multiple sclerosis, significant head trauma with persistent 
neurological cognitive deficits or complaints, Parkinson's disease, frontotemporal 
dementia, or other neurodegenerative diseases 
2) Abnormal liver function defined as AST and/or ALT > 3 times the upper limit of 
normal 
3) Renal insufficiency as defined by a serum creatinine > 1.5 times the upper limit of 
normal 
4) Recent (less than 1 year) cholecystectomy or the presence of post-cholecystectomy 
syndrome or biliary obstruction 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 33 of 92 
5) Clinically significant unstable medical condition (other than AD) that in the Site 
Investigator opinion would pose a risk to the participant if they were to participate in the 
study  
6) Any contraindication to undergo MRI studies such as: 
a. History of a cardiac pacemaker or pacemaker wires 
b. Metallic particles in the body 
c. Vascular clips in the head 
d. Prosthetic heart valves 
e.  Severe claustrophobia impeding ability to participate in an imaging study, or 
MRI findings that show one or more of the following: 
a. More than 4 incidental microhemorrhages 
b. Incidental lacunar infarcts with attributable signs or symptoms and with history 
of stroke 
c. Incidental meningiomas with attributable signs or symptoms 
d. Newly recognized meningioma  
7) Any major active or chronic psychiatric illness (e.g. depression, bipolar disorder, 
obsessive compulsive disorder, schizophrenia) that is not stable or well controlled within 
the previous year prior to baseline 
8) Any significant neurodevelopmental disability 
9) Current suicidal ideation or history of suicide attempt within five years of baseline or 
significant change from the screening and baseline C-SSRS at the discretion of the Site 
Investigator 
10) History of alcohol or other substance abuse or dependence within the past two years 
11) Any significant systemic illness or medical condition that could affect safety or 
compliance with study at the discretion of the Site Investigator 
12) Laboratory abnormalities in B12, TSH, or other common laboratory parameters that 
might contribute to cognitive dysfunction 
13) Current use of medications with psychoactive properties that may deleteriously affect 
cognition (e.g., anticholinergics, centrally-acting antihistamines, antipsychotics, sedative 
hypnotics, anxiolytics) 
14) Use of any investigational therapy being evaluated for the treatment of AD is prohibited 
beginning three months (90 days) prior to the Baseline Visit and throughout the study.   
16) Use of other investigational agents one month (28 days) prior to the Baseline Visit 
and for the duration of the trial. 
 
5.3 
Treatment Assignment Procedures 
Each subject who meets all eligibility criteria will be randomized to receive either therapy by twice 
daily sachet of AMX0035 (3g PB and 1g TUDCA) oral or matching placebo for approximately 24 
weeks of treatment. For the first week of study treatment the subjects will only take a single sachet 
daily and will be instructed to increase to two sachets daily at the Week 1 Telephone Call. 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 34 of 92 
5.3.1 Randomization Procedures 
The randomization scheme will be independently developed and will indicate the treatment 
assignment and the subject numbers to be used by each site. The randomization scheme will be 
developed and managed by the biostatistical team.  
 
5.3.2 Reasons for Withdrawal 
A study subject will be discontinued from participation in the study if: 
● Any clinical adverse event (AE), laboratory abnormality, concurrent illness, or other 
medical condition or situation occurs such that continued participation in the study is not 
in the best interest of the subject. 
● The subject meets any exclusion criteria (either newly developed or not previously 
recognized). 
Subjects are free to withdraw from participation in the study at any time upon request. 
 
5.3.3 Handling of Withdrawals 
A subject may choose to discontinue participation in the study at any time. However, the SI or 
designee will encourage subjects to continue with follow-up, regardless of their compliance with 
the study drug. If a subject permanently discontinues study drug, the SI or designee will encourage 
subjects to follow the study protocol under the intent-to-treat principle (ITT). These subjects will 
be encouraged to follow the study visits, off drug. Loss to follow-up should be prevented whenever 
possible. 
 
Any subject in the study who needs to begin the use of any prohibited medication (outlined in 
6.7.1), must immediately discontinue use of the study drug and should not begin use of the 
prohibited medication before an appropriate wash-out period occurs (please refer to the Site MOP 
for additional details). Subjects who permanently discontinue study drug should complete early 
study drug termination procedures per protocol without any study drug unblinding, if possible.  
Subjects who must permanently discontinue study drug may continue follow-up, per protocol. 
 
Early termination occurs when a subject withdraws consent, i.e., withdrawing his or her 
participation in future study procedures. The subject should then return any unused study drug and 
will be asked to return to the study site for an Early Discontinuation Visit. If possible, the Early 
Discontinuation visit should be done within 14 days of the last dose of IP (i.e., last dose of IP + 14 
days). The MRI and lumbar puncture may be done as soon as is practical and, if possible, within 
60 days of the last dose of IP (i.e., last dose of IP + 60 days). 
 
The Final Follow-Up Call is to occur 14 ± 5 days after the participant’s last dose of study drug. 
However, the Final Follow-Up Call is not required if the Early Discontinuation visit occurs 14 ± 
5 days after the last dose of study drug. 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 35 of 92 
Subjects who withdraw from the study due to adverse events will continue follow-up per protocol, 
as noted above. 
 
In the event a subject wishes to no longer have their personal health information used for the 
analysis of this study, he or she will notify the site in writing and future data will not be included 
in analysis. All data collected prior to the communication with the subject will be included in 
analysis. 
 
5.3.4 Termination of Study  
This study may be prematurely terminated if, in the opinion of the study PI, medical monitor, or 
sponsor, there is sufficient reasonable cause.  Written notification documenting the reason for 
study termination will be provided to the Site Investigator or sponsor by the terminating party. 
 
Circumstances that may warrant termination include, but are not limited to: 
● Determination of unexpected, significant, or unacceptable risk to subjects. 
● Enrollment is unsatisfactory. 
● Insufficient adherence to protocol requirements. 
● Data that are not sufficiently complete and/or evaluable.  
● Plans to modify, suspend, or discontinue development of the study drug. 
 
If the study is prematurely terminated or suspended, the sponsor will promptly inform the Site 
Investigators/institutions, and regulatory authorities of the termination or suspension and the 
reason(s) for the termination or suspension. The IRB/IEC will also be informed promptly and 
provided the reason(s) for the termination or suspension by the sponsor or by the Site 
Investigator/institution, as specified by the applicable regulatory requirement(s). 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 36 of 92 
6 
TREATMENTS ADMINISTERED 
 
6.1 
Treatments 
 
6.1.1 Study Product Description 
AMX0035 is a combination therapy comprising two active pharmaceutical ingredients, Sodium 
Phenylbutyrate (PB) and Tauroursodeoxycholic acid (TUDCA). 
 
Phenylbutyrate is an approved compound in the United States for urea cycle disorders and is 
marketed in the US as Buphenyl®. There is an existing USP monograph for this material. 
The chemical structure for PB is provided below. 
 
Chemical structure of PB: 
The active drug substance, PB, is manufactured by
 under cGMP 
conditions. The manufacture and controls for PB are described in Drug Master File No. 
. 
The specifications for PB are identical to those of the Ph.Eur. 
 
The active drug substance, TUDCA, is currently marketed in Italy under the brand name 
Tudcabil®. TUDCA is exported to China and Turkey under the brand name Taurolite® and is 
used clinically for the treatment of cholesterol gallstones. TUDCA has been used for the treatment 
of cholestatic liver diseases including primary cirrhosis, pediatric familial intrahepatic cholestasis 
and primary sclerosing cholangitis and cholestasis due to cystic fibrosis. To our knowledge, there 
are no other uses of TUDCA. It is marketed in the United States on websites such as Amazon as a 
dietary supplement to “promote liver health”. 
 
 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 37 of 92 
The chemical structure for TUDCA is provided below. 
Chemical structure TUDCA: 
The active drug substance TUDCA is manufactured by 
  
The specifications for TUDCA are identical to those used by the supplier. 
 
A powder filled sachet will be used as the AMX0035 drug product. The drug product will be filled 
under cGMP conditions in an aluminum foil lined sachet. 
 
The sachet will contain 2 active study drug ingredients and excipients. 
 
6.1.2 Placebo 
A matching placebo will be used to maintain blinding. The placebo sachets for this study will 
match the corresponding AMX0035 sachets in size, color, taste, and presentation. 
 
Sachets containing placebo will include sweeteners and excipients, but no active study drug 
ingredients. 
 
Administration of matching placebo will be the same as for subjects in the treatment group. 
 
6.2 
Acquisition 
Upon receipt of the study treatment supplies, an inventory must be performed and a drug receipt 
log filled out and signed by the person accepting the shipment.  It is important that the designated 
study staff count and verify that the shipment contains all the items noted in the shipment 
inventory. Any damaged or unusable study drug in each shipment will be documented in the study 
files. The Site Investigator must notify the study sponsor of the presence of any damaged or 
unusable study treatments that were supplied to the site. 
 
6.2.1 Formulation, Packaging, and Labeling 
The study drug is prepackaged in kits containing 98 sachets. Each subject will receive, at 
minimum, a kit at the Baseline, Week 6, Week 12, and Week 18 Visits. Additional kits may be 
assigned and dispensed with Sponsor approval to accommodate disruptions to the visit schedule 
because of the COVID-19 pandemic. The SI is responsible for ensuring the integrity of packaged 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 38 of 92 
study drug prior to dispensing. Each individual subject kit must be dispensed as provided with no 
further repackaging or labeling done at the investigational site, unless required by the institution 
per institutional polices. 
 
6.2.2 Product Storage and Stability 
The SI must ensure that all investigational drug supplies are stored in a locked, safe area at 
controlled room temperature (15-25°C) with access limited to authorized study staff. 
Investigational drug supplies should not be repackaged in any way.  
 
Once subjects are given kits, they will be asked to store them away from moisture at room 
temperature. Stability has been assessed both at ICH standard and accelerated conditions for each 
of the individual active ingredients. Each active ingredient was found to be stable for over five 
years. Drug product will receive regular stability testing over the course of the study to ensure 
product stability. One-month stability will be verified prior to initiation of the proposed trial. 
Subjects should contact the SI in the case of damaged kits. The SI or site staff will coordinate with 
sponsor to determine appropriate remediation.  
 
6.3 
Dosage, Preparation and Administration of Study Intervention/Investigational 
Product 
Subjects will open the sachet of AMX0035 and add it to a cup or other container. Subjects will 
then add approximately 8 oz. (1 cup) of room temperature water, stir until the powder is mostly 
dissolved, and consume the drink completely. It is normal for a small amount of powder to remain 
undissolved. Subjects should consume within one hour after the powder is added to water. Subjects 
may consume other beverages after consumption of study drug; however, subjects should not mix 
study drug with any liquid other than water. 
 
6.4 
Modification of Study Intervention/Investigational Product for a Subject 
Any dosage adjustment, along with the reason(s) and dates of adjustment, will be documented in 
the CRF for each subject requiring this manipulation. The SI or designated licensed physician Sub-
Investigator may reduce the dosage of study drug or discontinue the study drug for AEs thought 
to be related to the study drug or for other reasons during the trial (the reason and dates of 
suspension or dose reduction must be documented in CRF).  If the AE is mild or moderate, the 
dosage may be reduced until the event improves.  The SI or designated licensed physician Sub-
Investigator may then choose to resume the higher dosage or maintain the subject at a reduced 
dosage.  
 
If the AE is serious or life threatening, and deemed to be definitely related to drug, the study drug 
will be discontinued immediately. Study subjects must remain off the study drug permanently. 
Subjects may not resume study drug.  All AEs will be followed to resolution. 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 39 of 92 
6.4.1 Dosage Discontinuation 
Reasons for discontinuation of study medication may include an AE, Medical Monitor or SI 
recommendation, sponsor termination, protocol deviation, loss-to-follow-up, subject request, or 
death. All serious adverse events (SAEs) that occur in a subject who has discontinued early must 
be recorded and reported within 24-hours of awareness.   
 
Study subjects who discontinue study drug prematurely (early termination from study) and decide 
to not remain in the intention-to-treat (ITT) portion of the study will be encouraged to return for a 
Final Safety/Early Termination Visit and participate in a Follow-Up Telephone Call as outlined in 
Section 5.3.3. All subjects who discontinue study drug early and choose to remain in the ITT 
portion of the study will be encouraged to follow the study visits, off drug, up to the time of the 
Final Follow-up Telephone Call.   
 
6.5 
Accountability Procedures for AMX0035 
At the completion of the study, there will be a final reconciliation of drug shipped, drug consumed, 
and drug remaining. This reconciliation will be logged on the drug reconciliation form, signed, 
and dated. Any discrepancies noted will be investigated, resolved, and documented prior to return 
or destruction of unused study drug.  Drug destroyed on site will be documented in the study files. 
 
6.6 
Assessment of Subject Compliance with AMX0035 
Subjects will be instructed to return unused study medication containers (optional to return empty 
sachets) at each on-site clinic visit or the Early Discontinuation Visit. Site personnel will review 
the unused study medication and log in drug reconciliation form to determine compliance. 
 
In the event that a remote visit occurs, each subject will be instructed to use study drug from the 
new kit, regardless of the amount of study drug remaining from any previous kit in the subject’s 
possession. Drug accountability and compliance will occur at the next on-site clinic visit.  
 
Non-compliance will be defined as taking less than 80% or more than 125% of study medication 
as determined by unused sachet counts. If a study subject is non-compliant with study medication, 
the SI and staff should re-educate and train the subject in administration of study drug.  Data 
indicating non-compliance will be used in the end of study analysis. 
 
6.7 
Prior and Concomitant Therapy 
Throughout the study, SIs may prescribe concomitant medications or treatments deemed necessary 
to provide adequate supportive care provided that the medications are licensed in the United States. 
Study subjects should not receive other experimental agents for the duration of the study. This 
includes marketed agents at experimental dosages that are being evaluated for the treatment of AD. 
All concomitant medications and/or treatments and significant non-drug therapies including 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 40 of 92 
supplements and assistive devices, received by a subject should be recorded on the appropriate 
source document and eCRF. 
 
Any small molecule investigational therapy being used or evaluated for the treatment of AD is 
prohibited beginning 3 months (84 days) prior to the Baseline Visit and throughout the study.  Any 
immunotherapy investigational therapy is prohibited beginning 1 year (365 days) prior to the 
Baseline Visit and throughout the study. 
 
6.7.1 Prohibited Medications and Contraindications 
Prohibited Medications 
Throughout the course of the trial, study subjects should not be treated with the following 
medications.  If a Site Investigator learns that a subject has begun therapy with any of these 
medications, this should be reported to the Coordination Center immediately and action should be 
taken to discontinue the prohibited medication.  If, for safety or health reasons, or by subject 
choice, the prohibited medication cannot be stopped, then the study medication should be stopped. 
 
Prohibited medications include but are not limited to: 
 
● HDAC Inhibitors including: 
○ Valproate 
○ Vorinostat (Zolinza) 
○ Romidepsin 
○ Chidamide 
○ Panobinostat 
○ Lithium 
○ Butyrate 
○ Suramin 
  
● Probenecid 
  
● Bile Acid Sequestrants including: 
○ Cholestyramine and Cholestyramine Light 
○ Questran and Questran Light 
○ Welchol 
○ Colestid and Colestid Flavored 
○ Prevalite 
  
Note on Antacids Within Two Hours of AMX0035 Administration: 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 41 of 92 
Antacids containing Aluminum hydroxide or smectite (aluminum oxide) may not be taken 
within two hours of administration of AMX0035 as they inhibit absorption of TUDCA. 
These include: 
○ Alamag 
○ Alumina and Magnesia 
○ Antacid, Antacid M and Antacid Suspension 
○ Gen-Alox 
○ Kudrox 
○ M.A.H. 
○ Maalox HRF and Maalox TC 
○ Magnalox 
○ Madroxal 
○ Mylanta and Mylanta Ultimate 
○ Ri-Mox 
○ Rulox 
 
Aricept, Exelon, Razadyne, Namenda – If on any of these drugs, treatment must have started for 
no less than 3 months (84 days) prior to baseline and the dosing regimen must have remained 
stable for 6 weeks (42 days) prior to baseline.  The Investigator anticipates that the dosing regimen 
at baseline will remain unchanged throughout participation in the study or must not have been 
discontinued from any of these drugs within one month (28 days) prior to Baseline Visit or start 
one of these drugs during the course of the study. 
 
Pregnancy & Nursing Mothers 
There are no adequate and well-controlled studies in pregnant women. Subjects or partners of male 
subjects should not become pregnant during the study or 30 days after stopping study drug. If a 
female subject becomes pregnant, study treatment must be discontinued immediately.  
 
It is not known whether AMX0035 is excreted in human milk. Caution should be exercised; 
therefore, no subject should nurse an infant while participating in this study. 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 42 of 92 
7 
STUDY SCHEDULE 
No study procedures should be performed prior to the signing of the informed consent form (ICF). 
All subjects will sign an ICF prior to undergoing any study tests or procedures. The consenting 
process must be completed and documented by the SI, Sub-Investigator or by an IRB approved 
study personnel that has been delegated to consent subjects by the SI.  
 
At the discretion of the SI, the Screening and Week 24/Early Discontinuation visit assessments 
can be completed on multiple study visits. However, all cognitive testing must be performed on a 
single day. 
 
Blood samples should be drawn at the end of the visit; however, the order of testing will be at the 
discretion of each SI. 
 
Visit windows are consecutive calendar days, and the target visit dates, except the Final Follow-
Up Call, are calculated from the Baseline Visit (Day 0 of study drug administration).  The target 
date for the Final Follow-Up Call is calculated from the last dose of study drug. 
 
Subjects who withdraw consent or early terminate from the study (i.e., discontinue study drug) 
will be asked to return for an Early Discontinuation Visit and, as needed, have a Final Follow-Up 
Call. 
 
Ideally, any remote visit will be conducted using a HIPAA-compliant video conferencing platform. 
If video conferencing is not available or not feasible, remote visits may be conducted by phone.  
 
Sites may send study drug to participants’ residences. When transferring study drug to a 
participant, all reasonable efforts should be made to maintain the correct temperature. If possible, 
sites should use the Sponsor-selected vendor who will manage the shipments from the site to the 
subject using a certified shipping container and temperature monitor. Study drug is to be provided 
to subjects only after reviewing and documenting concomitant medications and therapies, and 
Adverse Events. Each subject will be instructed to use study drug from the new kit after receipt 
and verification of condition, regardless of the amount of study drug remaining from any previous 
kit in the subject’s possession. 
 
The longest period a subject may continue taking study drug without having completed the safety 
assessments listed below is 16 weeks/112 days. 
• ECG 
• Safety Labs: Hematology (Complete Blood Count with Differential), Complete Chemistry 
Panel, Liver Function Tests, and Urinalysis 
• Vital Signs 
• C-SSRS 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 43 of 92 
 
7.1 
Screening Visit  
The following procedures will be performed at an office visit to determine the subject’s eligibility 
for the study and the completion of assessments and parameters will take approximately 3-4 hours: 
o Obtain written informed consent from subject 
o Assess inclusion and exclusion criteria to determine subject eligibility 
o Obtain medical history and demographics 
o Review and document concomitant medications and therapies 
o Obtain AD diagnosis history, medical history, and demographic information 
o Assess and document adverse events (AEs) after subject signs informed consent form (ICF) 
o Measure vital signs (blood pressure, heart and breathing rates, temperature) including 
height and weight 
o Perform physical and neurological examinations 
o Perform 12-lead ECG (Electrocardiogram) 
o Administer Montreal Cognitive Assessment (MoCA) 
o Administer the C-SSRS Screening Version questionnaire 
o Administer Geriatric Depression Scale 
o Administer Neuropsychiatric Inventory Questionnaire (NPI-Q) 
o Perform MRI Scan (to be completed anytime between the Screening and up to 7 days prior 
to the Baseline Visit) 
o  Collect blood samples for 
o Clinical laboratory assessments including Hematology (CBC with differential), 
o Complete Chemistry Panel, Liver Function Tests 
o Collect urine sample for urinalysis 
o Perform lumbar puncture to collect CSF for biomarker analysis (to be completed anytime 
between the Screening Visit and up to 7 days prior to the Baseline Visit, pre-dose) 
o Schedule the Baseline Visit  
 
7.1.1 Screen Failures 
Any subject who signs consent will be considered enrolled in the study. If a subject fails screening, 
at a minimum, the following information should be captured and entered in the Electronic Data 
Capture (EDC) System: 
o Inclusion/Exclusion Criteria 
o Demographics 
o Reason for screen failure 
 
7.2 
Baseline Visit 
This visit will take place no more than 28+5 days after the Screening Visit.  The following 
procedures will be performed and will take approximately 3-4 hours: 
o Confirm eligibility criteria are still met 
o Randomize subject  
o Review and document concomitant medications and therapies 
o Review and document Adverse Events  


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 44 of 92 
o Measure vital signs (blood pressure, heart and breathing rates, temperature) 
o Administer DSRS 
o Administer FAQ 
o Administer Neuropsychiatric Inventory Questionnaire (NPI-Q) if not performed at 
screening 
o Administer ADAS-Cog  
o Administer the C-SSRS Since Last Visit questionnaire 
o Collect blood samples for: 
o Biomarkers 
o Genetic analysis 
o Administer first dose of study drug. The healthcare staff member will advise the subject on 
appropriate delivery. 
o Dispense 6 weeks of study drug  
 
7.3 
Week 1 Phone Call 
This visit will take place 7±1 day after the Baseline Visit.  The following procedures will be 
performed and will take approximately 15 minutes: 
o Review and document Adverse Events  
o Ask about study drug compliance and accountability 
o Notify subjects of increase from one sachet per day to two sachets per day 
 
7.4 
Week 6 Visit 
This visit will take place 42±14 days after the Baseline Visit.  The following procedures will be 
performed and will take approximately 30 minutes –1 hour. To the extent possible, the Week 6 
visit may be done remotely. If completed remotely, unused study drug will be collected, and 
compliance determined, at the next in-person visit. If allowed by local regulations and local IRB 
this visit can be performed at the subject’s residence or preferred location: 
o Review and document concomitant medications and therapies 
o Review and document Adverse Events  
o Administer MoCA 
o Administer the C-SSRS questionnaire (Since Last Visit) 
o Ask about study drug compliance and accountability 
o Collect any unused study drug (optional empty study drug sachets) 
o Dispense 6 weeks of study drug  
o Schedule next study visit 
 
7.5 
Week 12 Visit 
This visit will take place 84±28 days after the Baseline Visit. 
It is preferred that the Week 12 visit be conducted at the site with the participant physically present. 
If it is not possible to complete an in-person Week 12 visit at the site, the safety assessments below 
must be completed by Week 16/Day 112 for the subject to remain on study drug. Sites may make 
alternative arrangements to complete these assessments per institutional and IRB policy. 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 45 of 92 
• ECG 
• Safety Labs: Hematology (Complete Blood Count with Differential), Complete Chemistry 
Panel, Liver Function Tests, and Urinalysis 
• Vital Signs 
• C-SSRS 
If completed remotely, unused study drug will be collected, and compliance determined, at the 
next in-person visit. 
The following procedures will be performed and will take approximately 2-3 hours: 
o Measure vital signs (blood pressure, heart and breathing rates, temperature) 
o Review and document concomitant medications and therapies 
o Review and document Adverse Events  
o Ask about study drug compliance and accountability 
o Administer ADAS-Cog   
o Administer DSRS 
o Administer FAQ 
o Administer Neuropsychiatric Inventory Questionnaire (NPI-Q) 
o Administer the C-SSRS questionnaire (Since Last Visit) 
o Perform a 12-Lead ECG 
o Collect blood for: 
o Routine safety lab tests (chemistry and hematology assessment) 
o Biomarkers 
o Pharmacokinetics (PK) 
o Collect urine sample for urinalysis 
o Collect any unused study drug (optional empty study drug sachets) 
o Dispense 6 weeks of study drug 
o Schedule next study visit 
 
7.6 
Week 18 Visit 
This visit will take place 126±14 days after the Baseline Visit.  The following procedures will be 
performed and will take approximately 30 minutes – 1 hour. To the extent possible, the Week 18 
visit may be done remotely. If completed remotely, unused study drug will be collected, and 
compliance determined, at the next in-person visit. If allowed by local regulations and local IRB 
this visit can be performed at the subject’s residence or preferred location:  
o Review and document concomitant medications and therapies 
o Review and document Adverse Events  
o Administer MoCA 
o Administer the C-SSRS questionnaire (Since Last Visit) 
o Collect any unused study drug (optional empty study drug sachets) 
o Ask about study drug compliance and accountability 
o Dispense 6 weeks of study drug  
o Schedule next study visit 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 46 of 92 
7.7 
Week 24 Final Study Visit/Early Discontinuation Visit  
This visit will take place 168±28 days after the Baseline Visit. 
All reasonable efforts should be made to complete the Week 24 or Early Discontinuation visit at 
the site with the participant physically present. However, if COVID-19 related restrictions (e.g., 
site closure, travel restrictions) make it impossible to conduct an in-person clinic visit during the 
specified window, then any assessment that can be performed remotely should be completed as an 
unscheduled visit during the Week 24 window. The actual Week 24 visit, with all of the 
assessments indicated on the SOA, may be postponed for up to 12 weeks and treatment extended. 
The maximum duration a subject may be on IP is 40 weeks. Safety checks (i.e., ECG, safety labs, 
vital signs, and C-SSRS) must be completed, at minimum, every 16 weeks/112 days. If safety 
assessments are performed so that the Week 24 visit may be postponed, the assessments should be 
documented as an unscheduled visit. 
If possible, an Early Discontinuation visit should be done within 14 days of the last dose of IP (i.e., 
last dose of IP + 14 days). The MRI and lumbar puncture may be done as soon as is practical and, 
if possible, within 60 days of the last dose of IP (i.e., last dose of IP + 60 days). 
 
The following procedures will be performed and will take 3-4 hours: 
o Measure vital signs (blood pressure, heart and breathing rates, temperature) including 
weight 
o Review and document concomitant medications and therapies 
o Review and document Adverse Events 
o Perform Physical and neurological exam 
o Ask about study drug compliance and accountability 
o Administer ADAS-Cog   
o Administer DSRS 
o Administer FAQ 
o Administer Neuropsychiatric Inventory Questionnaire (NPI-Q) 
o Administer MoCA 
o Perform MRI scan 
o Perform lumbar puncture to collect CSF for biomarker analysis (can be collected up to 7 
days prior to this visit.  If the early discontinuation visit occurs up to 7 days after initiation 
of study drug, then the LP does not need to be completed) 
o Administer the C-SSRS questionnaire (Since Last Visit) 
o Perform a 12-Lead ECG 
o Collect blood for: 
o Routine safety lab tests (chemistry and hematology assessment) 
o Biomarkers 
o PK (will not be done for subjects completing an Early Discontinuation Visit) 
o Collect urine sample for urinalysis 
o Collect any unused study drug (optional empty study drug sachets) 
o Ask about study drug compliance and accountability 
o Schedule final follow-up telephone call as needed 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 47 of 92 
7.7.1 Final Follow-up Telephone Call 
A follow-up phone call will take place after the Week 24 visit and within 14±5 days after the 
subject’s last dose of study drug.  For participants who discontinue treatment early, the Final 
Follow-Up Call is not required if the Early Discontinuation visit occurs 14 ± 5 days after 
administration of the last dose of study drug. 
 
The following will be performed and will take approximately 15 minutes: 
o Review and document concomitant medications and therapies 
o Assess and document AEs, including AEs specified in 9.2.3 
 
7.8 
Protocol Deviations 
A protocol deviation is any noncompliance with the clinical trial protocol, Good Clinical Practice 
(GCP).  The noncompliance may be either on the part of the subject, the SI, or the study site staff. 
In the event of deviations, corrective actions are to be developed by the site in conjunction with 
the coordinating team and implemented promptly. 
 
 
All deviations from the protocol must be addressed in the subject’s source documents. Protocol 
deviations must be sent to the local IRB per their guidelines and entered in the Protocol Deviations 
Log in the EDC system.  
 
7.9 
Missed Visits and Procedures  
Missed visits and any procedures not performed (not attempted) for reasons other than illness, 
injury or progressive disability (i.e. subject is physically unable to perform test) will be reported 
as protocol deviations. Multiple missed study procedures, due to COVID-19, that does not affect 
data integrity or patient safety, will be documented and combined into one (1) minor protocol 
deviation. 
 
Procedures or visits not performed due to illness, injury or disability, including procedures that 
were attempted but failed (i.e. blood samples unable to be drawn after multiple attempts, or weight 
unable to be obtained due to subject immobility) will not be reported as protocol deviations.   
 
Study drug compliance that is outside the limits set in the study operations manual will be reported 
as a protocol deviation.   
 
Details and specific instructions regarding protocol deviations, including any exceptions to this 
standard procedure, are found in the study operations manual. 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 48 of 92 
8 
CLINICAL ASSESSMENTS AND OUTCOME MEASURES  
 
8.1 
Clinical Variables 
Assessments will be performed at designated time-points throughout the study for clinical 
evaluation.  In addition to the assessments evaluated below, subjects will provide information 
related to demographics, medical and AD diagnostic history, and concomitant medication usage. 
 
8.1.1 Vital Signs, Height, & Weight 
Vital signs will be obtained after the subject has been in a seated position for several minutes.  
Vital signs, including blood pressure, heart rate, respiratory rate and body temperature will be 
assessed at Screening, Baseline, Week 12, and Week 24/Early Discontinuation Visit. Height will 
only be collected once at the Screening Visit. Weight will be collected when a physical exam is 
done at the Screening and Week 24/Early Discontinuation Visit. 
 
If the subject cannot attend a visit at the site to have vitals measured because of COVID-19, other 
arrangements may be made to measure vitals as allowed per institution and local IRB policy. 
 
8.1.2 Clinical Laboratory Assessments 
The following laboratory tests will be performed for safety purposes at Screening, Week 12, and 
Week 24/Early Discontinuation Visits: 
o Hematology with differential panel: complete blood count with differential (hematocrit, 
hemoglobin, platelet count, RBC indices, total RBC, Total WBC, and WBC & differential). 
o Blood chemistry panel/liver function tests (LFTs): alanine aminotransferase (ALT 
(SGPT)), aspartate aminotransferase (AST (SGOT)), albumin, alkaline phosphatase 
(ALP), bicarbonate, blood urea nitrogen, calcium, chloride, creatinine, glucose, 
magnesium, phosphate, potassium, sodium, total bilirubin and total protein. 
o Urinalysis: albumin, appearance, bilirubin, blood, color, glucose, ketones, nitrate, pH, 
protein, specific gravity, urobilinogen and WBC screen. 
o B12 and TSH will be assessed at Screening Visit only as common laboratory assessments 
that may contribute to cognitive dysfunction. 
 
All subjects will have safety laboratory tests at the designated visits outlined in the protocol. These 
samples will be analyzed at a central laboratory. The SI may order additional testing, if thought to 
be necessary, to further assess an adverse event (AE) or if there is any suspicion that a subject may 
be pregnant, throughout the course of the study. 
 
If the subject cannot attend a visit at the site to have samples collected because of COVID-19, 
other arrangements may be made for sample collection and analysis as allowed per institution and 
local IRB policy (e.g., sample may be analyzed by site or third-party laboratory). 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 49 of 92 
8.1.3 Blood Draw and Urine Sample 
Subjects will provide additional blood samples at baseline for genetic analysis and at Baseline, 
Week 12, and Week 24/Early Discontinuation Visits for biomarkers. All samples will be 
anonymized and labeled with a code that will not include any identifiable information. The samples 
are for research purposes only. Although genetic information may be analyzed, no genetic 
information will be given to the subject. 
 
There is no scheduled date by which the samples will be destroyed. Samples may be stored for 
research until they are used, damaged, decayed, or otherwise unfit for analysis. Subjects have the 
option of declining participation in this portion of the study at any time by withdrawing their 
consent to have their sample used.  However, it will not be possible to destroy samples that may 
have already been used.   
 
Additionally, the central laboratory will store ship blood samples for pharmacokinetic analysis. 
The central laboratory facility will prepare kits for every site detailing the sampling protocol.  
 
8.1.4 12-Lead Electrocardiogram (ECG) 
A standard 12-lead ECG will be performed at Screening, Week 12, and Week 24/Early 
Discontinuation Visits. Tracings will be reviewed by a central ECG reader and a copy of the 
tracings will be kept at clinic sites as part of source documentation. The central ECG reader will 
provide standard ECG devices to each site as well as training. Board-certified cardiologists from 
the central ECG reader will review all ECGs. 
 
If the subject cannot attend a visit at the site to have an ECG performed because of COVID-19, 
arrangements may be made to complete the ECG elsewhere using a device not provided by the 
central reader as allowed per institution and local IRB policy. 
 
8.1.5 Physical and Neurological Examination 
A physical and neurological examination will be performed at Screening and Week 24/Early 
Discontinuation Visits. The following systems will be examined: general appearance, head, eyes, 
ears, nose, throat, neck, chest, heart, abdomen, extremities, edema, peripheral vascular, skin and 
appendages, musculoskeletal, central nervous system and back. 
 
8.1.6 Geriatric Depression Scale (GDS) 
The Geriatric Depression Scale (Short Form) will be performed at the Screening Visit only. The 
GDS is a questionnaire designed to identify and quantify the presence of depression in the elderly. 
The scale consists of 15 yes/no questions related to how the subject has felt over the previous 
week. The GDS includes items to which positive and negative answers are indicative of a symptom 
of depression. One point is given for each such appropriate answer, with a possible total of 15 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 50 of 92 
points. Total scores of 0-5 are considered normal and scores of 6-15 are considered indicative of 
depression. A GDS less than 7 is required for inclusion in the study. 
 
8.1.7 Columbia Suicide Severity Rating Scale (C-SSRS) 
The US FDA recommends the use of a suicidality assessment instrument that maps to the 
Columbia Classification Algorithm for Suicide Assessment (C-CASA)40. The C-CASA was 
developed to assist in coding suicidality data accumulated during the conduct of clinical trials of 
antidepressant drugs. The Columbia Suicide Severity Rating Scale (C-SSRS)23 will be utilized in 
this trial. The C-SSRS involves a series of questions designed to detect possible suicidal thinking 
and behavior. 
 
At the Screening Visit, the C-SSRS Screening Version will be administered.  This version is used 
to assess suicidality over a specified time-period.  The Since Last Visit Version of the C-SSRS 
will be administered at Baseline, Week 6, Week 12, Week 18 and Week 24/Early Discontinuation 
Visits. This version of the scale assesses suicidality since the subject’s last visit. 
 
8.1.8 Adverse Events 
Adverse events (AEs) will be documented at each study visit, including the Screening Visit once 
the informed consent form has been signed by the subject, and at all study visits, including the 
Final Follow-up Telephone Call 14 days (± 5 days) after the last dose of study drug.  Information 
on adverse effects of study medication and on inter-current events will be determined at each visit 
by direct questioning of the subjects, review of concomitant medications, and vital sign results. 
 
8.2 
Outcome Measures 
 
8.2.1 Functional Activities Questionnaire (FAQ) 
The FAQ is a brief informant-administered rating scale used to determine a subjects’ level of 
functional independence when performing a range of instrumental activities of daily living 
(IADLs), with repeat assessments useful for monitoring performance in these areas over time47. 
The FAQ total score (ranging from 0-30) reflects the sum of ordinal ratings (0 = fully independent, 
1 = has difficulty but does by self, 2 = requires assistance, and 3 = dependent) across ten items 
assessing a variety of functional activities (i.e., preparing a balanced meal, financial management 
skills, and shopping), with higher scores indicating increasing levels of dependence. For activities 
not normally undertaken by a person, a score of 1 is assigned if the informant believes the subject 
would be unable to complete the task if required, or a score of 0 is assigned if the informant 
believes the subject could successfully carry out the task if needed. Overall, the FAQ is a sensitive 
marker of functional impairment among individuals with varying dementia severity43, and has been 
shown to differentiate mild cognitive impairment from early Alzheimer’s Disease with 80% 
sensitivity and 87% specificity49. The FAQ demonstrates high reliability (exceeding 0.90), takes 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 51 of 92 
about 5 minutes to complete, and requires limited rater training to administer47.  The FAQ will be 
administered at the Baseline, Week 12, and Week 24/Early Discontinuation Visits. 
 
8.2.2 Dementia Severity Rating Scale (DSRS) 
The DSRS is a brief 12-item questionnaire administered to an informant that assesses a subjects’ 
functional abilities44 and offers a global characterization of everyday activities that may be 
impacted by neurodegenerative disease. The DSRS is designed in a multi-choice format with 
strong concurrent validity and parallel content to material covered on the Clinical Dementia Rating 
Scale (CDR), a commonly employed dementia staging instrument46. The DSRS is a highly reliable 
scale with an intra-class correlation of >90% for interrater reliability and Cronbach’s alpha > 0.70 
for internal consistency48, and has been shown to accurately discriminate between cognitive 
healthy individuals and dementia subjects of varying severity44,45. Further, the DSRS allows for a 
broad range of scores (total score 0-54) making it suitable to quantify a wide range of functional 
impairment without being hampered by floor effects seen in more advanced disease, while also 
making it sensitive to detecting incremental change in functional ability over time50. The DSRS 
takes about 5 minutes to administer, requires minimal rater training, and can be administered over 
the phone to study subjects if required. The DSRS will be administered at the Baseline, Week 12, 
and Week 24/Early Discontinuation Visits. 
 
8.2.3 Cognitive Evaluations 
Cognitive testing will include evaluations of the ADAS-Cog and Montreal – Cognitive Assessment 
(MoCA).  
 
The ADAS-Cog is validated and widely used as a primary cognitive outcome measure in AD 
pharmacotherapy studies. This is a psychometric instrument that evaluates memory (immediate 
and delayed word recall, word recognition), attention (number cancellation), reasoning (following 
commands), language (naming, comprehension), orientation, ideational praxis (placing letter in 
envelope) and constructional praxis (copying geometric designs), and executive functioning (maze 
completion). Scoring is in the range of 0 to 90 with a higher score indicating greater impairment. 
This test will be administered by experienced raters at each site at Baseline, Week 12, Week 
24/Early Discontinuation Visits. The ADAS-Cog will be the primary cognitive outcome measure 
for this study. 
 
If the ADAS-Cog is administered remotely, it should be completed to the extent possible 
given the available technology.  If the ADAS-Cog cannot be completed remotely, then it 
should be documented as a minor deviation. 
Montreal Cognitive Assessment (MoCA) is commonly utilized questionnaire in clinical trials and 
research settings to measure levels of cognitive impairment. The MoCA measures five areas of 
cognitive function: orientation, visuospatial, attention and calculation, recall, and language. The 
MoCA will take approximately 10 minutes to complete. The test will be administered by 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 52 of 92 
experienced raters at each site at Screening, Week 6, Week 18, Week 24/Early Discontinuation 
Visit. See Appendix III (section 13.3) for the worksheet. 
The 3 available versions of the MoCA test will be administered by experienced raters at each site. 
Subjects may be given any version of the MoCA at the Screening Visit as long as they have NOT 
received the same MoCA version clinically within the last 3 months. A different version of the 
MoCA should be used at each subsequent visit until Week 24 or Early Termination visit (if 
applicable). The MoCA version used at a study visit should be accurately documented in Source 
Document and within the EDC for each visit. 
Re-screening: In cases where the subject screen fails due to the MoCA score being out of the 
required inclusionary range at the Screening Visit, the subject may be re-screened; a minimum of 
one month must have passed since their original MoCA assessment. If the subject’s MoCA score 
was < 10, they must have had a change in therapy or intervention that (in the opinion of the SI) 
may have an impact on the subject’s cognitive status. Subjects who move forward with a re-screen 
must be evaluated using a different MoCA version (7.1, 7.2 or 7.3) that was used at the original 
Screening Visit, and subjects may be re-screened only once. 
 
If the MoCA is administered remotely, it should be completed to the extent possible given the 
available technology.  If the MoCA cannot be completed remotely, then it should be documented 
as a minor deviation. 
 
8.2.4 Neuropsychiatric Inventory Questionnaire (NPI-Q) 
The Neuropsychiatric Inventory (NPI) measures dementia-related behavioral symptoms and is 
used to assess changes in psychological status.  There are several versions of the NPI including 
the NPI-Questionnaire (NPI-Q), NPI-Clinician (NPI-C) and the NPI-Nursing Home (NPI-NH).  
All examine 12 sub-domains of behavioral functioning including: hallucinations, delusions, 
agitation, dysphoria, anxiety, euphoria, apathy, disinhibition, irritability, aberrant motor activity, 
eating abnormalities, and night-time behavioral alternations. The NPI-Q is completed by a trained 
rater through interview with the subject's study partner. It is well-validated and extensively used 
in clinical trials in AD. The NPI-Q will be administered at the Screening or Baseline, Week 12 and 
Week 24/Early Discontinuation Visits. 
 
8.2.5 Lumbar Puncture for CSF Biomarker 
 
Cerebrospinal fluid (CSF) 
biomarkers 
 
 
 
 
 
 CSF samples will be collected prior to 
AMX0035 treatment, anytime between the screening visit and up to 7 days prior to the baseline 
visit the baseline visit and following 24 weeks of treatment at the final study visit or at the early 
discontinuation visit. 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 53 of 92 
 
Subjects will have a fasting morning CSF sample taken anytime between the Screening and up to 
7 days prior to the Baseline Visit (pre-dose) and the Week 24 and/or the Early Discontinuation 
Visit.  If the Early Discontinuation Visit occurs within 7 days after the initiation of study drug 
(Baseline Visit), then the LP does not need to be completed. Lumbar punctures (LPs) will be 
performed by qualified, experienced practitioners. Standard protocols will be used employing 
sterile conditions, local lidocaine anesthesia, and preferred use of the Sprotte 24-gauge needles, 
which minimizes incidence of post-LP headaches. Approximately 15-20 cc of CSF will be 
collected for CSF biomarker 
, as well as routine chemistry (protein, glucose) and cell count. 
 
8.2.6 Neuroimaging 
MRI Scans: In accordance with secondary study objectives, all subjects will undergo 3T structural 
and functional MRI will be completed anytime between the Screening and up to 7 days prior to 
Baseline Visit and Week 24 and/or the Early Discontinuation Visits to assess the effect of treatment 
on brain volume, cerebral perfusion, and brain connectivity. Each scan session will last 
approximately 35 minutes and include the following MR pulse sequences: high resolution T1-
weighted multi-echo MPRAGE for volumetric analysis, task-free blood oxygen level dependent 
(BOLD) sequence to measure resting neural connectivity, diffusion tensor imaging (DTI) to 
quantify white matter structural connectivity, susceptibility-weighted imaging (SWI), and a T2-
weighted fluid attenuated inversion recovery (FLAIR) sequence. Radiologist at each site will 
provide a clinical read. For volumetric analysis, high resolution T1-weighted images will undergo 
reconstruction and volumetric segmentation using the Freesurfer image analysis suite 
(http://surfer.nmr.mgh.harvard.edu/).  
 
8.2.7  Pharmacokinetics 
Plasma concentrations of both TUDCA and PB will be assessed at the Week 12 and Week 24 
(approximately at the same time as CSF sample, if taken on the same day).  The time of the 
previous two drug administrations and the time of the sample will be noted in the eCRF. A PK 
sample will not be taken at an Early Discontinuation Visit if the subject discontinued study drug 
more than 48 hours before the visit. 
 
8.2.8 Training and Validation 
All evaluators must be certified by the study PI to perform cognitive and psychiatric outcome 
assessments. It is strongly preferred that a single evaluator performs all measures with a given 
instrument throughout the study, if possible.  Please refer to Section G of the site MOP for a more 
detailed description of the training and certification for the outcome assessments. 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 54 of 92 
9 
SAFETY AND ADVERSE EVENTS 
The adverse event (AE) definitions and reporting procedures provided in this protocol comply with 
all applicable United States Food and Drug Administration (FDA) regulations and International 
Conference on Harmonization (ICH) guidelines. The Site Investigator will carefully monitor each 
subject throughout the study for possible adverse events. All AEs will be documented on CRFs 
designed specifically for this purpose.  It is also important to report all AEs, especially those that 
result in permanent discontinuation of the investigational product being studied, whether serious 
or non-serious. 
 
9.1 
Definitions of AEs, Suspected Adverse Drug Reactions & SAEs 
 
9.1.1 Adverse Event and Suspected Adverse Drug Reactions 
An adverse event (AE) is any unfavorable and unintended sign (including a clinically significant 
abnormal laboratory finding, for example), symptom, or disease temporally associated with a 
study, use of a drug product or device whether or not considered related to the drug product or 
device.  
 
Adverse drug reactions (ADR) are all noxious and unintended responses to a medicinal product 
related to any dose.  The phrase “responses to a medicinal product” means that a causal relationship 
between a medicinal product and an adverse event is at least a reasonable possibility, i.e., the 
relationship cannot be ruled out.  Therefore, a subset of AEs can be classified as suspected ADRs, 
if there is a suspected causal relationship to the medicinal product. 
 
Examples of adverse events include: new conditions, worsening of pre-existing conditions, 
clinically significant abnormal physical examination signs (i.e. skin rash, peripheral edema, etc.), 
or clinically significant abnormal test results (i.e. lab values or vital signs), with the exception of 
outcome measure results, which are not being recorded as adverse events in this trial (they are 
being collected, but analyzed separately). Stable chronic conditions (i.e., diabetes, arthritis) that 
are present prior to the start of the study and do not worsen during the trial are NOT considered 
adverse events.  Chronic conditions that occur more frequently (for intermittent conditions) or with 
greater severity, would be considered as worsened and therefore would be recorded as adverse 
events. 
 
Adverse events are generally detected in two ways: 
 
Clinical - symptoms reported by the subject or signs detected on examination. 
 
Ancillary Tests - abnormalities of vital signs, laboratory tests, and other diagnostic 
procedures (other than the outcome measures, the results of which are not being captured 
as AEs). 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 55 of 92 
For the purposes of this study, symptoms of clinically noteworthy progression/worsening of 
cognitive, behavioral or functional abilities will be recorded as AEs.     
 
The following measures of disease progression will not be recorded as AEs even if they worsen 
(they are being recorded and analyzed separately): ADAS-Cog, DSRS, and FAQ.  
 
If discernible at the time of completing the AE log, a specific disease or syndrome rather than 
individual associated signs and symptoms should be identified by the Site Investigator and 
recorded on the AE log.  However, if an observed or reported sign, symptom, or clinically 
significant laboratory anomaly is not considered by the Site Investigator to be a component of a 
specific disease or syndrome, then it should be recorded as a separate AE on the AE log.  Clinically 
significant laboratory abnormalities, such as those that require intervention, are those that are 
identified as such by the SI. 
 
Subjects will be monitored for AEs from the time they provide and sign consent until completion 
of their participation in the study (defined as death, consent withdrawal, loss to follow up, early 
study termination for other reasons or following completion of the entire study). Any treatment 
AE still present upon completion of treatment (including early discontinuation) should be 
monitored until resolution or until the AE is declared a chronic condition. 
 
An unexpected adverse event is any AE in which the specificity or severity of which is not 
consistent with the current Investigator’s Brochure. An unexpected, suspected adverse drug 
reaction is any unexpected adverse event that, in the opinion of the SI or Sponsor, has a reasonable 
possibility of being related to the investigational product. 
 
9.1.2 Serious Adverse Events 
A serious adverse event (SAE) is defined as an adverse event that meets any of the following 
criteria: 
1. Results in death. 
2. Is life threatening: that is, poses an immediate risk of death as the event occurred. 
a. This serious criterion applies if the study subject, in the view of the Site Investigator 
or Sponsor, is at immediate risk of death from the AE as it occurs.  It does not apply 
if an AE hypothetically might have caused death if it were more severe. 
3. Requires inpatient hospitalization or prolongation of existing hospitalization. 
a. Hospitalization for an elective procedure or a routinely scheduled treatment is not 
an SAE by this criterion because an elective or scheduled “procedure” or a 
“treatment” is not an untoward medical occurrence. 
4. Results in persistent or significant disability or incapacity. 
a. This serious criterion applies if the “disability” caused by the reported AE results 
in a substantial disruption of the subject’s ability to carry out normal life functions. 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 56 of 92 
5. Necessitates medical or surgical intervention to preclude permanent impairment of a body 
function or permanent damage to a body structure. 
6. Important medical events that may not result in death, are not life-threatening, or do not 
require hospitalization may also be considered SAEs when, based upon appropriate 
medical judgment, they may jeopardize the subject and may require medical or surgical 
intervention to prevent one of the outcomes listed in this definition.  Examples of such 
medical events include blood dyscrasias or convulsions that do not result in inpatient 
hospitalization, or the development of drug dependency or drug abuse. 
 
An inpatient hospital admission in the absence of a precipitating, treatment-emergent, clinical 
adverse event may meet criteria for "seriousness" but is not an adverse experience, and will 
therefore not be considered an SAE. An example of this would include a social admission (subject 
admitted for other reasons than medical, e.g., lives far from the hospital, has no place to sleep). 
 
A serious, suspected adverse drug reaction is an SAE that, in the opinion of the SI or Sponsor, 
there is a reasonable possibility is related to the investigational product. 
 
The SI is responsible for classifying adverse events as serious or non-serious. 
 
9.2 
Assessment and Recording of Adverse Events 
The Site Investigator will carefully monitor each subject throughout the study for possible AEs.  
All AEs will be documented on source document templates and eCRFs designed specifically for 
this purpose.  All AEs will be reported in the EDC system and compiled into reports for periodic 
reviewing by the Medical Monitor. The Medical Monitor shall promptly review all information 
relevant to the safety of the investigational product, including all serious adverse events (SAEs).  
Special attention will be paid to those that result in permanent discontinuation of the 
investigational product being studied, whether serious or non-serious. 
 
9.2.1 Assessment of Adverse Events 
At each visit (including telephone interviews), the subject will be asked if they have had any 
problems or symptoms since their last visit in order to determine the occurrence of adverse events.   
If the subject reports an adverse event, the Site Investigator will probe further to determine: 
1. Type of event 
2. Date of onset and resolution (duration) 
3. Severity (mild, moderate, severe) 
4. Seriousness (does the event meet the above definition for an SAE) 
5. Causality, relation to investigational product and disease 
6. Action taken regarding investigational product 
7. Outcome 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 57 of 92 
9.2.2 Relatedness of Adverse Event to Investigational Product 
The relationship of the AE to the investigational product should be specified by the Site 
Investigator, using the following definitions: 
 
1.  Not Related:          
Concomitant illness, accident, or event with no reasonable 
association with treatment. 
 
2.  Unlikely: 
The reaction has little or no temporal sequence from administration 
of the investigational product, and/or a more likely alternative 
etiology exists. 
 
3.  Possibly Related: 
The reaction follows a reasonably temporal sequence from 
administration of the investigational product and follows a known 
response pattern to the suspected investigational product; the 
reaction could have been produced by the investigational product or 
could have been produced by the subject’s clinical state or by other 
modes of therapy administered to the subject. (Suspected ADR) 
 
4.  Probably Related: 
The reaction follows a reasonably temporal sequence from 
administration of investigational product; is confirmed by 
discontinuation of the investigational product or by re-challenge; 
and cannot be reasonably explained by the known characteristics of 
the subject’s clinical state. (Suspected ADR) 
 
5.  Definitely Related: 
The reaction follows a reasonable temporal sequence from 
administration of investigational product; that follows a known or 
expected response pattern to the investigational product; and that is 
confirmed by improvement on stopping or reducing the dosage of 
the investigational product, and reappearance of the reaction on 
repeated exposure. (Suspected ADR) 
 
 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 58 of 92 
9.2.3 Adverse Events in Prior Human Experience with Each Individual Component 
Both TUDCA and PB have been evaluated individually in multiple patient populations. The most 
commonly reported adverse events are below: 
 
TUDCA: 
o A small number of subjects receiving TUDCA have presented with mild diarrhea, 
abdominal and pain 
o Rare incidences of skin rash and vomiting have been observed 
PB: 
o Menstrual irregularities, decreased appetite, sweat-like body odor, and bad taste Less 
common side effects include: nausea, vomiting, stomach upset, stomach pain, gastritis, 
headache, and skin rash. Rarely, cases of peptic ulcers, rectal bleeding, constipation, 
pancreatitis and renal tubular acidosis have been reported. 
o Hypoalbuminemia, metabolic acidosis, alkalosis, hyperchloremia, hyperuricemia, 
hypokalemia, hypophosphatemia, hyperphosphatemia and hypernatremia have been 
observed. 
 
9.2.4 Recording of Adverse Events 
All clinical adverse events are recorded in the Adverse Event (AE) Log in the subject’s study 
binder. The site should fill out the AE Log and enter the AE information into the EDC system 
within 48 hours of the site learning of a new AE or receiving an update on an existing AE.   
 
Please Note: Serious Adverse Events (SAEs) must be reported to the MGH Coordination Center 
within 24 hours of the site learning of the SAE.  
 
Entries on the AE Log (and into the EDC) will include the following: name and severity of the 
event, the date of onset, the date of resolution, relationship to investigational product, action taken, 
and primary outcome of event. 
 
9.3 
Adverse Events and Serious Adverse Events - Reportable Events 
The following are considered reportable events and must be reported to the MGH Coordination 
Center within 24 hours of the site being notified of the event. 
 
o All events that meet the above criteria for Serious Adverse Events (SAEs) 
o Dosage Changes (Dose Management) 
• Investigational Product Suspension, Reduction or Re-challenge 
• Investigational Product Discontinuation 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 59 of 92 
10 
DATA SAFETY MONITORING AND STATISTICAL ANALYSIS PLAN 
 
10.1 
Medical Monitoring 
A Medical Monitor independent of the trial conduct will be identified by the Study Sponsor. The 
Medical Monitor’s responsibilities will include a regular evaluation of the frequency, severity and 
type of AEs and SAEs reported by all sites in the study. The Medical Monitor will be a physician 
with expertise in Alzheimer’s disease and common chronic medical (e.g., renal and cardiac) 
conditions in this elderly patient population and with prior experience with the conduct of clinical 
trials (trial design, safety monitoring, and recruitment). All AEs will be collected and reported in 
the electronic data capture (EDC) system and compiled into bi-monthly blinded reports for 
periodic reviewing by the Medical Monitor. Any possibly, probably or definitely study drug 
related, serious adverse events (i.e. suspected unexpected serious adverse drug reactions, or 
SUSARs) and any death are considered events of interest and will be reported in real-time (within 
1 business day of Coordination Center (CC) awareness) to the Medical Monitor and to members 
of the PSC. The Medical Monitor will approve the format and content of the periodic safety report.  
The Medical Monitor shall promptly review all information relevant to the safety of the 
investigational product, including all serious adverse events (SAEs) and AEs unusual in the 
context of Alzheimer disease. Special attention will be paid to those that result in permanent 
discontinuation of the investigational product being studied, whether serious or non-serious. The 
Medical monitor may ask to receive the AE reports more frequently. The Medical Monitor will 
communicate their recommendations to the PSC.   
 
10.2 
Protocol Steering Committee  
The Protocol Steering Committee (PSC) is composed of the Principal Investigator of the study 
(serving as SC Chair), the study biostatistician, independent Investigator members with expertise in 
Alzheimer’s disease and study-related medical (e.g., renal and cardiac) conditions and priorities 
(trial recruitment and drug supply) and the Sponsor Acting Medical Director. The PSC is responsible 
for the design of the study protocol and analysis plan and oversees the clinical trial from protocol 
development to study analysis and publication. 
 
10.3 
Statistical Methods 
Complete details of efficacy and safety analyses will be provided in a separate Statistical 
Analysis Plan (SAP). 
 
10.3.1 Sample-Size Determination 
A sample size of approximately 100 randomization subjects was chosen based on feasibility and 
is not based solely in statistical considerations. Subjects will be randomized in a ratio of 3:2 (active 
versus placebo). In order to maximize study power for evaluation of efficacy end-points, a global 
test statistic will be used. The global test statistic will be a combination of 3 change-from-baseline 
to end-of-study endpoints (univariate components), including the following: 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 60 of 92 
o Cognition 
o Activities of Daily Living (ADL) 
o Total Hippocampal Brain Volume  
 
The global test statistic will be calculated for each subject as a mean percentile score across the 
above 3 component endpoints for each subject in the study. This mean percentile score will then 
be analyzed as the primary efficacy outcome variable. For purposes of power calculations, global 
test statistics can be characterized based on the assumed effect sizes of each of the 3 component 
endpoints and the correlations between each of the 3 pairs of component endpoints. 
 
Use of a global test statistic can handle the case of correlated univariate endpoints and provide 
substantially greater power than the use of univariate test statistics, even when the component 
univariate endpoints have unequal magnitudes of treatment effects in favor of the active treatment. 
We assume a correlation of 0.4 between the cognitive and ADL component endpoints and a 
correlation of 0.2 between the total hippocampal volume component endpoint and each of the other 
two components endpoints (i.e., the cognitive component endpoint and the ADL component 
endpoint), based upon historical analyses. By using 50% statistical power and the assumed effect 
sizes as inputs, we can obtain the “expected p-value” for 2 selected combinations of component 
endpoints of the composite. We do this in 2 stages, first for the combination of ADAS-Cog and 
ADL component endpoints, which have expected p-values of 0.09409 and 0.20184, respectively, 
resulting in a 2-component expected p-value of 0.077583. Then we combine the 2-component 
expected p-value with the expected p-value for Total Hippocampal Brain Volume (0.20184), to 
get a global test statistic expected p-value of 0.049756. 
 
Each of the 3 component scales may have a different sensitivity with respect to detecting change 
over time. The sensitivity is quantified using the Mean-to-Standard Deviation Ratio (MSDR), 
which is calculated by dividing the mean of the change-from-baseline score by the standard 
deviation of the change-from-baseline score. For change-from-baseline to 6 months, we assume 
the MSDR values for ADAS-Cog, ADL, Total Hippocampal Volume are 0.8, 0.6, and 0.6, 
respectively. We assume a 60% value for Percent of Placebo Effect (i.e., the decline for the active 
treatment group is only 40% of the decline of the Placebo group). This corresponds to effect size 
(assumed treatment difference divided by the common standard deviation) values of 0.48 for the 
Cognitive Endpoint, 0.36 for the ADL endpoint, and 0.36 for the Total Hippocampal Brain Volume 
endpoint. As described previously, using these expected p-values and the assumed correlations 
between each pair of these 3 endpoints results in an expected p-value of 0.049756 for the global 
test statistic. 
 
Using 100 randomized subjects (assuming either no subject dropout so that there are 100 
completers, or that imputation appropriately accounts for subject dropout), 50% power, a 
randomization ratio of 1:1, gives an effect size (corresponding to the use of the global test statistic) 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 61 of 92 
of 0.566; this indicates that that under these assumptions use of the global test statistic is equivalent 
to using a single component test statistic with an effect size of 0.566 (rather than the assumed effect 
sizes of 0.48 for ADAS-Cog, 0.36 for ADL, and 0.36 for Total Hippocampal Brain Volume). 
Another way to interpret this is that using of the global test statistic, corresponding to an assumed 
effect size of 0.566 for a single component endpoint, and using α = 0.05 results in a power of 
approximately 50% (50.1%). So, when the individual components of the global test statistic are in 
the same direction (and in favor of the active treatment group versus placebo), then use of a global 
test statistic generally provides more power than use of a single component. 
 
Although the power calculations (see table below) show 80% power for an assumed Percent of 
Placebo Effect value of 85%, a Percent of Placebo Effect value as small as 50% or 60% would still 
be clinically relevant and would be an encouraging indication for moving forward into a new study. 
As described previously, a Percent of Placebo Effect value of 60% corresponds to global test 
statistic p-value of approximately 0.05 (0.049756, 2-sided), an effect size of 0.566, and a power of 
approximately 50%. A global test statistic p-value of 0.10 (2-sided) would be an observed trend 
that would still be suggestive of a signal indicating that moving forward into a new study would 
be appropriate. This corresponds to Percent of Placebo Effect value of just under 50%: a Percent 
of Placebo Effect value of 50% corresponds to global test statistic p-value of approximately 0.095 
(0.09477, 2-sided), an effect size of 0.479, and a power of approximately 38% at a 2-sided 
alpha=0.05 level. 
 
Percent 
of 
Placebo 
Effect 
Cog. 
Effect 
Size 
ADL 
Effect 
Size 
Total 
Hipp. 
Brain 
Volume 
Effect 
Size 
Cog. 
Expected 
p-value 
(2-sided) 
ADL 
Expected 
p-value 
(2-sided) 
Total 
Hipp. 
Expected 
p-value 
(2-sided) 
Cog. & 
ADL 
Combined 
Expected 
p-value 
(2-sided) 
Global 
Test 
Statistic 
Expected 
p-value 
(2-sided) 
Global 
Test 
Statistic 
Effect 
Size 
Global 
Test 
Statistic 
Power 
(%) 
50% 
0.40 
0.30 
0.30 
0.15959 
0.27395 
0.27395 
0.135094 
0.09477 
0.479 
38.3 
60% 
0.48 
0.36 
0.36 
0.09409 
0.20184 
0.20184 
0.077583 
0.049756 
0.566 
50.1 
70% 
0.56 
0.42 
0.42 
0.05206 
0.14709 
0.14709 
0.042619 
0.024794 
0.651 
61.7 
80% 
0.64 
0.48 
0.48 
0.02727 
0.09409 
0.09409 
0.020349 
0.009933 
0.754 
74.4 
85% 
0.68 
0.51 
0.51 
0.01937 
0.07588 
0.07588 
0.013962 
0.006283 
0.803 
79.5 
90% 
0.72 
0.54 
0.54 
0.01358 
0.06069 
0.06069 
0.009432 
0.003896 
0.852 
84.0 
100% 
0.80 
0.60 
0.60 
0.00646 
0.03793 
0.03793 
0.004131 
0.001417 
0.951 
90.9 
 
Some additional examples of the global test statistic under various assumed Percent of Placebo 
Effect values and corresponding effect sizes (and using the pairwise correlations of 0.4, 0.2, and 
0.2 described previously) are given below, along with the examples described previously. (Note 
that a Percent of Placebo effect value of 0% means that active treatment declines as much as 
Placebo, a value of 50% means that active treatment declines half as much as Placebo, and a value 
of 100% means that the active treatment doesn’t decline at all over the 6-month treatment period.) 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 62 of 92 
 
10.3.2 Study Unblinding 
After database lock, the responsible statistician will request the treatment codes, the study will be 
unblinded, and the statistical analysis will be conducted.  
 
10.3.3 Safety Endpoints 
 
10.3.3.1 Safety Endpoints 
The primary safety end-point will be the incidence of treatment emergent Grade II-IV adverse events. 
 
Other safety endpoints are: 
o Incidence and severity of treatment emergent adverse events (AEs) 
o Clinical laboratory tests  
o Vital signs  
o Physical examinations 
o ECGs 
o Use of concomitant medications for treatment of AEs 
o C-SSRS 
 
10.3.3.2 Primary Efficacy Endpoints 
The primary efficacy endpoint will be a global test statistic for change from Baseline to 24 weeks 
as described in Section 10.2.1 (“Sample-Size Determination”). 
 
10.3.3.3 Secondary Efficacy Endpoints 
The change in the following assessments from Screening and/or Baseline to each post-baseline 
visit as described below based on the Schedule of Activities between the AMX0035 treatment 
group and the placebo treatment group in the ITT population:  
 
o Cognition Endpoint component for the global test statistic (Baseline, Week 12, and 
Week 24) 
o ADL Endpoint component for the global test statistic (Baseline, Week 12, and Week 
24) 
o Total Hippocampal Brain Volume (Screening/Baseline and Week 24) 
o Additional volumetric MRI brain volume parameters, to be defined in the 
SAP (Screening/Baseline and Week 24) 
o ADAS-Cog (Baseline, Week 12, and Week 24) 
o FAQ (Baseline, Week 12, and Week 24) 
o DSRS (Baseline, Week 12, and Week 24) 
o NPI-Q (Screening/Baseline, Week 12, and Week 24) 
o MoCA (Screening, Week 6, Week 18, and Week 24) 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 63 of 92 
Derivation for the Cognition Endpoint component and the ADL Endpoint component for the global 
test statistic will be designed to optimize sensitivity in the MCI and mild-to-moderate AD 
populations by using scales specific to each of these two populations (with some overlapping tests 
and some tests distinct to each population. The process of combining scores for each scale (i.e., 
Cognition Endpoint component and ADL Endpoint component) across the two populations will 
be described in detail the SAP. 
 
A Mixed-effects Model for Repeated Measures will be used to calculate differences at 12 and 24 
weeks, using baseline assessment as a covariate. 
 
Secondary efficacy endpoints will be assessed using MMRM. For each of the 3 component 
efficacy endpoints (based on Cognition, ADL, and Total Hippocampal Brain Volume) which are 
used to calculate the global test statistic, a sensitivity analysis using Pattern Mixture Models 
(PMM) as described in Section 10.3 (“Missing Data”) will be done to impute missing data at Week 
24. 
 
10.3.3.4 Volumetric MRI 
Observed Case analysis for differences in change of vMRI over 24 weeks. 
 
10.3.3.5 CSF 
 
 
10.3.4 Analysis Populations 
The safety population included all randomized subjects who received at least 1 dose of study 
medication. Subjects in the safety population will be analyzed based on the treatment they actually 
received, and not necessarily the one to which they were randomized. 
 
An intent-to-treat (ITT) approach was used to define the primary efficacy analysis population. For 
a given endpoint, all randomized subjects who received any study medication, had a baseline 
assessment, and had at least 1 post-baseline efficacy assessment for the primary efficacy endpoint 
will be included in the ITT population. In the ITT population, subjects who switched treatment 
groups over the course of the study will be analyzed based on their randomized treatment, and not 
necessarily the treatment they actually received. 
 
10.3.5 Analysis for Safety 
The Safety population will be used for analyses of each of the safety endpoints. All concomitant 
medications will be tabulated according to drug class and preferred term using the WHO 
dictionary. The safety data will be summarized by treatment group. Treatment AEs will be coded 
and graded using MedDRA grading criteria. The treatment groups will be compared with respect 
to occurrence of each adverse event and incidence of Grade II/IV adverse events. Withdrawal, 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 64 of 92 
abnormal laboratory tests, vital signs and use of concomitant medications used for treatment of 
AEs will be assessed to characterize the safety profile of the combination of PB and TUDCA. 
Compliance data will be determined for each visit and by treatment group. The time to subject 
refusal will be compared between treatment groups to better determine tolerability. This will be 
accomplished using a method of survival analysis that allows informative censoring due to death. 
Descriptive statistics denoting the changes from baseline to the final assessment visit with respect 
to key laboratory parameters and vital signs will also be provided. 
 
10.3.5.1 Adverse Events 
Adverse events (AE) occurring after the start of study drug dosing at Baseline will be 
summarized descriptively for the safety population. All AEs will be coded according to system 
organ class (SOC) and preferred term (PT) using a Medical Dictionary for Regulatory Activities 
(MedDRA) dictionary. Summary tables showing the number of subjects and percent within each 
category will be generated for each of the following types of adverse events and its relationship 
to study treatment (related to study treatment):  
o All events  
o Serious events  
o Deaths  
o Events leading to withdrawal  
o Severe events  
 
Treatment AEs will be coded and graded using MedDRA grading criteria. The treatment groups 
will be compared with respect to occurrence of each adverse event and incidence of Grade II/IV 
adverse events. Total number of adverse events will be compared between groups using Fisher's 
exact test. Any treatment AE still present upon completion of treatment (including early 
discontinuation) should be monitored until resolution or until the AE is declared a chronic 
condition. AEs will be monitored until they become chronic or have completely resolved. 
 
10.3.5.2 Laboratory Parameters 
Laboratory parameters will be summarized by visit. Descriptive statistics denoting the changes 
from baseline to the final assessment visit with respect to key laboratory parameters and vital signs 
will also be provided. Frequencies of high and low values with respect to the normal range will be 
displayed, as will shift tables comparing each treatment visit and Baseline visit by time point and 
treatment group. Abnormal laboratory tests will be compared between groups using Fisher's exact 
test.  
 
10.3.5.3 Other Safety Parameters 
Vital signs will be summarized across groups by visit using descriptive statistics, and at each 
outcome visit and at end of study. Physical examination findings and number of subjects will be 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 65 of 92 
summarized as the count and percentage of subjects by eCRF pre-defined categories at last visit. 
Change from baseline at last visit will be summarized in a shift table comparing baseline and last 
visit results. Concomitant medications will be summarized by treatment group, drug class and 
preferred term. The change in the C-SSRS score from Baseline to each post-baseline visit will be 
summarized between the active treatment group and the placebo treatment group. 
 
10.3.6 Analysis for Efficacy 
Analysis of primary and secondary efficacy endpoints will be performed on the ITT population. 
 
The primary efficacy analysis will be based on the use of a global test statistic as described in 
Section 10.3.1 (“Sample-Size Determination”). The null hypothesis will be that there is no 
difference between the treatment groups, and the corresponding alternative hypothesis is that 
treatment with AMX0035 will result in a statistically significant difference (in favor of the active 
treatment group) in the global test statistic score relative to the placebo group at Week 24 in the 
ITT population. As described in Section 10.3.1, the global test statistic p-value will be calculated 
using the 3 individual component p-values (corresponding to change from baseline to Week 24 for 
the Cognition Endpoint, ADL Endpoint, and Total Hippocampal Brain Volume) and the 3 pairwise 
correlations values between the 3 endpoints. 
 
The primary efficacy analysis using the global test statistic will be based on using the Pattern 
Mixture Model (PMM) approach described in Section 10.4 (“Missing Data”) in order to impute 
any missing data at Week 24 for the 3 component endpoints (i.e., Cognition Endpoint, ADL 
Endpoint, and Total Hippocampal Brain Volume). A secondary analysis using the global test 
statistic will be based on using observed cases. 
 
Analyses for secondary efficacy endpoints will be conducted using mixed models for repeated 
measures (MMRM). The mixed model analysis will compare the estimated change from baseline 
(CFB), or change from screening (as applicable), between active treatment and placebo in all 
efficacy outcome scores at each scheduled post-baseline visit. Separate repeated measures 
longitudinal models will be used for each efficacy endpoint. This analysis will assess whether there 
is a difference in estimated CFB values between treatment groups. SAS PROC MIXED will be 
used to fit the MMRM models, with CFB of each of the efficacy outcomes (e.g., ADAS-cog Total 
Score) as the response variable and certain covariates and fixed effects as will be specified in the 
SAP prior to study unblinding. Full details of these analysis will be provided in the SAP. 
 
Descriptive statistics for continuous variables will include number of subjects (n), mean, standard 
deviation (SD), median, minimum, maximum, first and third quartiles, unless otherwise noted. 
Frequencies and percentages will be calculated for categorical variables. Percentages will be 
calculated within each treatment group on the number of non-missing observations. 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 66 of 92 
Subgroup analysis (e.g., based on subgroups defined by gender, age, baseline MoCA score) will 
be performed in the ITT population. 
 
10.4 
Missing Data 
Subjects who drop out will have all available post-baseline data included in the analysis. In 
addition, some subjects may have missing data, because of visits completed remotely during the 
COVID-19 pandemic. The mixed model for repeated measures is based on an assumption of 
Missing at Random (MAR) and is designed to handle right-censored data for subjects who drop 
out of the study. An additional analysis will be performed as a sensitivity analysis in this study and 
will be a z-score based pattern mixture model (PMM) approach. The PMM will use an MAR 
assumption, and this sensitivity analysis will use a subject’s last observed value and the z-score of 
that observation as a carried forward value, assuming a pattern of progression similar to subjects 
within the same treatment group who completed each visit. At each subsequent visit, a value will 
be imputed such that it has the same z-score relative to that subject’s treatment group mean and 
standard deviation for completers at that visit. The first analysis is intended to estimate the 
treatment effect expected if all subjects continued on treatment. After imputation for the sensitivity 
analyses, the estimated change from baseline between active and placebo group will be assessed 
by fitting an analysis of covariance (ANCOVA) model. Further details for the handling of missing 
data, as well as a detailed description of the ANCOVA analysis model, will be provided in the 
SAP. 
 
10.5 
Stopping Rules 
The Study PI will review safety data throughout the trial and may stop the trial for safety. Any 
death will lead to prompt review by the Medical Monitor and Global Study PI.  Two or more of 
the same SAE deemed probably or definitely related to study drug by Site Investigators, will lead 
to prompt review by the Medical Monitor and Study PI. 
 
10.6 
Interim Analysis 
No interim analysis is planned. 
 
11 
DATA COLLECTION, MANAGEMENT AND MONITORING 
 
11.1 
Role of Data Management 
Data Management (DM) is the development, execution and supervision of plans, policies, 
programs, and practices that control, protect, deliver, and enhance the value of data and 
information assets. 
 
All data will be managed in compliance with NCRI policies, and applicable Sponsor and regulatory 
requirements. Site personnel will collect, transcribe, correct, and transmit the data onto source 
documents, Case Report Forms (CRFs), and other forms used to report, track and record clinical 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 67 of 92 
research data.  Clinical sites will be monitored to ensure compliance with data management 
requirements and Good Clinical Practices. DM is responsible for developing, testing, and 
managing clinical data management activities. 
 
11.1.1 Data Entry and Checks 
Site personnel are encouraged to enter information into the EDC system within 5 days of a study 
visit.  Data collection is the responsibility of the staff at the site under the supervision of the SI.  
During the study, the SI must maintain complete and accurate documentation for the study. 
 
The EDC includes password protection. An edit checking and data clarification query process will 
be put in place to ensure accuracy and completeness of the database. Logic and range checks as 
well as more sophisticated rules will be built into the EDC to provide immediate error checking of 
the data entered. The system has the capability to automatically create electronic queries for forms 
that contain data inputs that are out of range, missing, or not calculated correctly. Sites will only 
have access to queries concerning their subjects. 
 
11.1.2 Data Lock Process 
The application will have the ability to lock the database to prevent any modification of data once 
the study is closed.  Once this option is activated, every user will have Read-Only access to the 
data. The database can only be locked after each SI has signed off on their subjects and all queries 
have been resolved. 
 
11.1.3 Quality Assurance 
Protocol procedures are reviewed with the SI and associated personnel prior to the study to ensure 
the accuracy and reliability of data. Each SI must adhere to the protocol detailed in this document 
and agree that any changes to the protocol must be approved by the Coordination Center prior to 
seeking approval from the site IRB.  Each Site Investigator will be responsible for enrolling only 
those study subjects who have met protocol eligibility criteria. 
 
11.2 
Clinical Monitoring 
Study Monitors will visit each study site to review source documentation materials, informed 
consent forms, and confirm entered data and that data queries have been accurately completed, 
and again at a study close-out visit.  Study Monitors will also verify that SAEs and protocol 
deviations have been reported appropriately, as required. The Study Monitors will review clinical 
facilities, resources and procedures for evaluating study subjects and study drug dispensing.  
Subsequently, the Study Monitors will provide monitoring reports to the Project Manager and, if 
requested, will provide reports of protocol compliance to the Study PI. Completed informed 
consent forms from each subject must be available in the subject’s file and verified for proper 
documentation.  A document outlining the monitoring plan is provided to each Study Monitor. 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 68 of 92 
11.3 
Data Handling and Record Keeping 
The SI is responsible for ensuring the accuracy, completeness, legibility, and timeliness of the data 
reported.  All source documents should be completed in a neat, legible manner to ensure accurate 
interpretation of data. Dark ink is required to ensure clarity of reproduced copies.  When making 
changes or corrections, cross out the original entry with a single line, and initial and date the 
change.  Do not erase, overwrite, or use correction fluid or tape on the original.  
 
Source document templates (SDTs) will be provided for use and maintained for recording data for 
each subject enrolled in the study.  Data reported in the eCRF derived from source documents 
should be consistent with the source documents and discrepancies should be explained. The 
Coordination Center will provide guidance to SIs on making corrections to source documents and 
eCRFs. 
 
A patient Global Unique Identifier (GUID) will be used as the identifier for the participants 
included in the study. The GUID is an 11-character string that is generated using encryption 
technology licensed by the NCRI from the National Institutes of Health (NIH) in 2013.  
 
The GUID is generated on a secure website that utilizes 128-bit Secure Socket Layer (SSL). On 
the website, the GUID is generated using an irreversible encryption algorithm-it accepts twelve 
identifying data elements, (e.g. last name at birth, first name at birth, gender at birth, day, month 
and year of birth, city and country of birth, etc.), and produces a unique random-generated 
character string, or GUID. No identifying information is stored in the system; it is simply used to 
generate the GUID. If the same information is entered into the secure website in the future, the 
same GUID will be generated.  
 
11.3.1 Confidentiality 
Study subject medical information obtained in this study is confidential, and disclosure to third 
parties other than those noted below is prohibited. Upon the subject’s permission, medical 
information may be given to his or her personal physician or other appropriate medical personnel 
responsible for his or her welfare. All local and federal guidelines and regulations regarding 
maintaining study subject confidentiality of data will be adhered to. 
 
Data generated throughout study must be made available for inspection by representatives of the 
US FDA, the Office for Human Research Protections (OHRP), the Sponsor, all pertinent national 
and local health and regulatory authorities, the Coordination Center or their representative, Study 
Monitoring personnel, and all local IRBs. 
 
11.3.2 Study Discontinuation  
The study can be terminated at any time by the Sponsor, Medical Monitor, or FDA.  Reasons for 
terminating the study may include, but are not limited to, the following: 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 69 of 92 
● The incidence or severity of AEs in this or other studies indicates a potential health hazard 
to study subjects. 
● Study subject enrollment is unsatisfactory. 
● Data recording is inaccurate or incomplete. 
● Sponsor withdraws funding. 
 
11.3.3 Retention of Records 
US FDA regulations (21 CFR 312.62[c]) require that records and documents pertaining to the 
conduct of this study and the distribution of investigational drug, including CRFs (if applicable), 
consent forms, laboratory test results, and medical inventory records, must be retained by the SI 
for two years after marketing application approval.  If no application is filed, these records must 
be kept for two years after the investigation is discontinued and the US FDA and the applicable 
national and local health authorities are notified.  The Coordination Center or their representative 
will notify the Site Investigators of these events. The Site Investigators should retain all study 
documents and records until they are notified in writing by the Sponsor or their representative.  
 
11.3.4 Publications 
The Study PI of the clinical trial,
, along with the sponsor, Amylyx Pharmaceuticals, 
Inc., will be responsible for publication of results from this trial. Their responsibilities will include 
the following: 
● Analysis and interpretation of data gathered in this study. 
● Dissemination of data in the form of a peer-reviewed publication. 
● Submit manuscripts to selected journals and address peer reviewers’ comments. 
● Submit abstracts to selected meetings and present data at the meetings. 
● Determine authorship on the basis of the Uniform Requirements for Manuscripts. 
 
 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 70 of 92 
12 
LITERATURE REFERENCES 
1. Zhou, Wenbo, et al. "Phenylbutyrate up-regulates the DJ-1 protein and protects neurons in 
cell culture and in animal models of Parkinson disease." Journal of Biological 
Chemistry 286.17 (2011): 14941-14951.  
2. Wright, Jerry M., et al. "Gene expression profile analysis of 4-phenylbutyrate treatment of 
IB3-1 bronchial epithelial cell line demonstrates a major influence on heat-shock 
proteins." Physiological Genomics 16.2 (2004): 204-211. 
3. Cuadrado-Tejedor, Mar, et al. "Phenylbutyrate is a multifaceted drug that exerts 
neuroprotective effects and reverses the Alzheimer s disease-like phenotype of a commonly 
used mouse model." Current Pharmaceutical Design 19.28 (2013): 5076-5084. 
4. Ricobaraza, Ana, et al. "Phenylbutyrate rescues dendritic spine loss associated with 
memory deficits in a mouse model of Alzheimer disease." Hippocampus 22.5 (2012): 
1040-1050. 
5. Wiley, Jesse C., Christina Pettan‐Brewer, and Warren C. Ladiges. "Phenylbutyric acid 
reduces amyloid plaques and rescues cognitive behavior in AD transgenic mice." Aging 
Cell 10.3 (2011): 418-428. 
6. Ricobaraza, Ana, et al. "Phenylbutyrate ameliorates cognitive deficit and reduces tau 
pathology in an Alzheimer's disease mouse model." Neuropsychopharmacology 34.7 
(2009): 1721. 
7. Ryu, Hoon, et al. "Sodium phenylbutyrate prolongs survival and regulates expression of 
anti‐apoptotic genes in transgenic amyotrophic lateral sclerosis mice." Journal of 
Neurochemistry 93.5 (2005): 1087-1098. 
8. Gardian, Gabriella, et al. "Neuroprotective effects of phenylbutyrate in the N171-82Q 
transgenic mouse model of Huntington's disease." Journal of Biological Chemistry 280.1 
(2005): 556-563. 
9. Corbett, Grant T., Avik Roy, and Kalipada Pahan. "Sodium phenylbutyrate enhances 
Astrocytic neurotrophin synthesis via protein kinase C (PKC)-mediated activation of 
cAMP-response 
element-binding 
protein 
(CREB)." Journal 
of 
Biological 
Chemistry 288.12 (2013): 8299-8312. 
10. Rodrigues, Cecília MP, et al. "Tauroursodeoxycholic acid prevents Bax-induced 
membrane 
perturbation 
and 
cytochrome 
C 
release 
in 
isolated 
mitochondria." Biochemistry 42.10 (2003): 3070-3080. 
11. Lo, Adrian C., et al. "Tauroursodeoxycholic acid (TUDCA) supplementation prevents 
cognitive impairment and amyloid deposition in APP/PS1 mice." Neurobiology of 
disease 50 (2013): 21-29. 
12. Dionísio, Pedro A., et al. "Amyloid-β pathology is attenuated by tauroursodeoxycholic acid 
treatment in APP/PS1 mice after disease onset." Neurobiology of aging 36.1 (2015): 228-
240. 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 71 of 92 
13. Nunes, Ana F., et al. "TUDCA, a bile acid, attenuates amyloid precursor protein processing 
and amyloid-β deposition in APP/PS1 mice." Molecular neurobiology 45.3 (2012): 440-
454. 
14. Rodrigues, Cecilia MP, et al. "Tauroursodeoxycholic acid reduces apoptosis and protects 
against neurological injury after acute hemorrhagic stroke in rats." Proceedings of the 
National Academy of Sciences 100.10 (2003): 6087-6092. 
15. Castro-Caldas, M., et al. "Tauroursodeoxycholic acid prevents MPTP-induced 
dopaminergic cell death in a mouse model of Parkinson’s disease." Molecular 
neurobiology 46.2 (2012): 475-486. 
16. Zhang, Yong-Jie, et al. "Aggregation-prone c9FTD/ALS poly (GA) RAN-translated 
proteins cause neurotoxicity by inducing ER stress." Acta Neuropathologica 128.4 (2014): 
505-524. 
17. Cudkowicz, Merit E., et al. "Phase 2 study of sodium phenylbutyrate in ALS." 
Amyotrophic Lateral Sclerosis 10.2 (2009): 99-106. 
18. Borovecki, F., et al. "Genome-wide expression profiling of human blood reveals 
biomarkers for Huntington's disease." Proceedings of the National Academy of Sciences of 
the United States of America 102.31 (2005): 11023-11028. 
19. Hogarth, Penelope, Luca Lovrecic, and Dimitri Krainc. "Sodium phenylbutyrate in 
Huntington's disease: A dose‐finding study." Movement Disorders 22.13 (2007): 1962-
1964. 
20. Elia, A., et al. "Tauroursodeoxycholic acid in the treatment of patients with amyotrophic 
lateral sclerosis." European Journal of Neurology 23.1 (2016): 45-52. 
21. Min, Ju-Hong, et al. "Oral solubilized ursodeoxycholic acid therapy in amyotrophic lateral 
sclerosis: a randomized cross-over trial." Journal of Korean Medical Science 27.2 (2012): 
200-206. 
22. Buphenyl 
Package 
Insert 
 
 
 
23. Gilbert, Jill, et al. "A phase I dose escalation and bioavailability study of oral sodium 
phenylbutyrate in patients with refractory solid tumor malignancies." Clinical Cancer 
Research 7.8 (2001): 2292-2300. 
24. Gore, Steven D., et al. "Impact of prolonged infusions of the putative differentiating agent 
sodium 
phenylbutyrate 
on 
myelodysplastic 
syndromes 
and 
acute 
myeloid 
leukemia." Clinical Cancer Research 8.4 (2002): 963-970. 
25. Wey, Hsiao-Ying, et al. "Insights into neuroepigenetics through human histone deacetylase 
PET imaging." Science Translational Medicine 8.351 (2016): 351ra106-351ra106. 
26. Zetterberg, Henrik, et al. "Association of cerebrospinal fluid neurofilament light 
concentration with Alzheimer disease progression." JAMA Neurology 73.1 (2016): 60-67. 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 72 of 92 
27. Constantinescu, Radu, et al. "Cerebrospinal fluid markers of neuronal and glial cell damage 
in patients with autoimmune neurologic syndromes with and without underlying 
malignancies." Journal of Neuroimmunology 306 (2017): 25-30. 
28. van Eijk, Jeroen JJ, et al. "CSF neurofilament proteins levels are elevated in sporadic 
Creutzfeldt-Jakob disease." Journal of Alzheimer's Disease 21.2 (2010): 569-576. 
29. Steinacker, Petra, et al. "Neurofilaments in blood and CSF for diagnosis and prediction of 
onset in Creutzfeldt-Jakob disease." Scientific Reports 6 (2016). 
30. Jabbari, Edwin, Henrik Zetterberg, and Huw R. Morris. "Tracking and predicting disease 
progression in progressive supranuclear palsy: CSF and blood biomarkers." J Neurol 
Neurosurg Psychiatry (2017): jnnp-2017. 
31. Craig-Schapiro, Rebecaa, et al. “YKL-40: a novel prognostic fluid biomarker for 
preclinical Alzheimer’s disease.” Biological psychiatry 68.10 (2010): 903-912. 
32. Comabella, Manuel, et al. “Cerebrospinal fluid chitinase 3-like 1 levels are associated with 
conversion to multiple sclerosis.” Brain 133.4 (2010): 1082-1093. 
33. Bonneh-Barkay, Dafna, et al. “YKL-40 expression in traumatic brain injury: an initial 
analysis.” Journal of Neurotrauma 27.7 (2010): 1215-1223. 
34. Janelidze, Shorena, et al. “Cerebrospinal fluid neurogranin and YKL-40 as biomarkers of 
Alzheimer’s disease.” Annals of Clinical and Translational Neurology 3.1 (2016): 12-20. 
35. Melah, Kelsey E., et al. “Cerebrospinal fluid markers of Alzheimer’s disease pathology 
and microglia activation are associated with altered white matter microstructure in 
asymptomatic adults at risk for Alzheimer’s disease.” Journal of Alzheimer’s Disease 50.3 
(2016): 873-886. 
36. Hayashi, Yasunori. "Long‐term potentiation: two pathways meet at neurogranin." The 
EMBO Journal 28.19 (2009): 2859-2860. 
37. Zhong, Ling, et al. "Increased prefrontal cortex neurogranin enhances plasticity and 
extinction learning." Journal of Neuroscience 35.19 (2015): 7503-7508. 
38. Portelius, Erik, et al. "Cerebrospinal fluid neurogranin: relation to cognition and 
neurodegeneration in Alzheimer’s disease." Brain 138.11 (2015): 3373-3385. 
39. Posner K, (et.al), Columbia Classification Algorithm of Suicide Assessment (C-CASA): 
Classification of Suicidal Events in the FDA’s Pediatric Suicidal Risk Analysis of 
Antidepressants, Am J Psychiatry, 2007, 164:1035-1043. 
40. September 2010 US FDA Draft Guidance for Industry Suicidality: Prospective Assessment 
of Occurrence in Clinical Trials 
41. TUDCA in new onset diabetes. Clinicaltrials.gov identifier NCT02218619. 
42. TUDCA and PB: effect on ER stress and metabolism. Clinicaltrial.gov identifier. 
NCT00771901. 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 73 of 92 
43. Castilla-Rilo, J., Lopez-Arrieta, J., Bermejo-Pareja, F., Ruiz, M., Sanchez-Sanchez, F., & 
Trincado, R. (2007). Instrumental activities of daily living in the screening of dementia in 
population studies: a systematic review and meta-analysis. Int J Geriatr Psychiatry, 22(9), 
829-836. doi:10.1002/gps.1747 
44. Clark, C. M., & Ewbank, D. C. (1996). Performance of the dementia severity rating scale: 
a caregiver questionnaire for rating severity in Alzheimer disease. Alzheimer Dis Assoc 
Disord, 10(1), 31-39.  
45. Mitchell, J. C., Dick, M. B., Wood, A. E., Tapp, A. M., & Ziegler, R. (2015). The utility 
of the Dementia Severity Rating Scale in differentiating mild cognitive impairment and 
Alzheimer disease from controls. Alzheimer Dis Assoc Disord, 29(3), 222-228. 
doi:10.1097/WAD.0000000000000057 
46. Moelter, S. T., Glenn, M. A., Xie, S. X., Chittams, J., Clark, C. M., Watson, M., & Arnold, 
S. E. (2015). The Dementia Severity Rating Scale predicts clinical dementia rating sum of 
boxes 
scores. 
Alzheimer 
Dis 
Assoc 
Disord, 
29(2), 
158-160. 
doi:10.1097/WAD.0000000000000031 
47. Pfeffer, R. I., Kurosaki, T. T., Harrah, C. H., Jr., Chance, J. M., & Filos, S. (1982). 
Measurement of functional activities in older adults in the community. J Gerontol, 37(3), 
323-329.  
48. Rikkert, M. G., Tona, K. D., Janssen, L., Burns, A., Lobo, A., Robert, P., . . . Waldemar, 
G. (2011). Validity, reliability, and feasibility of clinical staging scales in dementia: a 
systematic 
review. 
Am 
J 
Alzheimers 
Dis 
Other 
Demen, 
26(5), 
357-365. 
doi:10.1177/1533317511418954 
49. Teng, E., Becker, B. W., Woo, E., Knopman, D. S., Cummings, J. L., & Lu, P. H. (2010). 
Utility of the functional activities questionnaire for distinguishing mild cognitive 
impairment from very mild Alzheimer disease. Alzheimer Dis Assoc Disord, 24(4), 348-
353. doi:10.1097/WAD.0b013e3181e2fc84 
50. Xie, S. X., Ewbank, D. C., Chittams, J., Karlawish, J. H., Arnold, S. E., & Clark, C. M. 
(2009). Rate of decline in Alzheimer disease measured by a Dementia Severity Rating 
Scale. 
Alzheimer 
Dis 
Assoc 
Disord, 
23(3), 
268-274. 
doi:10.1097/WAD.0b013e318194a324 
 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 74 of 92 
13 
APPENDICES 
13.1 
Appendix I: Columbia-Suicide Severity Rating Scale (C-SSRS) Screening Version  
 
Information obtained from: http://www.cssrs.columbia.edu/ 
 
COLUMBIA-SUICIDE SEVERITY  
RATING SCALE  
(C-SSRS)  
Screening  
Version 1/14/09   
 Posner, K.; Brent, D.; Lucas, C.; Gould, M.; Stanley, B.; Brown, G.; Fisher, P.; Zelazny, J.; Burke, A.; Oquendo, M.; 
Mann, J.     
Disclaimer:  
This scale is intended to be used by individuals who have received training in its administration. The questions 
contained in the Columbia-Suicide Severity Rating Scale are suggested probes. Ultimately, the determination of the 
presence of suicidal ideation or behavior depends on the judgment of the individual administering the scale.  
  
  
Definitions of behavioral suicidal events in this scale are based on those used in The Columbia Suicide History  
Form, developed by John Mann, MD and Maria Oquendo, MD, Conte Center for the Neuroscience of Mental Disorders  
(CCNMD), New York State Psychiatric Institute, 1051 Riverside Drive, New York, NY, 10032. (Oquendo M. A.,  
Halberstam B. & Mann J. J., Risk factors for suicidal behavior: utility and limitations of research instruments. In M.B. 
First [Ed.] Standardized Evaluation in Clinical Practice, pp. 103 -130, 2003.)  
  
For reprints of the C-SSRS contact 
 New York State Psychiatric Institute, 1051 Riverside Drive, New 
York, New York, 10032; inquiries and training requirements contact 
  
  
© 2008 The Research Foundation for Mental Hygiene, Inc.  
 
 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 75 of 92 
SUICIDAL IDEATION  
Ask questions 1 and 2.  If both are negative, proceed to “Suicidal Behavior” section. If the answer to question 2 is “yes”, ask 
questions 3, 4 and 5.  If the answer to question 1 and/or 2 is “yes”, complete “Intensity of Ideation” section below.  
  
Past 60 Months 
1.  Wish to be Dead   
Subject endorses thoughts about a wish to be dead or not alive anymore, or wish to fall asleep 
and not wake up.  Have you wished you were dead or wished you could go to sleep and not 
wake up?   
  
  
  
If yes, describe: _____________________________________________________________________________________________ 
__________________________________________________________________________________________________________ 
__________________________________________________________________________________________________________ 
  
Yes       No 
          □          □ 
2.  Non-Specific Active Suicidal Thoughts  
General, non-specific thoughts of wanting to end one’s life/commit suicide (e.g., “I’ve thought about killing myself”) without 
thoughts of ways to kill oneself/associated methods, intent, or plan.   
Have you actually had any thoughts of killing yourself?  
  
If yes, describe: _____________________________________________________________________________________________ 
__________________________________________________________________________________________________________ 
__________________________________________________________________________________________________________ 
 
Yes       No 
          □          □ 
3.  Active Suicidal Ideation with Any Methods (Not Plan) without Intent to Act  
Subject endorses thoughts of suicide and has thought of at least one method during the assessment period. This is different than a 
specific plan with time, place or method details worked out (e.g., thought of method to kill self but not a specific plan).  Includes 
person who would say, “I thought about taking an  
overdose but I never made a specific plan as to when, where or how I would actually do it…..and I would never go 
through with it.” Have you been thinking about how you might do this?  
  
If yes, describe: _____________________________________________________________________________________________ 
__________________________________________________________________________________________________________ 
__________________________________________________________________________________________________________ 
 
Yes       No 
          □          □ 
4.  Active Suicidal Ideation with Some Intent to Act, without Specific Plan  
Active suicidal thoughts of killing oneself and subject reports having some intent to act on such thoughts, as opposed to “I have 
the thoughts but I definitely will not do anything about them.”  
Have you had these thoughts and had some intention of acting on them?   
  
If yes, describe: _____________________________________________________________________________________________ 
__________________________________________________________________________________________________________ 
__________________________________________________________________________________________________________ 
 
Yes       No 
          □          □ 
 
5.  Active Suicidal Ideation with Specific Plan and Intent  
Thoughts of killing oneself with details of plan fully or partially worked out and subject has some intent to carry it out.  
 
 
 
 
 
Yes       No 
          □          □ 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 76 of 92 
Have you started to work out or worked out the details of how to kill yourself? Do you intend to carry out this plan?  
If yes, describe: _____________________________________________________________________________________________ 
__________________________________________________________________________________________________________ 
__________________________________________________________________________________________________________ 
 
INTENSITY OF IDEATION  
The following features should be rated with respect to the most severe type of ideation (i.e., 1-5 from above, with 1 being the least 
severe and 5 being the most severe). Ask about time he/she was feeling the most suicidal.   
                            Most Severe Ideation:                                                                                                                                           
Type # (1-5)   _____                                                   Description of  Ideation ______________________________ 
                                                
 
Most Severe  
Frequency  
How many times have you had these thoughts?   
(1) Less than once a week    (2) Once a week   (3)  2-5 times in week    (4) Daily or almost daily    (5) Many times each day  
  
____  
Duration  
When you have the thoughts, how long do they last?                                   (3) 1-4 hours/a lot of time 
(1) Fleeting - few seconds or minutes                                                        (4) 4-8 hours/most of day  
(2) Less than 1 hour/some of the time                                                       (5) More than 8 hours/persistent or 
continuous   
____  
Controllability  
Could/can you stop thinking about killing yourself or wanting to die if you want to?  
(1) Easily able to control thoughts                                                                (4) Can control thoughts with a lot of difficulty  
(2) Can control thoughts with little difficulty                                             (5) Unable to control thoughts  
(3) Can control thoughts with some difficulty                                           (0) Does not attempt to control thoughts  
____  
Deterrents  
Are there things - anyone or anything (e.g., family, religion, pain of death) - that stopped you from wanting to die or acting on 
thoughts of committing suicide?  
(1) Deterrents definitely stopped you from attempting suicide           (4) Deterrents most likely did not stop 
you   
(2) Deterrents probably stopped you                                                        (5) Deterrents definitely did not stop you  
(3) Uncertain that deterrents stopped you                                              (0) Does not apply  
____  
Reasons for Ideation  
What sort of reasons did you have for thinking about wanting to die or killing yourself?  Was it to end the pain or stop the way  
you were feeling (in other words you couldn’t go on living with this pain or how you were feeling) or was it to get attention, 
revenge or a reaction from others? Or both?  
(1) Completely to get attention, revenge or a reaction from others        (4) Mostly to end or stop the pain (you couldn’t go on  
(2) Mostly to get attention, revenge or a reaction from others                     living with the pain or how you were feeling)  
(3) Equally to get attention, revenge or a reaction from others               (5) Completely to end or stop the pain (you couldn’t go 
on         and to end/stop the pain                                                                         living with the pain or  how you were feeling)                  
(0)  Does not apply  
  
  
  
  
____  
2  
  
 
 
 
 
 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 77 of 92 
SUICIDAL BEHAVIOR  
(Check all that apply, so long as these are separate events; must ask about all types)  
Past 60 Years or 
Lifetime 
Actual Attempt:   
A potentially self-injurious act committed with at least some wish to die, as a result of act. Behavior was in part thought of as 
method to kill oneself. Intent does not have to be 100%.  If there is any intent/desire to die associated with the act, then it can be 
considered an actual suicide attempt. There does not have to be any injury or harm, just the potential for injury or harm. If person 
pulls trigger while gun is in mouth but gun is broken so no injury results, this is considered an attempt.    
Inferring Intent: Even if an individual denies intent/wish to die, it may be inferred clinically from the behavior or circumstances. For 
example, a highly lethal act that is clearly not an accident so no other intent but suicide can be inferred (e.g., gunshot to head, 
jumping from window of a high floor/story). Also, if someone denies intent to die, but they thought that what they did could be 
lethal, intent may be inferred.   
Have you made a suicide attempt?  
 
Have you done anything to harm yourself?  
 
Have you done anything dangerous where you could have died?  
 
What did you do?  
 
Did you______ as a way to end your life?   
 
Did you want to die (even a little) when you_____?   
 
Were you trying to end your life when you _____?  
 
Or did you think it was possible you could have died from_____?  
 
Or did you do it purely for other reasons / without ANY intention of killing yourself (like to relieve stress, feel better, get sympathy, 
or get something else to happen)?  (Self-Injurious Behavior without suicidal intent) 
 
If yes, describe: _____________________________________________________________________________________________ 
__________________________________________________________________________________________________________ 
__________________________________________________________________________________________________________ 
Has subject engaged in Non-Suicidal Self-Injurious Behavior?  
  
       Yes      No  
  □           □  
  
  
  
  
  
  
  
  Total # of  
  Attempts  
  
______ 
 
  
  
  
  
   
 Yes      No  
  □          □  
Interrupted Attempt:    
When the person is interrupted (by an outside circumstance) from starting the potentially self-injurious act (if not for that, actual 
attempt would have occurred).  
Overdose: Person has pills in hand but is stopped from ingesting.  Once they ingest any pills, this becomes an attempt rather than an 
interrupted attempt. Shooting: Person has gun pointed toward self, gun is taken away by someone else, or is somehow prevented 
from pulling trigger. Once they pull the trigger, even if the gun fails to fire, it is an attempt. Jumping: Person is poised to jump, is 
grabbed and taken down from ledge. Hanging: Person has noose around neck but has not yet started to hang - is stopped from 
doing so.  
Has there been a time when you started to do something to end your life but someone or something stopped you before you actually 
did anything? 
  
If yes, describe: _____________________________________________________________________________________________ 
__________________________________________________________________________________________________________ 
__________________________________________________________________________________________________________ 
 
  
Yes      No  
□   □  
  
  
Total # of 
interrupted  
  
______  
  


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 78 of 92 
Aborted Attempt:    
When person begins to take steps toward making a suicide attempt, but stops themselves before they actually have engaged in any 
self-destructive behavior.  
Examples are similar to interrupted attempts, except that the individual stops him/herself, instead of being stopped by something 
else.  
Has there been a time when you started to do something to try to end your life but you stopped yourself before you actually did 
anything?  
If yes, describe: _____________________________________________________________________________________________ 
__________________________________________________________________________________________________________ 
__________________________________________________________________________________________________________ 
 
  
Yes      No  
□   □  
  
Total # of aborted  
  
______  
Preparatory Acts or Behavior:  
Acts or preparation towards imminently making a suicide attempt. This can include anything beyond a verbalization or thought, such 
as assembling a specific method (e.g., buying pills, purchasing a gun) or preparing for one’s death by suicide (e.g., giving things away, 
writing a suicide note).   
Have you taken any steps towards making a suicide attempt or preparing to kill yourself (such as collecting pills, getting a gun, 
giving valuables away or writing a suicide note)?  
If yes, describe: _____________________________________________________________________________________________ 
__________________________________________________________________________________________________________ 
__________________________________________________________________________________________________________ 
 
  
 
Yes      No  
         □          □  
Suicidal Behavior:  
Suicidal behavior was present during the assessment period?  
 
Suicide: 
 
Yes      No 
     □          □ 
 
Yes      No 
     □          □ 
 
 
Answer for Actual Attempts Only  
Most 
Recent  
Attempt 
Date:  
Most 
Lethal         
Attempt 
Date:  
Initial/First   
Attempt Date:  
Actual Lethality/Medical Damage:    
0. No physical damage or very minor physical damage (e.g., surface scratches).  
1. Minor physical damage (e.g., lethargic speech; first-degree burns; mild bleeding; sprains).  
2. Moderate physical damage; medical attention needed (e.g., conscious but sleepy, somewhat 
responsive; second-degree burns; bleeding of major vessel).  
3. Moderately severe physical damage; medical hospitalization and likely intensive care required (e.g., 
comatose with reflexes intact; third-degree burns less than 20% of body; extensive blood loss but can 
recover; major fractures).  
4. Severe physical damage; medical hospitalization with intensive care required (e.g., comatose without 
reflexes; third degree burns over 20% of body; extensive blood loss with unstable vital signs; major 
damage to a vital area).  
5. Death  
 
Enter Code 
 
 
 
______ 
 
 
 
Enter Code 
 
 
 
______ 
 
 
 
Enter Code 
 
 
 
______ 
 
 
Potential Lethality: Only Answer if Actual Lethality=0  
Likely lethality of actual attempt if no medical damage (the following examples, while having no actual 
medical damage, had potential for very serious lethality: put gun in mouth and pulled the trigger but gun 
fails to fire so no medical damage; laying on train tracks with oncoming train but pulled away before run 
over).  
  
0 = Behavior not likely to result in injury  
1 = Behavior likely to result in injury but not likely to cause death  
 
Enter Code 
 
 
 
______ 
 
 
Enter Code 
 
 
 
______ 
 
 
 
Enter Code 
 
 
 
______ 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 79 of 92 
2 = Behavior likely to result in death despite available medical care   
 
 
 
13.2 
Appendix II: Columbia-Suicide Severity Rating Scale (C-SSRS) Since Last Visit 
Version 
 
Information obtained from: http://www.cssrs.columbia.edu/ 
 
 
 
C-SSRS (COLUMBIA – SUICIDE SEVERITY RATING SCALE – SINCE LAST VISIT) 
 
Since Last Visit Version 1/14/09 
 
Posner, K.; Brent, D.; Lucas, C.; Gould, M.; Stanley, B.; Brown, G.; Fisher, P.; Zelazny, J.; Burke, A.; Oquendo, M.; Mann, J. 
 
Disclaimer: 
This scale is intended to be used by individuals who have received training in its administration. The questions contained in 
the Columbia-Suicide Severity Rating Scale are suggested probes. Ultimately, the determination of the presence of suicidal 
ideation or behavior depends on the judgment of the individual administering the scale. 
Definitions of behavioral suicidal events in this scale are based on those used in The Columbia Suicide History Form, 
developed by John Mann, MD and Maria Oquendo, MD, Conte Center for the Neuroscience of Mental Disorders (CCNMD), 
New York State Psychiatric Institute, 1051 Riverside Drive, New York, NY, 10032. (Oquendo M. A., Halberstam B. & Mann J. 
J., Risk factors for suicidal behavior: utility and limitations of research instruments. In M.B. First [Ed.] Standardized 
Evaluation in Clinical Practice, pp. 103 -130, 2003.) 
For reprints of the C-SSRS contact 
., New York State Psychiatric Institute, 1051 Riverside Drive, New York, 
New York, 10032; inquiries and training requirements contact 
 
 
© 2008 The Research Foundation for Mental Hygiene, Inc. 
 
 
 
 
 
 
 
 
 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 80 of 92 
 
 
 
 
 
 
 
 
SUICIDAL IDEATION  
Ask questions 1 and 2. If both are negative, proceed to “Suicidal Behavior” section. If the answer to 
question 2 is “yes”, ask questions 3, 4 and 5. If the answer to question 1 and/or 2 is “yes”, complete 
“Intensity of Ideation” section below.  
 
 
Since Last 
Visit 
1. Wish to be Dead  
Subject endorses thoughts about a wish to be dead or not alive anymore, or wish to fall asleep and not 
wake up.  
Have you wished you were dead or wished you could go to sleep and not wake up?  
If yes, describe: __________________________________________________________________________ 
_______________________________________________________________________________________
_______________________________________________________________________________________ 
_______________________________________________________________________________________ 
Yes    No 
□    □ 
 
2. Non-Specific Active Suicidal Thoughts  
General, non-specific thoughts of wanting to end one’s life/commit suicide (e.g., “I’ve thought about killing 
myself”) without thoughts of ways to kill oneself/associated methods, intent, or plan during the 
assessment period.  
Have you actually had any thoughts of killing yourself?  
If yes, describe: __________________________________________________________________________ 
_______________________________________________________________________________________
_______________________________________________________________________________________ 
_______________________________________________________________________________________ 
 
Yes    No 
□    □ 
3. Active Suicidal Ideation with Any Methods (Not Plan) without Intent to Act  
Subject endorses thoughts of suicide and has thought of at least one method during the assessment 
period. This is different than a specific plan with time, place or method details worked out (e.g., thought of 
method to kill self but not a specific plan). Includes person who would say, “I thought about taking an 
overdose but I never made a specific plan as to when, where or how I would actually do it…and I would 
never go through with it.”  
Have you been thinking about how you might do this?  
If yes, describe: __________________________________________________________________________ 
_______________________________________________________________________________________
_______________________________________________________________________________________ 
_______________________________________________________________________________________ 
 
Yes    No 
□    □ 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 81 of 92 
4. Active Suicidal Ideation with Some Intent to Act, without Specific Plan  
Active suicidal thoughts of killing oneself and subject reports having some intent to act on such thoughts, 
as opposed to “I have the thoughts but I definitely will not do anything about them.”  
Have you had these thoughts and had some intention of acting on them?  
If yes, describe: __________________________________________________________________________ 
_______________________________________________________________________________________
_______________________________________________________________________________________ 
_______________________________________________________________________________________ 
Yes    No 
□    □ 
 
5. Active Suicidal Ideation with Specific Plan and Intent  
Thoughts of killing oneself with details of plan fully or partially worked out and subject has some intent to 
carry it out.  
Have you started to work out or worked out the details of how to kill yourself? Do you intend to carry out 
this plan?  
If yes, describe: __________________________________________________________________________ 
_______________________________________________________________________________________
_______________________________________________________________________________________ 
_______________________________________________________________________________________ 
Yes    No 
□    □ 
 
INTENSITY OF IDEATION  
The following features should be rated with respect to the most severe type of ideation (i.e., 1-5 from 
above, with 1 being the least severe and 5 being the most severe).  
 
Most Severe Ideation:      _____           _________________________________________________  
                                          Type # (1-5)                                  Description of Ideation  
 
 
Most Severe 
Frequency  
How many times have you had these thoughts?  
(1) Less than once a week (2) Once a week (3) 2-5 times in week (4) Daily or almost daily (5) Many times 
each day  
 
____ 
Duration  
When you have the thoughts, how long do they last?  
(1) Fleeting - few seconds or minutes  
(2) Less than 1 hour/some of the time  
(3) 1-4 hours/a lot of time  
(4) 4-8 hours/most of day 
(5) More than 8 hours/persistent or continuous 
 
 
 
 
____ 
Controllability  
Could/can you stop thinking about killing yourself or wanting to die if you want to?  
(1) Easily able to control thoughts  
(2) Can control thoughts with little difficulty  
(3) Can control thoughts with some difficulty  
(4) Can control thoughts with a lot of difficulty 
(5) Unable to control thoughts 
(0) Does not attempt to control thoughts  
 
 
____ 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 82 of 92 
 
Deterrents  
Are there things - anyone or anything (e.g., family, religion, pain of death) - that stopped you from wanting 
to die or acting on thoughts of committing suicide?  
(1) Deterrents definitely stopped you from attempting suicide  
(2) Deterrents probably stopped you  
(3) Uncertain that deterrents stopped you  
(4) Deterrents most likely did not stop you  
(5) Deterrents definitely did not stop you 
(0) Does not apply 
 
 
 
 
____ 
Reasons for Ideation  
What sort of reasons did you have for thinking about wanting to die or killing yourself? Was it to end the 
pain or stop the way you were feeling (in other words you couldn’t go on living with this pain or how you 
were feeling) or was it to get attention, revenge or a reaction from others? Or both?  
(1) Completely to get attention, revenge or a reaction from others 
(2) Mostly to get attention, revenge or a reaction from others living with the pain or how you were feeling)  
(3) Equally to get attention, revenge or a reaction from others and to end/stop the pain living with the pain 
or how you were feeling)  
(4) Mostly to end or stop the pain (you couldn’t go on  
(5) Completely to end or stop the pain (you couldn’t go on 
(0) Does not apply  
 
 
 
 
 
 
 
____ 
 
 
SUICIDAL BEHAVIOR  
(Check all that apply, so long as these are separate events; must ask about all types)  
Since Last 
Visit 
Actual Attempt:  
A potentially self-injurious act committed with at least some wish to die, as a result of act. Behavior was in 
part thought of as method to kill oneself. Intent does not have to be 100%. If there is any intent/desire to 
die associated with the act, then it can be considered an actual suicide attempt. There does not have to be 
any injury or harm, just the potential for injury or harm. If person pulls trigger while gun is in mouth but 
gun is broken so no injury results, this is considered an attempt.  
Inferring Intent: Even if an individual denies intent/wish to die, it may be inferred clinically from the 
behavior or circumstances. For example, a highly lethal act that is clearly not an accident so no other intent 
but suicide can be inferred (e.g., gunshot to head, jumping from window of a high floor/story). Also, if 
someone denies intent to die, but they thought that what they did could be lethal, intent may be inferred.  
Have you made a suicide attempt?  
Have you done anything to harm yourself?  
Have you done anything dangerous where you could have died?  
What did you do?  
Did you______ as a way to end your life?  
Did you want to die (even a little) when you_____?  
Were you trying to end your life when you _____?  
Or did you think it was possible you could have died from_____?  
 
 
 
  
Yes    No 
□    □ 
    
Total # of 
Attempts 
 
 
______ 
 
 
 
 
 
 
Yes    No 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 83 of 92 
Or did you do it purely for other reasons / without ANY intention of killing yourself (like to relieve stress, 
feel better, get sympathy, or get something else to happen)? (Self-Injurious Behavior without suicidal 
intent)  
If yes, describe: __________________________________________________________________________ 
_______________________________________________________________________________________
_______________________________________________________________________________________ 
_______________________________________________________________________________________ 
 
Has subject engaged in Non-Suicidal Self-Injurious Behavior?  
□    □ 
Interrupted Attempt:  
When the person is interrupted (by an outside circumstance) from starting the potentially self-injurious act 
(if not for that, actual attempt would have occurred).  
Overdose: Person has pills in hand but is stopped from ingesting. Once they ingest any pills, this becomes 
an attempt rather than an interrupted attempt. Shooting: Person has gun pointed toward self, gun is taken 
away by someone else, or is somehow prevented from pulling trigger. Once they pull the trigger, even if 
the gun fails to fire, it is an attempt. Jumping: Person is poised to jump, is grabbed and taken down from 
ledge. Hanging: Person has noose around neck but has not yet started to hang - is stopped from doing so.  
Has there been a time when you started to do something to end your life but someone or something 
stopped you before you actually did anything?  
If yes, describe: __________________________________________________________________________ 
_______________________________________________________________________________________
_______________________________________________________________________________________ 
_______________________________________________________________________________________ 
 
Yes    No 
□    □ 
 
 
 
 
Total # of 
interrupted 
 
______ 
Aborted Attempt:  
When person begins to take steps toward making a suicide attempt, but stops themselves before they 
actually have engaged in any self-destructive behavior. Examples are similar to interrupted attempts, 
except that the individual stops him/herself, instead of being stopped by something else.  
Has there been a time when you started to do something to try to end your life but you stopped yourself 
before you actually did anything?  
 
Yes    No 
□    □ 
 
Total # of 
aborted 
If yes, describe: __________________________________________________________________________ 
_______________________________________________________________________________________ 
_______________________________________________________________________________________ 
_______________________________________________________________________________________ 
 
 
 
Preparatory Acts or Behavior:  
Acts or preparation towards imminently making a suicide attempt. This can include anything beyond a 
verbalization or thought, such as assembling a specific method (e.g., buying pills, purchasing a gun) or 
preparing for one’s death by suicide (e.g., giving things away, writing a suicide note).  
Have you taken any steps towards making a suicide attempt or preparing to kill yourself (such as collecting 
pills, getting a gun, giving valuables away or writing a suicide note)?  
If yes, describe: __________________________________________________________________________ 
 
 
Yes    No 
□    □ 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 84 of 92 
_______________________________________________________________________________________
_______________________________________________________________________________________ 
_______________________________________________________________________________________ 
Suicidal Behavior:  
Suicidal behavior was present during the assessment period?  
Yes    No 
□    □ 
 
Suicide:  
Yes    No 
□    □ 
Answer for Actual Attempts Only  
Most Lethal 
Attempt 
 
Date:_______ 
Actual Lethality/Medical Damage:  
0. No physical damage or very minor physical damage (e.g., surface scratches).  
1. Minor physical damage (e.g., lethargic speech; first-degree burns; mild bleeding; sprains).  
2. Moderate physical damage; medical attention needed (e.g., conscious but sleepy, somewhat responsive; 
second-degree burns; bleeding of major vessel).  
3. Moderately severe physical damage; medical hospitalization and likely intensive care required (e.g., 
comatose with reflexes intact; third-degree burns less than 20% of body; extensive blood loss but can 
recover; major fractures).  
4. Severe physical damage; medical hospitalization with intensive care required (e.g., comatose without 
reflexes; third-degree burns over 20% of body; extensive blood loss with unstable vital signs; major 
damage to a vital area).  
5. Death  
 
Enter Code 
 
 
 
______ 
Potential Lethality: Only Answer if Actual Lethality=0  
Likely lethality of actual attempt if no medical damage (the following examples, while having no actual 
medical damage, had potential for very serious lethality: put gun in mouth and pulled the trigger but gun 
fails to fire so no medical damage; laying on train tracks with oncoming train but pulled away before run 
over).  
0 = Behavior not likely to result in injury  
1 = Behavior likely to result in injury but not likely to cause death  
2 = Behavior likely to result in death despite available medical care  
 
Enter Code 
 
______ 
 
 
 
 
 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 85 of 92 
13.3 
Appendix III: Montreal Cognitive Assessment (MOCA) 
 
 
 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 86 of 92 
13.4 
Appendix IV: Dementia Severity Rating Scale (DSRS) 
 
PARTICIPANT’S NAME:____________________________ DATE:_________________ 
PERSON COMPLETING FORM:_____________________________________________ 
 
Please circle the most appropriate answer. 
 
Do you live with the participant? No Yes 
How much contact do you have with the participant? Less than 1 day per week 1 
day/week 2 days/week 3-4 days/week 
5 or more days per week 
Relationship to participant 
Self Spouse Sibling Child Other Family Friend Other ______________ 
 
In each section, please circle the number that most closely applies to the participant. This 
is a general form, so no one description may be exactly right -- please circle the answer that 
seems to apply most of the time. 
 
Please circle only one number per section, and be sure to answer all questions. 
 
MEMORY 
0 Normal memory. 
1 Occasionally forgets things that they were told recently. 
Does not cause many problems. 
2 Mild consistent forgetfulness. Remembers recent events but often forgets parts. 
3 Moderate memory loss. Worse for recent events. May not remember something you 
just told them. Causes problems with everyday activities. 
4 Substantial memory loss. Quickly forgets recent or newly-learned things. Can only 
remember things that they have known for a long time. 
5 Does not remember basic facts like the day of the week, when last meal was eaten 
or what the next meal will be. 
6 Does not remember even the most basic things. 
 
SPEECH AND LANGUAGE 
0 Normal ability to talk and to understand others. 
1 Sometimes cannot find a word, but able to carry on conversations. 
2 Often forgets words. May use the wrong word in its place. Some trouble expressing 
thoughts and giving answers. 
3 Usually answers questions using sentences but rarely starts a conversation. 
4 Answers questions, but responses are often hard to understand or don't make 
sense. Usually able to follow simple instructions. 
5 Speech often does not make sense. Can not answer questions or follow instructions. 
6 Does not respond most of the time. 
 
RECOGNITION OF FAMILY MEMBERS 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 87 of 92 
0 Normal - recognizes people and generally knows who they are. 
1 Usually recognizes grandchildren, cousins or relatives who are not seen frequently 
but may not recall how they are related. 
2 Usually does not recognize family members who are not seen frequently. Is often 
confused about how family members such as grandchildren, nieces, or nephews are 
related to them. 
3 Sometimes does not recognize close family members or others who they see 
frequently. May not recognize their children, brothers, or sisters who are not seen on 
a regular basis. 
4 Frequently does not recognize spouse or caregiver. 
5 No recognition or awareness of the presence of others. 
 
ORIENTATION TO TIME 
0 Normal awareness of time of day and day of week. 
1 Some confusion about what time it is or what day of the week, but not severe 
enough to interfere with everyday activities. 
2 Frequently confused about time of day. 
3 Almost always confused about the time of day. 
4 Seems completely unaware of time. 
 
ORIENTATION TO PLACE 
0 Normal awareness of where they are even in new places. 
1 Sometimes disoriented in new places. 
2 Frequently disoriented in new places. 
3 Usually disoriented, even in familiar places. May forget that they are already at 
home. 
4 Almost always confused about place. 
 
ABILITY TO MAKE DECISIONS 
0 Normal - as able to make decisions as before. 
1 Only some difficulty making decisions that arise in day-to-day life. 
2 Moderate difficulty. Gets confused when things get complicated or plans change. 
3 Rarely makes any important decisions. Gets confused easily. 
4 Not able to understand what is happening most of the time. 
 
SOCIAL AND COMMUNITY ACTIVITY 
0 Normal - acts the same with people as before 
1 Only mild problems that are not really important, but clearly acts differently from 
previous years. 
2 Can still take part in community activities without help. May appear normal to people 
who don't know them. 
3 Often has trouble dealing with people outside the home without help from caregiver. 
Usually can participate in quiet home activities with friends. The problem is clear to 
anyone who sees them. 
4 No longer takes part in any real way in activities at home involving other people. Can 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 88 of 92 
only deal with the primary caregiver. 
5 Little or no response even to primary caregiver. 
 
HOME ACTIVITIES AND RESPONSIBILITIES 
0 Normal. No decline in ability to do things around the house. 
1 Some problems with home activities. May have more trouble with money 
management (paying bills) and fixing things. Can still go to a store, cook or clean. 
Still watches TV or reads a newspaper with interest and understanding. 
2 Makes mistakes with easy tasks like going to a store, cooking or cleaning. Losing 
interest in the newspaper, TV or radio. Often can't follow a long conversation on a 
single topic. 
3 Not able to shop, cook or clean without a lot of help. Does not understand the 
newspaper or the TV. Cannot follow a conversation. 
4 No longer does any home-based activities. 
 
PERSONAL CARE - CLEANLINESS 
0 Normal. Takes care of self as well as they used to. 
1 Sometimes forgets to wash, shave, comb hair, or may dress in wrong type of 
clothes. Not as neat as they used to be. 
2 Requires help with dressing, washing and personal grooming. 
3 Totally dependent on help for personal care. 
 
EATING 
0 Normal, does not need help in eating food that is served to them. 
1 May need help cutting food or have trouble with some foods, but basically able to eat 
by themselves. 
2 Generally able to feed themselves but may require some help. May lose interest 
during the meal. 
3 Needs to be fed. May have trouble swallowing. 
 
CONTROL OF URINATION AND BOWELS 
0 Normal - does not have problems controlling urination or bowels except for physical 
problems. 
1 Rarely fails to control urination (generally less than one accident per month). 
2 Occasional failure to control urination (about once a week or less). 
3 Frequently fails to control urination (more than once a week). 
4 Generally fails to control urination and frequently can not control bowels. 
 
ABILITY TO GET FROM PLACE TO PLACE 
0 Normal, able to get around on their own. (May have physical problems that require a 
cane or walker). 
1 Sometimes gets confused when driving or taking public transportation, especially in 
new places. Able to walk places alone. 
2 Cannot drive or take public transportation alone, even in familiar places. Can walk 
alone outside for short distances. Might get lost if walking too far from home. 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 89 of 92 
3 Cannot be left outside alone. Can get around the house without getting lost or 
confused. 
4 Gets confused and needs help finding their way around the house. 
5 Almost always in a bed or chair. May be able to walk a few steps with help, but lacks 
sense of direction. 
6 Always in bed. Unable to sit or stand. 
 
Author: 
Dr. Christopher M Clark, Alzheimer’s Disease Core Center 
Department of Neurology, University of Pennsylvania, Philadelphia, Pennsylvania, USA 
 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 90 of 92 
13.5 
Appendix V: Functional Activities Questionnaire 
 
Administration 
 
Ask informant to rate patient’s ability using the following scoring system: 
• Dependent = 3 
• Requires assistance = 2 
• Has difficulty but does by self = 1 
• Normal = 0 
• Never did [the activity] but could do now = 0 
• Never did and would have difficulty now = 1 
 
Writing checks, paying bills, balancing checkbook 
 
Assembling tax records, business affairs, or papers 
 
Shopping alone for clothes, household necessities, or groceries 
 
Playing a game of skill, working on a hobby 
 
Heating water, making a cup of coffee, turning off stove after use 
 
Preparing a balanced meal 
 
Keeping track of current events 
 
Paying attention to, understanding, discussing TV, book, magazine 
 
Remembering appointments, family occasions, holidays, medications 
 
Traveling out of neighborhood, driving, arranging to take buses 
 
TOTAL SCORE:  
 
 
Evaluation 
 
Sum scores (range 0-30). Cutpoint of 9 (dependent in 3 or more activities) is 
recommended to indicate impaired function and possible cognitive 
impairment. 
 
 
 
 
 
 
 
 
 
 
 
Pfeffer RI et al. Measurement of functional activities in older adults in the community. J 
Gerontol 1982; 37(3):323-329. Reprinted with permission of The Gerontological Society of 
America, 1030 15th Street NW, Suite 250, Washington, DC 20005 via Copyright Clearance 
Center, Inc. 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 91 of 92 
13.6 
Appendix VI: Geriatric Depression Scale 
 
Choose the best answer for how you have felt over the past week: 
  
1. Are you basically satisfied with your life? YES / NO  
2. Have you dropped many of your activities and interests? YES / NO  
3. Do you feel that your life is empty? YES / NO  
4. Do you often get bored? YES / NO  
5. Are you in good spirits most of the time? YES / NO  
6. Are you afraid that something bad is going to happen to you? YES / NO  
7. Do you feel happy most of the time? YES / NO  
8. Do you often feel helpless? YES / NO  
9. Do you prefer to stay at home, rather than going out and doing new things? YES / NO  
10. Do you feel you have more problems with memory than most? YES / NO  
11. Do you think it is wonderful to be alive now? YES / NO  
12. Do you feel pretty worthless the way you are now? YES / NO  
13. Do you feel full of energy? YES / NO  
14. Do you feel that your situation is hopeless? YES / NO  
15. Do you think that most people are better off than you are? YES / NO  
 
Answers in bold indicate depression. Score 1 point for each bolded answer.  
 
A score > 5 points is suggestive of depression.  
A score ≥ 10 points is almost always indicative of depression.  
A score > 5 points should warrant a follow-up comprehensive assessment.  
 
Source: http://www.stanford.edu/~yesavage/GDS.html  
This scale is in the public domain.  
 
 
 
 
 
 
 
 
The Hartford Institute for Geriatric Nursing would like to acknowledge the original author of this Try This, Lenore 
Kurlowicz, PhD, RN, CS, FAAN, who made significant contributions to the field of geropsychiatric nursing and 
passed away in 2007. 
 
 


 
Version date 10 April 2020 
AMX-0035 in AD 
Protocol Number: AMX8000 
Version 4.0. 
Page 92 of 92 
13.7 
Appendix VII: Instructions to subjects 
 
The following instructions will be provided orally to the patient at the Baseline Visit by a 
healthcare staff member. Please have the Listerine® products (Pocketpaks® and Pocketmist®) 
available for demonstration. 
  
• Alert the patient that the study drug has a bitter taste, but that there are ways to make it 
more palatable (see below). 
  
•  Rip open the sachet of study drug and add it to a cup or other container and add 
approximately 8 oz. (1 cup) of room temperature water and stir vigorously. Study drug may 
require significant stirring or gentle crushing to dissolve. 
  
• The treatment should be taken within one hour of mixing into water. 
  
• Several things may be done to reduce the bad taste and make the drug more palatable: 
  
o Use Listerine Pocket Packs® (strips) or a Listerine PocketMist® (spray) immediately 
before and/or immediately after taking the drug. Use liberally to coat the mouth. This 
has been found to significantly mask the bitter taste. 
  
o Take a snack or a meal after taking your treatment. 
  
o Follow drug immediately with milk to remove taste from the mouth. 
  
o Avoid drinking fruit juice at the same time as the drug as this may make flavor worse. 
  
o Mixing the study drug with a liquid other than water should be avoided. 
  
 

SAP_001.pdf: 
  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 1 of 38 
 
 
 
 
 
 
 
 
 
Phase II Study to Assess the Safety, Tolerability, and Target 
Engagement of AMX0035, a Fixed Combination of Sodium 
Phenylbutyrate and Tauroursodeoxycholic Acid for the 
Treatment of Alzheimer’s Disease 
 
 
 
 
 
 
 
 
 
AMX8000 v0.1 20201008 
 
 


Amylyx Pharmaceuticals
Protocol AMX8000
Statistical Analysis Plan
Protocol Date and Version:  8 October 2020; v2.2
Page 2 of 38
 
Phase II Study to Assess the Safety, Tolerability, and 
Target Engagement of AMX0035, a Fixed Combination of 
Sodium Phenylbutyrate and Tauroursodeoxycholic Acid 
for the Treatment of Alzheimer’s Disease 
 
 By signing below, all parties accept that the analysis methods and data presentations are 
 acceptable and that this document is final. 
 
 
 
 
  
 
Date 
 
 
 
 
 
 
 
 
 
Date 
 
 
 
 
 
 
 
Date 
 
 
 
 
 
 
 
 
Date 
5/7/2021
5/7/2021
5/7/2021
5/8/2021


  
Amylyx Pharmaceuticals
Protocol AMX8000 
Statistical Analysis Plan
Protocol Date and Version:  8 October 2020; v2.2
Page 3 of 38
 
Modification History 
Unique 
Identifier for 
this Version 
 
 
Date of the 
Document 
Version 
 
 
 
Author 
Significant Changes 
from  
Previous Authorized 
Version 
0.1 
10 
Oct 
2020 
 
not applicable—first 
version 
0.2 
2 Nov 
2020 
add clarification to 
primary analysis and CSF 
markers gating;  
0.3 
3 Dec 
2020 
Add clairification to 
primary analysis and 
modify patient population 
definitions 
 
 
 
 
 
 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 4 of 38 
 
Table of Contents 
1 Abbreviations ............................................................................................. 6 
2 Introduction .............................................................................................. 13 
3 Trial Overview .......................................................................................... 13 
3.1 Design ..............................................................................................................13 
3.2 Study Objectives ..............................................................................................13 
3.2.1 Primary Objectives ........................................................................... 13 
3.2.2 Secondary Objectives....................................................................... 13 
 
3.3 Sample Size Determination ..............................................................................14 
3.4 Blinding and Unblinding..................................................................................16 
3.5 Study Drug Administration ..............................................................................16 
4 Patient Chronology .................................................................................. 16 
5 General Conditions for the Final Analysis ............................................ 16 
5.1 Definitions........................................................................................................16 
5.2 General Considerations for the Final Analysis ................................................17 
5.3 Interim Analysis ...............................................................................................18 
5.4 Changes to Statistical Analysis ........................................................................18 
5.5 Analysis Populations/Sets ................................................................................18 
5.5.1 All Patients Population .................................................................... 18 
5.5.2 Intent-to-Treat (ITT) Population ...................................................... 18 
5.5.3 Per Protocol (PP) Population ........................................................... 18 
5.5.4 Safety Population ............................................................................. 18 
5.6 Estimands, Intercurrent Events, and Missing Data ..........................................18 
5.7 Data Review .....................................................................................................20 
5.8 Missing Data ....................................................................................................20 
6 Study Conduct .......................................................................................... 20 
6.1 Treatment Assignments ...................................................................................20 
6.2 Enrollment, Demographics, and Baseline Characteristics ...............................21 
6.3 Patient Disposition and Protocol Deviations ...................................................21 
6.4 Extent of Exposure to Study Drug ...................................................................21 
6.5 Medical History ...............................................................................................21 
6.6 General Comments...........................................................................................22 
7 Efficacy Analyses ...................................................................................... 22 
7.1.1 Primary Endpoints ........................................................................... 22 
7.1.2 Secondary Endpoints (listed in hierarchical order) .......................... 22 
7.1.3 Biomarker Endpoints ....................................................................... 22 
7.2 Primary Efficacy Endpoints .............................................................................23 
7.2.1 Global Statistical Test ...................................................................... 23 
7.2.2 MADCOMS ..................................................................................... 23 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 5 of 38 
 
7.2.3 FAQ.................................................................................................. 24 
7.2.4 Total Hippocampal Brain Volume (volumetric MRI) ..................... 25 
7.3 Secondary Efficacy Endpoints .........................................................................25 
7.3.1 ADAS-Cog ....................................................................................... 25 
7.3.2 Dementia Severity Rating Scale (DSRS) ......................................... 26 
7.3.3 MoCA .............................................................................................. 26 
7.3.4 NPI-Q ............................................................................................... 26 
 
 
 
 
7.5 Statistical Evaluations ......................................................................................29 
7.5.1 Primary Analyses ............................................................................. 29 
7.5.2 Secondary Analyses ......................................................................... 32 
 
8 Safety ......................................................................................................... 34 
8.1 Safety Endpoints ..............................................................................................34 
8.2 Analysis Populations Evaluated for Safety ......................................................34 
8.3 Statistical Methods for Safety Endpoints .........................................................34 
8.4 Adverse Events ................................................................................................34 
8.5 Vital Signs ........................................................................................................35 
8.6 Electrocardiogram ............................................................................................35 
8.7 Clinical Laboratory Evaluations ......................................................................36 
8.8 Physical and Neurological Exams ...................................................................36 
8.9 C-SSRS ............................................................................................................36 
9 Other Listings ........................................................................................... 36 
10 Bibliography ........................................................................................... 37 
 
 
 
 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 6 of 38 
 
1 Abbreviations 
AE 
Adverse Event/Adverse Experience 
AD 
Alzheimer’s disease 
ADAS-Cog 
Alzheimer’s Disease Assessment Scale – Cognitive Subscale 
ALS 
Amyotrophic Lateral Sclerosis 
BOLD 
Blood Oxygen-Level Dependent Imaging 
CNS 
Central Nervous System 
CRF 
Case Report Form 
CSF 
Cerebrospinal Fluid 
C-SSRS 
Columbia Suicide Severity Rating Scale 
DSRS 
Dementia Severity Rating Scale 
eCRF 
Electronic Case Report Form 
FAQ 
Functional Activities Questionnaire 
FDA 
Food and Drug Administration 
g 
Gram 
GST 
Global Statistical Test 
IL 
Interleukin 
ITT 
Intention to Treat 
LP 
Lumbar Puncture 
MADCOMS 
Mild/Moderate AD Composite Scale 
MCI 
Mild Cognitive Impairment 
MedDRA 
Medical Dictionary for Regulatory Activities 
mITT 
Modified Intent to Treat 
MoCA 
Montreal – Cognitive Assessment 
MRI 
Magnetic Resonance Imaging 
N 
Number (typically refers to subjects) 
NfL 
Neurofilament Light Chain 
Ng 
Neurogranin 
NPI 
Neuropsychiatric Inventory 
NPI-Q 
Neuropsychiatric Inventory Questionnaire 
PB 
Sodium Phenylbutyrate 
PI 
Principal Investigator 
PK 
Pharmacokinetics 
PP 
Per Protocol 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 7 of 38 
 
SAE 
SAP 
SI 
Serious Adverse Event/Serious Adverse Experience 
Statistical Analysis Plan 
Site Investigator 
SOP 
Standard Operating Procedure 
TUDCA 
 
Tauroursodeoxycholic Acid 
 
US 
United States 
vMRI 
Volumetric Magnetic Resonance Imaging 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 8 of 38 
 
Table 1. Schedule of Assessments 
 
Screening 
Baseli
ne1 
Week 
1 
Phon
e Call 
Week 
615 
Week 
1216 
Week 
1815 
Week 
2417/Early 
Discontinuati
on18 
Final 
Follow-Up 
Call14 
-28 Days 
Day 0 
+5 
Days 
Day 7  
±1 
Days  
Day 42  
±14 
Days 
Day 
84 ±28 
Days 
Day 126  
±14 
Days 
Day 168  
±28 Days 
Last Dose of 
IP +14 ±5 
Days 
Written Informed consent 
X 
 
 
 
 
 
 
 
Inclusion/Exclusion Review 
X 
X 
 
 
 
 
 
 
Randomization2 
 
X 
 
 
 
 
 
 
Medical History/Demographics 
X 
 
 
 
 
 
 
 
AD Diagnosis History 
X 
 
 
 
 
 
 
 
Montreal - Cognitive Assessment 
(MoCA) 
X 
 
 
X 
 
X 
X 
 
DSRS 
 
X 
 
 
X 
 
X 
 
Geriatric Depression Scale 
X 
 
 
 
 
 
 
 
Vital Signs3 
X 
X 
 
 
X 
 
X 
 
FAQ 
 
X 
 
 
X 
 
X 
 
Physical Exam including Height 
and Weight4 
X 
 
 
 
 
 
X 
 
Neurology Exam5 
X 
 
 
 
 
 
X 
 
Safety labs6 
X 
 
 
 
X 
 
X 
 
12-Lead ECG (Electrocardiogram) 
X 
 
 
 
X 
 
X 
 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 9 of 38 
 
 
Screening 
Baseli
ne1 
Week 
1 
Phon
e Call 
Week 
615 
Week 
1216 
Week 
1815 
Week 
2417/Early 
Discontinuati
on18 
Final 
Follow-Up 
Call14 
-28 Days 
Day 0 
+5 
Days 
Day 7  
±1 
Days  
Day 42  
±14 
Days 
Day 
84 ±28 
Days 
Day 126  
±14 
Days 
Day 168  
±28 Days 
Last Dose of 
IP +14 ±5 
Days 
Neuropsychiatric 
Inventory 
Questionnaire (NPI-Q)  
X7 
 
 
X 
 
X 
 
ADAS-Cog 
 
X 
 
 
X 
 
X 
 
MRI Assessment8 
X 
 
 
 
 
X 
 
Adverse Events  
X 
X 
X 
X 
X 
X 
X 
X 
Concomitant Medications 
X 
X 
 
X 
X 
X 
X 
X 
Dispense Study Drug9 
 
X 
 
X 
X 
X 
 
 
Drug Accountability/Compliance 
 
 
X10 
X 
X 
X 
X 
 
Suicide Rating Scale (C-SSRS)11 
X 
X 
 
X 
X 
X 
X 
 
Blood draw for biomarker analysis 
 
X 
 
 
X 
 
X 
 
Lumbar puncture/CSF draw for 
biomarkers12 
 
X 
 
 
 
 
X 
 
Blood draw for pharmacokinetics13 
 
 
 
 
X 
 
X 
 
Blood draw for genetic analysis 
 
X 
 
 
 
 
 
 
1The Baseline Visit can be completed any time after the screening so long as all eligibility criteria are met and occur no more than 
28 +5 days after the Screening Visit. 
2Randomization should occur at the Baseline Visit. Randomization will entail entering a subject’s kit number into the electronic data 
capture system. 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 10 of 38 
 
3Vital signs include systolic and diastolic pressure in mmHg, respiratory rate/minute, heart rate/minute and temperature.  
4Height is only recorded once at the Screening Visit. 
5The standard Neurological Exam will be used for all subjects. 
6Safety labs include Hematology (CBC with differential), Complete Chemistry Panel, Liver Function Tests, B12 and TSH (at 
Screening Visit only) and Urinalysis.  
7 The NPI-Q Test can be performed either at the screening or baseline visit 
8The MRI assessment can be completed anytime between the Screening and up to 7 days prior to the Baseline Visit and will have a 
clinical read done locally. 
9First dose of study drug will be administered in clinic after ALL Baseline Visit procedures are completed. 
10Notify subjects of increase from one sachet per day to two sachets per day 
11C-SSRS Screening Version to be completed at Screening Visit only. C-SSRS Since Last Visit version to be completed at all 
other visits.  
12The first LP can be completed anytime between the Screening and up to 7 days prior to the Baseline Visit. 
13Take a single PK plasma sample on Visits 12 and 24 (same time as lumbar puncture). A PK sample will not be taken on subjects 
completing the Early Discontinuation Visit if the subject discontinued study drug more than 48 hours before the visit. 
14The Final Follow-Up Call is to occur 14 ± 5 days after the participant’s last dose of study drug. For participants who discontinue 
treatment early, the Final Follow-Up Call is not required if the Early Discontinuation visit occurs 14 ± 5 days after the last dose of 
study drug. 
15To the extent possible, the Week 6 and Week 18 visits may be done remotely. If the visit is done remotely, Drug 
Accountability/Compliance will occur at the next in-person clinic visit. 
16It is preferred that the Week 12 visit be conducted at the site with the participant physically present. If it is not possible to 
complete an in-person Week 12 visit at the site, the safety assessments below must be completed by Week 16/Day 112 for the 
subject to remain on study drug. Sites may make alternative arrangements to complete these assessments per institutional and IRB 
policy. 
• 
ECG 
• 
Safety Labs: Hematology (Complete Blood Count with Differential), Complete Chemistry Panel, Liver Function Tests, and Urinalysis 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 11 of 38 
 
• 
Vital Signs 
• 
C-SSRS 
17 The window for the Week 24 visit is Day 168 ± 28 days. However, if COVID-19 related restrictions (e.g., site closure, travel 
restrictions) make it impossible to conduct an in-person clinic visit during the specified window, then any assessment that can be 
performed remotely should be completed as an unscheduled visit during the Week 24 window. The actual Week 24 visit, with all 
of the assessments indicated on the SOA, may be postponed for up to 12 weeks and treatment extended. The maximum duration a 
subject may be on IP is 40 weeks. Safety checks (i.e., ECG, safety labs, vital signs, and C-SSRS) must be completed, at minimum, 
every 16 weeks/112 days. If safety assessments are performed so that the Week 24 visit may be postponed, the assessments should 
be documented as an unscheduled visit. 
18If possible, an Early Discontinuation visit should be done within 14 days of the last dose of IP (i.e., last dose of IP + 14 days). 
The MRI and lumbar puncture may be done as soon as is practical and, if possible, within 60 days of the last dose of IP (i.e., last 
dose of IP + 60 days). 
 
 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 12 of 38 
 
 Figure 1. Study workflow  
 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 13 of 38 
 
2 Introduction 
Alzheimer’s disease is characterized by the loss of neurons and synapses in the cerebral cortex 
and atrophy in the temporal and parietal lobes. Abnormal aggregates of amyloid plaques and 
neurofibrillary tangles are the primary histopathological findings of AD and are the target of 
many clinical trials. However, recent studies suggest that amyloid reduction may be less able 
to halt pathology after AD has progressed beyond the stage of mild cognitive impairment 
(MCI). At this stage, neuronal death and inflammatory pathways may contribute to disease 
progression to a greater degree than amyloid or tau. This suggests that there may be patient 
sub-groups that may not respond to amyloid-targeted therapies, yet may benefit from therapies 
targeting cell death and inflammation. 
AMX0035 is a combination of two compounds, Sodium Phenylbutyrate (PB) and 
Tauroursodeoxycholic Acid (TUDCA), that target the unfolded protein response (UPR) and 
bioenergetics stress, respectively. Both compounds are expected to cross the blood-brain-
barrier at therapeutic levels based on observed CNS target engagement observed in previous 
in vivo studies3,4,7,11,14 and are hypothesized to prevent neuronal death through distinct 
pathways.  Synergistic effect of these compounds has been found in preclinical models. 
3 Trial Overview 
3.1 Design 
This is a 24-week, phase II, longitudinal, multi-center, randomized, double-blind, placebo-
controlled trial to assess safety and tolerability of a fixed-dose combination of AMX0035 in 
subjects with MCI or dementia due to AD. Approximately 100 subjects will be randomized 
3:2 (active:placebo) to oral, twice daily sachet of active combination (TUDCA/PB) or placebo. 
3.2 Study Objectives 
3.2.1 Primary Objectives  
1. To compare the safety and tolerability of a fixed-dose combination of AMX0035 
(a TUDCA/PB combination) versus placebo in subjects with MCI (high or 
intermediate likelihood due to AD) or dementia due to AD over an approximate 
24-week treatment period; 
2. To determine the effects of AMX0035 treatment on AD progression as measured 
by a global statistical test (GST)  
3.2.2 Secondary Objectives  
1. To determine the effects of AMX0035 treatment on whole brain and regional 
brain atrophy, as assessed by volumetric Magnetic Resonance Imaging (vMRI); 
2. To measure the effects of treatment on functional MRI measures including 
connectivity with resting state BOLD; 
3. To assess the impact of AMX0035 on clinical symptoms as measured by ADAS-
Cog, DSRS, FAQ, and additional clinical outcomes; 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 14 of 38 
 
4. To assess the effect of AMX0035 on measures of neuropsychiatric symptoms, 
as assessed by the Neuropsychiatric Inventory Questionnaire (NPI-Q) 
 
The primary estimand is the effect of treatment as measured by a change from baseline in GST 
(comprised of Mild/Moderate AD Composite Scale (MADCOMS), FAQ, and hippocampal 
volume) estimated at 24 weeks relative to placebo in individuals with MCI (high or 
intermediate likelihood due to AD) or dementia due to AD. The study population for the 
primary estimand will be the intent to treat population.   
 
3.3 Sample Size Determination 
A sample size of approximately 100 randomized subjects was chosen based on feasibility and 
is not based solely in statistical considerations. Subjects will be randomized in a ratio of 3:2 
(active versus placebo). In order to maximize study power for evaluation of efficacy end-
points, a GST will be used. The GST will be a combination of 3 change-from-baseline to end-
of-study endpoints (univariate components): 
o Cognition (ADAS-Cog) 
o Functional Activities Questionnaire (FAQ) 
o Total Hippocampal Brain Volume  
For purposes of power calculations, GSTs can be characterized based on the assumed effect 
sizes of each of the 3 component endpoints and the correlations between each of the 3 pairs of 
component endpoints. 
We assume a correlation of 0.4 between the cognitive and FAQ component endpoints and a 
correlation of 0.2 between the total hippocampal volume component endpoint and each of the 
other two components endpoints (i.e., the cognitive component endpoint and the FAQ 
component endpoint), based upon historical analyses. By using 50% statistical power and the 
assumed effect sizes as inputs, we can obtain the “expected p-value” for 2 selected 
combinations of component endpoints of the composite. We do this in 2 stages, first for the 
combination of ADAS-Cog and FAQ component endpoints, which have expected p-values of 
0.09409 and 0.20184, respectively, resulting in a 2-component expected p-value of 0.077583. 
Then we combine the 2-component expected p-value with the expected p-value for Total 
Hippocampal Brain Volume (0.20184), to get a GST expected p-value of 0.049756. 
Each of the 3 component endpoints may have a different sensitivity with respect to detecting 
change over time. The sensitivity is quantified using the Mean-to-Standard Deviation Ratio 
(MSDR), which is calculated by dividing the mean of the change-from-baseline score by the 
standard deviation of the change-from-baseline score. For change-from-baseline to 6 months, 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 15 of 38 
 
we assume the MSDR values for ADAS-Cog, FAQ, Total Hippocampal Volume are 0.8, 0.6, 
and 0.6, respectively. We assume a 60% value for Percent of Placebo Effect (i.e., the decline 
for the active treatment group is only 40% of the decline of the Placebo group). This 
corresponds to effect size (assumed treatment difference divided by the common standard 
deviation) values of 0.48 for the Cognitive Endpoint, 0.36 for the FAQ endpoint, and 0.36 for 
the Total Hippocampal Brain Volume endpoint. Under these assumptions the resulting GST p-
value is 0.049756. 
Using 100 randomized subjects (assuming either no subject dropout so that there are 100 
completers, or that imputation appropriately accounts for subject dropout), 50% power, a 
randomization ratio of 1:1, gives an effect size (corresponding to the use of the GST) of 0.566; 
this indicates that that under these assumptions use of the GST is equivalent to using a single 
component test statistic with an effect size of 0.566 (rather than the assumed effect sizes of 
0.48 for ADAS-Cog, 0.36 for FAQ, and 0.36 for Total Hippocampal Brain Volume). Another 
way to interpret this is that using of the GST, corresponding to an assumed effect size of 0.566 
for a single component endpoint, and using α = 0.05 results in a power of approximately 50% 
(50.1%). So, when the individual components of the GST are in the same direction (and in 
favor of the active treatment group versus placebo), then use of a GST generally provides more 
power than use of a single component. 
Although the power calculations (Table 2) show 80% power for an assumed Percent of Placebo 
Effect value of 85%, a Percent of Placebo Effect value as small as 50% or 60% would still be 
clinically relevant and would be an encouraging indication for moving forward into a new 
study. As described previously, a Percent of Placebo Effect value of 60% corresponds to GST 
p-value of approximately 0.05 (0.049756, 2-sided), an effect size of 0.566, and a power of 
approximately 50%. A GST p-value of 0.10 (2-sided) would be an observed trend that would 
still be suggestive of a signal indicating that moving forward into a new study would be 
appropriate. This corresponds to Percent of Placebo Effect value of just under 50%: a Percent 
of Placebo Effect value of 50% corresponds to GST p-value of approximately 0.095 (0.09477, 
2-sided), an effect size of 0.479, and a power of approximately 38% at a 2-sided alpha=0.05 
level. 
Some additional examples of the GST under various assumed Percent of Placebo Effect values 
and corresponding effect sizes (and using the pairwise correlations of 0.4, 0.2, and 0.2 
described previously) are given below, along with the examples described previously. (Note 
that a Percent of Placebo effect value of 0% means that active treatment declines as much as 
Placebo, a value of 50% means that active treatment declines half as much as Placebo, and a 
value of 100% means that the active treatment doesn’t decline at all over the 6-month treatment 
period.) 
We included conservative estimates of power calculations based on ADAS-Cog.  The GST 
implemented in the analysis will incorporate MADCOMS, which has been previously shown 
to be more sensitive to change in mild to moderate populations (S Hendrix ADPD 2021).  
 


  
Amylyx Pharmaceuticals
Protocol AMX8000 
Statistical Analysis Plan
Protocol Date and Version:  8 October 2020; v2.2
Page 16 of 37
 
Table 2. Power of Global Test Statistic for total sample sizes of 50, 76, and 100 subjects for 
Protocol AMX8000 using a 3:2 randomization ratio 
Percent 
of 
Placebo 
Effect 
Cog. 
Effect 
Size 
FAQ 
Effect 
Size 
Total Hipp. 
Brain 
Volume 
Effect Size 
Global 
Test 
Statistic 
Effect 
Size 
Global 
Test 
Statistic 
Power (%) 
50 
Subjects 
Total 
Global 
Test 
Statistic 
Power 
(%) 
76 
Subjects 
Total 
Global 
Test 
Statistic 
Power 
(%) 
100 
Subjects 
Total 
50% 
0.40 
0.30 
0.30
0.479
36.9
52.2 
64.2
60% 
0.48 
0.36 
0.36
0.566
48.5
66.3 
78.4
70% 
0.56 
0.42 
0.42
0.651
60.0
78.2 
88.4
80% 
0.64 
0.48 
0.48
0.754
72.6
88.7 
95.5
85% 
0.68 
0.51 
0.51
0.803
77.8
92.2 
97.4
90% 
0.72 
0.54 
0.54
0.852
82.4
94.8 
98.5
100% 
0.80 
0.60 
0.60
0.951
89.7
97.9 
99.6
 
3.4 Blinding and Unblinding 
Once all eligibility criteria for the study have been met, the subject will be randomized by the 
biostatistical team with an allocation ratio of 3:2 by a computer-generated random sequence at 
the baseline visit. All participants and individuals employed by Amylyx or
 will be 
blinded to treatment groups until database unlock.  After database lock, 
 statisticians 
will request the treatment codes, the study will be unblinded and the statistical analysis will be 
conducted.  
3.5 Study Drug Administration 
Prepackaged AMX0035 sachets will be self-administered daily for 24 weeks.  AMX0035 dose 
is 3g PG and 1g TUDCA (active) or matching placebo. Individuals will take a single sachet 
daily for the first week.  Dosage will be increased to 2 sachets daily after 1 week (if tolerated) 
for the duration of study participation.  
4 Patient Chronology 
Study days will be numbered from Day 1, the first day of study medication intake.The duration 
of events, such as the duration of treatment, will be taken as the end date minus the start date 
(Day 1), plus 1. 
5 General Conditions for the Final Analysis 
5.1 Definitions 
Safety endpoints representing the change from baseline at a particular visit will be defined as 
the result at the visit minus the last non-missing result prior to the first dose of study 
medication. Should a baseline value be missing, then the corresponding screening value, if 
available, may be used. Efficacy endpoints representing the change from baseline at a  


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 17 of 38 
 
particular visit will be defined as the result at the visit minus the average of the non-missing 
results collected prior to the first dose of study medication.  Change from baseline will be 
missing for data collected prior to the first dose of study medication. Patients with a missing 
score for either baseline or the applicable visit will have a missing value for the change from 
baseline at that visit. 
Whether an improvement is represented by a positive or negative change from baseline will 
depend on the endpoint.  
5.2 General Considerations for the Final Analysis 
All analyses will be carried out in SAS version 9.3 or R version 3.4 or higher. 
Visits will be designated as Screening, Baseline/Week 1, Week 6, etc as defined in Table 1. 
Summaries will be shown with columns for each treatment group as well as a column for all 
patients in the study and applicable population. The number of subjects in the treatment group 
and population will be shown in the column header. Continuous data will be summarized with 
the number of non-missing values and their mean, standard deviation, median, minimum and 
maximum. Categorical data will be summarized as the count and percentage of distinct patients 
with each value. Unless noted otherwise and for a given analysis population (see section 6.3 
for definitions), the denominator will be the total number of subjects in this analysis population 
who belong to the treatment group. Summaries by visit will include only regularly scheduled 
visits. 
All data in the clinical database will be listed with the exception of prompt, drug label or data 
review / investigator signature pages. Listings will not be subset by analysis population. 
Listings will generally be sorted by patient number, parameter and visit date. Unscheduled 
visits will be listed, but they will generally not be summarized. 
If it happens that no patients qualify for a display the display will be produced with a note that 
“No patients qualify for the display.” For example, if there are no deaths then the applicable 
displays will be so noted. 
Further details appear in the mock display document. 
For safety summaries, the last pre-randomization measurement is defined as the baseline value. 
For efficacy measures baseline is defined as the last pre-randomization measurement.  
Visit windowing will be applied for analyses which use visit categories instead of actual 
number of days relative to dosing for each assessment. For categorical visit summaries, all 
visits including early termination assessments and unscheduled visits will be included with the 
closest scheduled post-baseline visit that includes the efficacy or safety assessment, based on 
number of days since Day 0. If an early termination visit and a regular visit (other than baseline) 
both fall within the same visit window, any non-missing efficacy assessments will be averaged, 
and a worst-case severity approach will be used for safety data.  
If partial dates are recorded for efficacy or safety outcomes, then partially missing 
start/beginning date (e.g. AE/Concomitant medication start date) will fill in the missing month 
with January and missing day with 1. For example, if month and day were both missing, then 
the date would be filled in with January 1st. Partially missing end/finishing date (e.g. 
AE/Concomitant medication end date) will be filled in with December and missing day with 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 18 of 38 
 
the last day of the month. For example, if month and day were both missing, then the date 
would be filled in with December 31st. For other outcomes (e.g. date of vital signs collection) 
fill in missing month with June (middle month) and missing day with the middle day of the 
month. For example, if month and day were both missing, then the value would be filled in 
with June 15th. 
Days will be converted to weeks by dividing by seven. Days will be converted to months by 
dividing by 30.417. Days will be converted to years by dividing by 365.25. All data collected 
during the study will be analyzed and reported unless stated otherwise. 
5.3 Interim Analysis 
No interim analysis of the data will be conducted.  
5.4 Changes to Statistical Analysis 
The statistical analysis plan does not deviate significantly from the protocol.  
 
5.5 Analysis Populations/Sets 
5.5.1 All Patients Population  
The All Patients Population is defined as patients with any record in the database. 
This population includes both screening and randomized subjects.  Population will 
be utilized for descriptive patient counts that include screening subjects. 
5.5.2 Intent-to-Treat (ITT) Population 
All randomized subjects will be included in the ITT population and will be analyzed 
as randomized.  The ITT population will be analyzed for efficacy in place of the 
mITT as per the recent FDA suggestion. 
5.5.3 Per Protocol (PP) Population 
The PP Population is defined as those ITT patients who took the study medication 
for 20 weeks or more and did not have any major protocol deviations. For 
programming purposes, they will be identified as having 80% compliance 
estimated from study drug return over the 24 week treatment period and having no 
major protocol violation as identified separately by the Sponsor Medical Director 
prior to database lock.  Analyses of the PP population will be analyzed as treated. 
5.5.4 Safety Population 
The safety population includes all randomized subjects who received at least 1 dose 
of study medication. Subjects in the safety population will be analyzed as treated. 
 
5.6 Estimands, Intercurrent Events, and Missing Data 
Summary of primary estimand:  


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 19 of 38 
 
In individuals with MCI (high or intermediate likelihood due to AD) or dementia due 
to AD, what is the effect of treatment taken for 24 weeks (estimated from the model) 
relative to placebo during the double-blind phase, in the protocol-defined ITT study 
population as measured by a GST that encompasses MADCOMS, FAQ, and 
hippocampal volume. 
1. Objective  
An estimate of efficacy which would potentially be supportive of proof of concept 
2. Estimand 
A. The population is the ITT population as defined by the protocol’s inclusion and 
exclusion criteria. 
B. Efficacy is measured by the estimated change from baseline at 24 weeks in the 
primary endpoint (GST) 
C. The treatment evaluated is the randomized treatment as it was assigned to study 
subjects. All types of intercurrent events are incorporated using a treatment policy 
strategy, which evaluates the randomized treatment as taken including missed or 
modified doses, drug discontinuation, and concurrent treatments. Deaths are not 
expected during the 24 week study. 
D. The mean change from baseline between treatment and control arms on the primary 
endpoint will be estimated at 24 weeks. A significant difference at a familywise error 
rate of 5% will be required for success. However we will consider a trending 
association (P<0.1) as proof of concept given the small sample size of the study. 
3. Primary estimator and missing data. 
The estimator is a continuous time MMRM using all available assessments. Due to the 
small sample size the model will be optimized by implementation of two composite 
covariates  that account for multiple baseline covariates in one variable. The composite 
covariate will be derived from blinded data and generated using the baseline model 
covariates (excluding treatment and visit) or the baseline model covariates* time 
interactions. The composite covariates will be included as a covariate in the model.   
Item scores that compose the GST for individuals that have right censored missing 
values and at least one baseline visit will be carried forward using LZCF.  If an 
individual is missing all post-baseline data, the z-score of the population baseline 
values will be used to estimate the LZCF within treatment groups for post-baseline 
visits. Interim visits for total hippocampal volume, which was assessed at baseline and 
24 weeks, will be imputed using straight line imputation at the observed or scheduled 
visit timepoints. Straight line imputation will also be performed for items that compose 
the GST (MADCOMS and FAQ) for timepoints with intermittent missing values (i.e. 
flanked by timepoints with data collected).  The 24 week estimate will be drawn from 
the MMRM model using the data imputed as described. 
LZCF assumes that subjects will follow the same trajectory after dropping out of the 
study, conditional on the model covariates as listed in Section 7.5.1.  However, if 
subjects tend to preferentially drop out due to study drug related events, it is possible 
that their post-dropout trajectory may differ from their pre-dropout trajectory.  In this 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 20 of 38 
 
case  the above specified assumption may not hold. A sensitivity analyses is proposed 
to assess this scenario. 
4. Sensitivity analyses and missing data.   
To assess the effect of LZCF on the primary outcome, the MMRM will be repeated 
without LZCF imputation and mean differences assessed. The primary analysis will 
incorporate hippocampal volume quantitation from cross-sectional data to meet the 
ITT population requirements.  A separate sensitivity analysis using the subset of data 
with longitudinal pairs will also be performed.  
5.7 Data Review 
Classification of deviations from the protocol as minor or major, and decisions regarding 
patient population assignments will be decided on a case-by-case basis without knowledge 
of the treatment assigned and before the database lock in a blinded data review meeting.  
After database lock, the responsible statistician will request the treatment codes, the study 
will be unblinded, and the statistical analysis will be conducted. 
5.8 Missing Data 
Patients who drop out will have all available post-baseline data included in the analysis, 
unless otherwise specified. Patients that lack information at a visit due to early termination, 
etc will be imputed using LZCF for efficacy analyses. LZCF allows imputation of the data 
such that individual trajectory carries on relative to the mean and standard deviation at each 
visit.  For individuals with only baseline data, baseline z-scores will be used to calculate 
LZCF for post-baseline visits within treatment groups. All patients will appear in each 
listing. Patients Excluded from One or More Analysis Sets (Listing 16.1.4), General 
Comments (Listing 16.1.7), Serious AEs (Listing 16.3.1.2), AEs Leading to 
Discontinuation or Death (Listing 16.3.2), and Clinically Significant Laboratory 
Abnormalities (Listing 16.3.4). Patients with no applicable data will be listed with “No 
Data” on the line.  
 
Additionally, patients with intermittant missing data will have values imputed using 
straight line imputation.  Right censored data will be imputed using LZCF.  In the event 
that a total score is missing individual items, LZCF or straight line imputation will be 
performed at the item level to fill in missing values prior to calculating total scores.  
6 Study Conduct  
6.1 Treatment Assignments 
Upon locking the database the study will be unblinded. Blinded reconciliation of 
demographic elements between this list and the clinical database will already have taken 
place. The treatment assignment will be given to each patient and 100% verified. 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 21 of 38 
 
6.2 Enrollment, Demographics, and Baseline Characteristics 
A summary table will be provided for the All Patients Population to show the study 
timelines: the earliest and latest date of screening visit, of study drug intake, and study 
participation as well as the duration in days of screening, treatment and study participation.  
A summary table will be provided for the Safety Population to summarize demographics, 
i.e. age, gender, race, height and weight at baseline. The table will be repeated for the ITT 
and PP Populations. The equality between treatment groups for each of these parameters 
will be tested with a t-test or Fisher’s exact test, as appropriate. 
The supportive listings will present all data on the Informed Consent / Demographics CRF 
page. The listings of disposition, drug dispensing and return, and vital signs also partly 
support these tables.  
6.3 Patient Disposition and Protocol Deviations 
A summary table will be provided for the All Patients Population to display the number of 
subjects randomized, Safety Population, ITT Population, and patients who completed or 
discontinued the study. Listings will be provided for the different reasons for screen failure, 
discontinuation, and exclusion from the analysis populations. Reasons for discontinuation 
will be taken from the End of Study form. Reasons for exclusion from the PP Population 
will be taken from the PP source documentation mentioned in Section 5.5.3.  
A summary table will be provided for all randomized patients to include those with at least 
one deviation. Major deviations as reported on corresponding eCRF will be summarized; 
within each classification the count and percent of each category that appears on the CRF 
will be displayed.  
Supportive listings will present all information on the Study Completion / Early 
Termination CRF page and the Protocol Deviations page. Another supportive listing will 
display patients excluded from any analysis population along with the reason(s) for 
exclusion.  
6.4 Extent of Exposure to Study Drug 
A summary table will be provided for the Safety Population stratified by treatment group 
to summarize the duration of treatment, total dose received, average dose per day and 
compliance. The count and percentage of subjects with compliance below 80% and above 
110% will be provided as an assessment of under/overdosing.   
The supportive listing will present all data on the Drug Dispensing and Return CRF page.  
6.5 Medical History 
Abnormal medical history findings are recorded by system. Patients with no abnormal 
medical history have a No at the top of the page and have the rest of the page blank. Patients 
with some abnormal history but also some normal systems have N/A for the normal 
systems.  
Findings are coded with the Medical Dictionary for Regulatory Affairs (MedDRA). The 
version number will be shown as a footnote in the displays. A listing will be provided of 
these data and will include all patients in the study. A summary table will be provided to 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 22 of 38 
 
show the count and percentage of patients with abnormal medical history by system organ 
class and preferred term. Patients will be counted at most once per term.  
6.6 General Comments 
A listing will be provided of all general comments recorded on the corresponding CRF 
page. 
Any deviations from the SAP will be described. 
7 Efficacy Analyses 
All efficacy endpoints will be characterized for association response to treatment over 
time and effect size for the purposes of designing an efficacy study using the ITT and Per 
Protocol populations. 
 
7.1.1 Primary Endpoints 
1) To assess the impact of AMX0035 on AD progression by assessing the 
performance of multiple outcome measures using a global statistical test (GST) 
(MADCOMS, FAQ, hippocampal volume (MRI)) for change from baseline to 24 
weeks. 
7.1.2 Secondary Endpoints (listed in hierarchical order) 
1. To assess the impact of AMX0035 on hippocampal volume. 
 
To assess the impact of AMX0035 on clinical symptoms as measured by: 
2. MADCOMS  
3. ADAS-Cog14 
4. FAQ 
5. DSRS 
6. MoCA 
7. Neuropsychiatric Inventory Questionnaire (NPI-Q) 
7.1.3 Biomarker Endpoints  
To determine the effects of AMX0035 treatment on: 
1. whole brain volume 
2. ventricular volume 
3. functional MRI measures including connectivity with resting state BOLD; 
4. cerebrospinal fluid (CSF) and plasma biochemical markers, including: 
• 
 
 
 
 
 
 
 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 23 of 38 
 
• 
 
 
  
 
 
 Primary Efficacy Endpoints 
7.2.1 Global Statistical Test 
A GST allows assessment of a global change in disease status/trajectory by standardizing 
and then combining measures. The GST will be a combination of 3 change from baseline 
to end of study endpoints (MADCOMS, FAQ, and total hippocampal brain volume).  The 
GST will be calculated for each subject as a mean score across the three component 
endpoints. This mean score will be analyzed as the primary efficacy outcome variable. 
7.2.2 MADCOMS 
ADAS-Cog 14 is  not specifically targeted to the mild/moderate stage of AD. A 
mild/moderate AD composite scale (MADCOMS) was previously optimized for the two 
distinct groups, mild AD (baseline MMSE 20-26) and moderate AD (baseline MMSE 14-
19).  The weighted composite was derived using PLS regression from ADAS-Cog, MMSE, 
and CDR individual items (S.Hendrix ADPD 2021).  
Moderate MADCOM=  
𝐶𝑜𝑚𝑝𝑟𝑒ℎ𝑒𝑛𝑠𝑖𝑜𝑛∗0.36390157 +  𝑊𝑜𝑟𝑑 𝐹𝑖𝑛𝑑𝑖𝑛𝑔∗0.10931155 
+  𝐼𝑑𝑒𝑎𝑡𝑖𝑜𝑛𝑎𝑙 𝑃𝑟𝑎𝑥𝑖𝑠∗0.42535667 +  𝑁𝑎𝑚𝑖𝑛𝑔 𝑂𝑏𝑗𝑒𝑐𝑡𝑠
∗0.65626894 +  𝑊𝑜𝑟𝑑 𝑅𝑒𝑐𝑜𝑔𝑛𝑖𝑡𝑖𝑜𝑛∗0.05159097 
+  𝑊𝑜𝑟𝑑 𝑅𝑒𝑐𝑎𝑙𝑙∗1.0698506 +  𝑆𝑝𝑜𝑘𝑒𝑛 𝐿𝑎𝑛𝑔𝑢𝑎𝑔𝑒
∗0.3019936 +  𝐻𝑜𝑚𝑒 𝑎𝑛𝑑 𝐻𝑜𝑏𝑏𝑖𝑒𝑠∗0.66529282 + 𝑀𝑒𝑚𝑜𝑟𝑦
∗0.12277257 − 𝑂𝑟𝑖𝑒𝑛𝑡𝑎𝑡𝑖𝑜𝑛 𝑡𝑜 𝑃𝑙𝑎𝑐𝑒∗0.23001218 
− 𝑆𝑝𝑒𝑙𝑙 𝐵𝑎𝑐𝑘𝑤𝑎𝑟𝑑∗0.07980965 − 𝐿𝑎𝑛𝑔𝑢𝑎𝑔𝑒 𝑎𝑛𝑑 𝑃𝑟𝑎𝑥𝑖𝑠
∗0.18954955 
Mild MADCOM= 
𝑊𝑜𝑟𝑑 𝐹𝑖𝑛𝑑𝑖𝑛𝑔∗0.39065568 +  𝑊𝑜𝑟𝑑 𝑅𝑒𝑐𝑎𝑙𝑙∗1.14084544 
+  𝑆𝑝𝑜𝑘𝑒𝑛 𝐿𝑎𝑛𝑔𝑢𝑎𝑔𝑒∗1.09895590 +  𝑃𝑒𝑟𝑠𝑜𝑛𝑎𝑙 𝐶𝑎𝑟𝑒
∗0.60865765 +  𝐶𝑜𝑚𝑚𝑢𝑛𝑖𝑡𝑦 𝐴𝑓𝑓𝑎𝑖𝑟𝑠∗0.15706995 
+  𝐽𝑢𝑑𝑔𝑚𝑒𝑛𝑡∗1.40920029 − 𝑂𝑟𝑖𝑒𝑛𝑡𝑎𝑡𝑖𝑜𝑛 𝑡𝑜 𝑇𝑖𝑚𝑒
∗0.27596627  
The current study collected DSRS (equivalent to CDR) and MoCA (equivalent to MMSE).  
The equivalent DSRS and MoCA test items were scaled to the MMSE or CDR test range 
and used to make MADCOMS.  
 
MMSE to MoCA conversion: 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 24 of 38 
 
MMSE Domain 
MoCA 
question(s) 
scale 
Orientation to Time 
17-20 
5/4 
Orientation to Place 
21-22 
5/2 
Attention and 
Calculation 
10 
5/3 
Recall 
14 
3/5 
Naming 
6 
2/3 
Repetition 
11 
1/2 
Commands 
9 
3/1 
Reading 
13 
1/2 
Drawing 
2 
1 
 
CDR to DSRS conversion: 
CDR Domain 
DSRS 
question(s) 
Memory 
1 
Orientation 
4-5 
Judgement and 
Problem Solving 
6 
Community Affairs 
7 
Home and Hobbies 
8 
Personal Care 
9 & 11 
DSRS values were converted to CDR scales by dividing the sum of the DSRS questions 
that make up the equivalent CDR domain score by the max score for those questions.  
Memory, orientation, judgement and problem solving, community affairs, as well as home 
and hobbies are multiplied by 4 to create 5 categories. That are assigned to 0,0.5,1,2, or 3 
by their rank value.  Personal care  scores are multiplied by 3 to create 4 categories that are 
assigned to 0,1,2, or 3 by their rank value. 
7.2.3 FAQ 
The FAQ, is a secondary endpoint, however included here due to inclusion in the GST.  
FAQ is a brief informant-administered rating scale used to determine a subjects’ level of 
functional independence when performing a range of instrumental activities of daily living 
(IADLs), with repeat assessments useful for monitoring performance in these areas over 
time47. The FAQ total score (ranging from 0-30) reflects the sum of ordinal ratings (0 = 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 25 of 38 
 
fully independent, 1 = has difficulty but does by self, 2 = requires assistance, and 3 = 
dependent) across ten items assessing a variety of functional activities (i.e., preparing a 
balanced meal, financial management skills, and shopping), with higher scores indicating 
increasing levels of dependence. For activities not normally undertaken by a person, a 
score of 1 is assigned if the informant believes the subject would be unable to complete 
the task if required, or a score of 0 is assigned if the informant believes the subject could 
successfully carry out the task if needed. Overall, the FAQ is a sensitive marker of 
functional impairment among individuals with varying dementia severity43, and has been 
shown to differentiate mild cognitive impairment from early Alzheimer’s Disease with 
80% sensitivity and 87% specificity49. The FAQ demonstrates high reliability (exceeding 
0.90), takes about 5 minutes to complete, and requires limited rater training to 
administer47.  The FAQ will be administered at the Baseline, Week 12, and Week 24/Early 
Discontinuation Visits. 
7.2.4 Total Hippocampal Brain Volume (volumetric MRI) 
Whole brain volume is a secondary endpoint included here due to incorporation in the 
GST.  Ventricular volume and hippocampal volume will be measured. MRI imaging 
of the brain will be performed in order to measure brain atrophy over time. Imaging 
will be performed using cross-sectional approach for baseline and week 24 samples as 
well as using the longitudinal approach for baseline and week 24 pairs. Results from 
vMRI studies suggest that the patterns of atrophy in AD can reliably be detected and 
tracked across time. Hippocampal volume derived from MRI correlates with 
histological hippocampal volume and degree of neuronal loss and AD pathology. 
Longitudinal MRI measures of regional and whole brain volumetric change provide 
a valuable complement to cognitive measures in that they are not influenced by 
temporary symptomatic improvements, and they may provide an early index of the 
study drug’s ability to reach the central nervous system and effect AD-related 
atrophy. 
7.3  Secondary Efficacy Endpoints 
7.3.1 ADAS-Cog 
The ADAS-Cog is validated and widely used as a primary cognitive outcome measure in 
AD pharmacotherapy studies. This is a psychometric instrument that evaluates memory 
(immediate and delayed word recall, word recognition), attention (number cancellation), 
reasoning (following commands), language (naming, comprehension), orientation, 
ideational praxis (placing letter in envelope) and constructional praxis (copying geometric 
designs), and executive functioning (maze completion). Scoring is in the range of 0 to 90 
with a higher score indicating greater impairment. This test will be administered by 
experienced raters at each site according to Table 1. 
 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 26 of 38 
 
7.3.2 Dementia Severity Rating Scale (DSRS) 
The DSRS is a brief 12-item questionnaire administered to an informant that assesses a 
subjects’ functional abilities44 and offers a global characterization of everyday activities 
that may be impacted by neurodegenerative disease. The DSRS is designed in a multi-
choice format with strong concurrent validity and parallel content to material covered on 
the Clinical Dementia Rating Scale (CDR), a commonly employed dementia staging 
instrument46. The DSRS is a highly reliable scale with an intra-class correlation of >90% 
for interrater reliability and Cronbach’s alpha > 0.70 for internal consistency48, and has 
been shown to accurately discriminate between cognitive healthy individuals and dementia 
subjects of varying severity44,45. Further, the DSRS allows for a broad range of scores (total 
score 0-54) making it suitable to quantify a wide range of functional impairment without 
being hampered by floor effects seen in more advanced disease, while also making it 
sensitive to detecting incremental change in functional ability over time50. The DSRS takes 
about 5 minutes to administer, requires minimal rater training, and can be administered 
over the phone to study subjects if required. The DSRS will be administered at the Baseline, 
Week 12, and Week 24/Early Discontinuation Visits. 
7.3.3 MoCA 
Montreal Cognitive Assessment (MoCA) is commonly utilized questionnaire in clinical 
trials and research settings to measure levels of cognitive impairment. The MoCA measures 
five areas of cognitive function: orientation, visuospatial, attention and calculation, recall, 
and language. The MoCA will take approximately 10 minutes to complete. The test will 
be administered by experienced raters at each site at Screening, Week 6, Week 18, Week 
24/Early Discontinuation Visit. See Appendix III (section 13.3) for the worksheet. 
The 3 available versions of the MoCA test will be administered by experienced raters at 
each site. Subjects may be given any version of the MoCA at the Screening Visit as long 
as they have NOT received the same MoCA version clinically within the last 3 months. A 
different version of the MoCA should be used at each subsequent visit until Week 24 or 
Early Termination visit (if applicable). The MoCA version used at a study visit should be 
accurately documented in Source Document and within the EDC for each visit. 
Re-screening: In cases where the subject screen fails due to the MoCA score being out of 
the required inclusionary range at the Screening Visit, the subject may be re-screened; a 
minimum of one month must have passed since their original MoCA assessment. If the 
subject’s MoCA score was < 10, they must have had a change in therapy or intervention 
that (in the opinion of the SI) may have an impact on the subject’s cognitive status. Subjects 
who move forward with a re-screen must be evaluated using a different MoCA version 
(7.1, 7.2 or 7.3) that was used at the original Screening Visit, and subjects may be re-
screened only once. 
7.3.4 NPI-Q 
The Neuropsychiatric Inventory (NPI) measures dementia-related behavioral symptoms 
and is used to assess changes in psychological status.  There are several versions of the NPI 
including the NPI-Questionnaire (NPI-Q), NPI-Clinician (NPI-C) and the NPI-Nursing 
Home (NPI-NH).  All examine 12 sub-domains of behavioral functioning including: 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 27 of 38 
 
hallucinations, delusions, agitation, dysphoria, anxiety, euphoria, apathy, disinhibition, 
irritability, aberrant motor activity, eating abnormalities, and night-time behavioral 
alternations. The NPI-Q is completed by a trained rater through interview with the subject's 
study partner. It is well-validated and extensively used in clinical trials in AD. The NPI-Q 
will be administered at the Screening or Baseline, Week 12 and Week 24/Early 
Discontinuation Visits. 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
  
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 28 of 38 
 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 29 of 38 
 
 
  
7.4.2.7 Additional Biomarkers 
Additional biomarker panels, focused on 
 
, will likely be performed in CSF and plasma.  
 
 
 
 
 
 
 
 
 
 
 
7.4.3 Pharmacokinetics 
Plasma and CSF concentrations for PB, TUDCA and their respective direct metabolites 
will be determined on the single PK samples taken on study visit 12 and 24 (week 24 only 
for CSF). The plasma concentrations are intended to approximate overall exposure at 
steady state in patients treated with AMX0035 and provide an estimate of endogenous bile 
acid concentrations in patients treated with placebo. PK analyses will be detailed in a 
separate document. 
7.5 Statistical Evaluations 
Efficacy analyses will be performed in the ITT and PP populations. The Per Protocol 
population analysis will include individuals within the per protocol population and visit 
data for individuals not in this population up until the point of non-compliance (4 
cumulative weeks of missed treatment or major protocol violation). 
 
7.5.1 Primary Analyses 
The GST will be a combination of 3 change-from-baseline to end-of-study endpoints 
(univariate components): 
o Cognition (MADCOMS) 
o Functional Activities Questionnaire (FAQ) 
o Total Hippocampal Brain Volume (cross-sectional data) 
 
The GST will be calculated for each subject as a mean zscore across the above 3 component 
endpoints for each subject in the study. This mean score will then be analyzed as the 
primary efficacy outcome variable.  
GST individual items with right censored data will be imputed using LZCF. Intermittently 
missing data will be imputed using straight line imputation. Straight line imputation or z-
scores will be calculated for each data collection timepoint in the study (baseline, week 6, 
week 12, week 18, week 24) .  Let Z be the imputed z-score, while x is the last observation 
at timepoint t1 and µ and σ are the mean and standard deviation of the next timepoint (t2) 
for which the data is missing. 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 30 of 38 
 
Zt2=(xt1 - µt2)/σt2 
Z-scores imputed relative to the group mean and standard deviation at each timepoint, will 
better preserve the slope of each arm and thus is more robust to differences in dropout rate 
across treatment. Individuals missing all post-baseline data will use the population baseline 
zscore to calculate LZCF by treatment group. GST will be calculated for each individual 
after LZCF is calculated for individual level items. LZCF imputations will be constrained 
by the range of the possible score for each measure. 
 A composite covariate will be calculated for the primary efficacy variable (GST) to 
adjust for baseline covariates as well as those that interact with time and will be included 
in the model. To calculate the composite, the change score (GST) is regressed on time.  
The residuals are regressed on the covariates listed below.  Individual composite 
coefficients for each covariate are multiplied by individual covariate values and summed. 
A separate covariate composite is calculated for baseline covariates and baseline 
covariates interacting with time. 
CFB will be analyzed by comparing the change between treatment group using a mixed 
model with repeated measures (MMRM). The MMRM will compare the estimated change 
from baseline between treatments for each primary endpoint. This analysis will assess 
whether there is a difference in estimated CFB between active and placebo groups.  
The MMRM with primary outcome CFB value as the response variable will include the 
following covariates and fixed effects: 
• 
Baseline composite covariate only: 
• Age (covariate); 
• baseline ADAS-Cog 
• baseline MOCA 
• baseline FAQ 
• baseline DSRS 
• baseline Hippocampal volume 
• AD/dementia status (fixed effect); 
• Concomittant use of AD medications 
• Level of Education (fixed effect split into categories of ≤12 years, >12 
years); 
• Sex (fixed effect); 
• APOE4 status (fixed effect, positive or negative); 
 
• 
Time composite covariate only: 
• time 
• Age*time; 
• baseline ADAS-Cog*time 
• baseline MOCA*time 
• baseline FAQ*time 
• baseline DSRS*time 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 31 of 38 
 
• baseline Hippocampal volume*time 
• AD/dementia status*time; 
• Concomittant use of AD medications*time 
• Level of Education*time (fixed effect split into categories of ≤12 
years, >12 years); 
• Sex*time; 
• APOE4 status*time (positive or negative); 
 
• 
Time (continuous time); 
• 
Time by treatment interaction (Time*Treatment); 
• 
Baseline Test Score of Efficacy Parameter (covariate); 
• 
Site (random effect); 
 
The covariance structure for the repeated measures in this model will be 
unstructured (UN). If UN does not converge for the model, the MMRM model will 
be simplified to allow convergence as described in the following paragraph. 
Variance components will be used as the covariance structure for the random site 
effect in the model. 
Any efficacy outcomes that do not converge using the specified primary model will 
be rerun using a first-order heterogeneous autoregressive (ARH[1]) covariance 
structure, and then a compound symmetry (CS) followed by variance components 
(VC) structures if ARH(1) doesn’t converge.  The covariance structure for the site 
random effect will be VC. 
Least-squares means will be estimated at each visit for the primary outcome.  The LS 
mean at the endpoint is interpreted as the expected CFB in the primary outcome at the 24 
week estimate drawn from the model within each group.  Least squares means and 
standard errors will be estimated from the mixed model at all timepoints (week 12 and 24) 
and will be shown for all analyses.  In addition, treatment differences, p-values, 95% 
confidence intervals for the difference, effect size, 95% confidence interval for the effect 
size, and an effect size based upon Cohen’s D will be displayed for each comparison.  
Effect size will be calculated by taking the difference of LSMEANS and dividing by the 
standard deviation (i.e. the standard error of the estimated difference multiplied by the 
squared degrees of freedom).  The equations below show how effect size and Cohen’s D 
effect size will be calculated. In the following formulas p stands for placebo group and t 
stands for treated), SE for standard error and df for degrees of freedom: 
𝐸𝑓𝑓𝑒𝑐𝑡 𝑆𝑖𝑧𝑒= 𝐿𝑆𝑀𝐸𝐴𝑁𝑡−𝐿𝑆𝑀𝐸𝐴𝑁𝑝
𝐿𝑆𝑀𝐸𝐴𝑁𝑃
 
Cohen’s d will be calculated using the following equation: 
Cohen’s 𝑑=
𝜇𝑡−𝜇𝑝
(𝑝𝑜𝑜𝑙𝑒𝑑 𝑆𝐷), 
where the pooled standard deviation (pooled SD) is defined as follows: 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 32 of 38 
 
𝑃𝑜𝑜𝑙𝑒𝑑 𝑆𝐷= √((𝑛𝑡−1)(𝑆𝐸𝑡 √𝑛𝑡 )2 + ((𝑛𝑝−1)(𝑆𝐸𝑝 √𝑛𝑝 )2
(𝑛𝑡+ 𝑛𝑝−1)
. 
The number of subjects with an observed efficacy outcome, mean, standard deviation, 
median, 25th percentile (Q1), 75th percentile (Q3), minimum and maximum will all be 
reported and accompany the estimates from the MMRM outlined in this section (Tables 
14.2.1-14.2.16).  
7.5.1.1 Covariate and Categorical Interaction Analyses 
The following variables will be assessed for interactions with the primary efficacy 
variable and time using the MMRM as described above: 
• baseline score (for outcome being analyzed) 
• baseline MoCA score 
• ApoE4(carrier/non-carrier; discrete) 
• ApoE4(number of E4 alleles; discrete) 
Estimates for continuous variables will be drawn at the first and third quartiles. 
An MMRM without imputation will be performed as a sensitivity analysis. The same 
MMRM parameters described above will be used. Additionally, an MMRM will be run for 
the primary analysis using MRI quantitative data generated with the longitudinal approach. 
7.5.2 Secondary Analyses 
All secondary endpoints CFB values will be analyzed using the MMRM described above. 
This analysis will assess whether or not there is a difference in estimated CFB values 
between treatment groups and placebo at the 24 week model estimate using least squares 
means estimates from the MMRM model. 
7.5.2.1 PK Analyses 
PK will be analyzed using the ITT population. Descriptive statistics will be provided for 
the AMX0035 and placebo treatment groups.  Additionally, correlations of  exposure 
values to clinical outcomes may be assessed, if possible, by correlation to  concentration 
data as well as summarization of outcomes data in the upper and lower PK tertiles. 
 
The PK concentration data collected prior to each dose may be used in a concentration 
response relationship analysis to assess correlation with each outcome which will mirror 
the primary analysis but replace the treatment variable with PK concentration. Analysis 
may be performed separately for each PK collection time as well as using the higher  of 
both PK timepoints. 
 
 
 
 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 33 of 38 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 34 of 38 
 
8 Safety 
8.1 Safety Endpoints 
Primary endpoint 
• incidence of treatment emergent Grade II-IV adverse events (includes moderate/ 
severe/ serious adverse events) 
Additional endpoints 
• 
Incidence and severity of treatment emergent adverse events (AEs) 
• 
Clinical laboratory tests  
• 
Vital signs  
• 
Physical examinations 
• 
ECGs 
• 
Use of concomitant medications for treatment of AEs 
• 
C-SSRS 
8.2 Analysis Populations Evaluated for Safety 
All analyses of safety will be performed on the Safety Population. 
8.3 Statistical Methods for Safety Endpoints 
A summary table will be provided for the Safety Population of the count and percentage of 
subjects with any safety endpoint. No hypothesis testing will be performed for safety variables. 
8.4 Adverse Events 
AEs reported on CRFs will be coded into system organ classes and preferred terms using 
the Medical Dictionary for Regulatory Activities (MedDRA v23.1). A treatment-emergent 
adverse event (TEAE) is defined as an AE with an onset date on or after the start of dosing. 
The adverse event summary will include only TEAEs. Any AEs that are not considered 
treatment-emergent will be provided in data listings only.  
 
The incidence of AEs will be summarized for the safety population. Although a preferred term 
or system organ class may be reported more than once for a subject, each subject will only be 
counted once in the incidence count for each category. If a subject has the same AE on multiple 
occasions, the highest severity (severe > moderate > mild) or drug relationship (definite > 
probable > possible > unlikely > not related) recorded for the event will be presented.  
 
Severity levels include: mild, moderate and severe. Relationships will be grouped into two 
categories for analysis: related and unrelated. Not related and unlikely will be categorized as 
“unrelated.” Possible, probable and definite will be categorized as “related.” If severity or drug 
relationship is missing no data imputation will be performed and no category of missing will 
be presented.  
 
Summary tables showing the number of subjects and percent within each category will be 
generated for each of the following types of adverse events: 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 35 of 38 
 
 
• All AEs; 
• Fatal Adverse Events; 
• AEs for Subjects who Died. 
• AEs with concomitant medications 
  
These summaries will present the number and percentage of subjects reporting an adverse 
event for each classification level. The denominators for calculating the percentages overall 
will be based on the number of subjects in the safety population. The denominators for 
calculating the percentages by treatment will be based on the number of subjects exposed to 
each treatment in the safety population. In addition to these summaries, all AEs will be 
summarized by action taken, seriousness, severity, and relationship to study drug. 
 
All AEs that occurred in 5% or more of all subjects (active and placebo) will be tabulated for 
the safety population. These results will be analyzed descriptively and their incidence rate and 
two-sided 95% confidence intervals will be summarized. In addition, the risk ratio and its 95% 
confidence intervals between active and placebo will be calculated in order to estimate the 
occurrence of side effects and adverse events.  
 
All SAEs, AEs leading to premature discontinuation from the study, AEs with fatal outcome, 
and AEs for subjects who died will also be provided in data listings by subject and preferred 
term. 
8.5 Vital Signs  
Each vital sign will be summarized by treatment and overall by visit, using descriptive statistics 
(mean, median, SD, minimum, maximum, and number of subjects) for the safety population. 
Additionally, descriptive summaries will be provided for CFB values for each treatment by 
visit for vital sign measurements collected during the study.  
 
The latest non-missing vital sign value collected prior to dosing will be used as the baseline 
values. The baseline values will usually be the vital signs recorded at the baseline visit. In the 
case of repeated vital signs, the last collected values within that visit will be used for the 
summary tables. 
 
Vital signs will be provided in a data listing by subject, visit, and parameter.   
8.6 Electrocardiogram 
ECG values and change from baseline values will be summarized by visit using descriptive 
statistics. ECG abnormalities will be summarized as the count and percentage of subjects in 
each treatment group. CFB will be summarized in a shift table crossing baseline and each visit 
result. The denominators for calculating the percentages will be the number of subjects in each 
treatment group who have an evaluation for both the screening and each visit in the safety 
population. These results will be analyzed descriptively and their incidence rate and two-sided 
95% confidence intervals will be summarized. 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 36 of 38 
 
8.7 Clinical Laboratory Evaluations 
Continuous blood clinical laboratory analytes absolute values and change from baseline values 
will be summarized by analyte and visit using descriptive statistics (mean, median, SD, 
minimum, maximum, and number of subjects). Mean line plots over time will be displayed for 
each analyte with separate lines for each treatment. Categorical laboratory analytes, classified 
as normal or abnormal, will be summarized by analyte and visit using the number and 
percentage of subjects in each category. The denominators for calculating the percentages will 
be based on the number of subjects with non-missing assessments at a particular visit for the 
safety population. The latest non-missing clinical laboratory tests collected prior to dosing will 
be used as the baseline values. 
 
Shifts to values outside of the normal range will be presented by analyte and will be 
summarized by the number and percentage of subjects with shifts. Shifts will be determined 
for analytes in which both the baseline value and the termination value are recorded. The 
denominators for calculating the percentages will be based on the number of subjects with non-
missing assessments for a particular analyte. 
 
Clinical laboratory results will be provided in data listings by subject, visit and analyte. 
Abnormal lab results will be provided in a separate listing by subject, center, analyte and visit. 
8.8 Physical and Neurological Exams 
Physical and neurological examination findings will be summarized as the count and 
percentage of subjects in each treatment group.  
8.9 C-SSRS 
The C-SSRS responses will be tabulated by visit, treatment group, question and response. All 
C-SSRS responses will also be provided in a data listing. 
 
9 Other Listings  
The following additional listings will be provided: 
• Subjects excluded from the safety, mITT, and PP populations; 
• Clinical laboratory results for hematology, blood chemistry and urinalysis;  
• Abnormal laboratory results; 
• Physical examination assessments; 
• Neurological examination assessments; 
• Concomitant medications; 
• Dose administration dates and times. 
Other Listings 
 
 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 37 of 38 
 
10  Bibliography 
[1] Blennow K, Mattsson N, Schöll M, Hansson O, Zetterberg H. Amyloid biomarkers in 
Alzheimer’s 
disease. 
Trends 
Pharmacol 
Sci 
2015;36:297–309. 
https://doi.org/https://doi.org/10.1016/j.tips.2015.03.002. 
[2] Mattsson N, Insel PS, Palmqvist S, Portelius E, Zetterberg H, Weiner M, et al. Cerebrospinal 
fluid tau, neurogranin, and neurofilament light in Alzheimer’s disease. EMBO Mol Med 
2016;8:1184–96. https://doi.org/https://doi.org/10.15252/emmm.201606540. 
[3] Gaetani L, Blennow K, Calabresi P, Di Filippo M, Parnetti L, Zetterberg H. Neurofilament 
light chain as a biomarker in neurological disorders. J Neurol Neurosurg &amp;Amp; 
Psychiatry 2019;90:870 LP – 881. https://doi.org/10.1136/jnnp-2018-320106. 
[4] Constantinescu R, Krýsl D, Bergquist F, Andrén K, Malmeström C, Asztély F, et al. 
Cerebrospinal fluid markers of neuronal and glial cell damage to monitor disease activity 
and predict long-term outcome in patients with autoimmune encephalitis. Eur J Neurol 
2016;23:796–806. https://doi.org/https://doi.org/10.1111/ene.12942. 
[5] Hall S, Öhrfelt A, Constantinescu R, Andreasson U, Surova Y, Bostrom F, et al. Accuracy of 
a Panel of 5 Cerebrospinal Fluid Biomarkers in the Differential Diagnosis of Patients With 
Dementia 
and/or 
Parkinsonian 
Disorders. 
Arch 
Neurol 
2012;69:1445–52. 
https://doi.org/10.1001/archneurol.2012.1654. 
[6] Petersen A, Gerges NZ. Neurogranin regulates CaM dynamics at dendritic spines. Sci Rep 
2015;5:11135. https://doi.org/10.1038/srep11135. 
[7] Portelius E, Zetterberg H, Skillbäck T, Törnqvist U, Andreasson U, Trojanowski JQ, et al. 
Cerebrospinal fluid neurogranin: relation to cognition and neurodegeneration in 
Alzheimer’s disease. Brain 2015;138:3373–85. https://doi.org/10.1093/brain/awv267. 
[8] Liu W, Lin H, He X, Chen L, Dai Y, Jia W, et al. Neurogranin as a cognitive biomarker in 
cerebrospinal fluid and blood exosomes for Alzheimer’s disease and mild cognitive 
impairment. Transl Psychiatry 2020;10:125. https://doi.org/10.1038/s41398-020-0801-2. 
[9] Isobe C, Abe T, Terayama Y. Levels of reduced and oxidized coenzyme Q-10 and 8-hydroxy-
2′-deoxyguanosine in the CSF of patients with Alzheimer’s disease demonstrate that 
mitochondrial oxidative damage and/or oxidative DNA damage contributes to the 
neurodegenerative process. J Neurol 2010;257:399–404. https://doi.org/10.1007/s00415-
009-5333-x. 
[10] Gerena Y, Menéndez-Delmestre R, Skolasky RL, Hechavarria RM, Pérez S, Hilera C, et al. 
Soluble insulin receptor as a source of insulin resistance and cognitive impairment  in HIV-
seropositive women. J Neurovirol 2015;21:113–9. https://doi.org/10.1007/s13365-014-
0310-2. 
[11] Gerena Y, Menéndez-Delmestre R, Delgado-Nieves A, Vélez J, Méndez-Álvarez J, Sierra-
Pagan JE, et al. Release of Soluble Insulin Receptor From Neurons by Cerebrospinal Fluid 
From  Patients With Neurocognitive Dysfunction and HIV Infection. Front Neurol 
2019;10:285. https://doi.org/10.3389/fneur.2019.00285. 


  
Amylyx Pharmaceuticals 
Protocol AMX8000 
Statistical Analysis Plan 
Protocol Date and Version:  8 October 2020; v2.2 
Page 38 of 38 
 
[12] Hughes TM, Rosano C, Evans RW, Kuller LH. Brain cholesterol metabolism, oxysterols, 
and dementia. J Alzheimers Dis 2013;33:891–911. https://doi.org/10.3233/JAD-2012-
121585. 
[13] Papassotiropoulos A, Lütjohann D, Bagli M, Locatelli S, Jessen F, Rao ML, et al. Plasma 
24S-hydroxycholesterol: a peripheral indicator of neuronal degeneration and  potential state 
marker 
for 
Alzheimer’s 
disease. 
Neuroreport 
2000;11:1959–62. 
https://doi.org/10.1097/00001756-200006260-00030. 
[14] Cuadrado E, Rosell A, Penalba A, Slevin M, Alvarez-Sabín J, Ortega-Aznar A, et al. 
Vascular MMP-9/TIMP-2 and neuronal MMP-10 up-regulation in human brain after stroke:  
a combined laser microdissection and protein array study. J Proteome Res 2009;8:3191–7. 
https://doi.org/10.1021/pr801012x. 
[15] Duits FH, Hernandez-Guillamon M, Montaner J, Goos JDC, Montañola A, Wattjes MP, et 
al. Matrix Metalloproteinases in Alzheimer’s Disease and Concurrent Cerebral  
Microbleeds. J Alzheimers Dis 2015;48:711–20. https://doi.org/10.3233/JAD-143186.