A Phase I Trial of the P97 Inhibitor CB-5339 in Patients With Advanced Solid Tumors and Lymphomas
Phase: PHASE1
Conditions: Aggressive Non-Hodgkin Lymphoma, Indolent Non-Hodgkin Lymphoma, Locally Advanced Malignant Solid Neoplasm, Metastatic Malignant Solid Neoplasm
Sponsor: National Cancer Institute (NCI)

i 
 
To:  
CTEP PIO 
From: 
Naoko Takebe, MD, PhD 
Date: 
March 4, 2021 
Re: 
Submission #3 to NCI Protocol #10349: “A Phase I Trial of the P97 Inhibitor CB-
5339 in Patients with Advanced Solid Tumors and Lymphomas” 
 
We would like to submit this amendment in response to CTEP disapproval of Amendment #02, 
which included a description about the recently opened Cleave-sponsored CB-5339 trial of 
patients with AML/myelodysplastic syndrome.  This amendment proposes enhanced evaluation 
of the first three patients entered on the NCI trial, specifically five days of inpatient monitoring 
during the first week of treatment.  Responses to CTEP administrative boilerplate 
recommendations are also included.  This study is only open at the NIH Clinical Center.  
 
Thank you for your consideration.   
 
I. 
 CTEP Comments Requiring a Response – Major Issues: 
# 
Section 
Comments 
1. 
SOC 
2.2.7 
Please discuss the language for the amendment for the SOC and section 2.2.7 with 
CTEP. Please submit the next summary of changes based on the previously 
approved version (amendment 1) 
 
The study team has discussed this amendment with CTEP; changes have been 
made in Section 2.2.7 and throughout the text (see heading III below). 
 
II. 
CTEP Recommendations: 
# 
Section 
Comments 
2. 
4.4.1 
Please revise the following excerpt as indicated. 
• To perform enrollments or request slot reservations:  Must be Be 
on an LPO roster, ETCTN Corresponding roster, or PO 
Participating Organization roster with the role of Registrar.  
Registrars must hold a minimum of an Associate Plus (AP) AP 
registration type. 
 
Response: these changes have been made 
 
3. 
4.3 
Please revise the following excerpt as indicated. 
 
Food and Drug Administration (FDA) regulations and National Cancer Institute (NCI) 
policy require all individuals contributing to NCI-sponsored trials to register and to renew 
their registration annually.  To register, all individuals must obtain a Cancer Therapy 
Evaluation Program (CTEP) Identity and Access Management (IAM) account at 
https://ctepcore.nci.nih.gov/iam.  In addition, persons with a registration type of 
Investigator (IVR), Non-Physician Investigator (NPIVR), or Associate Plus (AP) (i.e., 

ii 
 
# 
Section 
Comments 
clinical site staff requiring write access to Oncology Patient Enrollment Network (OPEN), 
Rave, or acting as a primary site contact) must complete their annual registration using 
CTEP’s web-based Registration and Credential Repository (RCR) at 
https://ctepcore.nci.nih.gov/rcr.   
 
Please revise the following excerpt as indicated. 
• AP:  clinical site staff (e.g., RN or CRA) with data entry access to 
CTSU applications such as the Roster Update Management 
System (RUMS), OPEN, Rave, acting as a primary site contact, or 
with consenting privileges (e.g., Roster Update Management 
System [RUMS], OPEN, Rave,), 
 
Please replace the paragraph specified below with the following language. 
 
In addition, all investigators acting as the Site-Protocol PI (Investigator listed on the IRB 
approval), consenting/treating/drug shipment investigator in OPEN, or as the Clinical 
Investigator (CI) on the DTL must be rostered at the enrolling site with a participating 
organization.  
 
In addition, all investigators act as the Site Protocol PI, consenting/treating/drug shipment, 
or as the CI on the DTL must be rostered at the enrolling site with a participating 
organization (i.e., Alliance). 
 
Response: these changes have been made 
 
4. 
4.4.2 
Please revise the following excerpt as indicated. 
 
Submit required forms and documents to the CTSU Regulatory Office via the Regulatory 
Submission Portal on the CTSU website.  
 
To access the Regulatory Submission Portal, log on to the CTSU members’ website, go to 
the Regulatory section, and select Regulatory Submission. 
To access the Regulatory Submission Portal, log on to the CTSU 
members’ website → Regulatory → Regulatory Submission. 
Institutions with patients waiting that are unable to use the Regulatory 
Submission Portal should alert the CTSU Regulatory Office immediately 
at 1-866-651-2878 in order to receive further instruction and support. 
Response: these changes have been made 
 
5. 
4.4.4 
Please delete the information within this subsection and replace with the following 
language. 
 
1.1.1 
Checking Site Registration Status 
 
Site’s registration status may be verified on the CTSU website.  

iii 
 
# 
Section 
Comments 
 
• Click on Regulatory at the top of the screen, 
• Click on Site Registration, and  
• Enter the site’s 5-character CTEP Institution Code and click on Go. 
o Additional filters are available to sort by Protocol, Registration 
Status, Protocol Status, and/or IRB Type. 
 
Note:  The status shown only reflects institutional compliance with site registration 
requirements as outlined within the protocol.  It does not reflect compliance with protocol 
requirements for individuals participating on the protocol or the enrolling investigator’s 
status with NCI or their affiliated networks. 
 
Response: these changes have been made 
 
6. 
9.3.1 
As it has been indicated that 10349 uses Rave-CTEP-AERS, please replace the 
language in this subsection with the following language. 
 
9.3.1 Rave-CTEP-AERS Integration 
 
The Rave Cancer Therapy Evaluation Program Adverse Event Reporting System 
(CTEP-AERS) integration enables evaluation of post-baseline AEs entered in 
Rave to determine whether they require expedited reporting, and facilitates entry 
in CTEP-AERS for those AEs requiring expedited reporting.    
 
All AEs that occur after baseline are collected in Medidata Rave using the 
Adverse Event form, which is available for entry at each treatment or reporting 
period, and used to collect AEs that start during the period or persist from the 
previous reporting period.  CRA will enter AEs that occur prior to the start of 
treatment on a baseline form that is not included in the Rave-CTEP-AERS 
integration.  AEs that occur prior to enrollment must begin and end on the 
baseline Adverse Event form and should not be included on the standard Adverse 
Events form that is available at treatment unless there has been an increase in 
grade. 
 
Prior to sending AEs through the rules evaluation process, site staff should verify 
the following on the Adverse Event form in Rave: 
 
• The reporting period (course/cycle) is correct, and 
• AEs are recorded and complete (no missing fields) and the form is 
query-free.  
 
The CRA reports AEs in Rave at the time the Investigator learns of the event.  If 
the CRA modifies an AE, it must be re-submitted for rules evaluation. 
 
Upon completion of AE entry in Medidata Rave, the CRA submits the AE for 
rules evaluation by completing the Expedited Reporting Evaluation form.  Both 
NCI and protocol-specific reporting rules evaluate the AEs submitted for 

iv 
 
# 
Section 
Comments 
expedited reporting.  A report is initiated in CTEP-AERS using information 
entered in Medidata Rave for AEs that meet reporting requirements.  The CRA 
completes the report by accessing CTEP-AERS via a direct link on the Medidata 
Rave Expedited Reporting Evaluation form. 
 
In the rare occurrence that Internet connectivity is lost, a 24-hour notification is to 
be made to CTEP by telephone at 301-897-7497.  Once internet connectivity is 
restored, the 24-hour notification that was phoned in must be entered immediately 
into CTEP-AERS using the direct link from Medidata Rave. 
 
Additional information about the CTEP-AERS integration is available on the 
CTSU website: 
 
• Study specific documents:  Protocols > Documents > Education and 
Promotion, and   
• Expedited Safety Reporting Rules Evaluation user guide:  
Resources > CTSU Operations Information > User Guides & Help 
Topics. 
 
NCI requirements for SAE reporting are available on the CTEP website:  
 
• NCI Guidelines for Investigators:  Adverse Event Reporting 
Requirements is available at 
https://ctep.cancer.gov/protocolDevelopment/electronic application
s/docs/aeguidelines.pdf. 
 
Response: these changes have been made 
 
7. 
12.2 
Please delete the language in this subsection and replace with the following. 
 
Data Reporting 
 
Medidata Rave is a clinical data management system being used for data collection for 
this trial/study.  Access to the trial in Rave is controlled through the CTEP-IAM system 
and role assignments.   
Requirements to access Rave via iMedidata: 
 
• 
A valid account, and  
• 
Assigned a Rave role on the LPO or PO roster at the enrolling site of:  Rave CRA, 
Rave Read Only, Rave CRA (LabAdmin), Rave SLA, or Rave Investigator.   
Rave role requirements: 
o 
Rave CRA or Rave CRA (Lab Admin) role, must have a minimum of an 
Associate Plus (AP) registration type, 
o 
Rave Investigator role, must be registered as an Non-Physician 
Investigator (NPIVR) or Investigator (IVR), and 

v 
 
# 
Section 
Comments 
o 
Rave Read Only role, site staff must have at a minimum an Associates 
(A) registration type. 
 
• 
Refer to https://ctep.cancer.gov/investigatorResources/default.htm for registration 
types and documentation required. 
 
If the study has a DTL, individuals requiring write access to Rave must also be assigned 
the appropriate Rave tasks on the DTL. 
 
Upon initial site registration approval for the study in Regulatory Support System (RSS), 
all persons with Rave roles assigned on the appropriate roster will be sent a study 
invitation e-mail from iMedidata.  To accept the invitation, site staff must log in to the 
Select Login (https://login.imedidata.com/selectlogin) using their CTEP-IAM username 
and password, and click on the accept link in the upper right-corner of the iMedidata 
page.  Site staff will not be able to access the study in Rave until all required Medidata 
and study specific trainings are completed.  Trainings will be in the form of electronic 
learnings (eLearnings), and can be accessed by clicking on the link in the upper right pane 
of the iMedidata screen.  If an eLearning is required and has not yet been taken, the link to 
the eLearning will appear under the study name in iMedidata instead of the Rave EDC 
link; once the successful completion of the eLearning has been recorded, access to the 
study in Rave will be granted, and a Rave EDC link will display under the study name.  
 
Site staff that have not previously activated their iMedidata/Rave account at the time of 
initial site registration approval for the study in RSS will receive a separate invitation from 
iMedidata to activate their account.  Account activation instructions are located on the 
CTSU website in the Data Management section under the Rave resource materials 
(Medidata Account Activation and Study Invitation Acceptance).  Additional information 
on iMedidata/Rave is available on the CTSU members’ website in the Data Management 
> Rave section at www.ctsu.org/RAVE/ or by contacting the CTSU Help Desk at 1-888-
823-5923 or by e-mail at ctsucontact@westat.com.   
 
Response: these changes have been made 
 
 
III. Changes made with this submission 
 
# 
Section 
Changes  
1 
cover 
Updated the list of associate investigators. 
 
2 
2.2 
2.2.7 
Updated the Background Section to describe the multicenter Cleave phase 1 
trial of CB-5339 trial in patients with AML.   
 
3 
Schema 
5 
7.1 
10 
 
Changed the study design such that the first 3 patients will be admitted to the 
NIH Clinical Center for the first week of treatment (days 1 – 5) and will return 
as out-patients on days 6 and 7 of that first week.  They will have daily 
physical examination and laboratory evaluation in addition to planned 
translational study sampling.  

vi 
 
 
 
4 
7.2.6 
Added shipping directions for ctDNA samples 
 
5 
10h 
Clarified that the cycle 1 day 1 or 2 ophthalmology questionnaire can be self-
administered by the patient rather than NEI staff.  
 
6 
10 
Corrected errors in PBMC blood sample collection and ECG timepoints in the 
study calendar. 
 
 
.

102 
TITLE:  A Phase 1 Trial of the p97 Inhibitor CB-5339 in Patients With Advanced Solid 
Tumors and Lymphomas 
 
Abbreviated title: Phase 1 CB-5339 
 
Corresponding Organization: LAO-NCI/National Cancer Institute LAO 
National Cancer Institute 
10 Center Drive, 12N226 
Bethesda, MD 20892 
 
Principal Investigator: 
Naoko Takebe, MD, PhD  
31 Center Drive 
Bethesda, MD, 20892 
(240) 781-3398 
Takeben@mail.nih.gov 
 
 
Participating Organizations (TBD)  
Limited participation to: LAO-NCI / National Cancer Institute LAO 
 
NCI Associate Investigators:  James Doroshow, MD, DCTD 
 
A. P. Chen, MD, DCTD 
Geraldine O’Sullivan Coyne, MD, PhD, DCTD 
Elad Sharon, MD, DCTD 
Howard Streicher, MD, DCTD 
Sheila Prindiville, MD, MPH, CCCT 
Abdul Rafeh Naqash, MD, DCTD 
Richard Piekarz, MD, PhD, DCTD 
Jessica Mukherjee, MS, CRNP, DCTD/NCI 
Non-NCI Associate  
Investigators: 
 
Lamin Juwara, CRNP, Leidos Biomed/FNLCR 
Ning Ma, CRNP Leidos Biomed/FNLCR 
Apurva Srivastava, PhD Leidos Biomed/FNLCR 
Tiarnan Keenan, MD, PhD, NEI 
Emily Chew, MD, NEI 
 
Referral Contact: 
Murielle Hogu, RN  
Bldg 10/RM 8D53  
 
Bethesda, MD 20892 
Phone: (240) 858-3335; Fax: (301) 451-5625  
 
murielle.hogu@nih.gov 
 
Statistician:  
Larry Rubinstein, PhD 
Rm 5W106 
9609 Medical Center Drive 

102 
Rockville, MD, 20850 
(240) 276-6026 
rubinsteinl@mail.nih.gov 
 
 
NCI Supplied Agent: 
CB-5339 tosylate (NSC 814100)  
 
IND #:  
 
 
Sponsor:  
DCTD, NCI  
 
NCT Number:    
 
 
 
NCT04449562 
 
Version Date:  
 
March 3, 2021 
 
 
 
 
 

102 
PRÉCIS 
Background: 
• Due to its critical role in protein homeostasis pathways, p97 is a promising target for the treatment of 
malignancies; tumor cells are considered to be dependent on components of the protein degradation 
machinery to maintain homeostasis and survive.  
• The p97 inhibitor CB-5339 has been well characterized in in vitro and in vivo studies and had 
demonstrated induction of an unfolded protein response, decreased cell viability, and apoptosis. 
 
Primary Objective: 
• To establish the safety, tolerability, and recommended phase 2 dose (RP2D) of CB-5339 administered 
orally on a schedule of once daily, 4 days on and 3 days off, in patients with advanced solid tumors and 
lymphomas 
 
Secondary Objectives: 
• To evaluate the pharmacokinetic profiles of CB-5339 
• To assess the preliminary antitumor activity of CB-5339 in patients with advanced solid tumors and 
lymphomas  
• To determine the effects of CB-5339 on the ubiquitin proteasome system and markers of cell death in pre- 
and post-treatment tumor biopsies and peripheral blood mononuclear cells (PBMCs) 
 
Exploratory Objectives: 
• To evaluate potential associations between CB-5339 activity and genomic alterations assessed in 
circulating tumor DNA 
 
Eligibility: 
• 
Patients ≥ 18 years of age must have histologically documented solid tumors whose disease has 
progressed on standard therapy or for which there is no available standard therapy or therapy known to 
prolong survival; or aggressive lymphoma who have refused or have no remaining curative options.  
Patients with indolent lymphomas must have undergone 3 or more prior regimens of therapy 
 
Study Design: 
• CB-5339 will be administered orally on a schedule of once daily, 4 days on and 3 days off, in 28-day 
cycles.  
• The trial will follow an accelerated titration design, changing to a traditional 3+3 dose escalation design 
(3-6 patients per cohort) once specified toxicity criteria are met.  A separate 15-patient expansion cohort 
will further explore pharmacodynamic endpoints and obtain additional pharmacokinetic data at the 
RP2D. 
• Once pharmacodynamic data are available at the RP2D, additional expansion cohorts may be considered 
to explore pharmacodynamic endpoints at lower dose levels (a protocol amendment will be submitted for 
these changes to the trial design). 
• Blood samples will be obtained for pharmacokinetic and pharmacodynamic analyses and to isolate 
circulating tumor DNA.  Tumor biopsies will be collected at baseline and 4-6 hours after drug 
administration in the expansion cohort only; an optional biopsy may be collected at disease progression. 
• Pharmacodynamic effects of CB-5339 will be assessed through a panel of markers including 
accumulation of lysine-48 (K48) specific polyubiquitinated substrates in the cytosol, upregulation of 
transcription factor CHOP in nucleus, and appearance of cleaved caspase-3 in the cytosol. 

102 
 
SCHEMA 
 
 
CB-5339 will be administered orally on a schedule of once daily, 4 days on and 3 days off, in 28-day cycles.  
The dose escalation table is provided on the next page.  The first three patients enrolled on this trial will be 
admitted to the Clinical Center hospital for five days of inpatient evaluation. 
  
The study will have an initial dose-escalation phase followed by a dose expansion phase of 15 patients. 
 
Blood and urine samples for pharmacokinetic analysis will be collected prior to CB-5339 administration 
on day 1 and then over the first 24 hours of cycle 1 (15 min, 30 min, 1hr, 2hr, 4hr, 6hr, 8hr*, 24hr post 
dose for all patients) and for the first 3 study patients only on cycle 1 day 4 (predose and 15 min, 30 min, 
1hr, 2hr, 4hr, 6hr, 8hr*, 24hr post dose).  *All PK collection is mandatory except for the 8-hr post dose. 
 
Peripheral blood mononuclear cells (PBMCs) will be collected prior to CB-5339 administration on day 1 and 
4-6 hours after receiving CB-5339 on day 1 (mandatory for all patients).  One additional blood sample 
(optional) may be collected at/near time of disease progression.   
 
Blood samples for circulating tumor DNA (ctDNA) may be collected prior to CB-5339 administration on day 
1 and then at the start of every cycle (mandatory only in expansion phase). 
 
Tumor biopsies will be mandatory during the expansion cohort only prior to CB-5339 administration and 4-6 
hours after receiving the first dose; an optional biopsy may be collected at/near disease progression.  Due to 
current uncertainties during the COVID-19 crisis, it may not be feasible to collect these samples due to 
institutional restrictions on research biopsies 
 

102 
 
Dose Escalation Schedule 
Dose level 
Dose of CB-5339 (mg/day, once daily 4 days on/3 days off weekly) 
-1 
25 mg/day; 3 days on/4 days off 
1 (starting) 
25 
2 
50 
3 
100 
4 
150 
5 
 225 
6 
300 

102 
TABLE OF CONTENTS 
PRÉCIS ........................................................................................................................................... 9 
SCHEMA ...................................................................................................................................... 10 
1. 
OBJECTIVES ................................................................................................................... 15 
1.1 
Primary Objectives ................................................................................................ 15 
1.2 
Secondary Objectives ............................................................................................ 15 
1.3 
Exploratory Objectives .......................................................................................... 15 
2. 
BACKGROUND ............................................................................................................... 15 
2.1 
The Therapeutic Rationale for p97 Inhibition ....................................................... 15 
2.2 
CB-5339 ................................................................................................................ 16 
2.3 
Rationale ................................................................................................................ 27 
2.4 
Correlative Studies Background ............................................................................ 27 
3. 
PATIENT SELECTION .................................................................................................... 30 
3.1 
Eligibility Criteria .................................................................................................. 30 
3.2 
Exclusion Criteria .................................................................................................. 31 
3.3 
Inclusion of Women and Minorities ...................................................................... 32 
3.4 
Research Eligibility Evaluation ............................................................................. 32 
4. 
REGISTRATION PROCEDURES ................................................................................... 32 
4.1 
Patient Registration in OPEN / IWRS ................................................................... 32 
4.2 
General Guidelines ................................................................................................ 33 
4.3 
Investigator and Research Associate Registration with CTEP ............................. 33 
4.4 
Site Registration .................................................................................................... 35 
5. 
TREATMENT PLAN ....................................................................................................... 37 
5.1 
Agent administration ............................................................................................. 38 
5.2 
Definition of Dose-Limiting Toxicity ................................................................... 39 
5.3 
Dose Expansion Cohort ......................................................................................... 40 
5.4 
General Concomitant Medication and Supportive Care Guidelines ..................... 41 
5.5 
Duration of Therapy .............................................................................................. 42 
5.6 
Duration of Follow-Up .......................................................................................... 43 
5.7 
Criteria for Removal from Study ........................................................................... 43 
5.8 
Dosing delays ........................................................................................................ 43 
5.9 
Dose Modifications ............................................................................................... 44 
5.10 
Visual Symptoms/Eye AEs Dose Modification Guidance .................................... 44 
6. 
PHARMACEUTICAL INFORMATION ......................................................................... 45 
6.1 
CB-5339 tosylate (NSC 814100) .......................................................................... 45 
7. 
BIOMARKER and CORRELATIVE STUDIES .............................................................. 47 
7.1 
Pharmacokinetic Analysis ....................................................................................... 1 
7.2 
Pharmacodynamic Assays ....................................................................................... 2 
7.3 
Biomarker Plan ........................................................................................................ 7 

102 
8. 
STATISTICAL CONSIDERATIONS ................................................................................ 9 
8.1 
Study Design/Endpoints .......................................................................................... 9 
8.2 
Sample Size/Accrual Rate ....................................................................................... 9 
8.3 
Analysis of Secondary and Exploratory Endpoints ............................................... 10 
9. 
ADVERSE EVENTS:  LIST AND REPORTING REQUIREMENTS ............................ 10 
9.1 
Comprehensive Adverse Events and Potential Risks List (CAEPR) .................... 10 
9.2 
Adverse Event Characteristics ............................................................................... 13 
9.3 
Expedited Adverse Event Reporting ..................................................................... 13 
9.4 
Routine Adverse Event Reporting ......................................................................... 16 
9.5 
Pregnancy .............................................................................................................. 16 
9.6 
Secondary Malignancy .......................................................................................... 16 
9.7 
Second Malignancy ............................................................................................... 17 
10. 
STUDY CALENDAR ....................................................................................................... 17 
11. 
MEASUREMENT OF EFFECT ....................................................................................... 19 
11.1 
Antitumor Effect – Solid Tumors .......................................................................... 19 
11.2 
Antitumor Effect – Hematologic Tumors ............................................................. 25 
12. 
STUDY OVERSIGHT AND DATA REPORTING / REGULATORY 
REQUIREMENTS ............................................................................................................ 27 
12.1 
Study Oversight ..................................................................................................... 27 
12.2 
Data Reporting ...................................................................................................... 28 
12.3 
Data Quality Portal ................................................................................................ 30 
12.4 
Collaborative Agreements Language .................................................................... 30 
12.5 
Genomic Data Sharing Plan .................................................................................. 32 
12.6 
NIH Human Data Sharing Plan ............................................................................. 32 
12.7 
Incidental/Secondary Findings Disclosure Procedure ........................................... 32 
13. 
HUMAN SUBJECTS PROTECTIONS ............................................................................ 33 
13.1 
Evaluation of Benefits and Risks/Discomforts ..................................................... 33 
13.2 
Consent and Assent Process and Documentation .................................................. 33 
13.3 
Procedure for Protecting Against or Minimizing Any Potential Risks ................. 34 
14. 
REFERENCES .................................................................................................................. 35 
APPENDIX A: PERFORMANCE STATUS CRITERIA ............................................................ 38 
APPENDIX B: PATIENT OPHTHALMOLOGIC QUESTIONNAIRE AND EYE 
EXAM ............................................................................................................................... 39 
APPENDIX C: PD/PK COLLECTION WORKSHEETS ............................................................ 44 
APPENDIX D: PATIENT STUDY DIARY ................................................................................. 50 
APPENDIX E: SOP FOR PBMC PREPARATION (PD) ............................................................ 52 

102 
APPENDIX F: PATIENT DRUG INTERACTIONS HANDOUT AND WALLET 
CARD ................................................................................................................................ 55 
 
 
 

102 
1. OBJECTIVES 
 
1.1 
Primary Objectives 
 
To establish the safety, tolerability, and recommended phase 2 dose (RP2D) of CB-5339 
administered orally on a schedule of once daily, 4 days on and 3 days off, in patients with 
advanced solid tumors and lymphomas 
 
1.2 
Secondary Objectives 
• To evaluate the pharmacokinetic profiles of CB-5339 
 
• To assess the preliminary antitumor activity of CB-5339 in patients with advanced solid 
tumors and lymphomas.  Although the clinical benefit of this agent has not been 
established, the intent of offering this treatment is to provide a possible therapeutic 
benefit, and thus the patient will be carefully monitored for tumor response and symptom 
relief in addition to safety and tolerability. 
 
• To determine the effects of CB-5339 on the ubiquitin proteasome system and on markers of 
cell death in pre- and post-treatment tumor biopsies and PBMCs 
1.3 
Exploratory Objectives 
• To evaluate potential associations between CB-5339 activity and genomic alterations 
assessed in circulating tumor DNA (ctDNA) 
 
2. BACKGROUND 
 
2.1 
The Therapeutic Rationale for p97 Inhibition 
 
Cancer cells carry numerous mutations and supernumerary chromosomes, making them likely to 
produce abnormal or excess proteins that must be eliminated (Vogelstein et al., 2013; Williams 
and Amon, 2009).  It has therefore been suggested that cancer cells are more dependent on 
components of the protein degradation machinery to maintain homeostasis and survive (Balch et 
al., 2008).  Several components of the degradation machinery have been reported to be 
overexpressed in cancer cells (Kharabi Masouleh et al., 2014; Mozos et al., 2011).  Of interest is 
p97, a ubiquitously expressed hexameric protein member of the AAA family of ATPases which is 
composed of 2 ATPase domains (D1 and D2), a N- terminal domain, and a C-terminal tail 
(Fessart et al., 2013).  
 
Through complex interactions with cofactors, p97 is involved in endocytosis, autophagy and 
protein trafficking but more importantly, in ubiquitin-dependent protein degradation processes 
(Figure 1).  p97 has a critical role in the ubiquitin proteasome system (UPS) where it chaperones 
subsets of proteins to the proteasome for degradation.  The UPS is composed of an enzymatic 
cascade that includes two ubiquitin activating enzymes (E1s), approximately 40 ubiquitin 
conjugating enzymes (E2s) and more than 500 ubiquitin ligases (E3s).  The concerted action of 
this enzyme cascade leads to the covalent attachment of the highly conserved 76 amino acid 

102 
protein, ubiquitin, to thousands of cellular substrates.  Ubiquitin itself can be internally modified 
by the conjugation of additional ubiquitin monomers to form poly-ubiquitin chains which, when 
attached via lysine-48 or lysine-11 of ubiquitin, target the substrate to degradation by the 26S 
proteasome; this lysine-48 Poly-Ub (K48-Poly-Ub) linkage is the predominant marker for 
proteins destined for protein degradation by the proteasome (Meyer et al., 2012).  p97 also 
functions in the cell’s alternate protein disposal pathway, the autophagy lysosome system (ALS) 
(Chou et al., 2011); cancer cells can become dependent on these two protein disposal pathways 
and therefore p97 inhibitors are anticipated to have measurable anticancer activity. 
 
Overexpression of p97 has been documented in several malignancies, and often in a manner 
relating to malignancy and outcome (Nadeau et al., 2015; Tsujimoto et al., 2004; Yamamoto et 
al., 2004a; Yamamoto et al., 2004b).  Due to its critical role in protein homeostasis pathways, p97 
has proven to be a promising target for the treatment of several malignancies.  Treatment of tumor 
cells with p97 inhibitors leads to accumulation of poly-ubiquitinated proteins, retention of 
endoplasmic reticulum-associated degradation substrates and generation of irresolvable 
proteotoxic stress, leading to activation of the apoptotic arm of the unfolded protein response 
(Anderson et al., 2015; Le Moigne et al., 2017; Zhou et al., 2015). 
 
 
Figure 1: p97 promotes protein degradation by acting as a protein segregase to remove proteins 
from membranous structures, chromatin, or complexes using the energy generated by ATP 
hydrolysis Reducing p97 levels causes ER stress and activates apoptosis through the unfolded 
protein response, a pathway that acts both to resolve unfolded protein stress and to trigger cell 
death when the buildup of such unfolded proteins becomes irresolvable (Buchberger et al., 2015; 
Deshaies, 2014; Le Moigne et al., 2017; Magnaghi et al., 2013).  Image:(Meyer et al., 2012)  
2.2 
CB-5339 
 
CB-5339 is Cleave Therapeutics’ second generation small-molecule inhibitor of p97.  Its activity 
is due to binding and inhibition of the D2 ATPase domain of p97, resulting in the disruption of 

102 
2.2.1 Preclinical Efficacy of CB-5339: in vitro studies  
 
The rationale supporting the clinical trials of the first-generation p97 inhibitor CB 5083 included 
preclinical activity in a variety of in vitro and in vivo models of solid tumors and lymphomas.  
CB-5339 shows similar activity to CB-5083 in all models tested to date, specifically 138 cancer 
cell lines representing a variety of tumor histologies including 5 myeloid leukemia lines 
(Figure 3).  The range in sensitivity to CB-5083 was narrow in this cell panel, with EC50 values 
ranging from 0.069 to 3.04 μM 72 hours after compound treatment.  Similarly, a narrow 
compound sensitivity range was also observed for CB-5339, with EC50 values spanning from 
0.053 to 3.04 μM.   
 
Figure 3: Sensitivity of a Panel of 138 Cancers Cell Lines to CB-5083 (left) or CB-5339 (right).  
Cell Lines are Ordered by EC50 Values. 
 
Data provided by Cleave Therapeutics also indicate that CB-5339-engages p97 in a similar way to 
CB-5083; both CB-5083 and CB-5339 bind to the same p97 binding pocket in the same manner 
(Figure 4).  

102 
CB-5083 resulted in a 33% TGI.  
 
AMO-1 multiple myeloma xenografts (Cleave Pharmacology Report 02-00015) 
 
The efficacy of 6 different CB-5339 dosing regimens were evaluated over a 12-day period in 
female SCID Beige mice bearing human AMO-1 multiple myeloma xenograft tumors.  The 
dosing regimens for CB-5339 were 1/W doses of 225 and 275 mg/kg (Groups 2 and 3, 
respectively), BIW doses of 150 and 200 mg/kg, and QD4/3 off doses of 80 or 100 mg/kg.  Other 
animals received QD4/3 off doses of 60 mg/kg CB-5083 (optimal dose in previously reported 
experiments) 
 
Figure 6: Very strong antitumor activity was 
seen for groups 2 and 3; weekly dosing of 
225 and 275 mg/kg resulted in TGI of 102% 
and 112%, respectively.  This strong 
antitumor response observed with the  
225 mg/kg QD1 dosing regimen was 
accompanied with a 16% mean regression on 
day 12, as well as 4/7 partial regressions and 
3/7 complete regressions within the study 
group.  Administration of 225 mg/kg CB-
5339 was generally tolerated, promoting a -
4.8% mean body weight loss on day 4.  In 
comparison, the 275 mg/kg 1/W dosing 
regimen was more efficacious with an 84% 
mean regression on day 12.  However, the 
activity observed at 275 mg/kg 1/W should be 
mitigated by the 3/8 drug-related deaths that occurred within this study group, suggesting that 
greater toxicity is associated with this dosing regimen.  Strong antitumor activity was also seen 
for the 200 mg/kg BIW dosing regimen, which resulted in a TGI of 109%.   
 
This response was accompanied with a 64% mean regression on day 12, as well as 2/7 partial 

102 
regression and 4/7 complete regression.  BIW administration of 200 mg/kg CB-5339 was 
generally tolerated, promoting a -4.1% mean body weight loss on day 8.  Of note, treatment with 
CB-5083 resulted in a TGI of 110% and a 68% mean regression on day 12, but the drug was not 
well tolerated in these experiments; CB-5083 can be highly active in the AMO-1 model and the 
activity observed here is comparable to that previously reported.  In conclusion, a variety of CB-
5339 dosing regimens showed strong antitumor activity against the human MM AMO-1 xenograft 
model.  
 
RPMI8226 multiple myeloma xenografts (Cleave Pharmacology Report 02-00014) 
 
The efficacy of 2 different doses of CB-5339 were evaluated over an 18-day period in female 
SCID Beige mice bearing human RPMI8226 multiple myeloma xenograft tumors.  The dosing 
regimens were QD4/3 off doses of 100 and 125 mg/kg CB-5339 (Groups 2 and 3, respectively); 
other animals received QD4/3 off doses of 60 mg/kg CB-5083 (optimal dose).   
 
Figure 7: Antitumor activity was 
seen for CB-5339 groups 2 and 3, 
with a 94% and 119% TGI, 
respectively.  The antitumor 
response observed with the 100 
mg/kg QD4/3 off dosing regimen 
was accompanied with 1/8 partial 
regressions within the study group.  
QD3/4 off administration of 100 
mg/kg of CB-5339 was generally 
tolerated.  In comparison, the 125 
mg/kg QD4/3 off dosing regimen 
resulted in a 26% mean regression 
on day 18, as well as 3/7 PR within 
the study group.  However, 1/7 drug 
related deaths and significant 
(>10%) weight losses were 
observed days 6-10 within this study 
group.  CB-5083 resulted in a 129% 
TGI and a 42% mean regression on day 18.  This strong antitumor response was accompanied 
with 5/8 PR within the study group.    
 
In conclusion, a QD4/3 off dosing regimen of 100 mg/kg of CB-5339, showed strong antitumor 
activity against a human MM RPMI8226 xenograft model.  

102 
2.2.3 Pharmacology of CB-5339 
The pharmacodynamics and pharmacokinetic profile of single-dose CB-5339 was determined in 
RPMI 8226 multiple myeloma (MM) tumor xenografts along with CB-5083 (Figure 8; 
Pharmacology Report 02-00013).  The data demonstrated that CB-5339, like CB-5083, achieved 
plasma levels sufficient to elicit a pharmacodynamic response specific to p97. The biomarkers 
modulated in the RPMI 8226 MM model were characteristic of a proteotoxic stress that engaged 
the tumor in the unfolded protein response pathway and subsequently, triggered the apoptosis of 
the tumor cells.  
 
 
Figure 8: RPMI8826 multiple myeloma xenografts treated with active doses of CB-5339 (NSC 
803952; 110 mg/kg) and CB-5083 (NSC788636; 60 mg/kg) (A) displayed largely similar K48-ub 
(B), CHOP (C), and cleaved caspase-3 (D) induction.  The 110 mg/kg dose of CB-5339 used in 
the PD studies was not specifically assessed for efficacy, but would, it is presumed, fall within the 
range of efficacy observed here for 100 mg/kg and 125 mg/kg CB-5339 administered on a QD3/4 
off schedule. 
 
CB-5339 exhibited transient peak plasma concentrations in the range of 2.14 to 41 μM between 1 
and 24 hr. CB-5083 plasma concentration ranged from 0.7 to 16.3 μM during the same interval.  
Concentrations of p97 inhibitors in tumor lysates generally mirrored the plasmatic concentrations.  
Dosage of CB-5339 and CB-5083 resulted in time-dependent increases in K48-Ub with peak 
levels obtained at later time points, past the peak plasma concentrations of the compound.  In 
alignment to what can be observed in sensitive solid tumor models (Le Moigne), significant 

102 
increased levels of CHOP protein were observed in the RPMI 8226 MM model, starting at 6 hr, 
and being sustained up to 10 hr post dosing. Both molecules, CB-5339 and CB- 5083, 
demonstrated similar induction of CHOP in intensity and durability in this experiment, with ~ 7- 
10-fold increase between 6 and 10 hr.  CHOP is described to be an ER stress marker in the 
unfolded protein response and has been shown to mediate programmed cell death (Barone et al., 
1994).  Induction of cPARP, an additional marker of apoptosis, could be detected at the10-hr time 
point in the RPMI 8226, with 4.3- fold and 53-fold increases for CB-5339 and CB-5083, 
respectively. 
 
The tosylate salt form of CB-5339 was selected for clinical development based on higher plasma 
exposure in dog compared to the free base form of CB-5339. 
 
2.2.4 Preclinical Toxicology of CB-5339 in Rats and Beagle Dogs  
 
Exploratory toxicology studies and IND-enabling studies have been conducted with Sprague-
Dawley rats and Beagle dogs.  The objectives of the exploratory studies were to determine the 
maximum tolerated dose MTD and to determine target organs of toxicity and any dose-limiting 
toxicities.  IND-enabling studies were conducted in rats and dogs to estimate the safe starting 
dose for clinical studies of CB-5339, to further characterize toxic effects with respect to target 
organs (clinical pathology and histopathology), and to evaluate reversibility of drug effects.   
 
Dose range finding in Beagle dogs: CB-5339 
This study evaluated the toxicity and toxicokinetics of CB-5339 in dogs after oral administration 
daily over two 4-day cycles (Days 1 through 4 and Days 8 through 11, with a 3-day washout 
period between the two cycles).  Doses of CB-5339 were 3.5, 7.5 and 15 mg/kg (de-escalated to 
10 mg/kg).  
Administration of 3.5 or 7.5 mg/kg/day CB-5339 via oral gavage was tolerated for two 4-day 
cycles, and a dose level of 10 mg/kg/day was tolerated for one 4-day cycle following a non-
tolerated dose of 15 mg/kg/day for 3 days.  Administration of 15 mg/kg/day resulted in body 
weight loss, reduced food consumption, and the moribund condition of one female after three 
daily doses in Cycle 1.  Clinical pathology findings consistent with dehydration, 
stress/inflammation, and findings secondary to decreased food consumption and body weight 
were noted for animals administered 15 mg/kg/day.  These findings, except the increased 
cholesterol, were not apparent on Day 12 after lowering the dose to 10 mg/kg/day for the second 
dosing cycle.  Therefore, the maximum-tolerated dose was considered 10 mg/kg/day, which 
corresponded to Day 11 combined sexes mean Cmax and AUC0-24 values of 702 ng/mL and 
3570 ng*hr/mL, respectively.  The no-observed-adverse-effect level (NOAEL) was 
7.5 mg/kg/day which corresponded to a Day 11 combined sexes mean Cmax and AUC0-24 values of 
827 ng/mL and 2090 ng*hr/mL, respectively.  
Final Repeat Dose Toxicity and Toxicokinetic Study in Beagle dogs (8376335) 
 
This study evaluated the toxicity and determined the toxicokinetics of CB-5339 when 
administered via oral gavage to dogs once daily over five 4-day cycles with 3-day washout 
periods between cycles, and to assess the reversibility or persistence of any effects after a 2-week 

102 
recovery phase.  The study included an assessment of CB-5339-related effects on ocular structure 
and function based on slit-lamp biomicroscopy and indirect ophthalmoscopy.  Male and female 
beagles were administered vehicle control article or 3.5, 7.5, or 10 mg/kg/day CB-5339.  CB-
5339-related clinical pathology effects were limited to minimally decreased red cell distribution 
width and mildly decreased absolute reticulocyte count in males administered 10 mg/kg/day with 
no signs of reversibility, except for absolute reticulocyte count in one male.  The test article was 
well tolerated at doses up to 10 mg/kg/day, with no adverse effects.  Thus, the NOAEL is 10 
mg/kg/day.  This dose level corresponded to mean Cmax and AUC values of 1240 ng/mL and 
3080 ng x hr/mL, respectively, in combined sexes on Day 32 of the dosing phase.  No significant 
CB-5339-related clinical observations, alterations in body weight or body weight gain, ocular or 
electroretinography abnormalities, electrocardiogram abnormalities, or anatomic pathology 
differences were noted for animals administered up to 10 mg/kg/day. 
 
Dose range finding in Rat: CB-5339  
This study evaluated the toxicity and toxicokinetics of CB-5339 when administered via oral 
gavage to rats daily over five 4-day cycles with 3-day washout periods between cycles.  Doses of 
CB-5339 in female rats were 3, 10, and 30 mg/kg; doses in male rats were 10, 30, and 60 (de-
escalated to 40) mg/kg.   
Mortality and adverse findings were noted in males administered 60 mg/kg/day and females 
administered 30 mg/kg/day; the cause of death was marrow hypocellularity and lymphoid 
depletion/necrosis.  Clinical pathology changes included minimally lower reticulocyte count and 
associated mean corpuscular hemoglobin concentration in males administered 30 mg/kg/day, 
minimally higher ALT in females administered 30 mg/kg/day and males administered 60/40 
mg/kg/day, and mildly lower triglyceride concentration in males administered 60/40 mg/kg/day.  
These clinical chemistry findings were reversed on Day 15 of the recovery phase.  CB-
5339-related microscopic findings included moderate marrow hypocellularity, marked pancreas 
acinar atrophy, and moderate glandular stomach mucosal atrophy in one female administered 
30 mg/kg/day, which were considered adverse because of similar microscopic findings noted in 
animals which were found dead, and slight lymphoid depletion/necrosis in the thymus in females 
administered 30 mg/kg/day, which were considered adverse because of similar microscopic 
findings noted in animals which were found dead. Thus, the no observed adverse effect level 
(NOAEL) is 40 mg/kg/day for males and 10 mg/kg/day for females.  These dose levels 
corresponded to mean Cmax and AUC values of 696 ng/mL and 5020 ng x hr/mL, respectively, in 
males and 258 ng/mL and 1070 ng x hr/mL, respectively, in females on Day 32 of the dosing 
phase. 
 
Final Repeat Dose Toxicity and Toxicokinetic Study in rats (8376333) 
 
This study evaluated the toxicity and determined the toxicokinetics of CB-5339 when 
administered via oral gavage to rats once daily over five 4-day cycles with 3-day washout 
periods between cycles, and assessed the reversibility, persistence, or delayed occurrence 
of any effects after a 2-week recovery phase.  Ophthalmic examinations were conducted once 
during the predose phase for all animals and once for all toxicity animals during Week 5 of the 
dosing phase 

102 
Male rats were administered 10, 30, or 60/40 mg/kg/day CB-5339 and female rats were 
administered 3, 10, or 30 mg/kg/day CB-5339.  Mortality and adverse findings were noted in 
males administered 60 mg/kg/day and females administered 30 mg/kg/day; microscopic 
evaluation established the cause of death was marrow hypocellularity and lymphoid 
depletion/necrosis.  Adverse decreases in body weights were observed during the dosing phase for 
males administered 60 mg/kg/day, following lowering of the dose level to 40 mg/kg/day, the body 
weight gain recovered.  Clinical pathology changes included minimally lower reticulocyte count 
and associated MCHC in males administered ≥ 30 mg/kg/day, minimally higher ALT in females 
administered 30 mg/kg/day and males administered 60/40 mg/kg/day, and mildly lower 
triglyceride concentration in males administered 60/40 mg/kg/day.  These clinical chemistry 
findings were reversed on Day 15 of the recovery phase.  CB-5339 related microscopic findings 
included moderate marrow hypocellularity, marked pancreas acinar atrophy, and moderate 
glandular stomach mucosal atrophy in one female administered 30 mg/kg/day, which were 
considered adverse because of similar microscopic findings in the animals found dead, and slight 
lymphoid depletion/necrosis in the thymus in females administered 30 mg/kg/day, again 
considered adverse because of similar microscopic findings in animals found dead.  At the 
recovery sacrifice, minimal spleen and thymic lymphoid depletion/necrosis was noted in one 
female administered 30 mg/kg/day, which indicated that recovery of lymphoid findings was in 
progress, but not yet complete.  The remaining findings noted at the terminal sacrifice were 
resolved.  No CB-5339-related ophthalmic findings were noted.   
 
No remarkable ophthalmic observations were noted with the exception of one female 
(3 mg/kg/day) with multiple foci of retinal hemorrhage in the left eye considered incidental.  
Effects noted for males administered 40 mg/kg/day and females administered 10 mg/kg/day were 
considered non-adverse due to the mild severity of findings and the lack of impact on animal 
health and wellbeing.  Thus, the NOAEL is 40 mg/kg/day for males and 10 mg/kg/day for 
females, confirming the dose-range finding study.  These dose levels corresponded to mean Cmax 
and AUC values of 696 ng/mL and 5020 ng*hr/mL, respectively, in males and 258 ng/mL and 
1070 ng*hr/mL, respectively, in females on Day 32 of the dosing phase. 
 
 
2.2.5 Eye Disorder Studies with CB-5339 
 
Clinical evaluation of Cleave Therapeutics’ first-in-class inhibitor of p97, CB-5083 in patients 
with advanced metastatic solid tumors (NCT02243917) and in lymphoid malignancies 
(NCT02223598) was halted due to dose-dependent toxicity related to PDE6 inhibition, including 
grade 2 chromatopsia, grade 2 photophobia, and grade 4 transient loss of vision that improved 
with drug discontinuation.  Reporting rates for at least 1 eye disorder on the solid tumor and 
lymphoma studies were 25 of 32 subjects (78%) and 5 of 12 subjects (42%), respectively (data 
from 2016 IB).  The median onset was day 1 for the solid tumor trial (range, 1 to 36), 60 to 90 
minutes after dosing, and with a median duration of 60 to 120 minutes.  Reports for the 
hematologic study were similar.   
 
In dog toxicology studies with CB-5339 performed for the current proposed study, all animals had 
a normal ophthalmic and electroretinography (ERG) examinations throughout all phases, except 
for one male in the dose-ranging study administered 3.5 mg/kg/day, in which the left eye had a 

102 
beagle dogs, which leads to a human dose of 32 mg.  Given the availability of 25 mg capsules for 
CB-5339 administration, we have set the human starting dose at 25 mg on the 4 days on and 3 
days off schedule (dose level -1 will reduce the frequency of administration by 25%).  Further 
dose escalation will reflect one capsule size per dose for patient convenience informed by 
Fibonacci sequence (Dose Escalation Table).   
 
PD results from the first 32 subjects on the CLC-101 solid tumor study of CB-5083 indicated that 
only subjects dosed at 590 mg CB-5083 or higher had measurable increases in K48-Poly-Ub of 
surrogate tissues (monocytes and B cells) at 2 hours post-dosing.  The magnitude of the blood cell 
K48-Poly-Ub increases seen in these subjects was similar to that seen in the blood of tumor 
bearing mice and rats indicative of target engagement by CB-5083.   
 
2.2.7 Clinical Trials of CB-5339 
 
CB-5339 is being evaluated in two phase 1 clinical studies.  Cleave Therapeutics is sponsoring a 
phase 1 trial of CB-5339 in patients with relapsed/refractory acute myeloid leukemia or 
relapsed/refractory intermediate or high risk myelodysplastic syndrome at several sites in the US 
and Australia (NCT04402541), and the NCI is conducting this current phase 1 trial in patients 
with solid tumors and lymphomas.  The dosing schedule of once daily, 4 days on and 3 days off, 
in 28-day cycles, and the starting dose of 25 mg, will be employed in both studies.  Both will also 
employ accelerated dose escalation strategies using single patient dose levels (this study reverts to 
standard 3+3 dose escalation as defined in Section 5.2.). 
 
2.3 
Rationale 
 
Based on its well characterized mechanism of action, preclinical data, and experience with 
Cleave’s previous-generation p97 inhibitor, CB-5339 may provide benefits to patients with 
advanced solid tumors and lymphomas refractory to standard-of-care treatments.  The anticancer 
effects of CB-5339 have been characterized in several in vitro and in vivo pharmacology studies 
and an ongoing trial in canine patients, demonstrating that it can elicit a variety of biological 
effects including induction of an unfolded protein response, decreased cell viability, and 
apoptosis.  The study-objective recommended phase 2 dose (RP2D) will be determined by the 
following: (1) a dose no higher than the maximum tolerated dose level; (2) obtaining exposures 
associated with preclinical biomarker activity; and (3) patient responses. 
 
 
2.4 
Correlative Studies Background 
 
As part of the NExT Program, the NCI’s Pharmacodynamic Assay Development and 
Implementation Section (PADIS), has developed a combination of 3 pharmacodynamic (PD) 
biomarkers to quantify the effect of Cleave Therapeutics’ p97 inhibitors (Srivastava et al., 2018). 
In vivo and in vitro PD response to the first generation p97 inhibitor CB-5083 (NSC-788636) was 
assessed via three major mechanisms by which p97 inhibitors act: 1) extraction of ubiquitinated 
substrates; 2) induction of unfolded protein response (UPR) due to ERAD; and 3) execution of 
apoptosis.  The polyubiquitinated proteins crosslinked through lysine-K48 of ubiquitin molecule 
(described as K48-ub) provided a specific measure of proteasome pathway blockage.  The 

102 
transcription factor CHOP (CCAAT-enhancer-binding protein homologous protein) assessed in 
the nuclear fraction of cell lysates provided a measure of UPR, and measurement of cleaved 
caspase-3 levels in the cytosolic fraction provided evidence of apoptosis (Figure 10).  These 3 
biomarkers were developed as sandwich immunoassays on the Luminex multiplex platform.  
 
Figure 10: HCT116 colon cancer xenografts treated with one dose of 100 mg/kg CB-5083 (NSC 
788636) displayed a significant PD induction of K48-ub, UPR, and apoptosis.  K48 ubiquitination 
in treated tumors peaked within an hour after treatment but remained significant for up to 24 
hours.  The induction of nuclear CHOP and cytosolic cleaved caspase-3 were maximal 6 hours 
after treatment. 
 
Analytical validity of the K48-ub and CHOP assays were determined for reproducibility and 
dilution linearity using xenograft tumor lysates processed by established methodology (Srivastava 
et al, 2016).  Fitness-for-purpose validation of K48-ub and CHOP assays were demonstrated in 
HCT116 and RPMI8226 xenograft studies using CB-5083 (unpublished data presented in this 
protocol).  Analytical and fitness-for-purpose validation of caspase-3 has been described earlier 
(Srivastava et al, 2016).  
 
Preliminary studies with CB-5339 have indicated that it induces a PD response that is 
substantially the same in terms of timing and extent to that observed with CB-5083 (Figure 8).  A 
clinical trial of CB-5339 in pet dogs with naturally occurring solid tumors, lymphomas, and 
multiple myeloma is currently underway by the NCI’s Comparative Oncology Program in 
collaboration with Cleave Therapeutics, the NCI Experimental Therapeutics (NExT) Program, 
and the NCI Division of Cancer Therapy and Diagnosis.  The trial design is a fixed schedule, dose 
escalation study and includes biopsy and PBMC collection for assessment of PD response at three 
timepoints post-dose (Figure 10).  Preliminary data collected to date also indicate that both K-48 
ubiquitin linked protein and CHOP mRNA-based measurements can be performed in PBMCs 
(Figure 11), justifying collection of these cells on this current trial.   

102 
 
3. PATIENT SELECTION 
 
3.1 
Eligibility Criteria  
3.1.1 Patients with histologically documented metastatic or locally advanced (not amenable to 
surgery) solid tumors whose disease has progressed on standard therapy or for which there 
is no available standard therapy or therapy known to prolong survival; or aggressive 
lymphoma who have refused or have no remaining curative options (e.g., stem cell 
transplant).   Patients with indolent lymphomas must have undergone 3 or more prior 
regimens of therapy.   
3.1.2 Any prior therapy must have been completed ≥4 weeks (6 weeks for nitrosoureas and 
mitomycin C) or, if known, ≥5 half-lives of the prior agent (whichever is shorter) prior to 
enrollment on protocol (minimum of 1 week between prior therapy and study enrollment), 
and the participant must have recovered to eligibility levels from prior toxicity.  Prior 
definitive radiation should have been completed ≥4 weeks or palliative radiation should 
have been completed ≥2 weeks prior to study enrollment and all associated toxicities 
resolved to eligibility levels (patients on study may be eligible for palliative radiotherapy 
to non-targeted lesions after 2 cycles of therapy at the PI’s discretion).  Patients must be 
≥2 weeks since any investigational agent administered as part of a Phase 0 study (where a 
sub-therapeutic dose of drug is administered) at the PI’s discretion and should have 
recovered to grade 1 or baseline from any toxicities. 
 
3.1.3 Patients who have had prior monoclonal antibody therapy must have completed that 
therapy ≥6 weeks (or 3 half-lives of the antibody, whichever is shorter) prior to enrollment 
on protocol (minimum of 1 week between prior therapy and study enrollment).   
3.1.4 Age ≥18 years.  Because no dosing or adverse event data are currently available on the use 
of CB-5339 in patients <18 years of age, children are excluded from this study, but will be 
eligible for future pediatric trials.   
3.1.5 ECOG performance status ≤2 (Karnofsky ≥60%, see Appendix A) and life expectancy > 3 
months, 
3.1.6 Patients must have adequate organ and marrow function as defined below: 
− 
absolute neutrophil count 
 
≥1,500/mcL 
− 
platelets  
 
≥100,000/mcL (solid tumor patients) 
 
 
 
≥75,000/mcL (lymphoma patients) 
− 
total bilirubin 
 
≤ 1.5 x institutional upper limit of normal (ULN) 
− 
AST(SGOT)/ALT(SGPT) 
 
≤3 × institutional ULN 
− 
creatinine  
 
≤ 1.5 x institutional ULN 
OR 
 
60 mL/min/1.73 m2 for patients with creatinine levels 
above 1.5X institutional normal 
3.1.7 The effects of CB-5339 on the developing human fetus are unknown.  For this reason and 
because p97 inhibitors agents may be teratogenic, women of child-bearing potential and 
men must agree to use adequate contraception (hormonal or barrier method of birth 
control; abstinence) prior to study entry and for the duration of study participation and for 

102 
4 months afterwards.  Should a woman become pregnant or suspect she is pregnant while 
she or her partner is participating in this study, she should inform her treating physician 
immediately.  Men treated or enrolled on this protocol must also agree to use adequate 
contraception prior to the study, for the duration of study participation, and 4 months after 
completion of CB-5339 administration. 
3.1.8 Ability to understand and the willingness to sign a written informed consent document. 
3.1.9 Subjects on the expansion cohort must also be willing to undergo two core biopsy 
procedures and have a lesion amenable to biopsy. 
3.1.10 Left ventricular ejection fraction ≥ the lower limit of normal by ECHO at entry.  
3.1.11 Mean QT interval corrected for heart rate (QTc) <470 ms using Fridericia’s Correction.  
 
 
3.2 
Exclusion Criteria 
3.2.1 Patients who have had chemotherapy or radiotherapy within 4 weeks (6 weeks for 
nitrosoureas or mitomycin C) prior to entering the study.  
3.2.2 Patients who have not recovered from adverse events due to prior anti-cancer therapy (i.e., 
have residual toxicities > Grade 1) with the exception of alopecia.  
3.2.3 Patients who are receiving any other investigational agents. 
 
3.2.4 Patients with clinically significant illnesses which would compromise participation in the 
study, including but not limited to active or uncontrolled infection, immune deficiencies, 
Hepatitis B, Hepatitis C, active tuberculosis, uncontrolled asthma, symptomatic congestive 
heart failure, unstable angina pectoris, uncontrolled cardiac arrhythmia, myocardial 
infarction within the past 6 months, cerebral vascular accident/stroke within the past 6 
months, or psychiatric illness/social situations that would limit compliance with study 
requirements.   
• Human immunodeficiency virus (HIV)-infected patients on effective anti-retroviral 
therapy with undetectable viral load within 6 months are eligible for this trial. 
• For patients with evidence of chronic hepatitis B virus (HBV) infection, the HBV 
viral load must be undetectable on suppressive therapy, if indicated. 
 
3.2.5 Patients with known brain metastases or carcinomatous meningitis are excluded from 
this clinical trial, with the exception of patients whose brain metastatic disease status has 
remained stable for ≥ 4 weeks after treatment of the brain metastases.  Patients on anti-
seizure medications may be enrolled at the discretion of the Principal Investigator 
providing that these patients are taking non-enzyme- inducing anti-seizure medications or 
can be converted to these. 
3.2.6 Pregnant women are excluded from this study because CB-5339 may have the potential 
for teratogenic or abortifacient effects.  Because there is an unknown but potential risk for 
adverse events in nursing infants secondary to treatment of the mother with this agent, 
breastfeeding should be discontinued if the mother is treated with CB-5339.   
 

102 
3.2.7 Current or previous history of sight-threatening retinal disease, including (but not limited 
to) proliferative diabetic retinopathy, severe retinal vascular disease, and advanced age-
related macular degeneration. 
 
3.2.8 Patients with a history of QT-prolongation or of Torsades de pointes (TdP), or of taking 
QT-prolonging drugs, are not eligible. 
 
 
3.3 
Inclusion of Women and Minorities 
 
This study will be open to all individuals regardless of gender, ethnicity, or race provided 
that the aforementioned inclusion and exclusion criteria are met.  For safety reasons, 
pregnant women and children are excluded from this study.  To date, there is no 
information that suggests that differences in CB-5339 drug metabolism or effect on tumor 
would be expected in one ethnic group compared to another.  Efforts will be made to 
extend accrual to each representative population, but a balance must be struck between 
participant safety considerations and limitations on the number of individuals exposed to 
potentially ineffective treatments on the one hand and the need to explore racial/ethnic 
aspects of clinical research on the other hand.  If differences in outcome that correlate to 
ethnic identity are noted, a follow-up study may be written to investigate those differences 
more fully. 
 
3.4 
Research Eligibility Evaluation 
 
3.4.1 A complete history and physical examination (including height, weight, vital signs, and 
performance score) will be conducted within 8 days prior to enrollment.  This will include 
evaluation of measurable disease, ECG, and determination of performance status.  
 
3.4.2 Diagnostic imaging studies, ophthalmology exam, and ECHO evaluation must be 
performed within 28 days prior to enrollment. 
 
3.4.3 Laboratory Evaluation: Baseline laboratory data are to be obtained within 8 days prior to 
enrollment: 
• Hematological Profile: CBC with differential 
• Biochemical Profile: electrolytes, BUN, creatinine, glucose, AST, ALT, bilirubin, 
calcium, phosphorous, albumin, magnesium, alkaline phosphatase, LDH (with uric 
acid for patients with lymphoma) 
• Urinalysis 
• Serum pregnancy test for female participants of childbearing potential. 
 
 
4. REGISTRATION PROCEDURES 
 
4.1 
Patient Registration in OPEN / IWRS 
4.1.1 OPEN / IWRS 
 

102 
The Oncology Patient Enrollment Network (OPEN) is a web-based registration system available on 
a 24/7 basis.  OPEN is integrated with CTSU regulatory and roster data and with the Lead Protocol 
Organization (LPOs) registration/randomization systems or Theradex Interactive Web Response 
System (IWRS) for retrieval of patient registration/randomization assignment.  OPEN will populate 
the patient enrollment data in NCI’s clinical data management system, Medidata Rave. 
 
Requirements for OPEN access:   
 
• A valid CTEP-IAM account. 
• To perform enrollments or request slot reservations:  Must be on an LPO roster, ETCTN 
Corresponding roster, or PO roster with the role of Registrar.  Registrars must hold a 
minimum of an Associate Plus (AP) registration type. 
• The registrar(s) must hold the OPEN Registrar task on the DTL for the site. 
• Have an approved site registration for a protocol prior to patient enrollment. 
 
To assign an Investigator (IVR) or Non-Physician Investigator (NPIVR) as the treating, crediting, 
consenting, drug shipment (IVR only), or receiving investigator for a patient transfer in OPEN, 
the IVR or NPIVR must list the IRB number used on the site’s IRB approval on their Form FDA 
1572 in RCR.  If a DTL is required for the study, the IVR or NPIVR must be assigned the 
appropriate OPEN-related tasks on the DTL. 
 
Prior to accessing OPEN, site staff should verify the following: 
 
• Patient has met all eligibility criteria within the protocol stated timeframes, and  
• All patients have signed an appropriate consent form and HIPAA authorization form (if 
applicable). 
 
Note:  The OPEN system will provide the site with a printable confirmation of registration and 
treatment information.  Please print this confirmation for your records.  
 
Access OPEN at https://open.ctsu.org or from the OPEN link on the CTSU members’ website.  
Further instructional information is in the OPEN section of the CTSU website at 
https://www.ctsu.org or https://open.ctsu.org.  For any additional questions, contact the CTSU 
Help Desk at 1-888-823-5923 or ctsucontact@westat.com. 
 
4.2 
General Guidelines 
 
Following registration, patients should begin protocol treatment within 8 days.  Issues that would 
cause treatment delays should be discussed with the Principal Investigator.  If a patient does not 
receive protocol therapy following registration, the patient’s registration on the study may be 
canceled.  The Study Coordinator should be notified of cancellations as soon as possible. 
 
4.3 
Investigator and Research Associate Registration with CTEP 
 
Food and Drug Administration (FDA) regulations and National Cancer Institute (NCI) policy 
require all individuals contributing to NCI-sponsored trials to register and to renew their 

102 
https://ctep.cancer.gov/investigatorResources/default.htm.  For questions, please contact the RCR 
Help Desk by email at RCRHelpDesk@nih.gov. 
 
4.4 
Site Registration 
 
IRB Approval 
 
Sites participating with the NCI Central Institutional Review Board (NCI CIRB) must submit the 
Study Specific Worksheet for Local Context (SSW) to the CIRB using IRBManager to indicate 
their intent to open the study locally.  The NCI CIRB’s approval of the SSW is automatically 
communicated to the CTSU Regulatory Office, but sites are required to contact the CTSU 
Regulatory Office at CTSURegPref@ctsu.coccg.org to establish site preferences for applying NCI 
CIRB approvals across their Signatory Network.  Site preferences can be set at the network or 
protocol level.  Questions about establishing site preferences can be addressed to the CTSU 
Regulatory Office by emailing the email address above or calling 1-888-651-CTSU (2878). 
 
In addition, the Site-Protocol PI (i.e., the investigator on the IRB/REB approval) must meet the 
following five criteria to complete processing of the IRB/REB approval record: 
• Holds an Active CTEP status, 
• Rostered at the site on the IRB/REB approval (applies to US and Canadian sites only) and 
on at least one participating roster, 
• If using NCI CIRB, rostered on the NCI CIRB Signatory record, 
• Includes the IRB number of the IRB providing approval in the Form FDA 1572 in the RCR 
profile, and 
• Holds the appropriate CTEP registration type for the protocol.  
 
Additional Requirements: 
 
Additional requirements to obtain an approved site registration status include: 
• An active Federalwide Assurance (FWA) number, 
• An active roster affiliation with the Lead Protocol Organization (LPO) or a Participating 
Organization, and 
• Compliance with all protocol-specific requirements (PSRs). 
 
4.4.1 Downloading Regulatory Documents 
 
Download the site registration forms from the protocol-specific page located on the CTSU 
members’ website.  Permission to view and download this protocol and its supporting documents 
is restricted based on person and site roster assignment.  To participate, the institution and its 
associated investigators and staff must be associated with the LPO or a Participating Organization 
on the protocol.  
 
• Log on to the CTSU members’ website (https://www.ctsu.org) using your CTEP-IAM 
username and password, 
• Click on Protocols in the upper left of your screen 
o Enter the protocol number in the search field at the top of the protocol tree, or 

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o Click on the By Lead Organization folder to expand, then select LAO-NCI, and 
protocol number 10349, 
• Click on Documents, select Site Registration, and download and complete the forms 
provided.  (Note:  For sites under the CIRB initiative, IRB data will load automatically to 
the CTSU as described above.)  
 
 
4.4.2 Submitting Regulatory Documents 
 
Submit required forms and documents to the CTSU Regulatory Office via the Regulatory 
Submission Portal on the CTSU website.  
 
To access the Regulatory Submission Portal, log on to the CTSU members’ website, go to the 
Regulatory section, and select Regulatory Submission. 
 
Institutions with patients waiting that are unable to use the Regulatory Submission Portal should 
alert the CTSU Regulatory Office immediately at 1-866-651-2878 in order to receive further 
instruction and support. 
 
4.4.3 Delegation of Tasks Log (DTL) 
 
Each site must complete a protocol-specific DTL using the DTL application in the Delegation 
Log section on the CTSU members’ website.  The Clinical Investigator (CI) is required to review 
and electronically sign the DTL prior to the site receiving an Approved site registration status and 
enrolling patients to the study.  To maintain an approved site registration status the CI must re-
sign the DTL at least annually and when a new version of the DTL is released; and activate new 
task assignments requiring CI sign-off.  Any individual at the enrolling site on a participating 
roster may initiate the site DTL.  Once the DTL is submitted for CI approval, only the designated 
DTL Administrators or the CI may update the DTL.  Instructions on completing the DTL are 
available in the Help Topics button in the DTL application and include a Master Task List, which 
describes DTL task assignments, CI signature, and CTEP registration requirements 
 
4.4.4 Checking Site Registration Status 
 
A site’s registration status may be verified on the CTSU website.  
 
• Click on Regulatory at the top of the screen, 
• Click on Site Registration, and  
• Enter the site’s 5-character CTEP Institution Code and click on Go. 
o Additional filters are available to sort by Protocol, Registration Status, Protocol 
Status, and/or IRB Type. 
 
Note:  The status shown only reflects institutional compliance with site registration requirements 
as outlined within the protocol.  It does not reflect compliance with protocol requirements for 
individuals participating on the protocol or the enrolling investigator’s status with NCI or their 
affiliated networks. 

102 
 
5. TREATMENT PLAN 
 
This is a first-in-human, open-label phase 1 trial of oral CB-5339 in adult patients with advanced 
metastatic solid tumors and lymphoid malignancies.  The study will be conducted in two parts, an 
initial dose-escalation phase followed by a dose expansion phase at the recommended phase 2 
dose (RP2D) in the same patient population.  Additional expansion cohorts may be considered to 
explore pharmacodynamic endpoints at lower dose levels (a protocol amendment will be 
submitted for these changes to the trial design).   
 
Patients will be required to maintain a study diary documenting when the doses were taken, and 
any associated side effects (Appendix D).  Patients will be asked to return the diary to the clinic 
staff at the end of each cycle.   
 
Patient evaluations will be performed throughout the study as described below.  Baseline history, 
physical examination, laboratory evaluations, and ECG must be conducted within 8 days prior to 
start of protocol therapy.  If protocol therapy is started within 8 days of the eligibility screening 
evaluations (see Section 3.4), the results from these screening evaluations may be used as baseline 
measurements.  If > 8 days have passed since the screening evaluations, the medical history, 
physical examination, laboratory evaluations, and ECG must be repeated prior to starting protocol 
therapy.   
Baseline tumor imaging must be performed within 28 days prior to start of protocol therapy.  If 
protocol therapy is started within 28 days of the eligibility screening tumor imaging, the screening 
evaluation imaging results may be used as baseline measurements; if > 28 days have passed since 
the screening evaluation tumor imaging, the imaging must be repeated prior to starting protocol 
therapy. 
History and physical examination will be performed at baseline (within 8 days of the start of 
protocol therapy), during weeks 1, 2, 3, and 4 of cycle 1, and at the start of every cycle thereafter 
(within 3 days prior to treatment).  Physical examinations will include O2 saturation measured by 
pulse oximeter.   
 
The first three patients on study will be admitted to the NIH Clinical Center for 5 days of in-
patient evaluation followed by out-patient evaluation at the day hospital on days 6 and 7 (vital 
check, PO2, serum chemistries, and CBC).   
 
 
Labs (CBC with differential; serum chemistries) will be performed at baseline (within 8 days of 
the start of protocol therapy), during weeks 1, 2, 3, and 4 of cycle 1, and at the start (+/- 1 day 
during the cycle and up to 3 days before start of a new cycle) and during week 1 of every cycle 
thereafter.  For the first three patients enrolled on the study who will receive their initial week of 
treatment as inpatients, labs will also be performed on Cycle 1 Day 2 prior to CB-5339, on Day 3 
based on the result from Day 2, on Day 4 prior to CB-5339, on Day 6 (Sunday at the Day 
Hospital), and on Day 8 (C1W2) 
 
ECG will be performed at baseline (within 8 days of the start of protocol therapy) and will be 

102 
performed on day 1 pre-dose and at 2 hours post dose/the time to peak concentration of every 
subsequent cycle, and as clinically indicated. 
 
Blood and urine samples for correlative PD and PK studies will be collected from all patients as 
described in Section 7.    
 
Paired tumor biopsies will be collected at baseline and then 4-6 hours after receiving the first dose 
in the expansion cohort; an optional biopsy may be collected at disease progression or “pre-
progression” (defined as a 10-19% increase in tumor volume as shown on a restaging scan).   
 
NEI associate investigators will perform an ophthalmology examination that includes optical 
coherence tomography (OCT), color vision testing, and a questionnaire on all patients during 
screening.  The questionnaire will be repeated after treatment on cycle 1 day 1 or 2; the 
questionnaire and eye examinations can be repeated by NEI as clinically indicated.  Details about 
the questionnaire and eye examinations can be found in Appendix B along with thresholds for 
pre-existing visual impairment.  Patients should be encouraged to report any vision changes to the 
study team immediately.  
 
CB-5339 is administered orally on a schedule of once daily, 4 days on and 3 days off (28-day 
cycle).  Dose escalation will continue until the RP2D (MTD) is established.  Intra-patient dose 
escalation will be permitted; refer to Section 5.2 regarding conditions for permitted intra-patient 
dose escalation.  
 
Dose Escalation Schedule 
Dose level 
Dose of CB-5339 (mg/day, once daily 4 days on/3 days off weekly) 
-1 
25 mg/day; 3 days on/4 days off 
1 (starting) 
25 
2 
50 
3 
100 
4 
150  
5 
225 
6 
300 
 
5.1 
Agent administration 
CB-5339 will be administered once daily, 4 days on and 3 days off, in 28-day cycles.  CB-
5339 capsules should be taken in a fasted state, either 1 hour before or 2 hours after meals. 
Patients have a 6-hr window to make up for missed/vomited doses. 
 
Reported adverse events and potential risks are described in Section 9.  Appropriate dose 
modifications are described in Section 5.9.  No investigational or commercial agents or 
therapies other than those described below may be administered with the intent to treat the 
patient’s malignancy. 
 
After cycle 2, as a measure of patient compliance only, a cycle will be considered completed 
if 90% of the prescribed CB-5339 doses are administered. 

102 
 
 
5.2 
Definition of Dose-Limiting Toxicity 
 
Determination of dose-limiting toxicity (DLT) will be based on toxicities observed in the 
first cycle of therapy and felt to be at least possibly related to study drug.  A greater than 2-
week delay for AEs before cycle 2 would be considered a DLT. 
 
This study will follow design 3 of the Simon accelerated titration designs (Simon et al., 
1997). We will accrue to the next dose level only after we have established safety at lower 
dose levels.   
 
During this accelerated phase, there will be one patient per dose level.  After the first 
instance of a drug-related Grade 2 toxicity (during the first cycle) at any dose level, the 
accelerated phase will end, and dose escalation will be changed to a 3 + 3 design.  All 
decisions on dose expansion and DLT will be made on the first cycle of treatment.   
 
When the accelerated phase ends, the trial will go back to a traditional 3+3 design.  That is, 
additional patients will be placed on the dose level at which the last new patient was 
treated; 3 patients will be treated initially at each new dose level.  
 
 
Number of Patients with DLT 
at a Given Dose Level 
3+3 Escalation Decision Rule 
0 out of 3 
Enter 3 patients at the next dose level. 
≥2 
Dose escalation will be stopped.  This dose level will be declared the 
maximally administered dose (highest dose administered).  Three (3) 
additional patients will be entered at the next lowest dose level if only 
3 patients were treated previously at that dose. 
1 out of 3 
Enter at least 3 more patients at this dose level. 
• If 0 of these 3 patients experience DLT, proceed to the next dose 
level. 
• If 1 or more of this group suffer DLT, then dose escalation is 
stopped, and this dose is declared the maximally administered 
dose.  Three (3) additional patients will be entered at the next 
lowest dose level if only 3 patients were treated previously at that 
dose. 
≤1 out of 6 at highest dose level 
below the maximally 
administered dose 
This is generally the recommended phase 2 dose.  At least 6 patients 
must be entered at the recommended phase 2 dose. 
 
If ≥ 2 patients experience DLT on dose level -1, the study will be placed on hold and all data 
reviewed to make a decision about further evaluation of the study drug.  
 
DLT is defined as an adverse event that is related (possibly, probably, or definitely) to 

102 
administration of study drug and fulfills one of the following criteria: 
5.2.1 Inability to administer ≥ 75% of doses of study drug in the absence of toxicity unless due 
to patient non-compliance. 
5.2.2 Any treatment-related death 
5.2.3 All ≥ Grade 3 toxicities, with the exceptions noted below. 
 
The following toxicities are NOT considered as DLTs: 
5.2.4 Alopecia 
5.2.5 Grade 3 fatigue, asthenia, anorexia, or constipation 
5.2.6 Grade 3 nausea, vomiting, or diarrhea not requiring hospitalization, tube feeding, total 
parenteral nutrition, or prolonged hospitalization 
5.2.7 Grade 3 alkaline phosphatase (ALP) or lactate dehydrogenase (LDH)  
5.2.8 Grade 3 bilirubin elevation that is asymptomatic, returns to ≤ Grade 2 levels in ≤ 7 days, 
and is not related to liver pathology (i.e., predominantly indirect bilirubin, Gilbert’s 
syndrome) 
5.2.9 Grade 3 electrolyte abnormality that improves to ≤ Grade 1 after 48 hours with appropriate 
management. 
5.2.10 Any degree of leukopenia or lymphopenia (except when associated with grade 4 
neutropenia that lasts > 5 days) will not be considered dose limiting  
5.2.11 Grade 3 or 4 neutropenia or thrombocytopenia lasting <5 days 
 
Aspartate aminotransferase (AST) or alanine aminotransferase (ALT) ≥3 × upper limit of normal 
(ULN) with total bilirubin ≥2 × ULN, alkaline phosphatase < 2 × ULN (FDA “Hy’s Law”) would 
be considered a DLT when determined to be related to study drug.  Any other toxicity considered 
relevant by the investigator may be considered a DLT after discussion with CTEP.   
 
Intra-patient dose escalation will be permitted if: a) there is no toxicity > Grade 1 that is related 
(possibly, probably, or definitely) to the study drug at the initial dose level experienced by that 
patient, b) higher doses have been evaluated and completed without DLT, and c) the patient’s 
disease is either stable or has progressed.  Doses may be escalated, provided conditions a–c are 
met, up to the last evaluated dose level NOT associated with DLT. 
 
5.3 
Dose Expansion Cohort 
 
Once the RP2D is reached, an additional 15 patients will be treated at this dose to further explore 
pharmacodynamic endpoints and obtain additional pharmacokinetic data.  For the expansion 
cohort, patients will continue to be monitored for occurrence of toxicities that meet the definition 
DLT after cycle 1.  Once pharmacodynamic data are available, additional expansion cohorts may 
be considered to explore pharmacodynamic endpoints at lower dose levels (a protocol amendment 
will be submitted for these changes to the trial design). 
 

102 
5.4 
General Concomitant Medication and Supportive Care Guidelines 
 
All patients will be provided with the best available supportive care.  All concurrent medications 
should be documented prior to initiation of treatment and periodically reviewed with the patient.  
It is not known which CYP enzymes are involved in the metabolism of CB-5339, and CB-5339 
appears to be a potential inhibitor of CYP2C19 and 2C9 in vitro. Therefore, for patients enrolled 
in the dose-escalation phase, avoid concomitant use of drugs that are strong inhibitors of CYP 
enzymes during the dose escalation phase, and substrates of CYP2C19 and 2C9 with narrow 
therapeutic indices, as this may affect the determination of the recommended phase 2 dose.  
During the expansion phase, any concomitant use of CB-5339 and drugs that are strong inhibitors 
of CYP enzymes or substrates with narrow therapeutic indices for CYP2C19 (e.g., diazepam) or 
CYP2C9 (e.g., warfarin, phenytoin, many sulfonylureas (tolbutamide, glyburide, glibenclamide, 
glipizide, glimepiride) will be monitored closely.  Consult http://medicine.iupui.edu/flockhart/ for 
frequently updated information on drug interactions with cytochrome P450 isoenzymes.   
 
Patients on study may be eligible for palliative radiotherapy to non-targeted lesions after 
completing 2 cycles of therapy at the Principal Investigator’s discretion. 
 
5.4.1 Nausea/Vomiting: Anti-emetics will not be administered routinely prior to CB-
5339.  However, if a patient develops nausea/vomiting, anti-emetics such as but 
not limited to prochlorperazine, metoclopramide, 5-HT3 antagonists, or aprepitant 
may be given.  In addition, if a patient develops nausea and/or vomiting that is 
Grade 2 or greater, anti-emetics may be instituted prophylactically at the discretion 
of the investigator.  Nausea and vomiting will be considered refractory if it does 
not resolve to grade 2 or less with a combination of at least 2 anti-emetics within 
24 hours.  
5.4.2 Diarrhea: Subjects will not be given anti-diarrhea medication prophylactically.  If 
diarrhea develops and does not have an identifiable cause other than study drug 
administration, addition of anti-motility agents such as tincture of opium 
(deodorized 10%), Lomotil (diphenoxylate HCl 2.5 mg + atropine sulfate 0.025 
mg/tablet) dosed according to the package insert, or loperamide 4 mg po after the 
first unformed stool with 2 mg po with every 2 hours as long as unformed stools 
continue (4 mg every 4 hours while asleep) may be used.  No more than 16 mg of 
loperamide should be taken during a 24-hour period).  This regimen can be 
repeated for each diarrheal episode and will continue for 12 hours after the first 
formed stool.  Diarrhea will be considered refractory if it does not resolve within 
24 hours ≤ to Grade 2 with the above measures.  If the patient develops blood or 
mucus in the stool, dehydration, or hemodynamic instability, or fever along with 
the diarrhea, anti-diarrheals will be discontinued and the patient will be treated 
with IV fluids and antibiotics as medically indicated.  Other potentially helpful 
treatments may also be administered, such as somatostatin analogues, 
propantheline bromide, etc. 
5.4.3 Electrolyte Abnormalities: If hypokalemia, hypophosphatemia, or 

102 
hypomagnesemia occur, the patient may receive oral or IV supplementation to 
correct the abnormality.  If hyponatremia occurs, the patient may receive 0.9% 
sodium chloride intravenously to correct the abnormality. 
5.4.4 Neutropenia: Febrile neutropenia is a life-threatening complication requiring 
hospitalization and urgent broad-spectrum antibiotics, as well as an aggressive 
search for the source and microbial cause of the episode.  If clinically indicated, 
filgastrim will be administered according to accepted guidelines (ASCO or 
Clinical Center).  Study medication will not be reinitiated until at least 24 hours 
after filgrastim administration. 
5.4.5 Anemia: Symptomatic anemia should be treated with red blood cell transfusion 
and is recommended if the hemoglobin falls below 8 g/dL.  The initiation of 
erythropoietic therapy for the management of chemotherapy-induced anemia 
follows the American Society of Hematology/ASCO clinical practice guidelines 
(http://www.asco.org). 
5.4.6 Thrombocytopenia: Thrombocytopenia will be treated conservatively.  In the 
absence of bleeding, or a necessary invasive procedure, platelet transfusions 
should be given for a platelet count ≤10,000/mm3.  If invasive procedure(s) is (are) 
planned, or the patient develops bleeding, platelet transfusions should be 
administered in accordance with the standard of practice, usually maintaining a 
platelet count above 50,000/mm3. 
 
 
5.5 
Duration of Therapy 
 
In the absence of treatment delays due to adverse event(s), treatment may continue until one of 
the following criteria applies: 
 
• 
Disease progression 
• 
Intercurrent illness that prevents further administration of treatment 
• 
Significant toxicity occurs despite 2 dose reductions or no lower dose level exists, 
• 
Patient decides to withdraw from the study 
• 
General or specific changes in the patient's condition render the patient unacceptable for 
further treatment in the judgment of the investigator 
• 
Patient non-compliance 
• 
Pregnancy 
• 
Termination of the study by sponsor 
• 
The drug manufacturer can no longer provide the study agent 
 
The reason(s) for protocol therapy discontinuation, the reason(s) for study removal, and the 
corresponding dates must be documented in the Case Report Form (CRF). 
 
5.5.1 Study Discontinuation and Closure 
 
This study may be temporarily suspended or prematurely terminated if there is sufficient 

102 
reasonable cause.  If the study is prematurely terminated or suspended, the Principal Investigator 
will promptly inform study participants and the IRB and will provide the reason(s) for the 
termination or suspension.  Study participants will be contacted, as applicable, and be informed of 
changes to study visit schedule. 
 Circumstances that may warrant termination or suspension include, but are not limited to: 
• Determination of unexpected, significant, or unacceptable risk to participants 
• Demonstration of efficacy that would warrant stopping    
• Insufficient compliance to protocol requirements 
• Data that are not sufficiently complete and/or evaluable 
• Determination that the primary endpoint has been met 
• Determination of futility 
 
The Study may resume once concerns about safety, protocol compliance, and data quality are 
addressed, and satisfy the IRB and/or Food and Drug Administration (FDA). 
 
 
5.6 
Duration of Follow-Up 
 
Patients will be followed for 30 days after the last dose is administered or until one of the 
following occurs: patient enrolls on another protocol, patient receives standard of care, or death, 
whichever comes first.  The follow-up will consist of a phone call between Days 27-30 after the 
last dose to evaluate adverse events that were ongoing and any new events that might be deemed 
related to the therapy.  Any patients with unresolved toxicity  Grade 2 at the time of the post-
study clinical follow-up visit will be followed with clinic visits or phone calls as appropriate until 
resolution of the toxicity to less than Grade 2 or stabilization of the toxicity. 
 
5.7 
Criteria for Removal from Study 
Patients will be removed from study for one of the following reasons: completed 30-day follow 
up period or toxicities are unresolved but stabilized, patient enrolls on another protocol, or patient 
receives standard of care.  The reason for study removal and the date the patient was removed 
must be documented in the medical record and communicated to Central Registration per Section 
4. 
 
 
5.8 
Dosing delays  
 
Doses of CB-5339 will be held or modified only for adverse events that are felt to be at least 
possibly related to study drug.  Treatment may be delayed for a maximum of 2 weeks for 
resolution of toxicities; in case toxicities do not resolve as defined below, the patient will not 
receive further therapy on this protocol and will be followed for resolution of toxicities.  Dose 
modifications are intended for within-cycle and start of next cycle changes.  If administration of 
CB-5339 is interrupted for any reason, it will not be made up, and counting of the cycle days will 
continue. 
 
Patients will be allowed up to 2 dose reductions.  For patients on dose level 1, the dose will be 
reduced to dose level -1 (25 mg/day; 3 days on/4 days off each week q 28-day cycles).  Patients 

102 
who require a dose reduction will not have the dose re-escalated.   
 
Treatment may be delayed for a maximum of 1 day during a cycle due to unavoidable scheduling 
conflicts.   
 
5.9 
Dose Modifications 
 
5.9.1 Grade 2 drug-related toxicity: therapy will not be interrupted for Grade 2 toxicities with 
the exception of ocular toxicity.  
5.9.2 Grade 3-4 drug-related non-hematologic toxicities: CB-5339 will be held until toxicities 
recover to ≤ grade 1 or baseline (with the exception of alopecia) prior to re-initiating 
therapy at the next lower dose level.  Electrolyte abnormalities will not require dose 
reduction if resolution to grade 1 or less is documented within 48 hours.  Dose 
modifications for nausea, vomiting, and diarrhea will be made only if they are refractory 
to treatment (refer to Section 5.4).  Diarrhea, nausea, and vomiting that fail to resolve to  
Grade 2 within 24 hours despite adequate medical management are considered refractory.  
5.9.3 Grade 3 hematologic toxicities: drug will be held for grade 3 hematologic toxicities, 
except leucopenia in the absence of neutropenia or lymphopenia, until resolution of 
toxicity to at least a grade 1 or baseline.  Dose modification for grade 3 hematologic 
toxicity will be made only if the patient has recurrent grade 3 hematologic toxicity 
despite appropriate supportive care, e.g., growth factors; those experiencing recurrent 
grade 3 hematological toxicity despite optimal management may be dose reduced to the 
lower dose level.   
5.9.4 Grade 4 drug-related hematologic toxicities of thrombocytopenia and neutropenia: CB-
5339 will be held until toxicities recover to ≤ grade 1 and therapy re-initiated at the next 
lower dose level.  Agent will not be held or dose modified for leucopenia in the absence 
of neutropenia or lymphopenia.  
5.9.5 All patients with grade 4 cardiac, respiratory, or neurologic toxicities at least possibly 
attributable to the investigational drug will be taken off treatment.  
 
5.10 Visual Symptoms/Eye AEs Dose Modification Guidance 
5.10.1 Subjects with visual symptoms should contact the study team to discuss stopping CB-
5339 until resolution of the symptoms and undergo an unscheduled eye exam per the 
protocol-defined ophthalmology questionnaire (Appendix B).  Patients will also be 
encouraged to avoid bright light and wear sunglasses. In subjects with identifiable 
objective findings by the ophthalmologist that is assessed to be medically important, CB-
5339 should be held.  If no such findings are identified, dosing may resume once the 
symptoms have resolved at the next lowest dose level with CTEP medical monitor 
approval.  If visual symptoms do not resolve after 7 days, the subject should be taken off 
treatment.  Optical coherence tomography (OCT) may be performed if indicated by the 
NEI associate investigators.   
5.10.2 Subjects with confirmed OCT abnormalities associated with clinically significant effects 
to ocular function or confirmed clinically significant decrease in visual acuity not 
 

102 
attributable to an event unrelated to drug therapy (e.g., trauma, ocular surface disease, or 
retinal changes consistent with an underlying diagnosis such as retinal hemorrhages in a 
patient with a coagulopathy, vitreous hemorrhage in a diabetic or progression of 
choroidal neovascularization in a patient with macular degeneration, concomitant 
medications), will have study drug held for a total of 7 calendar days inclusive, after 
which CB-5339 will be withdrawn if the visual acuity has not improved to within 10 
letters of baseline as determined by ETDRS visual acuity methods (or its equivalent using 
Snellen testing).  If the visual acuity has improved and the subject is experiencing benefit 
from treatment, CB-5339 dosing may resume at the next lowest dose level, with CTEP 
medical monitor approval. 
 
 
6. PHARMACEUTICAL INFORMATION 
 
A list of the adverse events and potential risks associated with CB-5339 agent can be found in 
Section 9. 
 
6.1 
CB-5339 tosylate (NSC 814100)  
 
Chemical name:  1-(4-(benzylamino)-5,6,7,8 – tetrahydropyrido[2,3-d]pyrimidin-2yl)-2-methyl-
1H-indole-4-carboxamide 4-methylbenzenesulfonate 
 
Other names: CB-5339  
 
Classification:  Small molecule, selective, ATP-competitive inhibitor of p97 
 
Mode of Action: Binds and inhibits the AAA ATPase domain of p97, resulting in the disruption 
of the ubiquitin proteasome system, accumulation of cellular polyubiquitinated proteins, 
generating endoplasmic reticulum stress and leading to cellular apoptosis by disrupting cellular 
restoration of protein homeostasis. 
 
Molecular formula: C31H21N6O4S 
M.W.: 
584.69 
  
Description:  CB-5339 tosylate drug substance is a white to off-white powder. 
  
Storage requirements:  Store bottles at controlled room temperature 20-25oC; brief excursions 
permitted between 15°-30°C (59°-86°F) [see USP Controlled Room Temperature].  Do not 
remove the desiccant. 
If a storage temperature excursion is identified, promptly return capsules to controlled room 
temperature and quarantine the supplies.  Provide a detailed report of the excursion (including 
documentation of temperature monitoring and duration of the excursion) to 
PMBAfterHours@mail.nih.gov for determination of suitability. 
 
How Supplied: CB-5339 tosylate is supplied by Cleave Therapeutics add distributed by the 
Pharmaceutical Management Branch, CTEP, DCTD, NCI as capsules containing 25 mg or 75 mg of 
CB-5339 free-base equivalent.  Capsules are provided in 60 cc HDPE bottles with induction seals 

102 
and child-resistant polypropylene plastic caps.  Each bottle contains 30 capsules with a desiccant 
pack.  Capsule descriptions are as follows: 
 
25 mg capsules:  hard gelatin, White Opaque, size 4 and contain the inactive ingredients: 
microcrystalline cellulose, mannitol, croscarmellose sodium, polaxamer, silicone dioxide and 
magnesium stearate.  
 
75 mg capsules: hard gelatin, Swedish Orange, size 1, and contain the inactive ingredients: 
microcrystalline cellulose, mannitol, croscarmellose sodium, polaxamer, silicone dioxide and 
magnesium stearate.  
  
Stability:   Shelf life stability testing of the intact bottles are on-going.  It is recommended that 
capsules are dispensed in the original manufacturer’s container.  If capsules must be repackaged, 
they are to be repackaged from the manufacturer-supplied white HDPE bottle into a pharmacy-
supplied white HDPE bottle for dispensing purposes. 
 
Route of administration: oral; capsules should be taken on an empty stomach (i.e., either 1 hour 
before or 2 hours after meals) with water. 
 
Potential Drug Interactions: In vitro studies suggest CB-5339 tosylate is hepatically metabolized, 
with metabolic pathways not fully defined. 
 
In vitro, CB-5339 tosylate showed moderate inhibition of CYP2C9 and CYP2C19, and weak 
inhibition of CYP1A2 and CYP2D6.  CB-5339 tosylate did not inhibit CYP3A4.  Use caution 
when co-administered with CYP2C9 and CYP2C19 substrates.   
 
In vitro, CB-5339 tosylate is > 98% protein-bound in human plasma.  Use caution when co-
administered with other medications that are highly protein-bound. 
 
Patient Care Implications: CB-5339 tosylate must not be administered to pregnant or nursing 
females.  Women study participants of reproductive potential and fertile men study participants 
and their partners must abstain or use effective contraception while receiving study treatment and 
for at least 4 months after the last dose.  
 
Availability: CB-5339 is an investigational agent supplied to investigators by the Division of 
Cancer Treatment and Diagnosis (DCTD), NCI.  CB-5339 is provided to the NCI under a 
Collaborative Agreement between the Pharmaceutical Collaborator and the DCTD, NCI (see 
Section 12.3). 
 
6.1.1 Agent Ordering and Agent Accountability 
 
NCI-supplied agents may be requested by eligible participating Investigators (or their authorized 
designee) at each participating institution.  The CTEP-assigned protocol number must be used 
for ordering all CTEP-supplied investigational agents.  The eligible participating investigators at 
each participating institution must be registered with CTEP, DCTD through an annual 
submission of FDA Form 1572 (Statement of Investigator), NCI Biosketch, Agent Shipment 

102 
Form, and Financial Disclosure Form (FDF).  If there are several participating investigators at 
one institution, CTEP-supplied investigational agents for the study should be ordered under the 
name of one lead participating investigator at that institution. 
 
The CTEP Pharmaceutical Management Branch (PMB) will provide direction as to when sites 
can order PMB-supplied agents. 
 
Submit agent requests through the PMB Online Agent Order Processing (OAOP) application.  
Access to OAOP requires the establishment of a CTEP Identity and Access Management (IAM) 
account and the maintenance of an “active” account status, a “current” password, and active 
person registration status.  For questions about drug orders, transfers, returns, or accountability, 
call or email PMB any time.  Refer to the PMB’s website for specific policies and guidelines 
related to agent management.   
 
Agent Inventory Records – The investigator, or a responsible party designated by the 
investigator, must maintain a careful record of the receipt, dispensing and final disposition of all 
agents received from the PMB using the appropriate NCI Investigational Agent (Drug) 
Accountability Record (DARF) available on the CTEP forms page.  Store and maintain separate 
NCI Investigational Agent Accountability Records for each agent, strength, formulation and 
ordering investigator on this protocol. 
 
Useful Links and Contacts 
• CTEP Forms, Templates, Documents:  http://ctep.cancer.gov/forms/ 
• NCI CTEP Investigator Registration:  RCRHelpDesk@nih.gov 
• PMB policies and guidelines: http://ctep.cancer.gov/branches/pmb/agent_management.htm  
• 
PMB Online Agent Order Processing (OAOP) application:  
https://ctepcore.nci.nih.gov/OAOP 
• CTEP Identity and Access Management (IAM) account: https://ctepcore.nci.nih.gov/iam/  
• CTEP IAM account help:  ctepreghelp@ctep.nci.nih.gov  
• IB Coordinator:  IBCoordinator@mail.nih.gov  
• PMB email:  PMBAfterHours@mail.nih.gov 
• PMB phone and hours of service: (240) 276-6575 Monday through Friday between 8:30 
am and 4:30 pm (ET) 
 
 
7. BIOMARKER AND CORRELATIVE STUDIES 
 
Blood and urine will be obtained from all patients to determine the PK of CB-5339; BSA additive 
should be included in the urine collection flask per Section 7.1.  Pre- and post-treatment tumor 
biopsies will be collected on the expansion cohort to measure the effects of CB-5339 on the 
ubiquitin proteasome system and on markers of cell death; PBMCs will be collected on the 
escalation cohort as surrogate markers for tumor effect.  Blood samples will also be collected for 
isolation of circulating tumor DNA (ctDNA) as an exploratory endpoint to identify potential 
genomic biomarkers of response in patients on the expansion cohort.   

102 
Record the date, planned time and actual time of collection for each specimen on the PK/PD 
sample collection sheet  
 
 
 
 

102 
Ophthalmologic Examination will be performed at screening and as clinically indicated.  
 
Ophthalmologic testing and biomicroscopic examinations should include assessment of the 
following in the order listed whenever possible. 
 
- 
Best corrected visual acuity (BCVA) using Early Treatment Diabetic Retinopathy Study 
(ETDRS) methodology.  The same methodology is to be used for the pre-study and 
follow-up examinations for each individual subject. 
- 
Slit lamp examination including assessment of the lids, lashes, conjunctiva, sclera, cornea, 
anterior chamber, iris, lens and anterior vitreous.   The slit lamp examination is repeated 
following dilation to better assess the lens and anterior vitreous. 
- 
Measurement of intra-ocular pressure. 
- 
Fundus examination.  This include assessment of the vitreous, retina, disc, macula, 
vessels, and periphery of each eye using dilated fundoscopy. 
- 
Spectral domain optical coherence tomography (OCT) of the macula and disc for both 
eyes.   The same type of device is to be used for the pre-study and follow-up examinations 
for each individual subject. 
- 
Standard field fundus photographs with the pupils dilated performed on each eye to aid in 
the evaluation of the optic nerve, vessels, macula, and periphery. 
- 
Color vision testing 
 
To be eligible for this research protocol, patients will be screened for pre-existing visual 
impairment.  Patients will be excluded if they do not meet the visual acuity threshold (best 
corrected visual acuity of 60 ETDRS letters [Snellen equivalent of 20/60] in either eye) and the 
visual field threshold (substantial visual field loss in one or both eyes). 
 
 
 
 
 
 
 

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APPENDIX C: PD/PK COLLECTION WORKSHEETS 
7.1 
Pharmacokinetic Analysis  
CB-5339 pharmacokinetics will be measured in plasma and urine from all patients during 
cycle 1 day 1 (the first 3 patients will also have PK blood collected on C1 D4) and during 
subsequent cycles for patients experiencing toxicity or who have undergone intra-patient 
dose escalation.  A stability additive must be included in urine samples as described below. 
PK parameters, including area under the plasma concentration versus time curve (AUC), 
maximum plasma concentration (Cmax), trough plasma concentration (Cmin), time to 
maximum plasma concentration (Tmax) and plasma terminal elimination half-life (T1/2) will 
be determined using appropriate PK models.  PK samples will be batched for analysis at 
the conclusion of the escalation phase and will not be used to determine escalation or 
expansion phase doses.  Note: the 8-hr post dose sample collection is optional pending data 
on agent stability in whole blood overnight until processing. 
 
One 0.5 mL K2EDTA tube (pediatric microtainer) will be obtained for each of the time 
points.  The actual time of collection will be noted for each sample, and the sample will be 
placed immediately on wet ice until processing to plasma.   
 
Blood will be collected at the following times (mandatory all patients except for the 8-hr 
post dose collection):   
• cycle 1 day 1 prior to CB-5339 administration  
• cycle 1 day 1 at 15, 30, and 60 minutes, 2hr, 4hr, 6hr, 8hr*, 24hr after CB-5339 
(before another dose is taken) 
 
Blood will also be collected at the following times for the first 3 patients only who will be 
admitted to the Clinical Center until Day 5 (all mandatory except for the 8-hr post dose 
collection):   
 
• cycle 1 day 4 predose and at 15, 30, and 60 minutes, 2hr, 4hr, 6hr, 8hr*, 24hr after 
CB-5339 (before another dose is taken) 
 
Patients who have been dose-adjusted will have optional PK samples collected prior to CB-
5339 administration on day 1 and then 1, 2, and 24 hours after drug administration (before 
another dose is taken) during the first cycle following dose adjustment only.   
 
The PK blood tubes/samples should be kept on ice until plasma can be recovered, at which 
time the plasma samples should be frozen (-70°C).  The plasma samples should be stored at 
-70°C, and shipped to the PK lab at the address below on dry ice. 
 
• 
Samples from the first three patients (hospitalized) will be sent in individual 
batches (i.e., all plasma from the patient’s day 1 and 4 collections) for “real-time” 
PK analysis by validated HPLC-MS/MS.  Subsequent patient samples can 
be stored and batched for shipment (approximately 48 samples/shipment).   
 
A baseline urine collection of 10 mL will be collected just before CB-5339 administration.  
1.5% BSA will be added to the sample and mixed well.  Urine will then be collected at 

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every void from 0 to 24 hours on cycle 1, day 1 for PK analysis.  Samples should be placed 
on wet ice immediately after collection and then refrigerated in the presence of 1.5% BSA.  
The total volume of urine collected for the 24-hour time period will be documented and a 
10-mL sample will be taken from the total volume and saved; the rest can be discarded.  
PK samples will be shipped to:  
 
Attn: Katherine Yahvah 
Alturas Analytics 
1324 Alturas Drive 
Moscow ID, 83843 
kyahvah@alturasanalytics.com 
 
Based upon the results of the initial measurements, sampling times may be adjusted but 
neither the total number of samples nor the total amount of blood will be increased. 
 
7.2 
Pharmacodynamic Assays 
 
Tumor core biopsies from patients on the expansion cohort only will be collected and processed 
as detailed below. 
 
7.2.1 Tumor biopsy collection 
After completion of the escalation phase, 15 additional patients will be enrolled in an 
expansion cohort at the RP2D for pharmacodynamic analysis.  Biopsies will be 
mandatory for all patients on the expansion cohort.  Given the known success rate for 
obtaining paired research biopsy samples in clinical studies at the Development 
Therapeutics Clinic, 15 patients will ensure an adequate number of usable paired biopsy 
samples are collected for meaningful analysis. 
 
Biopsies will be collected pre-treatment and then then 4-6 hours after receiving the first 
dose of CB-3559 on cycle 1 day 1.  An optional biopsy may be collected at disease 
progression or at “pre-progression” (a 10-19% increase in tumor volume as shown on a 
restaging scan).   
 
Given the limited number of patients providing biopsies, and the fact that tumor sampling 
will be limited to two timepoints, a multiplex biomarker strategy will be used to increase 
the likelihood of detecting a pharmacodynamic signal of drug action in the collected 
tumor tissue.  NCI’s Pharmacodynamic Assay Development and Implementation Section 
(PADIS), has developed a combination of 3 pharmacodynamic biomarkers to quantify the 
effect of CB-5339 (Srivastava et al., 2018) via the three major mechanisms by which p97 
inhibitors act: 1) extraction of ubiquitinated substrates; 2) induction of unfolded protein 
response (UPR) due to ERAD; and 3) execution of apoptosis.  The polyubiquitinated 
proteins crosslinked through lysine-K48 of ubiquitin molecule (described as K48-ub) 
provided a specific measure of proteasome pathway blockage.  The transcription factor 
CHOP (CCAAT-enhancer-binding protein homologous protein) assessed in the nuclear 
fraction of cell lysates provided a measure of UPR, and measurement of cleaved caspase-
3 levels in the cytosolic fraction provided evidence of apoptosis.  These 3 biomarkers 

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were developed as sandwich immunoassays on the Luminex multiplex platform; the 
multiplex approach maximizes the chances of finding a molecular response that will 
guide subsequent, more mature PD evaluations.  A priority use table for PD analysis is 
provided in Section 7.3.  Any biopsy tissue collected at progression/pre-progression will 
also be evaluated in these assays.   
 
 
7.2.2 Biopsy Procedure  
 
If feasible and considered safe by the interventional radiologist (percutaneous approach), 
dermatologist (percutaneous   or excisional approach), or ENT specialist (ENT 
approach), it is preferred that up to five cores ≥18-gauge in diameter and at least 1 cm in 
length, or equivalent, are obtained.  Excisional or ENT biopsy is allowed if indicated and 
can be used for analysis.  If a site is deemed appropriate for biopsy with minimal risk to 
the participant by agreement between the investigators and Interventional Radiology, a 
dermatologist, or an ENT specialist, an attempt at biopsy will be made.   
 
The biopsy procedure to be used in this protocol is described below; local anesthesia will 
be administered.  Such biopsies can be safely performed as evidenced by literature 
reports (Dowlati et al., 2001) as well as our experience at the Clinical Center.  Risks of 
the procedure include, but are not limited to, bleeding, infection, pain, and scarring.  Each 
site will follow local biopsy team SOPs for coagulant panel and platelets. 
 
The use of imaging to facilitate biopsies will be decided by members of the biopsy team 
and may include ultrasound, CT scan, or MRI.  Should CT scan be needed for biopsy, the 
number of scans for each procedure will be limited to the minimum number needed to 
safely obtain a biopsy.  Tumor biopsies and local anesthesia will be administered only if 
they are considered to be of low risk to the participant as determined by the investigators 
and the biopsy team.  
 
Baseline biopsies will be performed following patient enrolling on study.  If an initial 
attempt at biopsy is unsuccessful, the patient will be given an option to proceed with a 
repeated attempt.  A separate consent form must be signed for each biopsy procedure, so 
patients may choose not to undergo subsequent biopsies.  If the baseline biopsy is 
unsuccessful or the patient refuses to undergo subsequent biopsies, no further biopsies 
will be performed but the patient will remain on study, receive study medication, and 
other correlative studies will be performed.  The radiologist will be asked if the specimen 
came from center or periphery of the lesion; this location will be documented in the 
patient specimen log and, if possible, a photographic image of the needle position should 
be taken. 
 
7.2.3 Solid Tumor Biopsy Processing  
Biopsies should be collected, placed in pre-chilled cryogenic vials, and flash frozen in 
liquid nitrogen within 2 minutes of collection per DCTD SOP340507 
(https://dctd.cancer.gov/ResearchResources/biomarkers/docs/par/SOP340507_Biopsy_Frozen.pdf).  
The frozen biopsy specimens are transferred to PADIS on dry ice, where the core biopsy 

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samples are stored at -140°C, or colder, and subsequently processed within 7-10 days for 
analysis or as directed by the Principal Investigator.  Biopsy samples will be analyzed as 
described above; any additional cores will be flash-frozen and kept for future analysis in 
the Frederick National Laboratories CR Biorepository in liquid nitrogen freezers.  
Additional studies, if performed, will be conducted following an amendment to the current 
protocol. 
 
7.2.4 Archival Tissue Submission 
Archival tumor tissue submitted as a baseline specimen must have been collected within 3 
months prior to patient registration, and the patient must not have received any intervening 
cancer therapy since collection of the specimen.  Archival tissue must have been collected 
and processed according to SOP340507 
(https://dctd.cancer.gov/ResearchResources/biomarkers/docs/par/SOP340507_Biopsy_Frozen.pdf), 
including flash-freezing in liquid nitrogen, minimal cold ischemia time (< 5 minutes), and 
shipment on dry ice. 
 
Please send an email to FNLCR PD Specimen Central Receiving 
(NCI_PD_Support@mail.nih.gov) to advise that archival tissue is being prepared for 
shipment.  State “Protocol Name PD Specimens Ready for Shipment” in the subject 
line.  If needed, FNLCR PD Central Receiving can be contacted directly at 301-846-1951 
(primary) or 240-344-5697. 
 
7.2.5 Blood Collection for Peripheral Blood Mononuclear Cells (PBMCs) 
 
Whole blood will be collected aseptically by venipuncture or from a venous port into one 
6 mL NaHep tube and the cells pelleted per SOP (Appendix E).  
PBMC collection will be mandatory during both the dose escalation and expansion 
phases:  
• cycle 1 prior to CB-5339 administration  
• cycle 1 day 1, 4-6 hrs after drug administration   
• One additional blood sample (optional) may be collected at/near time of disease 
progression.   
 
Samples will be sent for K-48 ubiquitin linked protein and CHOP measurements in the 
laboratory of Dr. Apurva Srivastava, NCI-Frederick.   
 
7.2.6 Blood Collection for exploratory ctDNA Studies 
 
Whole blood (7.5 mL per collection) will be collected aseptically by venipuncture or 
from a venous port into one 10-mL Streck cell-free DNA tube.  Blood samples for should 
be shipped as soon as possible so they can be analyzed within 48 hours of collection 
(preferably, within 24 hours of collection).   
Blood samples for ctDNA will be optional during the dose escalation phase, mandatory 
during the expansion cohort:  

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• cycle 1 prior to CB-5339 administration  
• cycle 1 day 2 (at any time)   
• day 1 of every subsequent cycle (at any time) 
• One additional blood sample (optional) may be collected at/near time of disease 
progression.   
 
Testing and data analysis will be performed by MoCha on the Ilumina TSO 500 panel of 
oncology-related genes (non-CLIA).   
 
Ship ctDNA blood specimens at ambient temperature to:  
Attn: Alyssa Chapman/Ashley Hayes 
Molecular Characterization Lab 
Frederick National Laboratory for Cancer Research 
1050 Boyles Street 
Building 459 Room 125 
Frederick, MD 21702 
Phone: 301.846.1718 or 301.846.6973 
MoChaSampleReceiving@nih.gov 
 
7.2.7 Laboratory Contact 
At least 24 hours prior to sample collection, the research nurse will contact the NCI Phase 
I/II PK/PD Support Group in NIH Building 10: E-mail (preferred): NCIPK-
PDsupportgroup@mail.nih.gov, Pager (preferred): 102-12798, Phone: 240-858-3963, 
Fax: 301-480-5871.  Initial processing and shipping of the samples will be completed as 
described below.  Samples should be shipped as soon as possible. 
 
7.2.8 Sample Collection and Processing 
Biospecimens will be collected and processed using validated sops that will ensure both 
specimen quality and patient confidentiality pursuant to informed consent provisions.  
information about each specimen (e.g., blood, circulating tumor cells, per specific 
protocol) will be recorded on a pk/pd collection worksheet included in Appendix C.   
 
Using a computerized inventory system and a backup hardcopy process, all specimen 
collection and processing steps will be documented and the specific location of each 
specimen will be tracked.  Each new specimen collected will be assigned a unique 
barcode identifier that can be linked to the original specimen collected and other relevant 
information within the inventory system.  To ensure patient confidentiality, only 
containers used for the initial specimen collections will be labeled with patient identifiers.   
 
Only the barcode identifier will be applied to all subsequent specimen containers.  When 
specimens are processed and aliquoted, no patient information will be included on the new 
containers.  Original specimen containers will be discarded.  Only barcode-labeled 
specimens without patient identifiers will be shipped for analysis and/or storage.  Specimen 
labels will indicate: CTEP protocol number, unique patient accession number, 3-digit 
sample number (see list below), collection time, and total volume collected, as appropriate.  
Samples from sets of at least three patients will be grouped for scientific analysis. 

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Standardized 3-digit sample collection numbers: 
100 series: urine for PK 
200 series: blood for PK 
300 series: blood for PD 
800 series: blood for ctDNA 
 
The inventory process contains other security provisions sufficient to safeguard patient 
privacy and confidentiality.  Access to the inventory system and associated documents 
will be restricted to appropriate individuals.  Requests to use specimens stored in the 
repository must be approved.  The only patient information available in the inventory 
system will be the patient sex, diagnosis, and level of informed consent given.  SOPs 
ensure that any changes in informed consent made by a patient and relayed to the PI will 
be reflected in the inventory system to ensure that specimens are destroyed as 
appropriate.  All laboratory personnel will be trained to adhere to SOPs and will be 
monitored for high-quality performance. 
 
Any new use of these samples will require prospective IRB review and approval.  Access 
to these samples will only be granted following IRB approval of an additional protocol, 
granting the rights to use the material. 
 
If at any time, a patient withdraws from the study and does not wish for their existing 
samples to be utilized, the individual must provide a written request.  Following receipt 
of this request, the samples will be destroyed (or returned to the patient, if so requested), 
and reported as such to the IRB.  Any samples lost (in transit or by a researcher) or 
destroyed due to unknown sample integrity (i.e., broken freezer allows for extensive 
sample thawing, etc.) will be reported as such to the IRB. 
 
 

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8.3 
Analysis of Secondary and Exploratory Endpoints 
 
Once the MTD/RP2D is established, up to 15 additional patients will be enrolled to the expansion 
phase of the trial.  Mandatory tumor biopsies will be obtained in the expansion phase to assess for 
pharmacodynamic endpoints.  With up to 15 patients and a tumor biopsy QA criteria failure rate 
of 19% with respect to paired (pre- and post-dose) biopsies, we have a 95% likelihood of having 
at least 10 usable PD paired samples.  This will give us at least 90% power to detect a treatment 
related PD endpoint change of at least 1.8 SDs (with respect to the baseline values of the 
endpoint) at the 1-sided .01 significance level (to accommodate multiple comparisons). 
 
8.3.1 Evaluation of Response 
 
All patients included in the study must be assessed for response to treatment, even if there are 
major protocol treatment deviations or if they are ineligible.  Each patient will be assigned one of 
the following categories: 1) complete response, 2) partial response, 3) stable disease, 4) 
progressive disease, 5) early death from malignant disease, 6) early death from toxicity, 7) early 
death because of other cause, or 9) unknown (not assessable, insufficient data).  
 
All of the patients who met the eligibility criteria (with the possible exception of those who 
received no study medication) should be included in the main analysis of the response rate.  
Patients in response categories 4-9 should be considered to have a treatment failure (disease 
progression).  Thus, an incorrect treatment schedule or drug administration does not result in 
exclusion from the analysis of the response rate.   
 
8.3.2 Analysis of Exploratory Endpoints 
 
Exploratory evaluations will be performed, with results reported with appropriate caveats about 
the exploratory nature of the analysis, and without formal adjustment for multiple comparisons. 
 
9. ADVERSE EVENTS:  LIST AND REPORTING REQUIREMENTS  
 
Adverse event (AE) monitoring and reporting is a routine part of every clinical trial.  The 
following list of AEs (Section 9.1) and the characteristics of an observed AE (Sections 9.2 and 
9.3) will determine whether the event requires expedited reporting via the CTEP Adverse Event 
Reporting System (CTEP-AERS) in addition to routine reporting. 
 
9.1 
Comprehensive Adverse Events and Potential Risks List (CAEPR) 
 
The Comprehensive Adverse Events and Potential Risks list (CAEPR) provides a single list of 
reported and/or potential adverse events (AE) associated with an agent using a uniform 
presentation of events by body system.  In addition to the comprehensive list, a subset, the 
Specific Protocol Exceptions to Expedited Reporting (SPEER), appears in a separate column and 
is identified with bold and italicized text.  This subset of AEs (SPEER) is a list of events that are 
protocol specific exceptions to expedited reporting to NCI (except as noted below).  Refer to the 
'CTEP, NCI Guidelines: Adverse Event Reporting Requirements' 
http://ctep.cancer.gov/protocolDevelopment/electronic_applications/docs/aeguidelines.pdf for 

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9.2 
Adverse Event Characteristics  
 
• CTCAE term (AE description) and grade:  The descriptions and grading scales found 
in the revised NCI Common Terminology Criteria for Adverse Events (CTCAE) version 
5.0 will be utilized for AE reporting.  All appropriate treatment areas should have access 
to a copy of the CTCAE version 5.0.  A copy of the CTCAE version 5.0 can be 
downloaded from the CTEP website 
http://ctep.cancer.gov/protocolDevelopment/electronic applications/ctc.htm. 
 
• For expedited reporting purposes only:   
- 
AEs for the agent that are bold and italicized in the CAEPR (i.e., those listed in the 
SPEER column, Section 10.1) should be reported through CTEP-AERS only if the 
grade is above the grade provided in the SPEER. 
- 
Other AEs for the protocol that do not require expedited reporting are outlined in 
Section 9.3.4. 
 
• Attribution of the AE: 
- 
Definite – The AE is clearly related to the study treatment. 
- 
Probable – The AE is likely related to the study treatment. 
- 
Possible – The AE may be related to the study treatment. 
- 
Unlikely – The AE is doubtfully related to the study treatment. 
- 
Unrelated – The AE is clearly NOT related to the study treatment. 
 
9.3 
Expedited Adverse Event Reporting 
 
9.3.1 Rave-CTEP-AERS Integration 
 
The Rave Cancer Therapy Evaluation Program Adverse Event Reporting System (CTEP-
AERS) integration enables evaluation of post-baseline AEs entered in Rave to determine 
whether they require expedited reporting, and facilitates entry in CTEP-AERS for those 
AEs requiring expedited reporting.    
 
All AEs that occur after baseline are collected in Medidata Rave using the Adverse Event 
form, which is available for entry at each treatment or reporting period, and used to collect 
AEs that start during the period or persist from the previous reporting period.  CRA will 
enter AEs that occur prior to the start of treatment on a baseline form that is not included 
in the Rave-CTEP-AERS integration.  AEs that occur prior to enrollment must begin and 
end on the baseline Adverse Event form and should not be included on the standard 
Adverse Events form that is available at treatment unless there has been an increase in 
grade. 
 
Prior to sending AEs through the rules evaluation process, site staff should verify the 
following on the Adverse Event form in Rave: 
 
• The reporting period (course/cycle) is correct, and 
• AEs are recorded and complete (no missing fields) and the form is query-free.  

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The CRA reports AEs in Rave at the time the Investigator learns of the event.  If the CRA 
modifies an AE, it must be re-submitted for rules evaluation. 
 
Upon completion of AE entry in Medidata Rave, the CRA submits the AE for rules 
evaluation by completing the Expedited Reporting Evaluation form.  Both NCI and 
protocol-specific reporting rules evaluate the AEs submitted for expedited reporting.  A 
report is initiated in CTEP-AERS using information entered in Medidata Rave for AEs 
that meet reporting requirements.  The CRA completes the report by accessing CTEP-
AERS via a direct link on the Medidata Rave Expedited Reporting Evaluation form. 
 
In the rare occurrence that Internet connectivity is lost, a 24-hour notification is to be 
made to CTEP by telephone at 301-897-7497.  Once internet connectivity is restored, the 
24-hour notification that was phoned in must be entered immediately into CTEP-AERS 
using the direct link from Medidata Rave. 
 
Additional information about the CTEP-AERS integration is available on the CTSU 
website: 
 
• Study specific documents:  Protocols > Documents > Education and Promotion, 
and   
• Expedited Safety Reporting Rules Evaluation user guide:  Resources > CTSU 
Operations Information > User Guides & Help Topics. 
 
NCI requirements for SAE reporting are available on the CTEP website:  
 
• NCI Guidelines for Investigators:  Adverse Event Reporting Requirements is 
available at 
https://ctep.cancer.gov/protocolDevelopment/electronic applications/docs/aeguide
lines.pdf. 
 
9.3.2 Distribution of Adverse Event Reports 
 
CTEP-AERS is programmed for automatic electronic distribution of reports to the following 
individuals:  Principal Investigator and Adverse Event Coordinator(s) (if applicable) of the 
Corresponding Organization or Lead Organization, the local treating physician, and the Reporter 
and Submitter.  CTEP-AERS provides a copy feature for other e-mail recipients.  
 
9.3.3 Expedited Reporting Guidelines 
 
Use the NCI protocol number and the protocol-specific patient ID assigned during trial 
registration on all reports. 
 
Note:  A death on study requires both routine and expedited reporting, regardless of 
causality.  Attribution to treatment or other cause must be provided. 
 

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9.3.4 Additional Protocol-Specific Expedited Adverse Event Reporting Exclusions 
 
None.  
 
9.4 
Routine Adverse Event Reporting 
 
All Adverse Events must be reported in routine study data submissions.  AEs reported 
expeditiously through CTEP-AERS must also be reported in routine study data 
submissions. 
 
Adverse event data collection and reporting, which are required as part of every clinical trial, are 
done to ensure the safety of patients enrolled in the studies as well as those who will enroll in 
future studies using similar agents.  AEs are reported in a routine manner at scheduled times 
during the trial using Medidata Rave.  For this trial the Adverse Event CRF is used for routine AE 
reporting in Rave. 
 
9.5 
Pregnancy 
 
Although not an adverse event in and of itself, pregnancy as well as its outcome must be 
documented via CTEP-AERS.  In addition, the Pregnancy Information Form included within 
the NCI Guidelines for Adverse Event Reporting Requirements must be completed and submitted 
to CTEP.  Any pregnancy occurring in a patient or patient’s partner from the time of consent to 90 
days after the last dose of study drug must be reported and then followed for outcome.  Newborn 
infants should be followed until 30 days old.  Please see the “NCI Guidelines for Investigators: 
Adverse Event Reporting Requirements for DCTD (CTEP and CIP) and DCP INDs and IDEs” (at 
http://ctep.cancer.gov/protocolDevelopment/adverse effects.htm) for more details on how to 
report pregnancy and its outcome to CTEP.  
 
9.6 
Secondary Malignancy 
 
A secondary malignancy is a cancer caused by treatment for a previous malignancy (e.g., 
treatment with investigational agent/intervention, radiation or chemotherapy).  A secondary 
malignancy is not considered a metastasis of the initial neoplasm. 
 
CTEP requires all secondary malignancies that occur following treatment with an agent under an 
NCI IND/IDE be reported expeditiously via CTEP-AERS.  Three options are available to 
describe the event:  
 
• Leukemia secondary to oncology chemotherapy (e.g., acute myelocytic leukemia [AML])  
• Myelodysplastic syndrome (MDS)  
• Treatment-related secondary malignancy  
 
Any malignancy possibly related to cancer treatment (including AML/MDS) should also be 
reported via the routine reporting mechanisms outlined in each protocol.  
 

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9.7 
Second Malignancy 
 
A second malignancy is one unrelated to the treatment of a prior malignancy (and is NOT a 
metastasis from the initial malignancy).  Second malignancies require ONLY routine AE 
reporting unless otherwise specified. 
 
 
10. STUDY CALENDAR 
 
Baseline history, physical examination, laboratory evaluations, and ECG must be conducted 
within 8 days prior to start of protocol therapy.  If protocol therapy is started within 8 days of the 
eligibility screening evaluations (see Section 3.4), the results from these screening evaluations 
may be used as baseline measurements.  If > 8 days have passed since the screening evaluations, 
the medical history, physical examination, laboratory evaluations, and ECG must be repeated 
prior to starting protocol therapy.  Baseline tumor imaging must be performed within 28 days 
prior to start of protocol therapy.  If protocol therapy is started within 28 days of the eligibility 
screening tumor imaging, the screening evaluation imaging results may be used as baseline 
measurements; if > 28 days have passed since the screening evaluation tumor imaging, the 
imaging must be repeated prior to starting protocol therapy.  
 
Start of next cycle may be delayed for up to 1 week to accommodate scheduling conflicts.  
Treatments within a cycle may be delayed up to +/- 1 day to accommodate scheduling conflicts.  
History and physical examination and laboratory evaluations can be performed up to 3 days 
before the start of the next cycle.  The research team may perform additional safety/monitoring 
tests as clinically indicated. 
The first three patients will be admitted to the NIH Clinical Center for 5 days of in-patient 
evaluation followed by out-patient evaluation at the day hospital on days 6 and 7.  Monitoring 
(vital check, PO2, serum chemistries, and CBC) will be enhanced for these patients based on their 
clinical status (see chart)  
 

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18 
 
 
Pre-Study 
Eligibility 
Screening 
Baseline 
Clinical 
Evaluation 
Cycle 1 
Cycle 2  
Cycle 3 
onwards 
 
 
 
Wk
1 
Wk
2 
Wk
3 
Wk
4 
Wk
1 
Wk
2 
Wk
3 
Wk
4 
 
CB-5339a 
 
 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Informed consent 
X 
 
 
 
 
 
 
 
 
 
 
Demographics 
X 
 
 
 
 
 
 
 
 
 
 
Med. History 
X 
Xj 
 
 
 
 
X 
 
 
 
prior to 
treatment 
Physical examb 
X 
Xj 
X 
X 
X 
X 
X 
 
 
 
prior to 
treatment 
ECGb 
X 
Xj 
 
 
 
 
X 
 
 
 
X  
Urinalysis 
X 
Xj 
 
 
 
 
X 
 
 
 
 
Height and Weight 
X 
Xj 
 
 
 
 
X 
 
 
 
X 
Performance 
Status 
X 
Xj 
X 
X 
X 
X 
X 
 
 
 
X 
CBC w/diff, pltsc 
X 
Xj 
X 
X 
X 
X 
X 
 
 
 
X 
Serum chemistryc 
X 
Xj 
X 
X 
X 
X 
X 
 
 
 
X 
Tumor 
Measurementd 
X 
Xj 
 
 
 
 
 
 
 
 
X 
B-HCGe 
X 
Xj 
 
 
 
 
X 
 
 
 
prior to 
treatment 
PK blood and 
urinef  
 
 
X 
 
 
 
 
 
 
 
 
Blood samples for 
ctDNAh 
 
 
X 
 
 
 
X 
 
 
 
start of 
every cycle 
Blood samples for 
PBMCsg 
 
 
X 
 
 
 
 
 
 
 
 
Ophthalmic Exam/ 
Questionnairei 
X 
 
X 
 
 
 
 
 
 
 
 
ECHOj 
X 
 
 
Adverse event 
evaluation 
 
 
X………………………………………………....…X 
a. CB-5339 will be given once daily for 4 consecutive days followed by 3 days without drug 
(QD4/3-off weekly for 4 weeks in consecutive 28-day cycles as specified in the dose escalation 
table.  Drug is to be taken with water on an empty stomach, either 1 hour before or 2 hours 
after meals.  Patients 1-3 will be admitted to the NIH Clinical Center for 5 days of in-patient 
evaluation followed by out-patient evaluation at the day hospital on days 6 and 7 (vital check, 
PO2, serum chemistries, CBC). These first three patients will then resume treatment at the NIH 
Clinical Center on D8 (C1, Wk2) as outpatients. 
 
b. For patients enrolled on the study after the the first three subjects, physical examination 
including vital signs and O2 saturation level (pulse oximeter) will be conducted pre-study, 
during weeks 1, 2, 3, and 4 of cycle 1, and then at the start of every cycle thereafter (within 3 
days prior to treatment).  ECG will be performed at baseline (within 8 days of the start of 

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protocol therapy) and will be performed on day 1 pre-dose and at 2 hours post dose/the time to 
peak concentration of every subsequent cycle, and as clinically indicated. 
Serum chemistries (sodium, potassium, chloride, bicarbonate, BUN, creatinine, glucose, AST, 
ALT, bilirubin, calcium, phosphorous, albumin, magnesium, alkaline phosphatase, LDH (with 
uric acid for patients with lymphoma only) and CBC with differential and platelets will be 
performed pre-study; for patients 1-3 at the following times during week 1: day 2 prior to 
CB5339, Day 3 as needed based on the result from Day 2, Day 4 prior to CB5339, Day 6 prior 
to CB-5339, then Cycle 1 week 2 (Day 8) , during weeks, 2, 3, and 4 of cycle 1, and then at the 
start (within 3 days prior to treatment) during week 1 of every cycle thereafter.  Patients 4 
onwards will have serum chemistries performed pre-study and then during weeks 1, 2, 3, and 4 
of cycle 1, and then and at the start (within 3 days prior to treatment) during week 1 of every 
cycle thereafter.   
c. Radiologic examination will be performed at baseline and then every 2 cycles (3 cycles for 
patients on study for more than one year, 4 cycles for those on study more than 3 years). 
d. Urine pregnancy test (women of childbearing potential) will be conducted within 24 hours 
prior to CB-5339 administration at baseline, and within 24 hours prior to CB-5339 at the start 
of each cycle thereafter.   
e. Blood and urine for PK analysis will be obtained from all patients as specified in Section 7.1.  
f. Blood samples for PBMCs (mandatory for all patients except for an optional sample at/near 
disease progression) will be collected from patients as specified in Section 7.2. 
g. Blood samples for ctDNA (mandatory only during expansion phase) will be collected from 
patients as specified in Section 7.2. 
h. An ophthalmology examination and questionnaire will be conducted on all patients during 
screening by NEI investigators; the questionnaire will be repeated by the patient after treatment 
on cycle 1 day 1 or 2, and as clinically indicated with the eye exam per Appendix B.  
i. Values from eligibility screening tests may be used as baseline evaluation values if the test was 
performed within 8 days of start of protocol therapy (or, for radiologic evaluation, ECHO, and 
tumor measurement, within 28 days of start of protocol therapy).  See Section 3.4. 
 
 
 
 
11. MEASUREMENT OF EFFECT 
 
Although the clinical benefit of CB-5339 has not yet been established, the intent of offering this 
treatment is to provide a possible therapeutic benefit, and thus the patient will be carefully 
monitored for tumor response and symptom relief in addition to safety and tolerability.  Patients 
with measurable disease will be assessed by standard criteria.  For the purposes of this study, 
patients should be re-evaluated every 8 weeks (2 cycles; 3 cycles for patients on study more than 
one year, 4 cycles for those on study more than 3 years).  In addition to a baseline scan, 
confirmatory scans will also be obtained 4 weeks following initial documentation of an objective 
response. 
 
11.1 Antitumor Effect – Solid Tumors 
 

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Response and progression will be evaluated in this study using the new international criteria 
proposed by the revised Response Evaluation Criteria in Solid Tumors (RECIST) guideline 
(version 1.1) [Eur J Ca 45:228-247, 2009].  Changes in the largest diameter (unidimensional 
measurement) of the tumor lesions and the shortest diameter in the case of malignant lymph nodes 
are used in the RECIST criteria. 
 
11.1.1 Definitions 
 
Evaluable for toxicity.  All patients will be evaluable for toxicity from the time of their first 
treatment with CB-5339. 
 
Evaluable for objective response.  Only those patients who have measurable disease present at 
baseline, have received at least one cycle of therapy, and have had their disease re-evaluated (as 
defined in Section 11) will be considered evaluable for response.  These patients will have their 
response classified according to the definitions stated below.  (Note:  Patients who exhibit 
objective disease progression prior to the end of cycle 1 will also be considered evaluable.) 
 
Evaluable Non-Target Disease Response.  Patients who have lesions present at baseline that are 
evaluable but do not meet the definitions of measurable disease, have received at least one cycle 
of therapy, and have had their disease re-evaluated will be considered evaluable for non-target 
disease.  The response assessment is based on the presence, absence, or unequivocal progression 
of the lesions.  
 
11.1.2 Disease Parameters 
 
Measurable disease.  Measurable lesions are defined as those that can be accurately measured in 
at least one dimension (longest diameter to be recorded) as ≥20 mm (≥2 cm) by chest x-ray or as 
≥10 mm (≥1 cm) with CT scan, MRI, or calipers by clinical exam.  All tumor measurements must 
be recorded in millimeters (or decimal fractions of centimeters). 
 
Malignant lymph nodes.  To be considered pathologically enlarged and measurable, a lymph node 
must be ≥15 mm (≥1.5 cm) in short axis when assessed by CT scan (CT scan slice thickness 
recommended to be no greater than 5 mm [0.5 cm]).  At baseline and in follow-up, only the short 
axis will be measured and followed. 
 
Non-measurable disease.  All other lesions (or sites of disease), including small lesions (longest 
diameter <10 mm [<1 cm] or pathological lymph nodes with ≥10 to <15 mm [≥1 to <1.5 cm] 
short axis), are considered non-measurable disease.  Bone lesions, leptomeningeal disease, 
ascites, pleural/pericardial effusions, lymphangitis cutis/pulmonitis, inflammatory breast disease, 
and abdominal masses (not followed by CT or MRI), are considered as non-measurable. 
 
Note:  Cystic lesions that meet the criteria for radiographically defined simple cysts should not be 
considered as malignant lesions (neither measurable nor non-measurable) since they are, by 
definition, simple cysts. 
 
‘Cystic lesions’ thought to represent cystic metastases can be considered as measurable lesions, if 

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they meet the definition of measurability described above. However, if non-cystic lesions are 
present in the same patient, these are preferred for selection as target lesions. 
 
Target lesions.  All measurable lesions up to a maximum of 2 lesions per organ and 5 lesions in 
total, representative of all involved organs, should be identified as target lesions and recorded 
and measured at baseline.  Target lesions should be selected on the basis of their size (lesions with 
the longest diameter), be representative of all involved organs, but in addition should be those that 
lend themselves to reproducible repeated measurements.  It may be the case that, on occasion, the 
largest lesion does not lend itself to reproducible measurement in which circumstance the next 
largest lesion which can be measured reproducibly should be selected.  A sum of the diameters 
(longest for non-nodal lesions, short axis for nodal lesions) for all target lesions will be calculated 
and reported as the baseline sum diameters.  If lymph nodes are to be included in the sum, then 
only the short axis is added into the sum.  The baseline sum diameters will be used as reference to 
further characterize any objective tumor regression in the measurable dimension of the disease. 
 
Non-target lesions.  All other lesions (or sites of disease) including any measurable lesions over 
and above the 5 target lesions should be identified as non-target lesions and should also be 
recorded at baseline.  Measurements of these lesions are not required, but the presence, absence, 
or in rare cases unequivocal progression of each should be noted throughout follow-up.  
 
11.1.3 Methods for Evaluation of Measurable Disease 
 
All measurements should be taken and recorded in metric notation using a ruler or calipers.  All 
baseline evaluations should be performed as closely as possible to the beginning of treatment and 
never more than 4 weeks before the beginning of the treatment. 
 
The same method of assessment and the same technique should be used to characterize each 
identified and reported lesion at baseline and during follow-up.  Imaging-based evaluation is 
preferred to evaluation by clinical examination unless the lesion(s) being followed cannot be 
imaged but are assessable by clinical exam. 
 
Clinical lesions.  Clinical lesions will only be considered measurable when they are superficial 
(e.g., skin nodules and palpable lymph nodes) and ≥10 mm (≥1 cm) diameter as assessed using 
calipers (e.g., skin nodules).  In the case of skin lesions, documentation by color photography, 
including a ruler to estimate the size of the lesion, is recommended.  
 
Chest x-ray.  Lesions on chest x-ray are acceptable as measurable lesions when they are clearly 
defined and surrounded by aerated lung.  However, CT is preferable.  
 
Conventional CT and MRI.  This guideline has defined measurability of lesions on CT scan based 
on the assumption that CT slice thickness is 5 mm (0.5 cm) or less.  If CT scans have slice 
thickness greater than 5 mm (0.5 cm), the minimum size for a measurable lesion should be twice 
the slice thickness.  MRI is also acceptable in certain situations (e.g. for body scans).   
 
Use of MRI remains a complex issue.  MRI has excellent contrast, spatial, and temporal 
resolution; however, there are many image acquisition variables involved in MRI, which greatly 

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22 
impact image quality, lesion conspicuity, and measurement.  Furthermore, the availability of MRI 
is variable globally.  As with CT, if an MRI is performed, the technical specifications of the 
scanning sequences used should be optimized for the evaluation of the type and site of disease.  
Furthermore, as with CT, the modality used at follow-up should be the same as was used at 
baseline and the lesions should be measured/assessed on the same pulse sequence.  It is beyond 
the scope of the RECIST guidelines to prescribe specific MRI pulse sequence parameters for all 
scanners, body parts, and diseases.  Ideally, the same type of scanner should be used and the 
image acquisition protocol should be followed as closely as possible to prior scans.  Body scans 
should be performed with breath-hold scanning techniques, if possible. 
 
PET-CT.  At present, the low dose or attenuation correction CT portion of a combined PET-CT is 
not always of optimal diagnostic CT quality for use with RECIST measurements.  However, if the 
site can document that the CT performed as part of a PET-CT is of identical diagnostic quality to 
a diagnostic CT (with IV and oral contrast), then the CT portion of the PET-CT can be used for 
RECIST measurements and can be used interchangeably with conventional CT in accurately 
measuring cancer lesions over time.  Note, however, that the PET portion of the CT introduces 
additional data which may bias an investigator if it is not routinely or serially performed.   
 
Ultrasound.  Ultrasound is not useful in assessment of lesion size and should not be used as a 
method of measurement.  Ultrasound examinations cannot be reproduced in their entirety for 
independent review at a later date and, because they are operator dependent, it cannot be 
guaranteed that the same technique and measurements will be taken from one assessment to the 
next.  If new lesions are identified by ultrasound in the course of the study, confirmation by CT or 
MRI is advised.  If there is concern about radiation exposure at CT, MRI may be used instead of 
CT in selected instances. 
 
Endoscopy, Laparoscopy.  The utilization of these techniques for objective tumor evaluation is 
not advised.  However, such techniques may be useful to confirm complete pathological response 
when biopsies are obtained or to determine relapse in trials where recurrence following complete 
response (CR) or surgical resection is an endpoint. 
 
Tumor markers.  Tumor markers alone cannot be used to assess response.  If markers are initially 
above the upper normal limit, they must normalize for a patient to be considered in complete 
clinical response.  Specific guidelines for both CA-125 response (in recurrent ovarian cancer) and 
PSA response (in recurrent prostate cancer) have been published [JNCI 96:487-488, 2004; J Clin 
Oncol 17, 3461-3467, 1999; J Clin Oncol 26:1148-1159, 2008].  In addition, the Gynecologic 
Cancer Intergroup has developed CA-125 progression criteria which are to be integrated with 
objective tumor assessment for use in first-line trials in ovarian cancer [JNCI 92:1534-1535, 
2000]. 
 
Cytology, Histology.  These techniques can be used to differentiate between partial responses 
(PR) and complete responses (CR) in rare cases (e.g., residual lesions in tumor types, such as 
germ cell tumors, where known residual benign tumors can remain). 
 
The cytological confirmation of the neoplastic origin of any effusion that appears or worsens 
during treatment when the measurable tumor has met criteria for response or stable disease is 

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mandatory to differentiate between response or stable disease (an effusion may be a side effect of 
the treatment) and progressive disease. 
 
FDG-PET.  While FDG-PET response assessments need additional study, it is sometimes 
reasonable to incorporate the use of FDG-PET scanning to complement CT scanning in 
assessment of progression (particularly possible 'new' disease).  New lesions on the basis of FDG-
PET imaging can be identified according to the following algorithm:  
a. Negative FDG-PET at baseline, with a positive FDG-PET at follow-up is a sign of PD 
based on a new lesion. 
b. No FDG-PET at baseline and a positive FDG-PET at follow-up:  If the positive FDG-PET 
at follow-up corresponds to a new site of disease confirmed by CT, this is PD.  If the 
positive FDG-PET at follow-up is not confirmed as a new site of disease on CT, additional 
follow-up CT scans are needed to determine if there is truly progression occurring at that 
site (if so, the date of PD will be the date of the initial abnormal FDG-PET scan).  If the 
positive FDG-PET at follow-up corresponds to a pre-existing site of disease on CT that is 
not progressing on the basis of the anatomic images, this is not PD. 
c. FDG-PET may be used to upgrade a response to a CR in a manner similar to a biopsy in 
cases where a residual radiographic abnormality is thought to represent fibrosis or 
scarring.  The use of FDG-PET in this circumstance should be prospectively described in 
the protocol and supported by disease-specific medical literature for the indication.  
However, it must be acknowledged that both approaches may lead to false positive CR 
due to limitations of FDG-PET and biopsy resolution/sensitivity. 
 
Note:  A ‘positive’ FDG-PET scan lesion means one which is FDG avid with an uptake greater 
than twice that of the surrounding tissue on the attenuation corrected image. 
 
11.1.4 Response Criteria 
 
Evaluation of Target Lesions 
 
Complete Response (CR):  Disappearance of all target lesions.  Any pathological lymph nodes 
(whether target or non-target) must have reduction in short axis to <10 mm (<1 cm). 
 
Partial Response (PR):  At least a 30% decrease in the sum of the diameters of target lesions, 
taking as reference the baseline sum diameters. 
 
Progressive Disease (PD):  At least a 20% increase in the sum of the diameters of target lesions, 
taking as reference the smallest sum on study (this includes the baseline sum if that is the smallest 
on study).  In addition to the relative increase of 20%, the sum must also demonstrate an absolute 
increase of at least 5 mm (0.5 cm).  (Note:  the appearance of one or more new lesions is also 
considered progressions). 
 
Stable Disease (SD):  Neither sufficient shrinkage to qualify for PR nor sufficient increase to 
qualify for PD, taking as reference the smallest sum diameters while on study. 
 

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24 
Evaluation of Non-Target Lesions 
 
Complete Response (CR):  Disappearance of all non-target lesions and normalization of tumor 
marker level.  All lymph nodes must be non-pathological in size (<10 mm [<1 cm] short axis). 
 
Note:  If tumor markers are initially above the upper normal limit, they must normalize for a 
patient to be considered in complete clinical response. 
 
Non-CR/Non-PD:  Persistence of one or more non-target lesion(s) and/or maintenance of tumor 
marker level above the normal limits. 
 
Progressive Disease (PD):  Appearance of one or more new lesions and/or unequivocal 
progression of existing non-target lesions.  Unequivocal progression should not normally trump 
target lesion status.  It must be representative of overall disease status change, not a single lesion 
increase. 
 
Although a clear progression of “non-target” lesions only is exceptional, the opinion of the 
treating physician should prevail in such circumstances, and the progression status should be 
confirmed at a later time by the review panel (or Principal Investigator). 
 
Evaluation of Best Overall Response 
 
The best overall response is the best response recorded from the start of the treatment until 
disease progression/recurrence (taking as reference for progressive disease the smallest 
measurements recorded since the treatment started).  The patient's best response assignment will 
depend on the achievement of both measurement and confirmation criteria. 
 
For Patients with Measurable Disease (i.e., Target Disease) 
 
Target 
Lesions 
Non-Target 
Lesions 
New Lesions 
Overall 
Response 
Best Overall Response when 
Confirmation is Required* 
CR 
CR 
No 
CR 
≥4 wks. Confirmation** 
CR 
Non-CR/Non-PD 
No 
PR 
≥4 wks. Confirmation** 
CR 
Not evaluated 
No 
PR 
PR 
Non-CR/Non-
PD/not evaluated 
No 
PR 
SD 
Non-CR/Non-
PD/not evaluated 
No 
SD 
Documented at least once ≥4 wks. 
from baseline** 
PD 
Any 
Yes or No 
PD 
no prior SD, PR or CR 
Any 
PD*** 
Yes or No 
PD 
Any 
Any 
Yes 
PD 
 
See RECIST 1.1 manuscript for further details on what is evidence of a new lesion. 
**    Only for non-randomized trials with response as primary endpoint. 
***  In exceptional circumstances, unequivocal progression in non-target lesions may be accepted as 
disease progression. 
 
Note:  Patients with a global deterioration of health status requiring discontinuation of treatment 
without objective evidence of disease progression at that time should be reported as 

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“symptomatic deterioration.”  Every effort should be made to document the objective 
progression even after discontinuation of treatment. 
 
For Patients with Non-Measurable Disease (i.e., Non-Target Disease) 
 
Non-Target Lesions 
New Lesions 
Overall Response 
CR 
No 
CR 
Non-CR/non-PD 
No 
Non-CR/non-PD* 
Not all evaluated 
No 
not evaluated 
Unequivocal PD 
Yes or No 
PD 
Any 
Yes 
PD 
 
‘Non-CR/non-PD’ is preferred over ‘stable disease’ for non-target disease since SD is increasingly 
used as an endpoint for assessment of efficacy in some trials so to assign this category when no 
lesions can be measured is not advised 
 
11.1.5 Duration of Response 
 
Duration of overall response:  The duration of overall response is measured from the time 
measurement criteria are met for CR or PR (whichever is first recorded) until the first date that 
recurrent or progressive disease is objectively documented (taking as reference for progressive 
disease the smallest measurements recorded since the treatment started). 
 
The duration of overall CR is measured from the time measurement criteria are first met for CR 
until the first date that progressive disease is objectively documented. 
 
 
Duration of stable disease:  Stable disease is measured from the start of the treatment until the 
criteria for progression are met, taking as reference the smallest measurements recorded since the 
treatment started, including the baseline measurements.  
 
 
11.2 Antitumor Effect – Hematologic Tumors 
Response in patients with lymphoma will be assessed using the International Working Group 
Consensus Response Evaluation Criteria In Lymphoma (RECIL 2017) (Younes et al., 2017).   
 
11.2.1 CT/MRI measurements 
Assessment of tumor burden will use the sum of the longest diameters (SLD).  In subjects with 
disseminated disease, a maximum of 3 target lesions should be selected to estimate tumor 
response.  
 
Target lesions should be selected per the following criteria: 
• Target lesions should be selected from lesions of the largest size that can be measured 
reproducibly and preferably representing multiple sites and organs.  
 
• Lymph nodes:  
o Lymph nodes can be considered target lesions if the lymph node longest diameter 
measures ≥15 mm.  
o A lymph node measuring between 10 and 14 mm is considered abnormal but should 

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not be selected as a target lesion.  
o Lymph nodes measuring <10 mm in diameter are considered normal and cannot be 
used as target lesions. 
• In certain anatomical sites (inguinal, axillary, and portocaval), normal lymph 
nodes may exist in a narrow, elongated form, and such nodes should not be 
selected as target lesions if alternatives are available.  
 
• Extranodal lesions are selected as target lesions if they have a soft tissue component, 
based on their size and the ease of reproducibility of repeated measurements, with a 
minimum measurement of the longest diameter of ≥15 mm. 
 
• Nontarget lesions:  
o All other lesions should be identified as nontarget lesions and should be recorded at 
baseline, without the need to measure them. 
o Nontarget lesions should be followed and reported as present, absent, or clear 
progression. 
 
11.2.2 FDG-PET measurements  
FDG-PET is only required to confirm a CR. 
 
Scoring is semi-quantitative using the Deauville 5-point scale (Deauville 5PS).  It is a simple tool 
based on visual interpretation of [18F]2-fluoro-2-deoxy-D-glucose (FDG) uptake.  It takes 
advantage of two reference points of the individual subject, which have demonstrated relatively 
constant uptake on serial imaging.  The two reference organs are the mediastinum and the liver. 
The scale ranges from 1 to 5, where 1 is best and 5 is the worst. Each FDG-avid (or previously 
FDG-avid) lesion is rated independently: 
1. 
no uptake or no residual uptake (when used interim)  
2. 
slight uptake, but below blood pool (mediastinum)  
3. 
uptake above mediastinal, but below or equal to uptake in the liver  
4. 
uptake slightly to moderately higher than liver 
5. 
markedly increased uptake or any new lesion (on response evaluation)  
 
11.2.3 Bone marrow biopsy and aspirate 
A bone marrow biopsy and aspirate are only required to confirm a CR. 
 
11.2.4 RECIL 2017: Response categories based on assessment of target lesions  
 
 
% Change in sum of diameters of target lesions from nadir 
CR 
PR 
MRa 
SD 
PD 
% change 
from 
baseline 
• Complete 
disappearance 
of all target 
lesions and all 
nodes with 
long axis <10 
mm 
• ≥30% 
≥30% decrease 
in the sum of 
longest 
diameters of 
target lesions but 
not a CR 
≥10% decrease 
in the sum of 
longest 
diameters of 
target lesions but 
not a PR (<30%) 
<10% decrease 
or ≤20% 
increase in the 
sum of longest 
diameters of 
target lesions 
• >20% 
increase in 
the sum of 
longest 
diameters of 
target lesions 
• For small 
lymph nodes 

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% Change in sum of diameters of target lesions from nadir 
CR 
PR 
MRa 
SD 
PD 
decrease in 
the sum of 
longest 
diameters of 
target lesions 
(PR) with 
normalization 
of FDG-PET 
measuring 
<15 mm post 
therapy, a 
minimum 
absolute 
increase of 5 
mm and the 
long diameter 
should exceed 
15 mm 
• Appearance 
of a new 
lesion 
FDG-PET 
Normalization 
of FDG-PET 
(Deauville 
score 1-3) 
Positive 
(Deauville 
score 4-5) 
Any 
Any 
Any 
Bone 
marrow 
involvement 
Not involved 
Any 
Any 
Any 
Any 
New lesions 
No 
No 
No 
No 
Yes or No 
CR, complete response; CT, computerized tomography; FDG-PED, [18F]2-fluoro-2-deoxy-D-glucose; 
MR, minor response; PD, progression of disease; PR, partial response; SD, stable disease 
a A provisional category.  Table is as shown in (Younes et al., 2017). 
 
 
12. STUDY OVERSIGHT AND DATA REPORTING / REGULATORY 
REQUIREMENTS 
 
Adverse event lists, guidelines, and instructions for AE reporting can be found in Section 9. 
 
12.1 Study Oversight 
 
This protocol is monitored at several levels, as described in this section.  The Protocol Principal 
Investigator is responsible for monitoring the conduct and progress of the clinical trial, including 
the ongoing review of accrual, patient-specific clinical and laboratory data, and routine and 
serious adverse events; reporting of expedited adverse events; and accumulation of reported 
adverse events from other trials testing the same drug(s).  The Protocol Principal Investigator and 
statistician have access to the data at all times through the CTMS web-based reporting portal.   
 
For the Phase 1 portion of this study, all decisions regarding dose escalation/expansion/de-
escalation require sign-off by the Protocol Principal Investigator through the CTMS/IWRS.  In 
addition, for the Phase 1 portion, the Protocol Principal Investigator will have at least monthly, or 
more frequently, conference calls with the Study Investigators and the CTEP Medical Officer(s) 
to review accrual, progress, and adverse events and unanticipated problems.  
 

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All Study Investigators at participating sites who register/enroll patients on a given protocol are 
responsible for timely submission of data via Medidata Rave and timely reporting of adverse 
events for that particular study.  This includes timely review of data collected on the electronic 
CRFs submitted via Medidata Rave. 
 
All studies are also reviewed in accordance with the enrolling institution’s data safety monitoring 
plan. 
 
12.2 Data Reporting 
 
Medidata Rave is a clinical data management system being used for data collection for this 
trial/study.  Access to the trial in Rave is controlled through the CTEP-IAM system and role 
assignments.   
Requirements to access Rave via iMedidata: 
 
• 
A valid account, and  
• 
Assigned a Rave role on the LPO or PO roster at the enrolling site of:  Rave CRA, Rave 
Read Only, Rave CRA (Lab Admin), Rave SLA, or Rave Investigator.   
Rave role requirements: 
o Rave CRA or Rave CRA (Lab Admin) role, must have a minimum of an Associate 
Plus (AP) registration type, 
o Rave Investigator role, must be registered as an Non-Physician Investigator 
(NPIVR) or Investigator (IVR), and 
o Rave Read Only role, site staff must have at a minimum an Associates (A) 
registration type. 
 
• 
Refer to https://ctep.cancer.gov/investigatorResources/default.htm for registration types 
and documentation required. 
 
If the study has a DTL, individuals requiring write access to Rave must also be assigned the 
appropriate Rave tasks on the DTL. 
 
Upon initial site registration approval for the study in Regulatory Support System (RSS), all 
persons with Rave roles assigned on the appropriate roster will be sent a study invitation e-mail 
from iMedidata.  To accept the invitation, site staff must log in to the Select Login 
(https://login.imedidata.com/selectlogin) using their CTEP-IAM username and password, and 
click on the accept link in the upper right-corner of the iMedidata page.  Site staff will not be able 
to access the study in Rave until all required Medidata and study specific trainings are 
completed.  Trainings will be in the form of electronic learnings (eLearnings), and can be 
accessed by clicking on the link in the upper right pane of the iMedidata screen.  If an eLearning 
is required and has not yet been taken, the link to the eLearning will appear under the study name 
in iMedidata instead of the Rave EDC link; once the successful completion of the eLearning has 
been recorded, access to the study in Rave will be granted, and a Rave EDC link will display 
under the study name.  
 
Site staff that have not previously activated their iMedidata/Rave account at the time of initial site 

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registration approval for the study in RSS will receive a separate invitation from iMedidata to 
activate their account.  Account activation instructions are located on the CTSU website in the 
Data Management section under the Rave resource materials (Medidata Account Activation and 
Study Invitation Acceptance).  Additional information on iMedidata/Rave is available on the 
CTSU members’ website in the Data Management > Rave section at www.ctsu.org/RAVE/ or by 
contacting the CTSU Help Desk at 1-888-823-5923 or by e-mail at ctsucontact@westat.com.   
 
12.2.1 Method 
 
This study will be monitored by the Clinical Trials Monitoring Service (CTMS).  Data will be 
submitted to CTMS at least once every two weeks via Medidata Rave (or other modality if 
approved by CTEP).  Information on CTMS reporting is available at 
http://www.theradex.com/clinicalTechnologies/?National-Cancer-Institute-NCI-11.  On-site 
audits will be conducted three times annually (one annual site visit and two data audits).  For 
CTMS monitored studies, after users have activated their accounts, please contact the Theradex 
Help Desk at (609) 619-7862 or by email at CTMSSupport@theradex.com for additional support 
with Rave and completion of CRFs. 
 
12.2.2 Responsibility for Data Submission 
 
For ETCTN trials, it is the responsibility of the PI(s) at the site to ensure that all investigators at 
the ETCTN Sites understand the procedures for data submission for each ETCTN protocol and 
that protocol specified data are submitted accurately and in a timely manner to the CTMS via the 
electronic data capture system, Medidata Rave.   
 
Data are to be submitted via Medidata Rave to CTMS on a real-time basis, but no less than once 
every 2 weeks.  The timeliness of data submissions and timeliness in resolving data queries will 
be tracked by CTMS.  Metrics for timeliness will be followed and assessed on a quarterly basis.  
For the purpose of Institutional Performance Monitoring, data will be considered delinquent if it 
is greater than 4 weeks past due. 
 
Data from Medidata Rave and CTEP-AERS is reviewed by the CTMS on an ongoing basis as data is 
received.  Queries will be issued by CTMS directly within Rave.  The queries will appear on the 
Task Summary Tab within Rave for the CRA at the ETCTN to resolve.  Monthly web-based reports 
are posted for review by the Drug Monitors in the IDB, CTEP.  Onsite audits will be conducted by 
the CTMS to ensure compliance with regulatory requirements, GCP, and NCI policies and 
procedures with the overarching goal of ensuring the integrity of data generated from NCI-sponsored 
clinical trials, as described in the ETCTN Program Guidelines, which may be found on CTEP 
(http://ctep.cancer.gov/protocolDevelopment/electronic applications/adverse events.htm) and 
CTSU websites. 
 
An End of Study CRF is to be completed by the PI and is to include a summary of study 
endpoints not otherwise captured in the database, such as (for phase 1 trials) the recommended 
phase 2 dose (RP2D) and a description of any dose-limiting toxicities (DLTs).  CTMS will utilize 
a core set of eCRFs that are Cancer Data Standards Registry and Repository (caDSR) compliant 
(http://cbiit.nci.nih.gov/ncip/biomedical-informatics-resources/interoperability-and-

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semantics/metadata-and-models).  Customized eCRFs will be included when appropriate to meet 
unique study requirements.  The PI is encouraged to review the eCRFs, working closely with 
CTMS to ensure prospectively that all required items are appropriately captured in the eCRFs 
prior to study activation.  CTMS will prepare the eCRFs with built-in edit checks to the extent 
possible to promote data integrity. 
CDUS data submissions for ETCTN trials activated after March 1, 2014, will be carried out by 
the CTMS contractor, Theradex.  CDUS submissions are performed by Theradex on a monthly 
basis.  The trial’s lead institution is responsible for timely submission to CTMS via Rave, as 
above. 
 
Further information on data submission procedures can be found in the ETCTN Program 
Guidelines (http://ctep.cancer.gov/protocolDevelopment/electronic_applications/adverse_events.htm). 
 
12.3 Data Quality Portal 
 
The Data Quality Portal (DQP) provides a central location for site staff to manage unanswered 
queries and form delinquencies, monitor data quality and timeliness, generate reports, and review 
metrics.  
 
The DQP is located on the CTSU members’ website under Data Management.  The Rave Home 
section displays a table providing summary counts of Total Delinquencies and Total Queries.  
DQP Queries, DQP Delinquent Forms, and the DQP Reports modules are available to access 
details and reports of unanswered queries, delinquent forms, and timeliness reports.  Review the 
DQP modules on a regular basis to manage specified queries and delinquent forms. 
 
The DQP is accessible by site staff that are rostered to a site and have access to the CTSU 
website.  Staff that have Rave study access can access the Rave study data using a direct link on 
the DQP. 
 
To learn more about DQP use and access, click on the Help icon displayed on the Rave Home, 
DQP Queries, and DQP Delinquent Forms modules. 
 
Note:  Some Rave protocols may not have delinquent form details or reports specified on the 
DQP.  A protocol must have the Calendar functionality implemented in Rave by the Lead 
Protocol Organization (LPO) for delinquent form details and reports to be available on the 
DQP.  Site staff should contact the LPO Data Manager for their protocol regarding questions 
about Rave Calendaring functionality.  
 
 
12.4 Collaborative Agreements Language 
 
The agent supplied by CTEP, DCTD, NCI used in this protocol is provided to the NCI under a 
Collaborative Agreement (CRADA) between the Pharmaceutical Company (hereinafter referred 
to as “Collaborator”) and the NCI Division of Cancer Treatment and Diagnosis.  Therefore, the 
following obligations/guidelines, in addition to the provisions in the “Intellectual Property Option 

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to Collaborator”  
(http://ctep.cancer.gov/industryCollaborations2/intellectual_property.htm) contained within the 
terms of award, apply to the use of the Agent(s) in this study: 
 
1. Agent may not be used for any purpose outside the scope of this protocol, nor can Agent be 
transferred or licensed to any party not participating in the clinical study.  Collaborator data 
for Agent are confidential and proprietary to Collaborator and shall be maintained as such by 
the investigators.  The protocol documents for studies utilizing Agents contain confidential 
information and should not be shared or distributed without the permission of the NCI.  If a 
copy of this protocol is requested by a patient or patient’s family member participating on the 
study, the individual should sign a confidentiality agreement.  A suitable model agreement can 
be downloaded from: http://ctep.cancer.gov. 
 
2. For a clinical protocol where there is an investigational Agent used in combination with 
another Agent, each the subject of different Collaborative Agreements, the access to and use 
of data by each Collaborator shall be as follows (data pertaining to such combination use shall 
hereinafter be referred to as "Multi-Party Data”): 
 
a. NCI will provide all Collaborators with prior written notice regarding the existence and 
nature of any agreements governing their collaboration with NCI, the design of the 
proposed combination protocol, and the existence of any obligations that would tend to 
restrict NCI's participation in the proposed combination protocol. 
 
b. Each Collaborator shall agree to permit use of the Multi-Party Data from the clinical trial 
by any other Collaborator solely to the extent necessary to allow said other Collaborator to 
develop, obtain regulatory approval or commercialize its own Agent. 
 
c. Any Collaborator having the right to use the Multi-Party Data from these trials must agree 
in writing prior to the commencement of the trials that it will use the Multi-Party Data 
solely for development, regulatory approval, and commercialization of its own Agent. 
 
3. Clinical Trial Data and Results and Raw Data developed under a Collaborative Agreement 
will be made available to Collaborator, the NCI, and the FDA, as appropriate and unless 
additional disclosure is required by law or court order as described in the IP Option to 
Collaborator (http://ctep.cancer.gov/industryCollaborations2/intellectual_property.htm).  
Additionally, all Clinical Data and Results and Raw Data will be collected, used and disclosed 
consistent with all applicable federal statutes and regulations for the protection of human 
subjects, including, if applicable, the Standards for Privacy of Individually Identifiable Health 
Information set forth in 45 C.F.R. Part 164. 
 
4. When a Collaborator wishes to initiate a data request, the request should first be sent to the 
NCI, who will then notify the appropriate investigators (Group Chair for Cooperative Group 
studies, or PI for other studies) of Collaborator's wish to contact them. 
 
5. Any data provided to Collaborator for Phase 3 studies must be in accordance with the 
guidelines and policies of the responsible Data Monitoring Committee (DMC), if there is a 

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DMC for this clinical trial. 
 
6. Any manuscripts reporting the results of this clinical trial must be provided to CTEP by the 
Group office for Cooperative Group studies or by the principal investigator for non-
Cooperative Group studies for immediate delivery to Collaborator for advisory review and 
comment prior to submission for publication.  Collaborator will have 30 days from the date of 
receipt for review.  Collaborator shall have the right to request that publication be delayed for 
up to an additional 30 days to ensure that Collaborator’s confidential and proprietary data, in 
addition to Collaborator’s intellectual property rights, are protected.  Copies of abstracts must 
be provided to CTEP for forwarding to Collaborator(s) for courtesy review as soon as possible 
and preferably at least three (3) days prior to submission, but in any case, prior to presentation 
at the meeting or publication in the proceedings.  Press releases and other media presentations 
must also be forwarded to CTEP prior to release.  Copies of any manuscript, abstract and/or 
press release/ media presentation should be sent to: 
ncicteppubs@mail.nih.gov 
 
The Regulatory Affairs Branch will then distribute them to Collaborator.  No publication, 
manuscript or other form of public disclosure shall contain any of Collaborator’s confidential/ 
proprietary information. 
 
12.5 Genomic Data Sharing Plan 
 
N/A: no whole-exome sequencing data will be generated for research purposes on this study. 
 
12.6 NIH Human Data Sharing Plan 
What data will be shared?  
We will share human data generated in this research for future research as follows: 
x De-identified data in an NIH-funded or approved public repository  
x Identified data in BTRIS (automatic for activities in the Clinical Center)  
x De-identified or identified data with approved outside collaborators under appropriate 
agreements  
 
How and where will the data be shared?  
Data will be shared through:  
x An NIH-funded or approved public repository: clinicaltrials.gov 
x BTRIS (automatic for activities in the Clinical Center)  
x Approved outside collaborators under appropriate individual agreements  
x Publication and/or public presentations  
 
When will the data be shared?  
x At the time of publication or shortly thereafter 
 
12.7 Incidental/Secondary Findings Disclosure Procedure 
 
N/A 
 

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13. HUMAN SUBJECTS PROTECTIONS 
 
This study will be open to all individuals regardless of gender, ethnicity, or race, provided that the 
aforementioned inclusion and exclusion criteria are met.  Patients for this study will be recruited 
through internal referral, our physician referral base, and through various cancer information 
hotlines (i.e., Clinical Studies Support Center, 1-800-4Cancer).  To date, there is no information 
that suggests that differences in drug metabolism or effect on tumor would be expected in one 
ethnic group compared to another.  Efforts will be made to extend accrual to each representative 
population, but a balance must be struck between participant safety considerations and limitations 
on the number of individuals exposed to potentially ineffective treatments on the one hand and the 
need to explore racial/ethnic aspects of clinical research on the other hand.  If differences in 
outcome that correlate to ethnic identity are noted, a follow-up study may be written to investigate 
those differences more fully. 
 
Because p97 inhibitors are likely to have teratogenic effects, pregnant and nursing women will be 
excluded from this trial.  Patients with unstable or serious medical conditions are excluded due to 
the possibility that the underlying condition may obscure the attribution of effect and adverse 
events with respect to CB-5339 and may limit study compliance.  
 
This study includes patients 18 years of age and older.  Because no clinical dosing or adverse 
event data are currently available on the use of CB-5339 in patients <18 years of age, children are 
excluded from this study, but may be eligible for future pediatric trials.   
 
13.1 Evaluation of Benefits and Risks/Discomforts 
There may or may not be any clinical benefit to a patient from participation in this trial.  
Their participation will benefit future cancer patients.  Potential risks include the possible 
occurrence of any of a range of side effects that are listed in the consent document.  The 
procedure for protecting against or minimizing risks will be to medically evaluate patients 
as described in Section 5.   Although no compensation is available, any injury will be fully 
evaluated and treated in keeping with the benefits or care to which participants are entitled 
under applicable regulations. 
 
13.2 Consent and Assent Process and Documentation 
An associate or principal investigator on the trial will inform patients of the purpose, 
alternatives, drug administration plan, research objectives, and follow-up of this trial.  The 
patient will be provided an IRB-approved consent for review and signature and his/her 
questions will be answered.  After a decision is made to enroll into the study, a signature 
will be obtained from the patient.  The original signed consent goes to Medical Records; a 
copy will be placed in the research record.  Patients will not be consented by telephone.  
 
All patients must have a signed informed consent form and an on-study (confirmation of 
eligibility) form filled out and signed by a participating investigator before entering on 
study.   
 

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13.3 Procedure for Protecting Against or Minimizing Any Potential Risks 
All care will be taken to minimize side effects, but they can be unpredictable in nature and 
severity.  This study may involve risks to patients, which are currently unforeseeable.  All 
patients will be monitored for side effects from taking study medication.  This research 
represents a greater than minimal risk to participants, but presents the prospect of direct 
benefit to individual subjects. 
 
 
 

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14. REFERENCES 
Anderson, Daniel J., Le Moigne, R., Djakovic, S., Kumar, B., Rice, J., Wong, S., Wang, J., Yao, 
B., Valle, E., Kiss von Soly, S., et al. (2015). Targeting the AAA ATPase p97 as an Approach to 
Treat Cancer through Disruption of Protein Homeostasis. Cancer Cell 28, 653-665. 
Balch, W.E., Morimoto, R.I., Dillin, A., and Kelly, J.W. (2008). Adapting Proteostasis for 
Disease Intervention. Science 319, 916-919. 
Barone, M.V., Crozat, A., Tabaee, A., Philipson, L., and Ron, D. (1994). CHOP (GADD153) and 
its oncogenic variant, TLS-CHOP, have opposing effects on the induction of G1/S arrest. Genes 
Dev 8, 453-464. 
Buchberger, A., Schindelin, H., and Hanzelmann, P. (2015). Control of p97 function by cofactor 
binding. FEBS Lett 589, 2578-2589. 
Chou, T.-F., Brown, S.J., Minond, D., Nordin, B.E., Li, K., Jones, A.C., Chase, P., Porubsky, 
P.R., Stoltz, B.M., Schoenen, F.J., et al. (2011). Reversible inhibitor of p97, DBeQ, impairs both 
ubiquitin-dependent and autophagic protein clearance pathways. Proceedings of the National 
Academy of Sciences 108, 4834-4839. 
Deshaies, R.J. (2014). Proteotoxic crisis, the ubiquitin-proteasome system, and cancer therapy. 
BMC Biol 12, 94. 
Dowlati, A., Haaga, J., Remick, S.C., Spiro, T.P., Gerson, S.L., Liu, L., Berger, S.J., Berger, 
N.A., and Willson, J.K. (2001). Sequential tumor biopsies in early phase clinical trials of 
anticancer agents for pharmacodynamic evaluation. Clin Cancer Res 7, 2971-2976. 
Fessart, D., Marza, E., Taouji, S., Delom, F., and Chevet, E. (2013). P97/CDC-48: Proteostasis 
control in tumor cell biology. Cancer Letters 337, 26-34. 
International Council for Harmonisation of Technical Requirements for Pharmaceuticals for 
Human Use, I. (2009). Nonclinical Evaluation for Anticancer Pharmaceuticals (S9), pp. Retrieved 
from https://www.ich.org/products/guidelines.html. 
Kharabi Masouleh, B., Geng, H., Hurtz, C., Chan, L.N., Logan, A.C., Chang, M.S., Huang, C., 
Swaminathan, S., Sun, H., Paietta, E., et al. (2014). Mechanistic rationale for targeting the 
unfolded protein response in pre-B acute lymphoblastic leukemia. Proceedings of the National 
Academy of Sciences 111, E2219-E2228. 
Le Moigne, R. Dose response and time course pharmacokinetic/pharmacodynamic analysis after 
single administration of CB-5083 in HCT116 xenograft tumors. Non-clinical study report RPT-
01-00010 Cleave Biosciences, Inc. 
Le Moigne, R., Aftab, B.T., Djakovic, S., Dhimolea, E., Valle, E., Murnane, M., King, E.M., 
Soriano, F., Menon, M.-K., Wu, Z.Y., et al. (2017). The p97 Inhibitor CB-5083 Is a Unique 
Disrupter of Protein Homeostasis in Models of Multiple Myeloma. Molecular Cancer 
Therapeutics 16, 2375-2386. 

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Magnaghi, P., D'Alessio, R., Valsasina, B., Avanzi, N., Rizzi, S., Asa, D., Gasparri, F., Cozzi, L., 
Cucchi, U., Orrenius, C., et al. (2013). Covalent and allosteric inhibitors of the ATPase VCP/p97 
induce cancer cell death. Nature Chemical Biology 9, 548. 
Meyer, H., Bug, M., and Bremer, S. (2012). Emerging functions of the VCP/p97 AAA-ATPase in 
the ubiquitin system. Nature Cell Biology 14, 117. 
Mozos, A., Roué, G., López-Guillermo, A., Jares, P., Campo, E., Colomer, D., and Martinez, A. 
(2011). The Expression of the Endoplasmic Reticulum Stress Sensor BiP/GRP78 Predicts 
Response to Chemotherapy and Determines the Efficacy of Proteasome Inhibitors in Diffuse 
Large B-Cell Lymphoma. The American Journal of Pathology 179, 2601-2610. 
Nadeau, M.-È., Rico, C., Tsoi, M., Vivancos, M., Filimon, S., Paquet, M., and Boerboom, D. 
(2015). Pharmacological targeting of valosin containing protein (VCP) induces DNA damage and 
selectively kills canine lymphoma cells. BMC Cancer 15, 479. 
Simon, R., Freidlin, B., Rubinstein, L., Arbuck, S.G., Collins, J., and Christian, M.C. (1997). 
Accelerated titration designs for phase I clinical trials in oncology. Journal of the National Cancer 
Institute 89, 1138-1147. 
Srivastava, A.K., Govindharajulu, J.P., Hollingshead, M.G., Stotler, H., Wang, F., Chou, T., 
Banfield, K., Tomaino, F., Stott, G., S., Doroshow, J.H., et al. (2018). Pharmacodynamics of first-
in-class p97 inhibitors that disrupt protein homeostasis in cancer. Journal of Clinical Oncology 
36; suppl, abstract e14539. 
Tsujimoto, Y., Tomita, Y., Hoshida, Y., Kono, T., Oka, T., Yamamoto, S., Nonomura, N., 
Okuyama, A., and Aozasa, K. (2004). Elevated Expression of Valosin-Containing Protein (p97) Is 
Associated with Poor Prognosis of Prostate Cancer. Clinical Cancer Research 10, 3007-3012. 
Vogelstein, B., Papadopoulos, N., Velculescu, V.E., Zhou, S., Diaz, L.A., and Kinzler, K.W. 
(2013). Cancer Genome Landscapes. Science 339, 1546-1558. 
Williams, B.R., and Amon, A. (2009). Aneuploidy: Cancer's Fatal Flaw? Cancer Research 69, 
5289-5291. 
Yamamoto, S., Tomita, Y., Hoshida, Y., Iizuka, N., Kidogami, S., Miyata, H., Takiguchi, S., 
Fujiwara, Y., Yasuda, T., Yano, M., et al. (2004a). Expression Level of Valosin-Containing 
Protein (p97) Is Associated with Prognosis of Esophageal Carcinoma. Clinical Cancer Research 
10, 5558-5565. 
Yamamoto, S., Tomita, Y., Hoshida, Y., Iizuka, N., Monden, M., Yamamoto, S., Iuchi, K., and 
Aozasa, K. (2004b). Expression Level of Valosin-Containing Protein (p97) Is Correlated With 
Progression and Prognosis of Non-Small-Cell Lung Carcinoma. Annals of Surgical Oncology 11, 
697-704. 
Younes, A., Hilden, P., Coiffier, B., Hagenbeek, A., Salles, G., Wilson, W., Seymour, J.F., Kelly, 
K., Gribben, J., Pfreunschuh, M., et al. (2017). International Working Group consensus response 
evaluation criteria in lymphoma (RECIL 2017). Annals of Oncology 28, 1436-1447. 

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Zhou, H.-J., Wang, J., Yao, B., Wong, S., Djakovic, S., Kumar, B., Rice, J., Valle, E., Soriano, F., 
Menon, M.-K., et al. (2015). Discovery of a First-in-Class, Potent, Selective, and Orally 
Bioavailable Inhibitor of the p97 AAA ATPase (CB-5083). Journal of Medicinal Chemistry 58, 
9480-9497. 
 
 
 
 

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APPENDIX A: PERFORMANCE STATUS CRITERIA 
 
ECOG Performance Status Scale 
Karnofsky Performance Scale 
Grade 
Descriptions 
Percent 
Description 
0 
Normal activity.  Fully active, able 
to carry on all pre-disease 
performance without restriction. 
100 
Normal, no complaints, no evidence 
of disease. 
90 
Able to carry on normal activity; 
minor signs or symptoms of disease. 
1 
Symptoms, but ambulatory.  
Restricted in physically strenuous 
activity, but ambulatory and able 
to carry out work of a light or 
sedentary nature (e.g., light 
housework, office work). 
80 
Normal activity with effort; some 
signs or symptoms of disease. 
70 
Cares for self, unable to carry on 
normal activity or to do active work. 
2 
In bed <50% of the time.  
Ambulatory and capable of all 
self-care, but unable to carry out 
any work activities.  Up and about 
more than 50% of waking hours. 
60 
Requires occasional assistance, but 
is able to care for most of his/her 
needs. 
50 
Requires considerable assistance and 
frequent medical care. 
3 
In bed >50% of the time.  Capable 
of only limited self-care, confined 
to bed or chair more than 50% of 
waking hours. 
40 
Disabled, requires special care and 
assistance. 
30 
Severely disabled, hospitalization 
indicated.  Death not imminent. 
4 
100% bedridden.  Completely 
disabled.  Cannot carry on any 
self-care.  Totally confined to bed 
or chair. 
20 
Very sick, hospitalization indicated. 
Death not imminent. 
10 
Moribund, fatal processes 
progressing rapidly. 
5 
Dead. 
0 
Dead. 
 
 
 

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Ophthalmologic Examination will be performed at screening and as clinically indicated.  
 
Ophthalmologic testing and biomicroscopic examinations should include assessment of the 
following in the order listed whenever possible. 
 
- 
Best corrected visual acuity (BCVA) using Early Treatment Diabetic Retinopathy Study 
(ETDRS) methodology.  The same methodology is to be used for the pre-study and 
follow-up examinations for each individual subject. 
- 
Slit lamp examination including assessment of the lids, lashes, conjunctiva, sclera, cornea, 
anterior chamber, iris, lens and anterior vitreous.   The slit lamp examination is repeated 
following dilation to better assess the lens and anterior vitreous. 
- 
Measurement of intra-ocular pressure. 
- 
Fundus examination.  This include assessment of the vitreous, retina, disc, macula, 
vessels, and periphery of each eye using dilated fundoscopy. 
- 
Spectral domain optical coherence tomography (OCT) of the macula and disc for both 
eyes.   The same type of device is to be used for the pre-study and follow-up examinations 
for each individual subject. 
- 
Standard field fundus photographs with the pupils dilated performed on each eye to aid in 
the evaluation of the optic nerve, vessels, macula, and periphery. 
- 
Color vision testing 
 
To be eligible for this research protocol, patients will be screened for pre-existing visual 
impairment.  Patients will be excluded if they do not meet the visual acuity threshold (best 
corrected visual acuity of 60 ETDRS letters [Snellen equivalent of 20/60] in either eye) and the 
visual field threshold (substantial visual field loss in one or both eyes). 
 
 
 
 
 
 
 

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APPENDIX D: PATIENT STUDY DIARY 
 
Today’s date _____________________ 
 
 
    Agent:  CB-5339   Dose: ___________ 
Patient Name_____________________  (initials acceptable)  
Patient Study ID ___________________ 
 
INSTRUCTIONS TO THE PATIENT: 
1. 
Complete one form for each cycle (28 days, or 4 weeks) of treatment. 
2. 
 You will take ________ capsules (____ mg per capsule) of CB-5339 once daily on days 1-4 each 
week for each cycle. Take your dose at approximately the same time each day.  CB-5339 should be taken with 
water only on an empty stomach (that is, at least 1 hour before or 2 hours after a meal). 
3.   Record the date and times when you took CB-5339.   
4.    If you miss or vomit the dose within 6 hours, please make a note of this in the Comments column and do 
not make up the dose. 
5. 
If you have any comments or notice any side effects, please record them in the Comments column.  If you 
have any changes in vision, please call the study team immediately.  
6. 
Please bring this form and any unused CB-5339 when you return for each appointment. 
Day 
Date 
Time of CB-5339 
dose 
Dose 
Taken   
Comments 
1 
Week 1 
 
 
 
2 
 
 
 
 
3 
 
 
 
 
4 
 
 
 
 
5 
Do not take CB-5339 today 
 
6 
Do not take CB-5339 today 
 
7 
Do not take CB-5339 today 
 
8 
Week 2 
 
 
 
9 
 
 
 
 
10 
 
 
 
 
11 
 
 
 
 
12 
Do not take CB-5339 today 
 
13 
Do not take CB-5339 today 
 
14 
Do not take CB-5339 today 
 

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15 
Week 3 
 
 
 
16 
 
 
 
 
17 
 
 
 
 
18 
 
 
 
 
19 
Do not take CB-5339 today 
 
20 
Do not take CB-5339 today 
 
21 
Do not take CB-5339 today 
 
22 
Week 4 
 
 
 
23 
 
 
 
 
24 
 
 
 
 
25 
 
 
 
 
26 
Do not take CB-5339 today 
 
27 
Do not take CB-5339 today 
 
28 
Do not take CB-5339 today 
 
 
Patient’s signature:_______________________________________________________________ 
 
 
 
 
 
 
 
 
 
 
 

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APPENDIX E: SOP FOR PBMC PREPARATION (PD) 
 
1. Whole blood collected in green-top (sodium heparin, BD Diagnostics, Cat# 367878, size 13x100mm) collection 
tubes (5-6 mL/tube).  
 
2. Depending on total blood collection (5-15 mL from 1-3 tubes), prepare separate 50mL PBMC separation tubes.  
Each separation tube can hold a maximum of 7.5 mL of blood (if >7.5 mL blood, prepare two tubes).  Bring Ficoll 
(Ficoll-Paque PLUS< GE Healthcare, Cat# 17144002) to room temperature.  Add 10 mL Ficoll to each 50-mL tube.  
3. If total amount of blood is >7.5 mL, pool whole blood from 2-3 green-top (sodium heparin) collection tubes into 
one 50 mL tube.  
4. Dilute pooled whole blood 1:1 (one-part blood one-part PBS) with 1x PBS (from step-3), close the tube and mix 
slowly by inverting tube.  
5. Carefully overlay 15 mL of diluted blood+PBS mixture on top of the Ficoll layer using a 25 mL pipettor set on the 
lowest speed to avoid mixing the blood and Ficoll.  This step is critical for the purity of PBMCs.  To avoid mixing 
blood and Ficoll, the tube should be held at an angle and the blood mixture released very slowly.  It is important to 
not layer >15 mL because it may decrease the total PBMC yield/mL of blood.  
6. Centrifuge 50 mL tubes (from step-5) at 800xG for 30min at room temperature in a swing-out rotor.  
Importantly, the rotor breaks must be inactivated to prevent mixing of phases.  Equally important is any changes 
in temperature (use of pre-cooled centrifuge) can change the density ratios and have an impact on the separation 
quality.  
7. The PBMCs will be in the cloudy middle buffy layer (sometimes not clearly differentiated).  Collect PBMCs by 
carefully inserting a 5 mL pipette and collecting all buffy layer, which varies in content.  Transfer buffy layer to a 
new labeled 50 mL tube, a little excess (1-2 mL) to capture all buffy layer is acceptable.  Each buffy layer should be 
collected in a separate tube to allow for adequate dilution of Ficoll.  Dilute contents with 1x PBS to a total volume 
of 50 mL (min 5x buffy layer volume – 50 mL total).  
 
 
 
8. Centrifuge tubes from step-7 at 300xG for 7 min at room temperature.  
 

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9. There should be a visible cell pellet at the bottom of the tube.  Carefully aspirate supernatant (without touching 
the cell pellet) from each 50 mL tube and discard.  Resuspend the cell pellet in 1.5 mL 1x PBS.  If more than one 
tube is processed per patient, then combine suspended cells into one 50 mL tube.  For two tubes there will be a 
total of 3 mL cell suspension.  
10. For counting, prepare a 1:10 dilution of sample using PBS (20 µL sample + 180 µL 1x PBS).  
11. Refer to the SOP Appendix-3 (next page) for cell counting.  Cells can also be counted using AO/PI stain (Necelon, 
Cat# CS2-0106-5mL); mix 20 µL of 1:10 sample dilution with 20 µL of dye (1:2 dilution), count using Cellometer, 
record counts for calculation of total number of cells.  
12. Centrifuge tubes from step-9 at 500xG for 5 min at room temperature, aspirate supernatant and discard.  
Resuspend cell pellet in 1 mL of ice cold 1X PBS and transfer (split cells) to only two 1.5 mL microcentrifuge tubes.  
13. Centrifuge the samples at 10,000g for 5 minutes at 4°C, carefully completely remove supernatant (residual PBS 
interferes with cell extraction) and snap-freeze on dry ice.  
 
 

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APPENDIX F: PATIENT DRUG INTERACTIONS HANDOUT AND WALLET CARD 
 
Information for Patients, Their Caregivers and Non-Study Healthcare Team on Possible Interactions with 
Other Drugs and Herbal Supplements  
 
Patient Name: 
      
Diagnosis: 
      
Trial #: 10349 
      
Study Doctor: 
Study Doctor Phone #: 
Study Drug(s): CB-5339 
 
 
Please show this paper to all your healthcare providers (doctors, physician assistants, nurse practitioners, 
pharmacists), and tell them you are taking part in a clinical trial sponsored by the National Cancer Institute.  
 
These are the things that your healthcare providers need to know: 
 
CB-5339 may interact with certain specific liver enzymes or medications that are considered highly protein-bound. 
 
Explanation 
CYP 
Isoenzymes  
The enzymes in question are CYP2C9 and CYP2C19. CB-5339 moderately inhibits these 
enzymes and may affect other drugs that are broken down by these enzymes. 
Protein-
Binding 
CB-5339 binds to a high percentage of proteins in your blood and may affect the activity of other 
drugs that also bind highly to these proteins or the other drugs may affect the activity of CB-5339.  
 
These are the things that you need to know: 
  
The study drug CB-5339 may interact with other drugs which can cause side effects.  For this reason, it is 
very important to tell your doctors about all your medicines, including: (a) medicines you are taking before 
this clinical trial, (b) medicines you start or stop taking during this clinical trial, (c) medicines you buy 
without a prescription (over-the-counter remedy), (d) herbals or supplements (e.g. St. John’s Wort). It is 
helpful to bring your medication bottles or an updated medication list with you.  
 
Before you enroll onto the clinical trial, your study doctor will work with your regular health care providers 
to review any medicines and herbal supplements that are considered substrates of CYP2C9 and CYP2C19 
and medicines considered highly protein-bound. 
 
• Please be very careful!  Over-the-counter drugs (including herbal supplements) may contain ingredients 
that could interact with your study drug.  Speak to your doctors or pharmacist to determine if there 
could be any side effects.  
  
• Make sure your doctor knows to avoid certain prescription medicines.  
o Use caution with any medicines considered substrates of CYP2C9 and CYP2C19. 
o Use caution with any medicines considered to be highly protein bound. 
  
• Your regular health care provider should check a frequently updated medical reference or call your 
study doctor before prescribing any new medicine or discontinuing any medicine.