WO2023002415A2 - Methods and compositions for anti-cd117 antibody drug conjugate (adc) treatment - Google Patents

Abstract

Disclosed are receptor occupancy assays for an anti-CD117 antibody drug conjugate, and related methods for treating a human subject.

Description

METHODS AND COMPOSITIONS FOR ANTI-CD117 ANTIBODY DRUG CONJUGATE (ADC) TREATMENT

Related Applications

This application claims priority to U.S. Provisional Application No. 63/223,937, filed on July 20, 2021. The entire contents of the priority application are incorporated by reference herein.

Sequence Listing

The instant application contains a Sequence Listing which has been submitted electronically in XML format and is hereby incorporated by reference in its entirety. Said copy, created on July 19, 2022, is named M103034_2280WO_0730_1_SL.xml and is 331 kilobytes in size.

Background

CD117 (also referred to as c-kit or Stem Cell Factor Receptor (SCRF)) is a single transmembrane, receptor tyrosine kinase that binds the ligand Stem Cell Factor (SCF). SCF induces homodimerization of CD117 which activates its tyrosine kinase activity and signals through both the P13-AKT and MAPK pathways (Kindblom et al., Am J. Path. 1998 152(5):1259).

CD117 was initially discovered as an oncogene and has been studied in the field of oncology (see, for example, Stankov et al. (2014) Curr Pharm Des. 20(17):2849-80). CD117 is highly expressed on hematopoietic stem cells (HSCs).

Although targeting CD117 represents a potential therapeutic target for treating diseases such as cancer, and as a conditioning agent for cell transplantation, e.g., given its expression on HSCs, the nature of treating such diseases presents unique challenges, including adverse effects of the cancer on bone marrow and hematologic function.

CD117 is highly expressed on hematopoietic stem cells (HSCs) and on acute myeloid leukemia (AML) tumor cells. This expression pattern makes CD117 a potential target for both conditioning and treating patients across a broad range of diseases. There remains, however, a need for a minimium safe and biologically effective (MSBE) dose of a therapeutic anti-CD117 antibody (or antibody drug conjugate (ADC)). CD117 receptor occupancy by a therapeutic anti-CD117 antibody (or ADC) can be measured and MSBE dose can be determined based on receptor occupancy. Summary

Described herein are compositions and methods for treating a human subject with an anti-CD117 antibody drug conjugate (ADC). In particular, methods and compositions disclosed herein may be used to determine dosing of the ADC for treatment of a human subject, e.g., treatment for cancer or as a conditioning agent. The methods described herein generally rely on receptor occupancy (RO) assays, e.g., flow cytometry RO assays. In certain embodiments, an RO assay is used to determine the percentage of available receptors, i.e., CD117, that are bound as a function of drug (antibody) concentration.

Provided herein is a method for treating a human subject in need thereof, comprising: determining CD117 receptor occupancy of a therapeutic anti-CD117 antibody on CD117 expressing cells from a human subject, said method comprising performing a receptor occupancy (RO) assay on a sample from the human subject, and determining the percent receptor occupancy of the therapeutic anti-CD117 antibody on CD117 expressing cells from the sample; and administering to the human subject an amount of the therapeutic anti- CD117 antibody that is less than 100 times an amount of the therapeutic anti-CD117 antibody sufficient to result in about 100% CD117 receptor occupancy as determined by the RO assay, wherein the therapeutic anti-CD117 antibody depletes CD117+ cells in the human subject thereby treating the human subject.

Also disclosed herein is a method for treating a human subject in need thereof, comprising: determining CD117 receptor occupancy of a therapeutic anti-CD117 antibody on CD117 expressing cells from a human subject, said method comprising performing a receptor occupancy (RO) assay on a sample from the human subject, and determining the percent receptor occupancy of the therapeutic anti-CD117 antibody on CD117 expressing cells from the sample; and administering to the human subject an amount of the therapeutic anti-CD117 antibody that is less than 50 times an amount of the therapeutic anti-CD117 antibody sufficient to result in about 100% CD117 receptor occupancy as determined by the RO assay, wherein the therapeutic anti-CD117 antibody depletes CD117+ cells in the human subject thereby treating the human subject.

Also disclosed herein is a method for treating a human subject in need thereof, comprising: determining CD117 receptor occupancy of a therapeutic anti-CD117 antibody on CD117 expressing cells from a human subject, said method comprising performing a receptor occupancy (RO) assay on a sample from the human subject, and determining the percent receptor occupancy of the therapeutic anti-CD117 antibody on CD117 expressing cells from the sample; and administering to the human subject an amount of the therapeutic anti-CD117 antibody that is less than 10 times an amount of the therapeutic anti-CD117 antibody sufficient to result in about 100% CD117 receptor occupancy as determined by the RO assay, wherein the therapeutic anti-CD117 antibody depletes CD117+ cells in the human subject thereby treating the human subject.

In one embodiment, the therapeutic anti-CD117 antibody comprises a heavy chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 105, 106, and 107, respectively, and comprises a light chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 108, 109, and 110, respectively.

In one embodiment, the therapeutic anti-CD117 antibody, or antigen binding fragment thereof, comprises a light chain variable region comprising the amino acid sequence set forth as SEQ ID NO: 104, and a heavy chain variable region comprising the amino acid sequence set forth as SEQ ID NO: 103.

In another embodiment, the therapeutic anti-CD117 antibody comprises a heavy chain having the amino acid sequence as set forth as SEQ ID NO: 138, and a light chain having an amino acid sequence set forth as SEQ ID NO: 144.

In one embodiment, the therapeutic anti-CD117 antibody is an lgG1 isotype.

In one embodiment, the human subject is administered an amount of the therapeutic anti-CD117 antibody that is less than an amount of the therapeutic anti-CD117 antibody sufficient to result in about 100% CD117 receptor occupancy as determined by the RO assay.

In one embodiment, the human subject is administered an amount of the therapeutic anti-CD117 antibody that is less than an amount of the therapeutic anti-CD117 antibody sufficient to result in about 90% CD117 receptor occupancy as determined by the RO assay.

In one embodiment, the human subject is administered an amount of the therapeutic anti-CD117 antibody that is less than an amount of the therapeutic anti-CD117 antibody sufficient to result in about 80% CD117 receptor occupancy as determined by the RO assay.

In one embodiment, the human subject is administered an amount of the therapeutic anti-CD117 antibody that is less than an amount of the therapeutic anti-CD117 antibody sufficient to result in about 70% CD117 receptor occupancy as determined by the RO assay.

In one embodiment, the human subject is administered an amount of the therapeutic anti-CD117 antibody that is less than an amount of the therapeutic anti-CD117 antibody sufficient to result in about 60% CD117 receptor occupancy as determined by the RO assay.

In one embodiment, the human subject is administered an amount of the therapeutic anti-CD117 antibody that is less than an amount of the therapeutic anti-CD117 antibody sufficient to result in about 50% CD117 receptor occupancy as determined by the RO assay. In a further embodment, the RO assay comprises contacting the sample with an anti- CD117 antibody, or an antigen binding fragment thereof, that cross-blocks the therapeutic anti-CD117 antibody.

In yet another embodiment, the therapeutic anti-CD117 antibody that is administered to the human subject as an anti-CD117 antibody drug conjugate (ADC) comprising the therapeutic anti-CD117 antibody conjugated via a linker to an amatoxin.

In one embodiment, the ADC has the structure of formula (III):

or a stereoisomer thereof; wherein:

X is S or S(O); L is a linker;

Z is a chemical moiety formed by a coupling reaction between a reactive substituent Z' present on L and a reactive substituent present within the anti-CD117 antibody; and

Ab is the anti-CD117 antibody.

In another embodiment, the ADC has the structure of formula (Ilia) (SEQ ID NO:

286):

(Ilia). or formula (lllb) (SEQ ID NO: 287):

In one embodiment, L comprises one or more moieties selected from a bond, - (C=0)-, a -C(0)NH- group, an -0C(0)NH- group, C₁-C₆ alkylene, C₁-C₆ heteroalkylene, C2-C₆ alkenylene, C2-C₆ heteroalkenylene, C2-C₆ alkynylene, C2-C₆ heteroalkynylene, C₃- C₆ cycloalkylene, heterocycloalkylene, arylene, heteroarylene, a -(CH₂CH₂0)_P- group where p is an integer from 1-6; a solubility enhancing group, and a peptide; wherein each C1-C₆ alkylene, C1-C₆ heteroalkylene, C2-C₆ alkenylene, C2-C₆ heteroalkenylene, C2-C₆ alkynylene, C2-C₆ heteroalkynylene, C₃-C₆ cycloalkylene, heterocycloalkylene, arylene, or heteroarylene may optionally be substituted with from 1 to 5 substituents independently selected for each occasion from the group consisting of alkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, alkaryl, alkyl heteroaryl, amino, ammonium, acyl, acyloxy, acylamino, aminocarbonyl, alkoxycarbonyl, ureido, carbamate, aryl, heteroaryl, sulfinyl, sulfonyl, hydroxyl, alkoxy, sulfanyl, halogen, carboxy, trihalomethyl, cyano, hydroxy, mercapto, and nitro; or each C1-C₆ alkylene, C1-C₆ heteroalkylene, C2-C₆ alkenylene, C2-C₆ heteroalkenylene, C₂-C₆ alkynylene, C₂-C₆ heteroalkynylene, C₃-C₆ cycloalkylene, heterocycloalkylene, arylene, or heteroarylene may optionally be interrupted by one or more heteroatoms selected from O, S and N.

In still another embodiment, the ADC has the structure of formula (IV) (SEQ ID NO:

288):

a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein Ab is the anti- CD117 antibody.

In another embodiment, the ADC has the structure of formula (IVa) (SEQ ID NO:

289):

a stereoisomer thereof, or a pharmaceutically acceptable salt thereof.

In one embodiment, the ADC has the structure of formula (IVb) (SEQ ID NO: 290):

a stereoisomer thereof, or a pharmaceutically acceptable salt thereof.

Also disclosed herein is a method for determining receptor occupancy of a therapeutic anti-CD117 antibody on a CD117 expressing cell from a human subject, said method comprising performing a receptor occupancy (RO) assay on a sample obtained from a human subject, and determining the percent receptor occupancy of the therapeutic anti- CD117 antibody on the CD117 expressing cell from the sample, wherein the therapeutic anti-CD117 antibody comprises a heavy chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 105, 106, and 107, respectively, and comprises a light chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 108, 109, and 110, respectively.

In one embodiment, the RO assay comprises the steps of (a) contacting the sample with an amount of the anti-CD117 therapeutic antibody, (b) contacting the sample with an amount of a second anti-CD117 antibody, or an antigen-binding fragment thereof, that competes with the anti-CD117 therapeutic antibody for binding to CD117 on the CD117 expressing cell, wherein the second anti-CD117 antibody, or an antigen-binding fragment thereof, is labelled with a first detectable agent; (c) detecting the amount of the second antibody bound to the CD117 on the cell surface on the CD117 expressing cell in the sample, and (d) calculating the percentage of CD117 bound by the anti-CD117 therapeutic antibody, thereby determining receptor occupancy of the therapeutic anti-CD117 antibody.

Also disclosed herein is a method for determining receptor occupancy of a therapeutic anti-CD117 antibody on a CD117 expressing cell from a human subject who has been administered the therapeutic antibody, said method comprising performing a receptor occupancy (RO) assay on a sample from a human subject, and determining the percent receptor occupancy of the therapeutic anti-CD117 antibody on the CD117 expressing cell from the sample , and wherein therapeutic anti-CD117 antibody comprises a heavy chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 105, 106, and 107, respectively, and comprises a light chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 108, 109, and 110, respectively. In one embodiment, the RO assay comprises the steps of: (a) obtaining a sample from the human subject administered the therapeutic antibody; (b) contacting the sample with an amount of a second anti-CD117 antibody, or an antigen-binding fragment thereof, that competes with the anti-CD117 therapeutic antibody for binding to a CD117 receptor, wherein the second anti-CD117 antibody, or an antigen binding fragment thereof, is labelled with a first detectable agent; (c) detecting the amount of the second antibody bound to the CD117 receptor on the CD117 expressing cell in the sample, and (d) calculating the percentage of CD117 bound by the anti-CD117 therapeutic antibody, thereby determining receptor occupancy of the therapeutic anti-CD117 antibody

In one embodiment, the step of calculating the percentage of CD117 bound by the anti-CD117 therapeutic antibody further comprises the steps contacting the sample (or an equivalent sample) with an amount of a third anti-CD117 antibody, or an antigen-binding fragment thereof, that does not compete with the anti-CD117 therapeutic antibody for binding to a CD117 receptor, wherein the third anti-CD117 antibody, or an antigen-binding fragment thereof, is labelled with a second detectable agent, and detecting the amount of the third anti-CD117 antibody, or an antigen-binding fragment thereof, bound to the CD117 receptor on the CD117 expressing cell in the sample, thereby determining the total amount of the CD117 receptor on the CD117 expressing cell in the sample. In another embodiment, the second detectable agent is detected at a different emission wavelength than the first detectable agent.

In one embodiment, the receptor occupancy of the therapeutic anti-CD117 antibody is determined by detecting a signal from the first detectable agent, detecting a signal from the second detectable agent, and comparing the signals in order to determine the percent receptor occupancy.

In one embodiment, the detecting is determined using flow cytometry. In one embodiment, the second anti-CD117 antibody, or an antigen-binding fragment thereof, is an antigen binding fragment of the therapeutic antibody, a competitive anti-CD117 antibody that cross blocks the therapeutic antibody, or an antigen-binding fragment of a competitive anti-CD117 antibody that cross blocks the therapeutic antibody.

In one embodiment, the amount of the second anti-CD117 antibody is a saturating amount of the second anti-CD117 antibody.

In one embodiment, the amount of the third anti-CD117 antibody is a saturating amount of the third anti-CD117 antibody.

In one embodiment, the detectable agent is selected from the group consisting of a fluorescent label, a luminescent label, a bioluminescent label, a magnetic label, a radiolabel, and an enzyme.

In one embodiment, the detectable agent is a fluorescent label selected from the group consisting of phycoerythrin (PE), allophycocyanin (APC), BD Horizon Brilliant™ Violet 421 (BV421), BD Horizon Brilliant™ Violet 510 (BV510), BD Horizon Brilliant™ Violet 785 (BV785), fluorescein (FITC), PerCP-Cy5.5, and Alexa Fluor® 647 (AF647).

In one embodiment, the PE is phycoerythrin (PE)-Dazzle 594, PE/Cy5, PE/Cy5.5 and PE/Cy7. In one embodiment, the APC is allophycocyanin-Cy7.

In one embodiment, the third anti-CD117 antibody comprises antibody 104D2 conjugated to BV421.

In one embodiment, the second antibody is the anti-CD117 therapeutic antibody conjugated to phycoerythrin.

In one embodiment, the sample is obtained from the human subject immediately following administration of the anti-CD117 therapeutic antibody to the human subject. In another embodiment, the sample is obtained from the human subject at about 2 hours after administration of the anti-CD117 therapeutic antibody to the human subject. In another embodiment, the sample is obtained from the human subject at about 4 hours after administration of the anti-CD117 therapeutic antibody to the human subject. In another embodiment, the sample is obtained from the human subject at about 8 hours after administration of the anti-CD117 therapeutic antibody to the human subject. In another embodiment, the sample is obtained from the human subject at about 24 hours after administration of the anti-CD117 therapeutic antibody to the human subject. In another embodiment, the sample is obtained from the human subject at about 36 hours after administration of the anti-CD117 therapeutic antibody to the human subject. In another embodiment, the sample is obtained from the human subject at about 48 hours after administration of the anti-CD117 therapeutic antibody to the human subject.

In one embodiment, the sample comprises a CD117+ cell. In one embodiment, the sample comprises a leukemic blast cell, a hematopoietic stem cell (HSC), or a hematopoietic stem and progenitor cell (HSPC).

In one embodiment, the sample is whole blood or bone marrow from the human subject.

In one embodiment, the second anti-CD117 antibody, or the antigen binding fragment thereof, binds to the same epitope as the therapeutic antibody.

In one embodiment, the RO assay comprises contacting the sample with a) the anti- CD117 therapeutic antibody, the antigen binding fragment thereof, and b) a second antibody, or an antigen-binding fragment thereof, which is labelled and specifically binds to the therapeutic anti-CD117 antibody, or an antigen binding fragment thereof, and contacting the sample (or an equivalent sample) with a third anti-CD117 antibody, or an antigen-binding fragment thereof, which does not compete with the therapeutic anti-CD117 antibody for binding to human CD117, wherein the second antibody, or antigen-binding fragment thereof, does not cross react with the third anti-CD117 antibody, or an antigen-binding fragment thereof, and wherein the second anti-CD117 antibody, or antigen binding fragment thereof, is labelled with a first detectable agent and the third antibody, or an antigen-binding fragment thereof, is labeled with a second detectable agent.

In one embodiment, the therapeutic anti-CD117 antibody, or antigen binding fragment thereof, comprises a light chain variable region comprising the amino acid sequence set forth as SEQ ID NO: 104, and a heavy chain variable region comprising the amino acid sequence set forth as SEQ ID NO: 103.

In one embodiment, the therapeutic anti-CD117 antibody comprises a heavy chain having the amino acid sequence as set forth as SEQ ID NO: 138, and a light chain having an amino acid sequence set forth as SEQ ID NO: 144.

In one embodiment, the therapeutic anti-CD117 antibody is an lgG1 isotype.

In yet another embodiment, the method disclosed herein further comprises determining a dose of the therapeutic antibody for treating a human subject in need based on the percent receptor occupancy.

Also provided herein is a method of depleting CD117 expressing cells in a human subject, comprising administering an dose of an anti-CD117 antibody drug conjugate (ADC) comprising an anti-CD117 antibody conjugated to an amatoxin via a linker, to the human subject, wherein the dose is determined using the method of any one of the methods disclosed herein, and wherein the anti-CD117 antibody comprises a heavy chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 105, 106, and 107, respectively, and comprises a light chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 108, 109, and 110, respectively.

Another embodiment disclosed herein is a method of treating a human subject in need thereof, comprising administering an dose of an anti-CD117 antibody drug conjugate (ADC) comprising an anti-CD117 antibody conjugated to an amatoxin to the human subject, wherein the dose is determined using the method of any one of the methods disclosed herein, and wherein the anti-CD117 antibody comprises a heavy chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 105, 106, and 107, respectively, and comprises a light chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 108, 109, and 110, respectively.

Further provided is a method of conditioning a human subject, comprising administering an dose of an anti-CD117 antibody drug conjugate (ADC) comprising an anti- CD117 antibody conjugated to an amatoxin to the human subject, wherein the dose is determined using the method of any one of the methods disclosed herein, and wherein the anti-CD117 antibody comprises a heavy chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 105, 106, and 107, respectively, and comprises a light chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 108, 109, and 110, respectively.

In one embodiment, the sample is from the same human subject.

In one embodiment, the amount administered to the human subject is less than 1.1 times an amount of the therapeutic anti-CD117 antibody sufficient to result in about 100% CD117 receptor occupancy as determined by the RO assay.

In one embodiment, the dose resulted in at least about 80% receptor occupancy in the RO assay. In one embodiment, the dose resulted in at least about 85% receptor occupancy in the RO assay. In one embodiment, the dose resulted in at least about 90% receptor occupancy in the RO assay. In one embodiment, the dose resulted in at least about 95% receptor occupancy in the RO assay. In one embodiment, the dose resulted in at least about 99% receptor occupancy in the RO assay.

Also provided herein is a method of conditioning a human subject in need thereof, the method comprising administering to the human subject an amount of an anti-CD117 ADC sufficient to achieve and/or maintain a receptor occupancy of at least about 80% as determined according to any one of the methods disclosed herein, wherein the anti-CD117 ADC comprises an anti-CD117 antibody conjugated to an amatoxin, and wherein the anti- CD117 antibody comprises a heavy chain variable region comprising CDR1 , CDR2 and CDR3 as set forth in SEQ ID NO: 105, 106, and 107, respectively, and a light chain variable region comprising CDR1 , CDR2 and CDR3 as set forth in SEQ ID NO: 108, 109, and 110, respectively.

In one embodiment, the receptor occupancy achieved and/or maintained is at least about 85%. In one embodiment, the receptor occupancy achieved and/or maintained is at least about 90%. In one embodiment, the receptor occupancy achieved and/or maintained is at least about 95%. In one embodiment, the receptor occupancy achieved and/or maintained is at least about 99%. In one embodiment, the receptor occupancy achieved and/or maintained is about 100%. In certain embodiments, the ADC has the structure of formula (III) (SEQ ID NO: 285):

or a stereoisomer thereof; wherein: X is S or S(O);

L is a linker;

Z is a chemical moiety formed by a coupling reaction between a reactive substituent Z' present on L and a reactive substituent present within the anti-CD117 antibody; and Ab is the anti-CD117 antibody.

In another embodiment, the ADC has the structure of formula (Ilia) (SEQ ID NO:

286):

(Ilia). or formula (lllb) (SEQ ID NO: 287):

In one embodiment, L comprises one or more moieties selected from a bond, - (C=0)-, a -C(0)NH- group, an -0C(0)NH- group, C₁-C₆ alkylene, C₁-C₆ heteroalkylene, C2-C₆ alkenylene, C2-C₆ heteroalkenylene, C2-C₆ alkynylene, C2-C₆ heteroalkynylene, C₃- C₆ cycloalkylene, heterocycloalkylene, arylene, heteroarylene, a -(CH₂CH₂0)_P- group where p is an integer from 1-6, a solubility enhancing group, and a peptide; wherein each C1-C₆ alkylene, C1-C₆ heteroalkylene, C2-C₆ alkenylene, C2-C₆ heteroalkenylene, C2-C₆ alkynylene, C2-C₆ heteroalkynylene, C₃-C₆ cycloalkylene, heterocycloalkylene, arylene, or heteroarylene may optionally be substituted with from 1 to 5 substituents independently selected for each occasion from the group consisting of alkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, alkaryl, alkyl heteroaryl, amino, ammonium, acyl, acyloxy, acylamino, aminocarbonyl, alkoxycarbonyl, ureido, carbamate, aryl, heteroaryl, sulfinyl, sulfonyl, hydroxyl, alkoxy, sulfanyl, halogen, carboxy, trihalomethyl, cyano, hydroxy, mercapto, and nitro; or each C1-C₆ alkylene, C1-C₆ heteroalkylene, C2-C₆ alkenylene, C2-C₆ heteroalkenylene, C₂-C₆ alkynylene, C₂-C₆ heteroalkynylene, C₃-C₆ cycloalkylene, heterocycloalkylene, arylene, or heteroarylene may optionally be interrupted by one or more heteroatoms selected from O, S and N.

In one embodiment, the ADC has the structure of formula (IV) (SEQ ID NO: 288):

a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein Ab is the anti- CD117 antibody.

In one embodiment, the ADC has the structure of formula (IVa) (SEQ ID NO: 289):

In one embodiment, the ADC has the structure of formula (IVb) (SEQ ID NO: 290):

a stereoisomer thereof, or a pharmaceutically acceptable salt thereof.

In certain embodiments, the methods disclosed herein further comprise administering a stem cell transplant to the human subject. In one embodiment, the stem cell transplant comprises HSCs. In one embodiment, the stem cell transplant consists essentially of HSCs. In one embodiment, the HSCs are allogeneic.

In certain embodiments, the human subject has a disorder that would benefit from CD117+ cell depletion. In one embodiment, the human subject is in need of a cell transplant.

In another embodiment, the human subject has a stem cell disorder.

In still another embodiment, the human subject has cancer or an autoimmune disease.

In one embodiment, the cancer is a hematological cancer. In one embodiment, the hematological cancer is leukemia. In one embodiment, the leukemia is acute myeloid leukemia.

In one embodiment, the leukemia is acute lymphoblastic leukemia or chronic lymphocytic leukemia. In one embodiment, the hematological cancer is myelodysplastic syndrome.

Also provided herein is a method for determining receptor occupancy of a therapeutic anti-CD117 antibody on CD117 expressing cells from a human subject, said method comprising performing a receptor occupancy (RO) assay on a sample from a human subject, and determining the percent receptor occupancy of the therapeutic anti-CD117 antibody on CD117 expressing cells from the sample, wherein the therapeutic anti-CD117 antibody comprises a heavy chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 105, 106, and 107, respectively, and comprises a light chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 108, 109, and 110, respectively.

Brief Description of the Drawings

Fig. 1 depicts a schematic of an assay for selecting fluorophores for a receptor occupancy assay.

Figs. 2A and 2B graphically depict the results of an assay to measure the geometric mean fluorescence intensity (gMFI) of various antibodies labeled with a variety of detectable agents in the presence of CD117+ cells (Kasumi-1 cells; Fig. 2A) and a negative control (Kasumi-1 KO cells; Fig. 2B).

Fig.3 summarizes the results of an assay to measure the geometric mean fluorescence intensity (gMFI) of various antibodies labeled with a variety of detectable agents in the presence of CD117+ cells (Kasumi-1 cells) and a negative control (Kasumi-1 KO cells).

Fig.4 depicts a schematic of a whole blood spike-in assay.

Figs. 5A and 5B graphically depicts flow cytometry data for a whole blood spike-in assay using a spike of Kasumi-1 cells and the anti-CD117 antibody 104D2-labeled with phycoerythrin (i.e., “104D2-PE”; Fig. 5A)) in comparison to a control sample without a spike of Kasumi-1 cells;(Fig. 5B).

Figs. 6A-6C depicts three different antibody cocktails, each having a different CD117 fluorophore (Figs. 6A-6C) for use in whole blood spike-in assays.

Fig.7 graphically depicts flow cytometry data for a whole blood spike-in assay to measure the geometric mean fluorescence intensity (gMFI) of various antibodies labeled with a variety of detectable agents.

Figs. 8A-8D summarizes the results of an assay comparing the dynamic range of Brilliant Violet™ 421 (BV421 ; Figs. 8A and 8D) to phycoerythrin (PE; Figs. 8B and 8D) and Alexa Fluor 647 (AF647; Fig. 8C and 8D).

Fig.9 depicts the results of a receptor occupancy assay using various fluorophore- labeled antibodies. Detailed Description

Described herein are compositions and methods relating to dosing regimens for administering an anti-CD117 antibody drug conjugates (ADCs) to a human patient in need thereof, e.g., as a conditioning agent for a cell transplant or for treating cancer or an autoimmune disease.

Definitions

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood to one of ordinary skill in the art to which this invention pertains. Otherwise, certain terms used herein have the meanings as set forth in the specification.

It must be noted that as used herein and in the appended claims, the singular forms "a," "an," and "the" include plural reference unless the context clearly dictates otherwise.

As used herein, the term “about” refers to a value that is within 10% above or below the value being described.

As used herein, the term “amatoxin” refers to a member of the amatoxin family of peptides which are generally produced by Amanita phalloides mushrooms, or a derivative thereof, such as a variant or derivative thereof capable of inhibiting RNA polymerase II activity. Amatoxins may be isolated from a variety of mushroom species (e.g., Amanita phalloides, Gaiehna marginata, Lepiota brunneo-incarnata) or may be prepared semi- synthetically or synthetically. A member of this family, oc-amanitin, is described in Wieland, Int. J. Pept. Protein Res.1983, 22(3):257-276. A derivative of an amatoxin may be obtained by chemical modification of a naturally occurring compound ("semi-synthetic"), or may be obtained from an entirely synthetic source. Synthetic routes to various amatoxin derivatives are disclosed in, for example, U.S. Patent No. 9,676,702 and in Perrin et al., J. Am. Chem. Soc. 2018, 140, p. 6513-6517, each of which is incorporated by reference herein in their entirety with respect to synthetic methods for preparing and derivatizing amatoxins. Amatoxins useful in conjunction with the compositions and methods described herein include compounds such, as, but not limited to, compounds of Formula (I), a-amanitin, b-amanitin, y- amanitin, e-amanitin, amanin, amaninamide, amanullin, amanullinic acid, and proamanullin.

As used herein, the term "antibody" refers to an immunoglobulin molecule that specifically binds to, or is immunologically reactive with, a particular antigen, and includes monoclonal, chimeric antibodies, humanized antibodies, heteroconjugate antibodies (e.g., bi- tri- and quad-specific antibodies, diabodies, triabodies, and tetrabodies), and antigen binding fragments of antibodies, including, for example, Fab', F(ab')2, Fab, Fv, rlgG, and scFv fragments. Antibodies described herein are generally isolated or recombinant. "Isolated," when used herein refers to a polypeptide, e.g., an antibody, that has been identified and separated and/or recovered from a cell or cell culture from which it was expressed. Ordinarily, an isolated antibody will be prepared by at least one purification step. Thus, an "isolated antibody," refers to an antibody which is substantially free of other antibodies having different antigenic specificities. For instance, an isolated antibody that specifically binds to CD117 is substantially free of antibodies that specifically bind antigens other than CD117.

Generally, antibodies comprise heavy and light chains containing antigen binding regions. Each heavy chain is comprised of a heavy chain variable region (abbreviated herein as HCVR or VH) and a heavy chain constant region. The heavy chain constant region is comprised of three domains, CH1 , CH2 and CH3. Each light chain is comprised of a light chain variable region (abbreviated herein as LCVR or VL) and a light chain constant region. The light chain constant region is comprised of one domain, CL. The VH, and VL regions can be further subdivided into regions of hypervariability, termed complementarity determining regions (CDR), interspersed with regions that are more conserved, termed framework regions (FR). As used herein, the term “complementarity determining region” (CDR) refers to a hypervariable region found both in the light chain and the heavy chain variable domains of an antibody. Each VH and VL is composed of three CDRs and four FRs, arranged from amino-terminus to carboxyl-terminus in the following order: FR1 , CDR1 , FR2, CDR2, FR3, CDR3, FR4. The variable regions of the heavy and light chains contain a binding domain that interacts with an antigen. The constant regions of the antibodies can mediate the binding of the immunoglobulin to host tissues or factors, including various cells of the immune system (e.g., effector cells) and the first component (Clq) of the classical complement system.

The amino acid positions that delineate a hypervariable region of an antibody can vary, depending on the context and the various definitions known in the art. Some positions within a variable domain may be viewed as hybrid hypervariable positions in that these positions can be deemed to be within a hypervariable region under one set of criteria while being deemed to be outside a hypervariable region under a different set of criteria. One or more of these positions can also be found in extended hypervariable regions. The antibodies described herein may contain modifications in these hybrid hypervariable positions. The variable domains of native heavy and light chains each contain four framework regions that primarily adopt a b-sheet configuration, connected by three CDRs, which form loops that connect, and in some cases form part of, the b-sheet structure. The CDRs in each chain are held together in close proximity by the framework regions in the order FR1-CDR1-FR2-CDR2-FR3-CDR3-FR4 and, with the CDRs from the other antibody chains, contribute to the formation of the target binding site of antibodies (see Kabat et al., Sequences of Proteins of Immunological Interest, National Institute of Health, Bethesda,

MD., 1987). In certain embodiments, numbering of immunoglobulin amino acid residues is performed according to the immunoglobulin amino acid residue numbering system of Kabat et al., unless otherwise indicated (although any antibody numbering scheme, including, but not limited to IMGT and Chothia, can be utilized).

The term “antigen-binding fragment” or “antigen binding portion” as used interchangeably herein, refers to one or more fragments of an antibody that retains the ability to specifically bind to the target antigen of the instant antibody from which it is derived. The antigen-binding function of an antibody can be performed by fragments of a full-length antibody. Examples of antigen-binding fragments include, but are not limited to: (i) a Fab fragment, a monovalent fragment consisting of the V_L, V_H, CL, and CH1 domains; (ii) a F(ab')2 fragment, a bivalent fragment containing two Fab fragments linked by a disulfide bridge at the hinge region; (iii) a Fd fragment consisting of the V_H and CH1 domains; (iv) a Fv fragment consisting of the V_L and V_H domains of a single arm of an antibody, (v) a dAb including V_H and V_L domains; (vi) a dAb fragment that consists of a V_H domain (see, e.g., Ward et al., Nature 341 :544-546, 1989); (vii) a dAb which consists of a V_H or a V_L domain; (viii) an isolated complementarity determining region (CDR); and (ix) a combination of two or more (e.g., two, three, four, five, or six) isolated CDRs which may optionally be joined by a synthetic linker. Furthermore, although the two domains of the Fv fragment, V_L and V_H, are coded for by separate genes, they can be joined, using recombinant methods, by a linker that enables them to be made as a single protein chain in which the V_L and V_H regions pair to form monovalent molecules (known as single chain Fv (scFv); see, for example, Bird et al., Science 242:423-426, 1988 and Huston et al., Proc. Natl. Acad. Sci. USA 85:5879-5883, 1988). These antibody fragments can be obtained using conventional techniques known to those of skill in the art, and the fragments can be screened for utility in the same manner as intact antibodies. Antigen-binding fragments can be produced by recombinant DNA techniques, enzymatic or chemical cleavage of intact immunoglobulins, or, in certain cases, by chemical peptide synthesis procedures known in the art.

As used herein, the term “scFv” refers to a single chain Fv antibody in which the variable domains of the heavy chain and the light chain from an antibody have been joined to form one chain. scFv fragments contain a single polypeptide chain that includes the variable region of an antibody light chain (V_L) (e.g., CDR-L1, CDR-L2, and/or CDR-L3) and the variable region of an antibody heavy chain (V_H) (e.g., CDR-H1 , CDR-H2, and/or CDR- H3) separated by a linker. The linker that joins the V_L and V_H regions of a scFv fragment can be a peptide linker composed of proteinogenic amino acids. The term "monoclonal antibody" as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical and/or bind the same epitope, except for possible variant antibodies, e.g., containing naturally occurring mutations or arising during production of a monoclonal antibody preparation, such variants generally being present in minor amounts. In contrast to polyclonal antibody preparations, which typically include different antibodies directed against different determinants (epitopes), each monoclonal antibody of a monoclonal antibody preparation is directed against a single determinant on an antigen. Thus, the modifier "monoclonal" indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method.

An "intact" or "full length" antibody, as used herein, refers to an antibody having two heavy (H) chain polypeptides and two light (L) chain polypeptides interconnected by disulfide bonds. Each heavy chain is comprised of a heavy chain variable region (abbreviated herein as HCVR or VH) and a heavy chain constant region. The heavy chain constant region is comprised of three domains, CH1 , CH2 and CH3. Each light chain is comprised of a light chain variable region (abbreviated herein as LCVR or VL) and a light chain constant region. The light chain constant region is comprised of one domain, CL. The VH, and VL regions can be further subdivided into regions of hypervariability, termed complementarity determining regions (CDR), interspersed with regions that are more conserved, termed framework regions (FR). Each VH and VL is composed of three CDRs and four FRs, arranged from amino-terminus to carboxyl-terminus in the following order: FR1 , CDR1 , FR2, CDR2, FR3, CDR3, FR4. The variable regions of the heavy and light chains contain a binding domain that interacts with an antigen. The constant regions of the antibodies can mediate the binding of the immunoglobulin to host tissues or factors, including various cells of the immune system (e.g., effector cells) and the first component (Clq) of the classical complement system.

As used herein, the term “conjugate” refers to a compound formed by the chemical bonding of a reactive functional group of one molecule, such as an antibody or antigen binding fragment thereof, with an appropriately reactive functional group of another molecule, such as a cytotoxin described herein. The foregoing conjugates are also referred to interchangeably herein as a “drug antibody conjugate”, an “antibody drug conjugate” and an “ADC”. In one embodiment, an ADC is formed by the chemical bonding of a reactive functional group of one molecule, such as an antibody or antigen-binding fragment thereof, with an appropriately reactive functional group of another molecule, such as a cytotoxin described herein. Conjugates may include a linker between the two molecules bound to one another, e.g., between an antibody and a cytotoxin. Examples of linkers that can be used for the formation of a conjugate include peptide-containing linkers, such as those that contain naturally occurring or non-naturally occurring amino acids, such as D-amino acids. Linkers can be prepared using a variety of strategies described herein and known in the art. Depending on the reactive components therein, a linker may be cleaved, for example, by enzymatic hydrolysis, photolysis, hydrolysis under acidic conditions, hydrolysis under basic conditions, oxidation, disulfide reduction, nucleophilic cleavage, or organometallic cleavage (see, for example, Leriche et al., Bioorg. Med. Chem., 20:571-582, 2012).

As used herein, the term “anti-CD117 antibody” or "an antibody that binds to CD117" refers to an antibody that is capable of binding CD117, e.g., human CD117 (hCD117) with sufficient affinity such that the antibody is useful as a diagnostic and/or therapeutic agent in targeting CD117.

The term “therapeutic antibody”, as used herein, refers to an antibody that can be used for treating or conditioning a human subject. The term is intended to include a naked antibody as well as an antibody that may be conjugated to a cytotoxin, thus forming an antibody drug conjugate (ADC). In one embodiment, a therapeutic antibody is an anti- CD117 antibody, e.g., Ab85, which is conjugated to an amatoxin for conditioning or treating a human subject in need thereof.

The term “cross competes" refers to the ability of an antibody or antibody fragment to interfere with the binding of other antibodies or antibody fragments to a specific antigen in a standard competitive binding assay. An antibody or antigen binding fragment that cross competes with another is a “competitive antibody”. The ability or extent to which an antibody, antibody fragment or other antigen-binding moieties is able to interfere with the binding of another antibody or antibody fragment to a specific antigen, and, therefore whether it can be said to cross-compete, can be determined using standard competition binding assays. One suitable assay involves the use of the Biacore technology (e.g. by using the BIAcore 3000 instrument (Biacore, Uppsala, Sweden)), which can measure the extent of interactions using surface plasmon resonance technology. Another assay for measuring cross-competing uses an ELISA-based approach. A high throughput process for "epitope binning" antibodies based upon their cross-competition is described in International Patent Application No. WO 2003/48731.

"Binds the same epitope as" means the ability of an antibody or antibody fragment to bind to a specific antigen whereby it binds to the same epitope as the exemplified antibody when using the same epitope mapping technique for comparing the antibodies or fragments thereof. The epitopes of the exemplified antibody and other antibodies can be determined using epitope mapping techniques. Epitope mapping techniques are well known in the art. For example, conformational epitopes are readily identified by determining spatial conformation of amino acids such as by, e.g., hydrogen/deuterium exchange, x-ray crystallography and two-dimensional nuclear magnetic resonance.

As used herein, the term "consists essentially of," or variations such as "consist essentially of" or "consisting essentially of" as used throughout the specification and claims, indicate the inclusion of any recited integer or group of integers, and the optional inclusion of any recited integer or group of integers that do not materially change the basic or novel properties of the specified method, structure or composition.

As used herein, the terms “condition” and “conditioning” refer to processes by which a patient is prepared for receipt of a transplant, e.g., a transplant containing hematopoietic stem cells (HSCs). Such procedures promote the engraftment of a hematopoietic stem cell transplant (for instance, as inferred from a sustained increase in the quantity of viable hematopoietic stem cells within a blood sample isolated from a patient following a conditioning procedure and subsequent hematopoietic stem cell transplantation). According to the methods described herein, a patient may be conditioned for hematopoietic stem cell transplant therapy by administration to the patient of an anti-CD117 ADC. Administration of an anti-CD117 ADC to a patient in need of hematopoietic stem cell transplant therapy can promote the engraftment of a hematopoietic stem cell graft, for example, by selectively depleting endogenous hematopoietic stem cells, thereby creating a vacancy filled by an exogenous hematopoietic stem cell transplant.

As used herein, the term “hematopoietic stem cells” (“HSCs”) refers to immature blood cells having the capacity to self-renew and to differentiate into mature blood cells containing diverse lineages including but not limited to granulocytes (e.g., promyelocytes, neutrophils, eosinophils, basophils), erythrocytes (e.g., reticulocytes, erythrocytes), thrombocytes (e.g., megakaryoblasts, platelet producing megakaryocytes, platelets), monocytes (e.g., monocytes, macrophages), dendritic cells, microglia, osteoclasts, and lymphocytes (e.g., NK cells, B-cells and T-cells). Such cells may include CD34⁺ cells.

CD34⁺ cells are immature cells that express the CD34 cell surface marker.

As used herein, patients that are “in need of” a hematopoietic stem cell transplant include patients that exhibit a defect or deficiency in one or more blood cell types, as well as patients having a stem cell disorder, autoimmune disease, cancer, or other pathology described herein. Hematopoietic stem cells generally exhibit 1) multi-potency, and can thus differentiate into multiple different blood lineages including, but not limited to, granulocytes (e.g., promyelocytes, neutrophils, eosinophils, basophils), erythrocytes (e.g., reticulocytes, erythrocytes), thrombocytes (e.g., megakaryoblasts, platelet producing megakaryocytes, platelets), monocytes (e.g., monocytes, macrophages), dendritic cells, microglia, osteoclasts, and lymphocytes (e.g., NK cells, B-cells and T-cells), 2) self-renewal, and can thus give rise to daughter cells that have equivalent potential as the mother cell, and 3) the ability to be reintroduced into a transplant recipient whereupon they home to the hematopoietic stem cell niche and re-establish productive and sustained hematopoiesis. Hematopoietic stem cells can thus be administered to a patient defective or deficient in one or more cell types of the hematopoietic lineage in order to re-constitute the defective or deficient population of cells in vivo. For example, the patient may be suffering from cancer, and the deficiency may be caused by administration of a chemotherapeutic agent or other medicament that depletes, either selectively or non-specifically, the cancerous cell population. Additionally or alternatively, the patient may be suffering from a hemoglobinopathy (e.g., a non-malignant hemoglobinopathy), such as sickle cell anemia, thalassemia, Fanconi anemia, aplastic anemia, and Wiskott-Aldrich syndrome. The subject may be one that is suffering from adenosine deaminase severe combined immunodeficiency (ADA SCID), HIV/AIDS, metachromatic leukodystrophy, Diamond-Blackfan anemia, and Schwachman-Diamond syndrome. The subject may have or be affected by an inherited blood disorder (e.g., sickle cell anemia) or an autoimmune disorder. Additionally or alternatively, the subject may have or be affected by a malignancy, such as neuroblastoma or a hematologic cancer. For instance, the subject may have a leukemia, lymphoma, or myeloma. In some embodiments, the subject has acute myeloid leukemia, acute lymphoid leukemia, chronic myeloid leukemia, chronic lymphoid leukemia, multiple myeloma, diffuse large B-cell lymphoma, or non-Hodgkin’s lymphoma. In some embodiments, the subject has myelodysplastic syndrome. In some embodiments, the subject has an autoimmune disease, such as scleroderma, multiple sclerosis, ulcerative colitis, Crohn’s disease, Type 1 diabetes, or another autoimmune pathology described herein. In some embodiments, the subject is in need of chimeric antigen receptor T-cell (CART) therapy. In some embodiments, the subject has or is otherwise affected by a metabolic storage disorder. The subject may suffer or otherwise be affected by a metabolic disorder selected from the group consisting of glycogen storage diseases, mucopolysaccharidoses, Gaucher's Disease, Hurlers Disease, sphingolipidoses, metachromatic leukodystrophy, or any other diseases or disorders which may benefit from the treatments and therapies disclosed herein and including, without limitation, severe combined immunodeficiency, Wiscott-Aldrich syndrome, hyper immunoglobulin M (IgM) syndrome, Chediak-Higashi disease, hereditary lymphohistiocytosis, osteopetrosis, osteogenesis imperfecta, storage diseases, thalassemia major, sickle cell disease, systemic sclerosis, systemic lupus erythematosus, multiple sclerosis, juvenile rheumatoid arthritis and those diseases, or disorders described in "Bone Marrow Transplantation for Non-Malignant Disease," ASH Education Book, 1 :319-338 (2000), the disclosure of which is incorporated herein by reference in its entirety as it pertains to pathologies that may be treated by administration of hematopoietic stem cell transplant therapy. Additionally or alternatively, a patient “in need of” a hematopoietic stem cell transplant may one that is or is not suffering from one of the foregoing pathologies, but nonetheless exhibits a reduced level (e.g., as compared to that of an otherwise healthy subject) of one or more endogenous cell types within the hematopoietic lineage, such as megakaryocytes, thrombocytes, platelets, erythrocytes, mast cells, myeoblasts, basophils, neutrophils, eosinophils, microglia, granulocytes, monocytes, osteoclasts, antigen-presenting cells, macrophages, dendritic cells, natural killer cells, T-lymphocytes, and B-lymphocytes. One of skill in the art can readily determine whether one’s level of one or more of the foregoing cell types, or other blood cell type, is reduced with respect to an otherwise healthy subject, for instance, by way of flow cytometry and fluorescence activated cell sorting (FACS) methods, among other procedures, known in the art.

As used herein, the term “recipient” refers to a patient that receives a transplant, such as a transplant containing a population of hematopoietic stem cells. The transplanted cells administered to a recipient may be, e.g., autologous, syngeneic, or allogeneic cells.

The term "allogeneic" when used in reference to a cell transplant or graft broadly means any transplant which is not genetically identical to a patient recipient. More specifically, any transplant from any donor who is not an identical twin to a patient recipient, is referred to as an allogeneic transplant as these transplants are not genetically identical to a patient recipient. Thus, the term "donor" of an allogeneic transplant means any donor who is not an identical twin to a patient recipient.

As used herein, the term “sample” refers to a specimen (e.g., blood, blood component (e.g., serum or plasma), urine, saliva, amniotic fluid, cerebrospinal fluid, tissue (e.g., placental or dermal), pancreatic fluid, chorionic villus sample, and cells) taken from a subject.

As used herein, the terms “subject” and “patient”, used interchangeably herein, refer to an organism, such as a human, that receives treatment for a particular disease or condition as described herein. For instance, a patient, such as a human patient, may receive treatment prior to hematopoietic stem cell transplant therapy in order to promote the engraftment of exogenous hematopoietic stem cells.

As used herein, the phrase “substantially cleared from the blood” refers to a point in time following administration of a therapeutic agent to a patient when the concentration of the therapeutic agent in a blood sample isolated from the patient is such that the therapeutic agent is not detectable by conventional means (for instance, such that the therapeutic agent is not detectable above the noise threshold of the device or assay used to detect the therapeutic agent). A variety of techniques known in the art can be used to detect antibodies, antibody fragments, and protein ligands, such as ELISA-based detection assays known in the art or described herein. Additional assays that can be used to detect antibodies, or antibody fragments, include immunoprecipitation techniques and immunoblot assays, among others known in the art.

As used herein, the phrase "stem cell disorder" broadly refers to any disease, disorder, or condition that may be treated or cured by conditioning a subject's target tissues, and/or by ablating an endogenous stem cell population in a target tissue (e.g., ablating an endogenous hematopoietic stem or progenitor cell population from a subject's bone marrow tissue) and/or by engrafting or transplanting stem cells in a subject's target tissues. For example, Type I diabetes has been shown to be cured by hematopoietic stem cell transplant and may benefit from conditioning in accordance with the compositions and methods described herein. Additional disorders that can be treated using the compositions and methods described herein include, without limitation, sickle cell anemia, thalassemias, Fanconi anemia, aplastic anemia, Wiskott-Aldrich syndrome, ADA SCID, HIV/AIDS, metachromatic leukodystrophy, Diamond-Blackfan anemia, and Schwachman-Diamond syndrome. Additional diseases that may be treated using the patient conditioning and/or hematopoietic stem cell transplant methods described herein influde inherited blood disorders (e.g., sickle cell anemia) and autoimmune disorders, such as scleroderma, multiple sclerosis, ulcerative colitis, and Chrohn’s disease. Additional diseases that may be treated using the conditioning and/or transplantation methods described herein include a malignancy, such as a neuroblastoma or hematologic cancers, such as leukemia, lymphoma, and myeloma. For instance, the cancer may be acute myeloid leukemia, acute lymphoid leukemia, chronic myeloid leukemia, chronic lymphoid leukemia, multiple myeloma, diffuse large B-cell lymphoma, or non-Flodgkin’s lymphoma. Additional diseases treatable using the conditioning and/or transplantation methods described herein include myelodysplastic syndrome. In some embodiments, the subject has or is otherwise affected by a metabolic storage disorder. For example, the subject may suffer or otherwise be affected by a metabolic disorder selected from the group consisting of glycogen storage diseases, mucopolysaccharidoses, Gaucher's Disease, Hurlers Disease, sphingolipidoses, metachromatic leukodystrophy, or any other diseases or disorders which may benefit from the treatments and therapies disclosed herein and including, without limitation, severe combined immunodeficiency, Wiscott-Aldrich syndrome, hyper immunoglobulin M (IgM) syndrome, Chediak-Fligashi disease, hereditary lymphohistiocytosis, osteopetrosis, osteogenesis imperfecta, storage diseases, thalassemia major, sickle cell disease, systemic sclerosis, systemic lupus erythematosus, multiple sclerosis, juvenile rheumatoid arthritis and those diseases, or disorders described in "Bone Marrow Transplantation for Non-Malignant Disease," ASH Education Book, 1 :319-338 (2000), the disclosure of which is incorporated herein by reference in its entirety as it pertains to pathologies that may be treated by administration of hematopoietic stem cell transplant therapy.

As used herein, the terms “treat” or “treatment” refers to reducing the severity and/or frequency of disease symptoms, eliminating disease symptoms and/or the underlying cause of said symptoms, reducing the frequency or likelihood of disease symptoms and/or their underlying cause, and improving or remediating damage caused, directly or indirectly, by disease. Beneficial or desired clinical results include, but are not limited to, promoting the engraftment of exogenous hematopoietic cells in a patient following antibody conditioning therapy as described herein and subsequent hematopoietic stem cell transplant therapy. Additional beneficial results include an increase in the cell count or relative concentration of hematopoietic stem cells in a patient in need of a hematopoietic stem cell transplant following conditioning therapy and subsequent administration of an exogenous hematopoietic stem cell graft to the patient. Beneficial results of therapy described herein may also include an increase in the cell count or relative concentration of one or more cells of hematopoietic lineage, such as a megakaryocyte, thrombocyte, platelet, erythrocyte, mast cell, myeoblast, basophil, neutrophil, eosinophil, microglial cell, granulocyte, monocyte, osteoclast, antigen-presenting cell, macrophage, dendritic cell, natural killer cell, T- lymphocyte, or B-lymphocyte, following conditioning therapy and subsequent hematopoietic stem cell transplant therapy. Additional beneficial results may include the reduction in quantity of a disease-causing cell population, such as a population of cancer cells or autoimmune cells. Insofar as the methods disclosed herein are directed to preventing disorders, it is understood that the term "prevent" does not require that the disease state be completely thwarted. Rather, as used herein, the term preventing refers to the ability of the skilled artisan to identify a population that is susceptible to disorders, such that administration of the compounds disclosed herein may occur prior to onset of a disease. The term does not imply that the disease state is completely avoided. As used herein, the term “treatment” encompasses conditioning, unless otherwise indicated.

As used herein, the terms "variant" and "derivative" are used interchangeably and refer to naturally-occurring, synthetic, and semi-synthetic analogues of a compound, peptide, protein, or other substance described herein. A variant or derivative of a compound, peptide, protein, or other substance described herein may retain or improve upon the biological activity of the original material.

As used herein, the term “coupling reaction” refers to a chemical reaction in which two or more substituents suitable for reaction with one another react so as to form a chemical moiety that joins (e.g., covalently) the molecular fragments bound to each substituent. Coupling reactions include those in which a reactive substituent bound to a fragment that is a cytotoxin, such as a cytotoxin known in the art or described herein, reacts with a suitably reactive substituent bound to a fragment that is an antibody, or antigen binding fragment thereof, such as an antibody, antigen-binding fragment thereof, or specific anti-CD117 antibody that binds CD117 known in the art or described herein. Examples of suitably reactive substituents include a nucleophile/electrophile pair (e.g., a thiol/haloalkyl pair, an amine/carbonyl pair, or a thiol/a, b-unsaturated carbonyl pair, among others), a diene/dienophile pair (e.g., an azide/alkyne pair, among others), and the like. Coupling reactions include, without limitation, thiol alkylation, hydroxyl alkylation, amine alkylation, amine condensation, amidation, esterification, disulfide formation, cycloaddition (e.g., [4+2] Diels-Alder cycloaddition, [3+2] Huisgen cycloaddition, among others), nucleophilic aromatic substitution, electrophilic aromatic substitution, and other reactive modalities known in the art or described herein.

The term "acyl" as used herein refers to -C(=0)R, wherein R is hydrogen (“aldehyde”), C1-C12 alkyl, C2-C12 alkenyl, C2-C12 alkynyl, C3-C7 carbocyclyl, C6-C20 aryl, 5-10 membered heteroaryl, or 5-10 membered heterocyclyl, as defined herein. Non-limiting examples include formyl, acetyl, propanoyl, benzoyl, and acryloyl.

The term "C1-C12 alkyl" as used herein refers to a straight chain or branched, saturated hydrocarbon having from 1 to 12 carbon atoms. Representative C1-C12 alkyl groups include, but are not limited to, -methyl, -ethyl, -n-propyl, -n-butyl, -n-pentyl, and -n- hexyl; while branched C1-C12 alkyls include, but are not limited to, -isopropyl, -sec-butyl, - isobutyl, -tert-butyl, -isopentyl, and 2-methylbutyl. A C1-C12 alkyl group can be unsubstituted or substituted.

The term "alkenyl" as used herein refers to C2-C12 hydrocarbon containing normal, secondary, or tertiary carbon atoms with at least one site of unsaturation, i.e., a carbon- carbon, sp² double bond. Examples include, but are not limited to: ethylene or vinyl, -allyl, -1- butenyl, -2-butenyl, -isobutylenyl, -1-pentenyl, -2-pentenyl, -3-methyl-1-butenyl, -2-methyl-2- butenyl, -2,3-dimethyl-2-butenyl, and the like. An alkenyl group can be unsubstituted or substituted.

"Alkynyl" as used herein refers to a C2-C12 hydrocarbon containing normal, secondary, or tertiary carbon atoms with at least one site of unsaturation, i.e., a carbon- carbon, sp triple bond. Examples include, but are not limited to acetylenic and propargyl. An alkynyl group can be unsubstituted or substituted. "Aryl" as used herein refers to a C6-C20 carbocyclic aromatic group. Examples of aryl groups include, but are not limited to, phenyl, naphthyl and anthracenyl. An aryl group can be unsubstituted or substituted.

"Arylalkyl" as used herein refers to an acyclic alkyl radical in which one of the hydrogen atoms bonded to a carbon atom, typically a terminal or sp³ carbon atom, is replaced with an aryl radical. Typical arylalkyl groups include, but are not limited to, benzyl, 2-phenylethan-1-yl, 2-phenylethen-1-yl, naphthylmethyl, 2-naphthylethan-1-yl, 2- naphthylethen-1-yl, naphthobenzyl, 2-naphthophenylethan-1-yl and the like. The arylalkyl group comprises 6 to 20 carbon atoms, e.g. the alkyl moiety, including alkanyl, alkenyl or alkynyl groups, of the arylalkyl group is 1 to 6 carbon atoms and the aryl moiety is 5 to 14 carbon atoms. An alkaryl group can be unsubstituted or substituted.

“Cycloalkyl” as used herein refers to a saturated carbocyclic radical, which may be mono- or bicyclic. Cycloalkyl groups include a ring having 3 to 7 carbon atoms as a monocycle or 7 to 12 carbon atoms as a bicycle. Examples of monocyclic cycloalkyl groups include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, and cyclooctyl. A cycloalkyl group can be unsubstituted or substituted.

“Cycloalkenyl” as used herein refers to an unsaturated carbocyclic radical, which may be mono- or bicyclic. Cycloalkenyl groups include a ring having 3 to 6 carbon atoms as a monocycle or 7 to 12 carbon atoms as a bicycle. Examples of monocyclic cycloalkenyl groups include 1-cyclopent-1-enyl, 1-cyclopent-2-enyl, 1-cyclopent-3-enyl, 1 -cyclohex-1 - enyl, 1-cyclohex-2-enyl, and 1-cyclohex-3-enyl. A cycloalkenyl group can be unsubstituted or substituted.

"Heteroaralkyl" as used herein refers to an acyclic alkyl radical in which one of the hydrogen atoms bonded to a carbon atom, typically a terminal or sp3 carbon atom, is replaced with a heteroaryl radical. Typical heteroaryl alkyl groups include, but are not limited to, 2-benzimidazolylmethyl, 2-furylethyl, and the like. The heteroarylalkyl group comprises 6 to 20 carbon atoms, e.g. the alkyl moiety, including alkanyl, alkenyl or alkynyl groups, of the heteroarylalkyl group is 1 to 6 carbon atoms and the heteroaryl moiety is 5 to 14 carbon atoms and 1 to 3 heteroatoms selected from N, O, P, and S. The heteroaryl moiety of the heteroarylalkyl group may be a monocycle having 3 to 7 ring members (2 to 6 carbon atoms or a bicycle having 7 to 10 ring members (4 to 9 carbon atoms and 1 to 3 heteroatoms selected from N, O, P, and S), for example: a bicyclo[4,5], [5,5], [5,6], or [6,6] system.

"Heteroaryl" and "heterocycloalkyl" as used herein refer to an aromatic or non aromatic ring system, respectively, in which one or more ring atoms is a heteroatom, e.g. nitrogen, oxygen, and sulfur. The heteroaryl or heterocycloalkyl radical comprises 2 to 20 carbon atoms and 1 to 3 heteroatoms selected from N, O, P, and S. A heteroaryl or heterocycloalkyl may be a monocycle having 3 to 7 ring members (2 to 6 carbon atoms and 1 to 3 heteroatoms selected from N, O, P, and S) or a bicycle having 7 to 10 ring members (4 to 9 carbon atoms and 1 to 3 heteroatoms selected from N, O, P, and S), for example: a bicyclo[4,5], [5,5], [5,6], or [6,6] system. Heteroaryl and heterocycloalkyl can be unsubstituted or substituted.

Heteroaryl and heterocycloalkyl groups are described in Paquette, Leo A.; "Principles of Modern Heterocyclic Chemistry" (W. A. Benjamin, New York, 1968), particularly Chapters 1, 3, 4, 6, 7, and 9; "The Chemistry of Heterocyclic Compounds, A series of Monographs"

(John Wiley & Sons, New York, 1950 to present), in particular Volumes 13, 14, 16, 19, and 28; and J. Am. Chem. Soc. (1960) 82:5566.

Examples of heteroaryl groups include by way of example and not limitation pyridyl, thiazolyl, tetrahydrothiophenyl, pyrimidinyl, furanyl, thienyl, pyrrolyl, pyrazolyl, imidazolyl, tetrazolyl, benzofuranyl, thianaphthalenyl, indolyl, indolenyl, quinolinyl, isoquinolinyl, benzimidazolyl, isoxazolyl, pyrazinyl, pyridazinyl, indolizinyl, isoindolyl, 3H-indolyl, 1H- indazolyl, purinyl, 4H-quinolizinyl, phthalazinyl, naphthyridinyl, quinoxalinyl, quinazolinyl, cinnolinyl, pteridinyl, 4aH-carbazolyl, carbazolyl, phenanthridinyl, acridinyl, pyrimidinyl, phenanthrolinyl, phenazinyl, phenothiazinyl, furazanyl, phenoxazinyl, isochromanyl, chromanyl, imidazolidinyl, imidazolinyl, pyrazolidinyl, pyrazolinyl, benzotriazolyl, benzisoxazolyl, and isatinoyl.

Examples of heterocycloalkyls include by way of example and not limitation dihydroypyridyl, tetrahydropyridyl (piperidyl), tetrahydrothiophenyl, piperidinyl, 4-piperidonyl, pyrrolidinyl, 2-pyrrolidonyl, tetrahydrofuranyl, tetrahydropyranyl, bis-tetrahydropyranyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl, decahydroquinolinyl, octahydroisoquinolinyl, piperazinyl, quinuclidinyl, and morpholinyl.

By way of example and not limitation, carbon bonded heteroaryls and heterocycloalkyls are bonded at position 2, 3, 4, 5, or 6 of a pyridine, position 3, 4, 5, or 6 of a pyridazine, position 2, 4, 5, or 6 of a pyrimidine, position 2, 3, 5, or 6 of a pyrazine, position 2, 3, 4, or 5 of a furan, tetrahydrofuran, thiofuran, thiophene, pyrrole or tetrahydropyrrole, position 2, 4, or 5 of an oxazole, imidazole or thiazole, position 3, 4, or 5 of an isoxazole, pyrazole, or isothiazole, position 2 or 3 of an aziridine, position 2, 3, or 4 of an azetidine, position 2, 3, 4, 5, 6, 7, or 8 of a quinoline or position 1 , 3, 4, 5, 6, 7, or 8 of an isoquinoline. Still more typically, carbon bonded heterocycles include 2-pyridyl, 3-pyridyl, 4-pyridyl, 5- pyridyl, 6-pyridyl, 3-pyridazinyl, 4-pyridazinyl, 5-pyridazinyl, 6-pyridazinyl, 2-pyrimidinyl, 4- pyrimidinyl, 5-pyrimidinyl, 6-pyrimidinyl, 2-pyrazinyl, 3-pyrazinyl, 5-pyrazinyl, 6-pyrazinyl, 2- thiazolyl, 4-thiazolyl, or 5-thiazolyl. By way of example and not limitation, nitrogen bonded heteroaryls and heterocycloalkyls are bonded at position 1 of an aziridine, azetidine, pyrrole, pyrrolidine, 2- pyrroline, 3-pyrroline, imidazole, imidazolidine, 2-imidazoline, 3-imidazoline, pyrazole, pyrazoline, 2-pyrazoline, 3-pyrazoline, piperidine, piperazine, indole, indoline, 1H-indazole, position 2 of a isoindole, or isoindoline, position 4 of a morpholine, and position 9 of a carbazole, or beta-carboline. Still more typically, nitrogen bonded heterocycles include 1- aziridyl, 1-azetedyl, 1-pyrrolyl, 1-imidazolyl, 1-pyrazolyl, and 1-piperidinyl.

"Substituted” as used herein and as applied to any of the above alkyl, alkenyl, alkynyl, aryl, arylalkyl, cycloalkyl, heteroaryl, heterocyclyl, and the like, means that one or more hydrogen atoms are each independently replaced with a substituent. Unless otherwise constrained by the definition of the individual substituent, the foregoing chemical moieties, such as “alkyl”, “alkylene”, “heteroalkyl”, “heteroalkylene”, “alkenyl”, “alkenylene”, “heteroalkenyl”, “heteroalkenylene”, “alkynyl”, “alkynylene”, “heteroalkynyl”, “heteroalkynylene”, “cycloalkyl”, “cycloalkylene”, “heterocyclolalkyl”, heterocycloalkylene”, “aryl,” “arylene”, “heteroaryl”, and “heteroarylene” groups can optionally be substituted. Typical substituents include, but are not limited to, -X, -R, -OH, -OR, -SH, -SR, NH₂, -NHR, - N(R)₂, -N⁺(R)₃, -CX₃, -CN, -OCN, -SON, -NCO, -NCS, -NO, -N0₂, -N_3, -NC(=0)H, -NC(=0)R, -C(=0)H, -C(=0)R, -C(=0)NH₂, -C(=0)N(R)₂, -S0₃-, -S0₃H, -S(=0)₂R, -OS(=0)₂OR, - S(=0)₂NH₂, -S(=0)₂N(R)₂, -S(=0)R, -OP(=0)(OH)₂, -OP(=0)(OR)₂, -P(=0)(OR)₂, -PO₃, - P0₃H₂, -C(=0)X, -C(=S)R, -C0₂H, -C0₂R, -C0₂-, -C(=S)OR, -C(=0)SR, -C(=S)SR, - C(=0)NH_2, -C(=0)N(R)₂, -C(=S)NH₂, -C(=S)N(R)₂, -C(=NH)NH₂, and -C(=NR)N(R)₂; wherein each X is independently selected for each occasion from F, Cl, Br, and I; and each R is independently selected for each occasion from Ci-Ci₂ alkyl, C₆-C₂o aryl, C₃-Ci4 heterocycloalkyl or heteroaryl, protecting group and prodrug moiety. Wherever a group is described as "optionally substituted," that group can be substituted with one or more of the above substituents, independently for each occasion.

It is to be understood that certain radical naming conventions can include either a mono-radical or a di-radical, depending on the context. For example, where a substituent requires two points of attachment to the rest of the molecule, it is understood that the substituent is a di-radical. For example, a substituent identified as alkyl that requires two points of attachment includes di-radicals such as -CH₂-, -CH₂CH₂-, -CH₂CH(CH₃)CH₂-, and the like. Other radical naming conventions clearly indicate that the radical is a di-radical such as "alkylene," "alkenylene," “arylene,” “heterocycloalkylene,” and the like.

Wherever a substituent is depicted as a di-radical (i.e., has two points of attachment to the rest of the molecule), it is to be understood that the substituent can be attached in any directional configuration unless otherwise indicated. "Isomerism" means compounds that have identical molecular formulae but differ in the sequence of bonding of their atoms or in the arrangement of their atoms in space. Isomers that differ in the arrangement of their atoms in space are termed "stereoisomers." Stereoisomers that are not mirror images of one another are termed "diastereoisomers," and stereoisomers that are non-superimposable mirror images of each other are termed "enantiomers," or sometimes "optical isomers."

A carbon atom bonded to four non-identical substituents is termed a "chiral center." "Chiral isomer" means a compound with at least one chiral center. Compounds with more than one chiral center may exist either as an individual diastereomer or as a mixture of diastereomers, termed "diastereomeric mixture." When one chiral center is present, a stereoisomer may be characterized by the absolute configuration (R or S) of that chiral center. Absolute configuration refers to the arrangement in space of the substituents attached to the chiral center. The substituents attached to the chiral center under consideration are ranked in accordance with the Sequence Rule of Cahn, Ingold and Prelog. (Cahn et al., Angew. Chem. Inter. Edit. 1966, 5, 385; errata 511 ; Cahn et al., Angew. Chem. 1966, 78, 413; Cahn and Ingold, J. Chem. Soc. 1951 (London), 612; Cahn et al., Experientia 1956, 12, 81; Cahn, J. Chem. Educ. 1964, 41 , 116). A mixture containing equal amounts of individual enantiomeric forms of opposite chirality is termed a "racemic mixture."

The compounds disclosed in this description and in the claims may comprise one or more asymmetric centers, and different diastereomers and/or enantiomers of each of the compounds may exist. The description of any compound in this description and in the claims is meant to include all enantiomers, diastereomers, and mixtures thereof, unless stated otherwise. In addition, the description of any compound in this description and in the claims is meant to include both the individual enantiomers, as well as any mixture, racemic or otherwise, of the enantiomers, unless stated otherwise. When the structure of a compound is depicted as a specific enantiomer, it is to be understood that the coumponds disclosed herein are not limited to that specific enantiomer. Accordingly, enantiomers, optical isomers, and diastereomers of each of the structural formulae of the present disclosure are contemplated herein. In the present specification, the structural formula of the compound represents a certain isomer for convenience in some cases, but the present disclosure includes all isomers, such as geometrical isomers, optical isomers based on an asymmetrical carbon, stereoisomers, tautomers, and the like, it being understood that not all isomers may have the same level of activity. The compounds may occur in different tautomeric forms. The compounds according to the disclosure are meant to include all tautomeric forms, unless stated otherwise. When the structure of a compound is depicted as a specific tautomer, it is to be understood that the instant disclosure is not limited to that specific tautomer.

The compounds of any formula described herein include the compounds themselves, as well as their salts, and their solvates, if applicable. A salt, for example, can be formed between an anion and a positively charged group (e.g., amino) on a compound of the disclosure. Suitable anions include chloride, bromide, iodide, sulfate, bisulfate, sulfamate, nitrate, phosphate, citrate, methanesulfonate, trifluoroacetate, glutamate, glucuronate, glutarate, malate, maleate, succinate, fumarate, tartrate, tosylate, salicylate, lactate, naphthalenesulfonate, and acetate (e.g., trifluoroacetate). The term "pharmaceutically acceptable anion" refers to an anion suitable for forming a pharmaceutically acceptable salt. Likewise, a salt can also be formed between a cation and a negatively charged group (e.g., carboxylate) on a compound of the disclosure. Suitable cations include sodium ion, potassium ion, magnesium ion, calcium ion, and an ammonium cation such as tetramethylammonium ion. Examples of some suitable substituted ammonium ions are those derived from: ethylamine, diethylamine, dicyclohexylamine, triethylamine, butylamine, ethylenediamine, ethanolamine, diethanolamine, piperazine, benzylamine, phenylbenzylamine, choline, meglumine, and tromethamine, as well as amino acids, such as lysine and arginine. The compounds of the disclosure also include those salts containing quaternary nitrogen atoms.

Examples of suitable inorganic anions include, but are not limited to, those derived from the following inorganic acids: hydrochloric, hydrobromic, hydroiodic, sulfuric, sulfurous, nitric, nitrous, phosphoric, and phosphorous. Examples of suitable organic anions include, but are not limited to, those derived from the following organic acids: 2-acetyoxybenzoic, acetic, ascorbic, aspartic, benzoic, camphorsulfonic, cinnamic, citric, edetic, ethanedisulfonic, ethanesulfonic, fumaric, glucheptonic, gluconic, glutamic, glycolic, hydroxymaleic, hydroxynaphthalene carboxylic, isethionic, lactic, lactobionic, lauric, maleic, malic, methanesulfonic, mucic, oleic, oxalic, palmitic, pamoic, pantothenic, phenylacetic, phenylsulfonic, propionic, pyruvic, salicylic, stearic, succinic, sulfanilic, tartaric, toluenesulfonic, and valeric. Examples of suitable polymeric organic anions include, but are not limited to, those derived from the following polymeric acids: tannic acid, carboxymethyl cellulose.

Additionally, the compounds of the present disclosure, for example, the salts of the compounds, can exist in either hydrated or unhydrated (the anhydrous) form or as solvates with other solvent molecules. Non-limiting examples of hydrates include monohydrates, dihydrates, etc. Non-limiting examples of solvates include ethanol solvates, acetone solvates, etc. "Solvate" means solvent addition forms that contain either stoichiometric or non-stoichiometric amounts of solvent. Some compounds have a tendency to trap a fixed molar ratio of solvent molecules in the crystalline solid state, thus forming a solvate. If the solvent is water the solvate formed is a hydrate; and if the solvent is alcohol, the solvate formed is an alcoholate. Hydrates are formed by the combination of one or more molecules of water with one molecule of the substance in which the water retains its molecular state as H₂0. A hydrate refers to, for example, a mono-hydrate, a di-hydrate, a tri-hydrate, etc.

In addition, a crystal polymorphism may be present for the compounds or salts thereof represented by the formulae disclosed herein. It is noted that any crystal form, crystal form mixture, or anhydride or hydrate thereof, is included in the scope of the present disclosure.

Therapeutic Methods and Compositions

The present disclosure provides methods and compositions for treating a human subject with an antibody drug conjugate (ADC) comprising an anti-CD117 antibody conjugated to a cytotoxin (e.g., an amatoxin). The approach described herein provides for individualized or personalized dosing. A receptor occupancy (RO) assay can be used to determine the amount of the anti-CD117 ADC to be delivered, where an anti-CD117 antibody (or antigen binding fragment thereof) that is the same as the anti-CD117 antibody of the ADC is used as a therapeutic antibody in an RO assay. Alternatively, an antibody or antigen binding fragment that is competitive to the therapeutic antibody can be used in an RO assay to determine receptor saturation for a given concentration of the therapeutic antibody, fragment thereof, or competitive antibody or fragment thereof.

The RO assay can be used to guide dose escalation decisions, allowing the dose to be escalated until target saturation occurs. In other instances, the RO assay can be used to determine a patient’s maximum dose, where the maximum dose is the dose (or antibody concertation) resulting in 100% of receptors being bound. Alternatively, the RO assay and the determined receptor occupancy for a given antibody concertation can be used to confirm that a proposed dose is at or below a saturating dose.

Provided herein is a method for treating a human subject in need thereof, comprising determining CD117 receptor occupancy of a therapeutic anti-CD117 antibody on CD117 expressing cells from the human subject. The method includes performing a receptor occupancy (RO) assay on a sample from the human subject, and determining the percent receptor occupancy of the therapeutic anti-CD117 antibody on CD117 expressing cells from the sample followed by administration to the human subject of an amount of the therapeutic anti-CD117 antibody (or preferably an ADC comprising the therapeutic antibody) that is less than about 10 times, less than about 5 times, less than about 2 times, less than about 1.5 times, less than about 1.2 times, or less than about 1.1 times an amount of the therapeutic anti-CD117 antibody sufficient to result in about 100% CD117 receptor occupancy as determined by the RO assay.

In certain embodiments, the human subject is administered an amount of the therapeutic anti-CD117 antibody (or ADC thereof) that is less than an amount of the therapeutic anti-CD117 antibody (or ADC thereof) sufficient to result in about 100% CD117 receptor occupancy as determined by the RO assay.

In another embodiment, the human subject is administered an amount of the therapeutic anti-CD117 antibody (or ADC thereof) that is less than an amount of the therapeutic anti-CD117 antibody (or ADC thereof) sufficient to result in about 95% CD117 receptor occupancy as determined by the RO assay.

In another embodiment, the human subject is administered an amount of the therapeutic anti-CD117 antibody (or ADC thereof) that is less than an amount of the therapeutic anti-CD117 antibody (or ADC thereof) sufficient to result in about 90% CD117 receptor occupancy as determined by the RO assay.

In another embodiment, the human subject is administered an amount of the therapeutic anti-CD117 antibody (or ADC thereof) that is less than an amount of the therapeutic anti-CD117 antibody (or ADC thereof) sufficient to result in about 85% CD117 receptor occupancy as determined by the RO assay.

In another embodiment, the human subject is administered an amount of the therapeutic anti-CD117 antibody (or ADC thereof) that is less than an amount of the therapeutic anti-CD117 antibody (or ADC thereof) sufficient to result in about 80% CD117 receptor occupancy as determined by the RO assay.

Also disclosed herein is a method for depleting CD117 expressing cells in a human subject where a dose of an anti-CD117 antibody drug conjugate (ADC) comprising an anti- CD117 antibody conjugated to an amatoxin is administered to a human subject in need thereof. The dose is determined by an RO assay using the therapeutic anti-CD117 antibody of the ADC (or a competitive antibody thereof). In some embodiments, the dose is less than about 10 times, less than about 5 times, less than about 2 times, less than about 1.5 times, less than about 1.2 times, or less than about 1.1 times an amount of the therapeutic anti- CD117 antibody sufficient to result in about 100% CD117 receptor occupancy as determined by the RO assay.

In certain embodiments, the dose used for treatment of the human subject in need thereof resulted in at least about 80% receptor occupancy in the RO assay; at least about 85% receptor occupancy in the RO assay; at least about 90% receptor occupancy in the RO assay; at least about 95% receptor occupancy in the RO assay; at least about 99% receptor occupancy in the RO assay, or 100% receptor occupancy in the RO assay.

The methods disclosed herein can be used to condition a human subject with an anti- CD117 ADC where the human subject is undergoing a cell transplant, e.g., a stem cell transplant. The method can further include administering the transplant to the human subject, e.g., once the ADC has substantially cleared. In certain embodiments, the stem cell transplant is an HSC transplant.

In certain embodiments, the methods and compositions disclosed herein are used to treat a human subject having a stem cell disorder.

In addition, the compositions and methods described herein can be used to treat cancers directly, such as cancers characterized by cells that are CD117+. For instance, the compositions and methods described herein can be used to treat leukemia, particularly in patients that exhibit CD117+ leukemic cells. By depleting CD117+ cancerous cells, such as leukemic cells, the compositions and methods described herein can be used to treat various cancers directly. Exemplary cancers that may be treated in this fashion include hematological cancers, such as acute myeloid leukemia, acute lymphoid leukemia, chronic myeloid leukemia, chronic lymphoid leukemia, multiple myeloma, diffuse large B-cell lymphoma, and non-Hodgkin's lymphoma. In certain embodiments, the cancer is a hematological cancer.

Acute myeloid leukemia (AML) is a cancer of the myeloid line of blood cells, characterized by the rapid growth of abnormal white blood cells that build up in the bone marrow and interfere with the production of normal blood cells. AML is the most common acute leukemia affecting adults, and its incidence increases with age. The symptoms of AML are caused by replacement of normal bone marrow with leukemic cells, which causes a drop in red blood cells, platelets, and normal white blood cells. As an acute leukemia, AML progresses rapidly and may be fatal within weeks or months if left untreated. In one embodiment, the anti-CD117 ADCs described herein are used to treat AML in a human patient in need thereof. In certain embodiments the anti-CD117 ADC treatment depletes AML cells in the treated subjects. In some embodiments 50% or more of the AML cells are depleted. In other embodiments, 60% or more of the AML cells are depleted, or 70% or more of the AML cells are depleted, or 80% of more or 90% or more, or 95% or more of the AML cells are depleted.

The cancer may be a hematological cancer, such as leukemia or myelodysplastic syndrome. Examples of leukemia that may be treated using the methods and compositions disclosed herein include, but are not limited to, acute myeloid leukemia, acute lymphoblastic leukemia, or chronic lymphocytic leukemia. In addition, the compositions and methods described herein can be used to treat autoimmune disorders. For instance, an antibody, or antigen-binding fragment thereof, can be administered to a subject, such as a human patient suffering from an autoimmune disorder, so as to kill a CD117+ immune cell. The CD117+ immune cell may be an autoreactive lymphocyte, such as a T-cell that expresses a T-cell receptor that specifically binds, and mounts an immune response against, a self antigen. By depleting self-reactive, CD117+ cells, the compositions and methods described herein can be used to treat autoimmune pathologies, such as those described below. Additionally or alternatively, the compositions and methods described herein can be used to treat an autoimmune disease by depleting a population of endogenous hematopoietic stem cells prior to hematopoietic stem cell transplantation therapy, in which case the transplanted cells can home to a niche created by the endogenous cell depletion step and establish productive hematopoiesis. This, in turn, can re-constitute a population of cells depleted during autoimmune cell eradication.

Autoimmune diseases that can be treated using the compositions and methods described herein include, without limitation, psoriasis, psoriatic arthritis, Type 1 diabetes mellitus (Type 1 diabetes), rheumatoid arthritis (RA), human systemic lupus (SLE), multiple sclerosis (MS), inflammatory bowel disease (IBD), lymphocytic colitis, acute disseminated encephalomyelitis (ADEM), Addison's disease, alopecia universalis, ankylosing spondylitisis, antiphospholipid antibody syndrome (APS), aplastic anemia, autoimmune hemolytic anemia, autoimmune hepatitis, autoimmune inner ear disease (AIED), autoimmune lymphoproliferative syndrome (ALPS), autoimmune oophoritis, Balo disease, Behcet's disease, bullous pemphigoid, cardiomyopathy, Chagas' disease, chronic fatigue immune dysfunction syndrome (CFIDS), chronic inflammatory demyelinating polyneuropathy, Crohn's disease, cicatrical pemphigoid, coeliac sprue-dermatitis herpetiformis, cold agglutinin disease, CREST syndrome, Degos disease, discoid lupus, dysautonomia, endometriosis, essential mixed cryoglobulinemia, fibromyalgia-fibromyositis, Goodpasture's syndrome, Grave's disease, Guillain-Barre syndrome (GBS), Hashimoto's thyroiditis, Hidradenitis suppurativa, idiopathic and/or acute thrombocytopenic purpura, idiopathic pulmonary fibrosis, IgA neuropathy, interstitial cystitis, juvenile arthritis, Kawasaki's disease, lichen planus, Lyme disease, Meniere disease, mixed connective tissue disease (MCTD), myasthenia gravis, neuromyotonia, opsoclonus myoclonus syndrome (OMS), optic neuritis, Ord's thyroiditis, pemphigus vulgaris, pernicious anemia, polychondritis, polymyositis and dermatomyositis, primary biliary cirrhosis, polyarteritis nodosa, polyglandular syndromes, polymyalgia rheumatica, primary agammaglobulinemia, Raynaud phenomenon, Reiter's syndrome, rheumatic fever, sarcoidosis, scleroderma, Sjogren's syndrome, stiff person syndrome, Takayasu's arteritis, temporal arteritis (also known as "giant cell arteritis"), ulcerative colitis, collagenous colitis, uveitis, vasculitis, vitiligo, vulvodynia ("vulvar vestibulitis"), and Wegener's granulomatosis.

Other diseases and conditions that can be treated using the methods disclosed herein are provided in U.S. Patent No. 10,899,843, which is incorporated by reference herein.

In particular, the methods include determining the receptor occupancy for an anti- CD117 antibody (or a competitive antibody thereof) on cells, e.g., hematopoietic stem cells (HSCs) to determine the percentage of available receptors that are bound as a function of drug concentration. Receptor occupancy can be determined using receptor occupancy (RO) assay based on a sample from the human subject.

Note that throughout where the term “sample” is used, assays may be performed on the same sample or material obtained from the same sample. Thus, assays may be performed on a sample, meaning individual assays on material obtained from the same sample or the assay is performed on the same sample. In certain instances, the sample tested in the RO assay is obtained from the same subject who will be treated with the ADC comprising the anti-CD117 therapeutic antibody. In one embodiment, the sample is peripheral blood or bone marrow from the human subject.

A receptor occupancy assay is used to determine binding of a therapeutic antibody of interest. As a substitute of the therapeutic antibody, a competitive antibody may be used in an RO assay, which may bind to the same epitope as the therapeutic antibody or just cross block binding of the therapeutic antibody to the antigen. Thus, in the context of an RO assay, where a therapeutic antibody is referenced, a competitive antibody thereof may be used as an alternative in the assay.

A receptor occupancy assay generally provides a percentage of how many “receptors”, e.g., CD117, are bound by an amount of a compound of interest, e.g., a therapeutic anti-CD117 antibody or a competitive antibody. In the current disclosure, a receptor occupancy assay measures the percentage of CD117 that is bound by an amount of the antibody of interest, e.g., Ab85 which is an anti-CD117 antibody. The percentage of bound CD117 is dependent on the amount of antibody used in the assay. By determining the percentage of bound CD117 for a given amount of antibody, the amount of antibody can be adjusted in order to achieve the desired saturation percentage, e.g., at least about 80% receptor occupancy, at least about 85% receptor occupancy, at least about 90% receptor occupancy, at least about 95% receptor occupancy, at least about 96% receptor occupancy, at least about 97% receptor occupancy, at least about 98% receptor occupancy, at least about 99% receptor occupancy, or 100% receptor occupancy. It should be noted that when referring to a cell in reference to a free receptor assay or free and total receptor assay described herein, the term is intended to include a population of cells. For example, if a cell is contacted with a labelled anti-CD117 antibody, it is intended to also refer to a population of cells being contacted.

The methods disclosed herein are based, at least in part, on the discovery that receptor occupancy and cell surface expression of CD117, including HSCs from human patients in need of a stem cell transplant, are capable of being assessed by RO assays, such as a flow cytometry RO assay. In certain embodiments, the output of the RO assays contemplated herein can be used to select an appropriate dosage of a therapeutic antibody to be administered to a subject.

A flow cytometry receptor occupancy (RO) assay is an in vitro or ex vivo cell assay using flow cytometry to determine the percentage of available receptors on a cell. A flow cytometry RO assay can be used to determine the total number of available receptors on a cell, e.g., a hematopoietic stem cell (HSC) or a leukemic blast cell, from a given subject. In addition, depending on the type of antibody or antibodies used in the assay, the number of receptor sites occupied by an antibody of interest (e.g., therapeutic antibody) vs. the total number of available sites can be determined.

In one embodiment, a receptor occupancy assay is a free receptor occupancy assay, in which unbound (or unoccupied) receptors (e.g., CD117) on a cell are determined by contacting the cell with both the therapeutic antibody of interest and a competitive antibody. One of the two antibodies is labeled with a detectable agent. In a preferred embodiment, the competitive antibody is labeled with a detectable agent. The binding of the unlabeled antibody is then determined by measuring the signal from the detectable agent of the labeled antibody, which provides a means to then calculate the level of unoccupied receptors (e.g., CD117).

In another embodiment, a receptor occupancy assay is a free and total receptor occupancy assay, in which unbound (or unoccupied) receptors (e.g., CD117) on a cell are determined by contacting the cell with the therapeutic antibody of interest, a competitive antibody labeled with a first detectable agent, and a non-competitive antibody labeled with a second detectable agent, whereby the non-competitive antibody is used to determine the total number of receptors, e.g., CD117, on a cell surface. Such an assay measures the binding of a desired therapeutic antibody to its receptor site, e.g., CD117, by subtracting the signal from the second detectable agent (i.e., the non-competitive antibody, which provides the total number of available receptors on a cell) from the signal from the first detectable agent (i.e., the competitive antibody, which provides the number of unbound (or unoccupied) receptors). In this scenario, the non-competing antibody does not compete for binding with the therapeutic antibody of interest (or with the competitive antibody). This information can be useful in determining dosing in patients where the target may have differential expression depending on the patient, e.g., where the receptor level or cell numbers can markedly change (up or down) over time.

The methods disclosed herein can be used to determine dosing of an ADC comprising Ab85 conjugated via a linker to an amatoxin (described in more detail below). As such, there are a number of detection reagents that can be used to in RO assays for determining receptor occupancy of Ab85 (or an antigen binding fragment thereof) which is representative of an anti-CD117 ADC containing the Ab85 antibody. For example, an RO assay may use a labeled Ab85 (or an antigen binding fragment thereof). Such a label may be, for example, a fluorophore. A labeled Ab85 antibody (or an antigen binding fragment thereof) may be used in combination with an unlabeled competitive anti-CD117 antibody (or vice versa regarding labelling; one of the antibodies is labeled). A competitive antibody may, in some embodiments, bind to the same epitope as Ab85. In another embodiment, the therapeutic anti-CD117 antibody, e.g., Ab85, is not labeled but instead is contacted with an anti-idiotype antibody which specifically recognizes the therapeutic anti-CD117 antibody, e.g., Ab85.

In one embodiment, provided herein is a method for determining receptor occupancy of a therapeutic anti-CD117 antibody on CD117 expressing cells from a human subject, said method comprising performing a receptor occupancy (RO) assay on a sample from a human subject, and determining the percent receptor occupancy of the therapeutic anti-CD117 antibody on CD117 expressing cells from the sample.

Generally, the RO assay is used to determine the RO of the therapeutic antibody. In certain aspects to determine the therapeutic antibody RO, the therapeutic antibody is used.

In other embodiments, a surrogate antibody which represents the therapeutic antibody, e.g., an antibody that competes with the therapeutic antibody for antigen binding, is used.

In certain aspects, the method for determining receptor occupancy of a therapeutic anti-CD117 antibody on CD117 expressing cells from a human subject, comprises performing a receptor occupancy (RO) assay on a sample from a human subject, and determining the percent receptor occupancy of the therapeutic anti-CD117 antibody on CD117 expressing cells from the sample, wherein the therapeutic anti-CD117 antibody, e.g., an anitbody comprising a heavy chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 105, 106, and 107, respectively, and comprises a light chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 108, 109, and 110, respectively. The RO assay comprises contacting the sample with the anti-CD117 therapeutic antibody, detecting the amount of the anti-CD117 therapeutic antibody bound to CD117 expressing cells in the sample, and calculating the percentage of CD117 bound by the anti-CD117 therapeutic antibody. In certain embodiments, the RO assay comprises contacting the sample with an amount of a surrogate of the therapeutic antibody, where the surrogate is an antigen binding fragment of the therapeutic antibody, a competitive anti-CD117 antibody that cross blocks the therapeutic antibody, or an antigen-binding fragment of the competitive anti-CD117 antibody, detecting the amount of the surrogate bound to CD117 expressing cells in the sample, calculating the fraction of CD117 bound by the amount of the surrogate, and correlating the fraction of CD117 bound by the amount of the surrogate to an amount of the therapeutic antibody that would result in substantially the same fraction of CD117 being bound by the therapeutic antibody.

In one embodiment, an RO assay comprises contacting a sample from a human subject with the anti-CD117 therapeutic antibody, an antigen binding fragment thereof, a competitive anti-CD117 antibody thereof, or an antigen-binding fragment of the competitive anti-CD117 antibody, and contacting the sample (or an equivalent sample) with a second anti-CD117 antibody, or an antigen-binding fragment thereof, which does not cross block the therapeutic anti-CD117 antibody, wherein the competitive anti-CD117 antibody, or an antigen binding fragment thereof of the competitive anti-CD117 antibody, is labelled with a first detectable agent and the second anti-CD117 antibody, or an antigen-binding fragment thereof, is labeled with a second detectable agent. Inclusion of a second anti-CD117 antibody that does not cross block the therapeutic anti-CD117 antibody may be useful, for example, as a reference in instances where the therapeutic anti-CD117 antibody may at least partially obscure the output of an RO assay. As one non-limiting example, and without wishing to be bound by any theory, a therapeutic anti-CD117 antibody may antagonize CD117 thereby reducing the true number of CD117 molecules in a sample, e.g., by causing cell death or otherwise reducing the number of CD117 molecules on the surface of the cell.

A second anti-CD117 antibody that does not cross block the therapeutic anti-CD117 antibody may provide a reference for the RO assay to control for any loss of CD117 in the sample due to the therapeutic anti-CD117 antibody. In another embodiment, second anti- CD117 antibody that does not cross block the therapeutic anti-CD117 antibody may be useful, for example, for determining the total number of CD117 on a cell in the sample.

In one embodiment, an RO assay comprises contacting a sample from a human subject with a) the anti-CD117 therapeutic antibody, an antigen binding fragment thereof, the competitive anti-CD117 antibody, or an antigen binding fragment thereof, and b) a second antibody, or an antigen-binding fragment thereof, which is labelled and specifically binds to the therapeutic anti-CD117 antibody an antigen binding fragment thereof, the competitive anti-CD117 antibody, or an antigen binding fragment thereof. The sample is then contacted with a third anti-CD117 antibody, or an antigen-binding fragment thereof, which does not compete with the therapeutic anti-CD117 antibody for binding to human CD117, where the second antibody, or antigen-binding fragment thereof, does not cross react with the third anti-CD117 antibody, or an antigen-binding fragment thereof, and where the second anti- CD117 antibody, or antigen binding fragment thereof, is labelled with a first detectable agent and the third antibody, or an antigen-binding fragment thereof, is labeled with a second detectable agent.

In one embodiment, an RO assay comprises contacting a sample from a human subject with a) the therapeutic anti-CD117 antibody, an antigen binding fragment thereof, b) a second anti-CD117 antibody, or an antigen-binding fragment thereof, which is labelled with a first detectable agent and competes with the therapeutic anti-CD117 antibody for binding to human CD117, and c) a third anti-CD117 antibody, or an antigen-binding fragment thereof, which is labelled with a second detectable agent and does not compete with the therapeutic anti- CD117 antibody for binding to human CD117.

In one embodiment, an RO assay comprises contacting a sample from a human subject with a) the therapeutic anti-CD117 antibody, an antigen binding fragment thereof, the competitive anti-CD117 antibody, or an antigen binding fragment thereof, b) a second anti-CD117 antibody, or an antigen-binding fragment thereof, which is labelled with a first detectable agent and does not compete with the therapeutic anti- CD117 antibody for binding to human CD117, and c) a third antibody, or an antigen-binding fragment thereof, which is labeled with a second detectable agent and specifically binds to the therapeutic anti-CD117 antibody, an antigen binding fragment thereof, the competitive anti-CD117 antibody, or an antigen binding fragment thereof, and the second anti-CD117 antibody.

Any suitable detectable agent can be used in the RO assays described herein. In certain embodiments, the detectable agent is selected from the group consisting of a fluorescent label, a luminescent label, a bioluminescent label, a magnetic label, a radiolabel, and an enzyme. In one particular embodiment, the detectable agent is a fluorescent label (i.e., a fluorophore). In situations where two detectable agents are used to determine occupancy, different signals (e.g., different fluorophores) can be used to distinguish the variables. For example, a first detectable agent may be a first fluorophore, and a second detectable agent may be a second fluorophore which is detected at a different emission wavelength than the first detectable agent. Exemplary embodiments of fluorophores include, but are not limited to, phycoerythrin (PE), allophycocyanin (APC), BD Horizon Brilliant™ Violet 421 (BV421), BD Horizon Brilliant™ Violet 510 (BV510), BD Horizon Brilliant™ Violet 785 (BV785), fluorescein (FITC), PerCP-Cy5.5, and Alexa Fluor® 647 (AF647). In certain embodiments, the phycoerythrin is phycoerythrin (PE)-Dazzle 594, PE/Cy5, PE/Cy5.5 or PE/Cy7. In certain embodiments, the phycoerythrin is allophycocyanin is allophycocyanin- Cy7.

Receptor occupancy generally can be determined by measuring a signal from the first detectable agent, measuring a signal from the second detectable agent, and comparing the signals in order to determine the percent receptor occupancy.

In one embodiment, the percentage of therapeutic anti-CD117 antibody bound to CD117 expressing cells, as well as, or alternatively, mean fluorescent intensity (MFI) of bound antibody, will be quantified by a flow cytometry-based receptor occupancy assay. This assay can be performed on whole blood, peripheral blood and /or bone marrow aspirates. The receptor occupancy assay provides data to determine the amount and/or type of CD117 expressing cells that the therpaetuic antibody (or competitive antibody thereof) is interacting with. In certain embodiments, samples from a human subject suffering from a disease or disorder which is treatable with an HSC transplant are taken prior to treatment with the anti- CD117 ADC to determine an appropriate dose to achieve a level of receptor occupancy in the human subject. In other embodiments, samples from a human subject (e.g., a leukemic patient) are taken to determine the amount of CD117 expressed on a cell surface in order to determine an appropriate dose to achieve a level of receptor occupancy in the human subject. In certain other embodiments, samples from a human subject suffering from a disease or disorder which is treatable with an HSC transplant are taken after treatment with the anti-CD117 ADC to determine an appropriate dose to achieve a level of receptor occupancy in the human subject.

Anti-CD117 Antibodies

Amino acid sequences of anti-CD117 antibodies that can be used both in the RO assays described herein and in the therapeutic compositions described herein are described in U.S. Patent No. 10,899,843, which is incorporated by reference herein. The sequence tables provided herein (Tables 1 and 2) also describes amino acid sequences for anti- CD117 antibodies that can be used in the compositions and methods disclosed herein.

In one embodiment, an anti-CD117 antibody, or antigen binding fragment thereof, comprises a heavy chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 105, 106, and 107, respectively, and comprises a light chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 108, 109, and 110, respectively. In one embodiment, an anti-CD117 antibody, or antigen binding fragment thereof, comprises a light chain variable region comprising the amino acid sequence set forth as SEQ ID NO: 104, and a heavy chain variable region comprising the amino acid sequence set forth as SEQ ID NO: 103.

The heavy chain variable region (VH) amino acid sequence of Ab85 is provided below as SEQ ID NO: 103. The VH CDR amino acid sequences of Ab85 are underlined below and are as follows: NYWIG (VH CDR1 ; SEQ ID NO: 105); IINPRDSDTRYRPSFQG (VH CDR2; SEQ ID NO: 106); and HGRGYEGYEGAFDI (VH CDR3; SEQ ID NO: 107).

Ab85 VH sequence

EVQLVQSGAEVKKPGESLKISCKGSGYSFTNYWIGWVRQMPGKGLEWMAIINPRDSDTRY RPSFQGQVTISADKSISTAYLQWSSLKASDTAMYYCARHGRGYEGYEGAFDIWGQGTLVT VSS (SEQ ID NO: 103)

The light chain variable region (VL) amino acid sequence of Ab85 is provided below as SEQ ID NO: 104. The VL CDR amino acid sequences of Ab85 are underlined below and are as follows: RSSQGIRSDLG (VL CDR1 ; SEQ ID NO: 108); DASNLET (VL CDR2; SEQ ID NO: 109); and QQANGFPLT (VL CDR3; SEQ ID NO: 110).

Ab85 VL sequence

DIQMTQSPSSLSASVGDRVTITCRSSQGIRSDLGWYQQKPGKAPKLLIYDASNLETGVPSR FSGSGSGTDFTLTISSLQPEDFATYYCQQANGFPLTFGGGTKVEIK (SEQ ID NO: 104)

In one embodiment, an anti-CD117 antibody, or antigen binding fragment thereof, comprises a heavy chain having the amino acid sequence as set forth as SEQ ID NO: 130, and a light chain having an amino acid sequence set forth as SEQ ID NO: 144.

In certain embodiments, an anti-CD117 antibody is an lgG1 isotype. The anti-CD117 antibody comprising any of the sequences set forth in the Sequence Tables 1-2 can be an intact antibody and/or an lgG1 or an lgG4 isotype.

In one embodiment, the anti-CD117 antibody, or binding fragment thereof, comprises a variant Fc region, wherein said variant Fc region comprises at least one amino acid modification relative to a wild-type Fc region, such that said molecule has an altered affinity for an FcgammaR. Certain amino acid positions within the Fc region are known through crystallography studies to make a direct contact with FcyR. Specifically, amino acids 234- 239 (hinge region), amino acids 265-269 (B/C loop), amino acids 297-299 (C'/E loop), and amino acids 327-332 (F/G) loop (see Sondermann et al., 2000 Nature, 406: 267-273). For example, amino acid substitutions at amino acid positions 234 and 235 of the Fc region have been identified as decreasing affinity of an IgG antibody for binding to an Fc receptor, particularly an Fc gamma receptor (FcyR). In one embodiment, an anti-CD117 antibody described herein comprises an Fc region comprising an amino acid substituion at L234 and/or L235, e.g., L234A and L235A (EU index). Thus, the anti-CD117 antibodies described herein may comprise variant Fc regions comprising modification of at least one residue that makes a direct contact with an FcyR based on structural and crystallographic analysis. In one embodiment, the Fc region of the anti-CD117 antibody (or Fc containing fragment thereof) comprises an amino acid substitution at amino acid 265 according to the EU index as in Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, NH1 , MD (1991), expressly incorporated herein by references. The "EU index as in Kabat" or “EU index” refers to the numbering of the human lgG1 EU antibody and is used herein in reference to Fc amino acid positions unless otherwise indicated.

In one embodiment, the Fc region comprises a D265A mutation. In one embodiment, the Fc region comprises a D265C mutation.

In some embodiments, the Fc region of the anti-CD117 antibody (or fragment thereof) comprises an amino acid substitution at amino acid 234 according to the EU index as in Kabat. In one embodiment, the Fc region comprises a L234A mutation. In some embodiments, the Fc region of the anti-CD117 antibody (or fragment thereof) comprises an amino acid substitution at amino acid 235 according to the EU index as in Kabat. In one embodiment, the Fc region comprises a L235A mutation. In yet another embodiment, the Fc region comprises a L234A and L235A mutation. In a further embodiment, the Fc region comprises a D265C, L234A, and L235A mutation.

In certain aspects a variant IgG Fc domain comprises one or more amino acid substitutions resulting in decreased or ablated binding affinity for an FcgammaR and/or C1q as compared to the wild type Fc domain not comprising the one or more amino acid substitutions. Fc binding interactions are essential for a variety of effector functions and downstream signaling events including, but not limited to, antibody dependent cell-mediated cytotoxicity (ADCC) and complement dependent cytotoxicity (CDC). Accordingly, in certain aspects, an antibody comprising a modified Fc region (e.g., comprising a L234A, L235A, and a D265C mutation) has substantially reduced or abolished effector functions.

Affinity to an Fc region can be determined using a variety of techniques known in the art, for example but not limited to, equilibrium methods (e.g., enzyme-linked immunoabsorbent assay (ELISA); KinExA, Rathanaswami et al. Analytical Biochemistry, Vol. 373:52-60, 2008; or radioimmunoassay (RIA)), or by a surface plasmon resonance assay or other mechanism of kinetics-based assay (e.g., BIACORE™ analysis or Octet™ analysis (forteBIO)), and other methods such as indirect binding assays, competitive binding assays fluorescence resonance energy transfer (FRET), gel electrophoresis and chromatography (e.g., gel filtration). These and other methods may utilize a label on one or more of the components being examined and/or employ a variety of detection methods including but not limited to chromogenic, fluorescent, luminescent, or isotopic labels. A detailed description of binding affinities and kinetics can be found in Paul, W. E., ed., Fundamental Immunology,

4th Ed., Lippincott-Raven, Philadelphia (1999), which focuses on antibody-immunogen interactions. One example of a competitive binding assay is a radioimmunoassay comprising the incubation of labeled antigen with the antibody of interest in the presence of increasing amounts of unlabeled antigen, and the detection of the antibody bound to the labeled antigen. The affinity of the antibody of interest for a particular antigen and the binding off- rates can be determined from the data by scatchard plot analysis. Competition with a second antibody can also be determined using radioimmunoassays. In this case, the antigen is incubated with antibody of interest conjugated to a labeled compound in the presence of increasing amounts of an unlabeled second antibody.

In one embodiment, an anti-CD117 antibody described herein comprises an Fc region comprising L235A, L235A, and D265C (EU index). The antibodies of the invention may be further engineered to further modulate antibody half-life by introducing additional Fc mutations, such as those described for example in (Dall'Acqua et al. (2006) J Biol Chem 281: 23514-24), (Zalevsky et al. (2010) Nat Biotechnol 28: 157-9), (Hinton et al. (2004) J Biol Chem 279: 6213-6), (Hinton et al. (2006) J Immunol 176: 346-56), (Shields et al. (2001 ) J Biol Chem 276: 6591-604), (Petkova et al. (2006) Int Immunol 18: 1759-69), (Datta-Mannan et al. (2007) Drug Metab Dispos 35: 86-94), (Vaccaro et al. (2005) Nat Biotechnol 23: 1283- 8), (Yeung et al. (2010) Cancer Res 70: 3269-77) and (Kim et al. (1999) Eur J Immunol 29: 2819-25), and include positions 250, 252, 253, 254, 256, 257, 307, 376, 380, 428, 434 and 435. Exemplary mutations that may be made singularly or in combination are T250Q,

M252Y, 1253A, S254T, T256E, P2571, T307A, D376V, E380A, M428L, H433K, N434S, N434A, N434H, N434F, H435A and H435R mutations.

Thus, in one embodiment, the Fc region comprises a mutation resulting in a decrease in half life. An antibody having a short half-life may be advantageous in certain instances where the antibody is expected to function as a short-lived therapeutic, e.g., the conditioning step described herein where the antibody is administered followed by HSCs. Ideally, the antibody would be substantially cleared prior to delivery of the HSCs, which also generally express CD117 but are not the target of the anti-CD117 antibody, unlike the endogenous stem cells. In one embodiment, the Fc region comprises a mutation at position 435 (EU index according to Kabat). In one embodiment, the mutation is an H435A mutation. In one embodiment, the anti-CD117 antibody described herein has a half-life of equal to or less than 24 hours, equal to or less than 22 hours, equal to or less than 20 hours, equal to or less than 18 hours, equal to or less than 16 hours, equal to or less than 14 hours, equal to or less than 13 hours, equal to or less than 12 hours, or equal to or less than 11 hours. In one embodiment, the half-life of the antibody is 11 hours to 24 hours; 12 hours to 22 hours;

10 hours to 20 hours; 8 hours to 18 hours; or 14 hours to 24 hours

Antibodies may be produced using recombinant methods and compositions, e.g., as described in U.S. Pat. No. 4,816,567. In one embodiment, isolated nucleic acid encoding an anti-CD117 antibody described herein is provided. Such nucleic acid may encode an amino acid sequence comprising the VL and/or an amino acid sequence comprising the VH of the antibody (e.g., the light and/or heavy chains of the antibody). In a further embodiment, one or more vectors (e.g., expression vectors) comprising such nucleic acid are provided. In a further embodiment, a host cell comprising such nucleic acid is provided. In one such embodiment, a host cell comprises (e.g., has been transformed with): (1) a vector comprising a nucleic acid that encodes an amino acid sequence comprising the VL of the antibody and an amino acid sequence comprising the VH of the antibody, or (2) a first vector comprising a nucleic acid that encodes an amino acid sequence comprising the VL of the antibody and a second vector comprising a nucleic acid that encodes an amino acid sequence comprising the VH of the antibody. In one embodiment, the host cell is eukaryotic, e.g. a Chinese Hamster Ovary (CHO) cell or lymphoid cell (e.g., Y0, NS0, Sp20 cell). In one embodiment, a method of making an anti-CLL-1 antibody is provided, wherein the method comprises culturing a host cell comprising a nucleic acid encoding the antibody, as provided above, under conditions suitable for expression of the antibody, and optionally recovering the antibody from the host cell (or host cell culture medium).

For recombinant production of an anti-CD117 antibody, nucleic acid encoding an antibody, e.g., as described above, is isolated and inserted into one or more vectors for further cloning and/or expression in a host cell. Such nucleic acid may be readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of the antibody).

Suitable host cells for cloning or expression of antibody-encoding vectors include prokaryotic or eukaryotic cells described herein. For example, antibodies may be produced in bacteria, in particular when glycosylation and Fc effector function are not needed. For expression of antibody fragments and polypeptides in bacteria, see, e.g., U.S. Pat. Nos. 5,648,237, 5,789,199, and 5,840,523. (See also Charlton, Methods in Molecular Biology,

Vol. 248 (B.K.C. Lo, ed., Humana Press, Totowa, N.J., 2003), pp. 245-254, describing expression of antibody fragments in E. coli.) After expression, the antibody may be isolated from the bacterial cell paste in a soluble fraction and can be further purified.

Vertebrate cells may also be used as hosts. For example, mammalian cell lines that are adapted to grow in suspension may be useful. Other examples of useful mammalian host cell lines are monkey kidney CV1 line transformed by SV40 (COS-7); human embryonic kidney line (293 or 293 cells as described, e.g., in Graham et al., J. Gen Virol. 36:59 (1977)); baby hamster kidney cells (BHK); mouse sertoli cells (TM4 cells as described, e.g., in Mather, Biol. Reprod. 23:243-251 (1980)); monkey kidney cells (CV1); African green monkey kidney cells (VERO-76); human cervical carcinoma cells (HELA); canine kidney cells (MDCK; buffalo rat liver cells (BRL 3A); human lung cells (W138); human liver cells (Hep G2); mouse mammary tumor (MMT 060562); TRI cells, as described, e.g., in Mather et al., Annals N.Y. Acad. Sci. 383:44-68 (1982); MRC 5 cells; and FS4 cells. Other useful mammalian host cell lines include Chinese hamster ovary (CHO) cells, including DHFR- CHO cells (Urlaub et al., Proc. Natl. Acad. Sci. USA 77:4216 (1980)); and myeloma cell lines such as Y0, NS0 and Sp2/0. For a review of certain mammalian host cell lines suitable for antibody production, see, e.g., Yazaki and Wu, Methods in Molecular Biology, Vol. 248 (B. K. C. Lo, ed., Humana Press, Totowa, N.J.), pp. 255-268 (2003).

In one embodiment, the anti-CD117 antibody, or antigen binding fragment thereof, comprises variable regions having an amino acid sequence that is at least 95%, 96%, 97% or 99% identical to the SEQ ID Nos disclosed herein. Alternatively, the anti-CD117 antibody, or antigen binding fragment thereof, comprises CDRs comprising the SEQ ID Nos disclosed herein with framework regions of the variable regions described herein having an amino acid sequence that is at least 95%, 96%, 97% or 99% identical to the SEQ ID Nos disclosed herein in any of Tables land 2.

In one embodiment, the anti-CD117 antibody, or antigen binding fragment thereof, comprises a heavy chain variable region and a heavy chain constant region having an amino acid sequence that is disclosed herein (e.g., Tables 1 or 2). In another embodiment, the anti- CD117 antibody, or antigen binding fragment thereof, comprises a light chain variable region and a light chain constant region having an amino acid sequence that is disclosed herein (e.g., Tables 1or 2). In yet another embodiment, the anti-CD117 antibody, or antigen binding fragment thereof, comprises a heavy chain variable region, a light chain variable region, a heavy chain constant region and a light chain constant region having an amino acid sequence that is disclosed herein (e.g., Tables 1 and 2). TABLE 1 : ANTI-CD117 ANTIBODY SEQUENCES AND ANTIBODY CONSTANT REGION SEQUENCES

TABLE 2: ANTI-CD117 ANTIBODY SEQUENCES

AND ANTIBODY CONSTANT SEQUENCES

Anti-CD117 ADCs

Anti-CD117 antibodies, and antigen-binding fragments thereof, described herein in Tabels 1 and 2, e.g., Ab85, can be conjugated (linked) to a cytotoxin. In some embodiments, the cytotoxic molecule is conjugated to a cell internalizing anti-CD117 antibody, or antigen-binding fragment thereof as disclosed herein such that following the cellular uptake of the antibody, or fragment thereof, the cytotoxin may access its intracellular target and mediate hematopoietic cell death. An example of such an antibody is Ab85. Various cytotoxins can be conjugated to an anti-CD117 antibody or antigen-binding fragment thereof via a linker for use in the therapies described herein. As used herein, the terms "cytotoxin", "cytotoxic moiety", and "drug" are used interchangeably.

ADCs of the present invention therefore may be of the general formula Ab-(Z-L-D)_n, wherein an anti-CD117 antibody or antigen-binding fragment thereof (Ab) is conjugated (covalently linked) to a linker (L), and through a chemical moiety (Z), to a cytotoxic moiety (“drug,” D).

Accordingly, the anti-CD117 antibody or antigen-binding fragment thereof may be conjugated to a number of drug moieties as indicated by integer n, which represents the average number of cytotoxins per antibody. Any number of cytotoxins can be conjugated to the antibody, e.g., about 1 , about 2, about 3, about 4, about 5, about 6, about 7, or about 8.

In some embodiments, n is from 1 to 4. In some embodiments, n is from 1 to 3. In some embodiments, n is about 2. In some embodiments, n is about 1. The average number of drug moieties per antibody in preparations of ADC from conjugation reactions may be characterized by conventional means such as mass spectroscopy, ELISA assay, and HPLC. The quantitative distribution of ADC in terms of n may also be determined. In some instances, separation, purification, and characterization of homogeneous ADC where n is a certain value from ADC with other drug loadings may be achieved by means such as reverse phase HPLC or electrophoresis.

For some anti-CD117 ADCs, n may be limited by the number of attachment sites on the antibody. For example, where the attachment is a cysteine thiol, an antibody may have only one or several cysteine thiol groups, or may have only one or several sufficiently reactive thiol groups through which a linker may be attached. Generally, antibodies do not contain many free and reactive cysteine thiol groups which may be linked to a drug moiety; primarily, cysteine thiol residues in antibodies exist as disulfide bridges. In certain embodiments, an antibody may be reduced with a reducing agent such as dithiothreitol (DTT) or tricarbonylethylphosphine (TCEP), under partial or total reducing conditions, to generate reactive cysteine thiol groups. In certain embodiments, higher drug loading, e.g. n>5, may cause aggregation, insolubility, toxicity, or loss of cellular permeability of certain antibody-drug conjugates.

In certain embodiments, fewer than the theoretical maximum number of drug moieties are conjugated to an antibody during a conjugation reaction. An antibody may contain, for example, lysine residues that do not react with the drug-linker intermediate or linker reagent, as discussed below. Only the most reactive lysine groups may react with an amine-reactive linker reagent. In certain embodiments, an antibody is subjected to denaturing conditions to reveal reactive nucleophilic groups such as lysine or cysteine.

The loading (drug/antibody ratio) of an ADC may be controlled in different ways, e.g., by: (i) limiting the molar excess of drug-linker intermediate or linker reagent relative to antibody, (ii) limiting the conjugation reaction time or temperature, (iii) partial or limiting reductive conditions for cysteine thiol modification, (iv) engineering by recombinant techniques the amino acid sequence of the antibody such that the number and position of cysteine residues is modified for control of the number and/or position of linker-drug attachments. Cytotoxins

Cytotoxins suitable for use with the compositions and methods described herein include DNA-intercalating agents, (e.g., anthracyclines), agents capable of disrupting the mitotic spindle apparatus (e.g., vinca alkaloids, maytansine, maytansinoids, and derivatives thereof), RNA polymerase inhibitors (e.g., an amatoxin, such as a-amanitin, and derivatives thereof), and agents capable of disrupting protein biosynthesis (e.g., agents that exhibit rRNA N-glycosidase activity, such as saporin and ricin A-chain), among others known in the art.

In some embodiments, the cytotoxin is a microtubule-binding agent (for instance, maytansine or a maytansinoid), an amatoxin, pseudomonas exotoxin A, deBouganin, diphtheria toxin, saporin, an auristatin, an anthracycline, a calicheamicin, irinotecan, SN-38, a duocarmycin, a pyrrolobenzodiazepine, a pyrrolobenzodiazepine dimer, an indolinobenzodiazepine, an indolinobenzodiazepine dimer, or a variant thereof, or another cytotoxic compound described herein or known in the art.

Additional cytotoxins suitable for use with the compositions and methods described herein include, without limitation, 5-ethynyluracil, abiraterone, acylfulvene, adecypenol, adozelesin, aldesleukin, altretamine, ambamustine, amidox, amifostine, aminolevulinic acid, amrubicin, amsacrine, anagrelide, anastrozole, andrographolide, angiogenesis inhibitors, antarelix, anti-dorsalizing morphogenetic protein-1, antiandrogen, prostatic carcinoma, antiestrogen, antineoplaston, antisense oligonucleotides, aphidicolin glycinate, apoptosis gene modulators, apoptosis regulators, apurinic acid, asulacrine, atamestane, atrimustine, axinastatin 1, axinastatin 2, axinastatin 3, azasetron, azatoxin, azatyrosine, baccatin III derivatives, balanol, batimastat, BCR/ABL antagonists, benzochlorins, benzoylstaurosporine, beta lactam derivatives, beta-alethine, betaclamycin B, betulinic acid, bFGF inhibitors, bicalutamide, bisantrene, bisaziridinylspermine, bisnafide, bistratene A, bizelesin, breflate, bleomycin A2, bleomycin B2, bropirimine, budotitane, buthionine sulfoximine, calcipotriol, calphostin C, camptothecin derivatives (e.g., 10-hydroxy-camptothecin), capecitabine, carboxamide-amino-triazole, carboxyamidotriazole, carzelesin, casein kinase inhibitors, castanospermine, cecropin B, cetrorelix, chlorins, chloroquinoxaline sulfonamide, cicaprost, cis-porphyrin, cladribine, clomifene and analogues thereof, clotrimazole, collismycin A, collismycin B, combretastatin A4, combretastatin analogues, conagenin, crambescidin 816, crisnatol, cryptophycin 8, cryptophycin A derivatives, curacin A, cyclopentanthraquinones, cycloplatam, cypemycin, cytarabine ocfosfate, cytolytic factor, cytostatin, dacliximab, decitabine, dehydrodidemnin B, 2'deoxycoformycin (DCF), deslorelin, dexifosfamide, dexrazoxane, dexverapamil, diaziquone, didemnin B, didox, diethylnorspermine, dihydro-5-azacytidine, dihydrotaxol, dioxamycin, diphenyl spiromustine, discodermolide, docosanol, dolasetron, doxifluridine, droloxifene, dronabinol, duocarmycin SA, ebselen, ecomustine, edelfosine, edrecolomab, eflornithine, elemene, emitefur, epothilones, epithilones, epristeride, estramustine and analogues thereof, etoposide, etoposide 4'-phosphate (also referred to as etopofos), exemestane, fadrozole, fazarabine, fenretinide, filgrastim, finasteride, flavopiridol, flezelastine, fluasterone, fludarabine, fluorodaunorunicin hydrochloride, forfenimex, formestane, fostriecin, fotemustine, gadolinium texaphyrin, gallium nitrate, galocitabine, ganirelix, gelatinase inhibitors, gemcitabine, glutathione inhibitors, hepsulfam, homoharringtonine (HHT), hypericin, ibandronic acid, idoxifene, idramantone, ilmofosine, ilomastat, imidazoacridones, imiquimod, immunostimulant peptides, iobenguane, iododoxorubicin, ipomeanol, irinotecan, iroplact, irsogladine, isobengazole, jasplakinolide, kahalalide F, lamellarin-N triacetate, lanreotide, leinamycin, lenograstim, lentinan sulfate, leptolstatin, letrozole, lipophilic platinum compounds, lissoclinamide 7, lobaplatin, lometrexol, lonidamine, losoxantrone, loxoribine, lurtotecan, lutetium texaphyrin, lysofylline, masoprocol, maspin, matrix metalloproteinase inhibitors, menogaril, rnerbarone, meterelin, methioninase, metoclopramide, MIF inhibitor, ifepristone, miltefosine, mirimostim, mithracin, mitoguazone, mitolactol, mitomycin and analogues thereof, mitonafide, mitoxantrone, mofarotene, molgramostim, mycaperoxide B, myriaporone, N-acetyldinaline, N-substituted benzamides, nafarelin, nagrestip, napavin, naphterpin, nartograstim, nedaplatin, nemorubicin, neridronic acid, nilutamide, nisamycin, nitrullyn, octreotide, okicenone, onapristone, ondansetron, oracin, ormaplatin, oxaliplatin, oxaunomycin, paclitaxel and analogues thereof, palauamine, palmitoylrhizoxin, pamidronic acid, panaxytriol, panomifene, parabactin, pazelliptine, pegaspargase, peldesine, pentosan polysulfate sodium, pentostatin, pentrozole, perflubron, perfosfamide, phenazinomycin, picibanil, pirarubicin, piritrexim, podophyllotoxin, porfiromycin, purine nucleoside phosphorylase inhibitors, raltitrexed, rhizoxin, rogletimide, rohitukine, rubiginone B1, ruboxyl, safingol, saintopin, sarcophytol A, sargramostim, sobuzoxane, sonermin, sparfosic acid, spicamycin D, spiromustine, stipiamide, sulfinosine, tallimustine, tegafur, temozolomide, teniposide, thaliblastine, thiocoraline, tirapazamine, topotecan, topsentin, triciribine, trimetrexate, veramine, vinorelbine, vinxaltine, vorozole, zeniplatin, and zilascorb, among others.

Anti-CD117 antibodies, and antigen-binding fragments thereof, described herein can be conjugated to a cytotoxin that is a microtubule binding agent. As used herein, the term “microtubule-binding agent” refers to a compound which acts by disrupting the microtubular network that is essential for mitotic and interphase cellular function in a cell. Examples of microtubule-binding agents include, but are not limited to, maytasine, maytansinoids, and derivatives thereof, such as those described herein or known in the art, vinca alkaloids, such as vinblastine, vinblastine sulfate, vincristine, vincristine sulfate, vindesine, and vinorelbine, taxanes, such as docetaxel and paclitaxel, macrolides, such as discodermolides, cochicine, and epothilones, and derivatives thereof, such as epothilone B or a derivative thereof.

Maytansinoids

In some embodiments, the microtubule binding agent is a maytansine, a maytansinoid or a maytansinoid analog. Maytansinoids are mitototic inhibitors which bind microtubules and act by inhibiting tubulin polymerization. Maytansine was first isolated from the east African shrub Maytenus serrata (U.S. Pat. No. 3,896,111). Subsequently, it was discovered that certain microbes also produce maytansinoids, such as maytansinol and C-3 maytansinol esters (U.S. Pat. No. 4,151,042). Synthetic maytansinol and derivatives and analogues thereof are disclosed, for example, in U.S. Pat. Nos. 4,137,230; 4,248,870; 4,256,746; 4,260,608; 4,265,814; 4,294,757; 4,307,016; 4,308,268; 4,308,269; 4,309,428; 4,313,946; 4,315,929;

4,317,821 ; 4,322,348; 4,331 ,598; 4,361 ,650; 4,364,866; 4,424,219; 4,450,254; 4,362,663; and 4,371 ,533. Maytansinoid drug moieties are attractive drug moieties in antibody drug conjugates because they are: (i) relatively accessible to prepare by fermentation or chemical modification, derivatization of fermentation products, (ii) amenable to derivatization with functional groups suitable for conjugation through the non-disulfide linkers to antibodies, (iii) stable in plasma, and (iv) effective against a variety of tumor cell lines.

Examples of suitable maytansinoids include esters of maytansinol, synthetic maytansinol, and maytansinol analogs and derivatives. Included herein are any cytotoxins that inhibit microtubule formation and that are highly toxic to mammalian cells, as are maytansinoids, maytansinol, and maytansinol analogs, and derivatives.

Examples of suitable maytansinol esters include those having a modified aromatic ring and those having modifications at other positions. Such suitable maytansinoids are disclosed in U.S. Pat. Nos. 4,137,230; 4,151 ,042; 4,248,870; 4,256,746; 4,260,608; 4,265,814; 4,294,757 4,307,016; 4,308,268; 4,308,269; 4,309,428; 4,313,946; 4,315,929; 4,317,821 ; 4,322,348 4,331 ,598; 4,361 ,650; 4,362,663; 4,364,866; 4,424,219 ;4, 450, 254; 4,322,348; 4,362,663 4,371 ,533; 5,208,020; 5,416,064; 5,475,092; 5,585,499; 5,846,545; 6,333,410; 7,276,497; and 7,473,796, the disclosures of each of which are incorporated herein by reference as they pertain

In some embodiments, the immunoconjugates of the invention utilize the thiol- containing maytansinoid (DM1), formally termed N²'-deacetyl-N²'-(3-mercapto-1-oxopropyl)- maytansine, as the cytotoxic agent. DM1 is represented by the structural formula (V):

In another embodiment, the conjugates of the present invention utilize the thiol- containing maytansinoid N²'-deacetyl-N²'(4-methyl-4-mercapto-1 -oxopentyl)-maytansine (e.g., DM4) as the cytotoxic agent. DM4 is represented by the structural formula (VI):

Another maytansinoid comprising a side chain that contains a sterically hindered thiol bond is N²'-deacetyl-N-²'(4-mercapto-1-oxopentyl)-maytansine (termed DM3), represented by the structural formula (VII):

Each of the maytansinoids taught in U.S. Pat. Nos. 5,208,020 and 7,276,497, can also be used in the conjugate of the present invention. In this regard, the entire disclosure of 5,208,020 and 7,276,697 is incorporated herein by reference. Many positions on maytansinoids can serve as the position to chemically link the linking moiety. For example, the C-3 position having a hydroxyl group, the C-14 position modified with hydroxymethyl, the C-15 position modified with hydroxy and the C-20 position having a hydroxy group are all expected to be useful. In some embodiments, the C-3 position serves as the position to chemically link the linking moiety, and in some particular embodiments, the C-3 position of maytansinol serves as the position to chemically link the linking moiety. There are many linking groups known in the art for making antibody- maytansinoid conjugates, including, for example, those disclosed in U.S. Pat. Nos. 5,208,020, 6,441,163, and EP Patent No. 0425235 B1 ; Chari et al., Cancer Research 52:127-131 (1992); and U.S. 2005/0169933 A1, the disclosures of which are hereby expressly incorporated by reference. Additional linking groups are described and exemplified herein.

The present disclosure also includes various isomers and mixtures of maytansinoids and conjugates. Certain compounds and conjugates of the present invention may exist in various stereoisomeric, enantiomeric, and diastereomeric forms. Several descriptions for producing such antibody-maytansinoid conjugates are provided in U.S. Pat. Nos. 5,208,020, 5,416,0646,333,410, 6,441,163, 6,716,821, and 7,368,565, each of which is incorporated herein in its entirety.

A therapeutically effective number of maytansinoid molecules bound per antibody molecule can be determined by measuring spectrophotometrically the ratio of the absorbance at 252 nm and 280 nm. An average of 3 to 4 maytansinoid molecules conjugated per antibody molecule can enhancing cytotoxicity of target cells without negatively affecting the function or solubility of the antibody, although one molecule of toxin/antibody can enhance cytotoxicity over antibody alone. The average number of maytansinoid molecules/antibody or antigen binding fragment thereof can be, for example, 1-10 or 2-5.

Anthracyclines

In other embodiments, the antibodies and antigen-binding fragments thereof described herein can be conjugated to a cytotoxin that is an anthracycline molecule. Anthracyclines are antibiotic compounds that exhibit cytotoxic activity. Studies have indicated that anthracyclines may operate to kill cells by a number of different mechanisms including: 1) intercalation of the drug molecules into the DNA of the cell thereby inhibiting DNA-dependent nucleic acid synthesis; 2) production by the drug of free radicals which then react with cellular macromolecules to cause damage to the cells or 3) interactions of the drug molecules with the cell membrane [see, e.g., C. Peterson et al.," Transport And Storage Of Anthracycline In Experimental Systems And Human Leukemia" in Anthracvcline Antibiotics In Cancer Therapy; N.R. Bachur, "Free Radical Damage" id. at pp.97-102] Because of their cytotoxic potential anthracyclines have been used in the treatment of numerous cancers such as leukemia, breast carcinoma, lung carcinoma, ovarian adenocarcinoma and sarcomas [see e.g., P.H- Wiernik, in Anthracvcline: Current Status And New Developments p 11] Commonly used anthracyclines include doxorubicin, epirubicin, idarubicin and daunomycin.

Representative examples of anthracyclines include, but are not limited to daunorubicin (Cerubidine; Bedford Laboratories), doxorubicin (Adriamycin; Bedford Laboratories; also referred to as doxorubicin hydrochloride, hydroxy-daunorubicin, and Rubex), epirubicin (Ellence; Pfizer), and idarubicin (Idamycin; Pfizer Inc.) The anthracycline analog, doxorubicin (ADRIAMYCINO) is thought to interact with DNA by intercalation and inhibition of the progression of the enzyme topoisomerase II, which unwinds DNA for transcription. Doxorubicin stabilizes the topoisomerase II complex after it has broken the DNA chain for replication, preventing the DNA double helix from being resealed and thereby stopping the process of replication. Doxorubicin and daunorubicin (DAUNOMYCIN) are prototype cytotoxic natural product anthracycline chemotherapeutics (Sessa et al., (2007) Cardiovasc. Toxicol. 7:75-79).

In other embodiments, the anti-CD117 antibodies or antigen-binding fragments thereof described herein can be conjugated to a cytotoxin that is a pyrrolobenzodiazepine (PBD) or a cytotoxin that comprises a PBD. PBDs are natural products produced by certain actinomycetes and have been shown to be sequence selective DNA alkylating compounds. PBD cytotoxins include, but are not limited to, anthramycin, dimeric PBDs, and those disclosed in, for example, Hartley, J.A. (2011). “The development of pyrrolobenzodiazepines as antitumour agents.” Expert Opin. Inv. Drug, 20(6), 733-744; and Antonow, D.; Thurston,

D.E. (2011) “Synthesis of DNA-interactive pyrrolo[2,1-c][1 ,4]benzodiazepines (PBDs).”

Chem. Rev. 111 : 2815-2864.

Calicheamicins

I In other embodiments, the antibodies and antigen-binding fragments thereof described herein can be conjugated to a cytotoxin that is an enediyne antitumor antibiotic (e.g., calicheamicins, ozogamicin). The calicheamicin family of antibiotics are capable of producing double-stranded DNA breaks at sub-picomolar concentrations. Examples of calicheamicins suitable for use in the present invention are disclosed, for example, in U.S. Pat. No. 4,671 ,958; U.S. Pat. No. 4,970,198, U.S. Pat. No. 5,053,394, U.S. Pat. No. 5,037,651 ; and U.S. Pat. No. 5,079,233, which are incorporated herein in their entirety. Structural analogues of calicheamicin which may be used include, but are not limited to, those disclosed in, for example, Hinman et al., Cancer Research 53:3336-3342 (1993), Lode et al., Cancer Research 58:2925-2928 (1998), and the aforementioned U.S. patents to American Cyanamid.

Auristatins

Anti-CD117 antibodies, and antigen-binding fragments thereof, described herein can be conjugated to a cytotoxin that is an auristatin (U.S. Pat. Nos. 5,635,483; 5,780,588). Auristatins are anti-mitotic agents that interfere with microtubule dynamics, GTP hydrolysis, and nuclear and cellular division (Woyke et al (2001) Antimicrob. Agents and Chemother. 45(12):3580-3584) and have anticancer (U.S. Pat. No. 5,663,149) and antifungal activity (Pettit et al (1998) Antimicrob. Agents Chemother. 42:2961-2965). (U.S. Pat. Nos. 5,635,483; 5,780,588). The auristatin drug moiety may be attached to the antibody through the N- (amino) terminus or the C- (carboxyl) terminus of the peptidic drug moiety (WO 02/088172).

Exemplary auristatin embodiments include the N-terminus linked monomethylauristatin drug moieties DE and DF, disclosed in Senter et al, Proceedings of the American Association for Cancer Research, Volume 45, Abstract Number 623, presented Mar. 28, 2004, the disclosure of which is expressly incorporated by reference in its entirety. An exemplary auristatin embodiment is MMAE, wherein the wavy line indicates the point of covalent attachment to the linker of an antibody-linker conjugate (-L-Z-Ab, as described herein).

Another exemplary auristatin embodiment is MMAF, wherein the wavy line indicates the point of covalent attachment to the linker of an antibody-linker conjugate (-L-Z-Ab, as described herein), as disclosed in US 2005/0238649:

Auristatins may be prepared according to the methods of: U.S. Pat. No. 5,635,483; U.S. Pat. No. 5,780,588; Pettit et al (1989) J. Am. Chem. Soc. 111 :5463-5465; Pettit et al (1998) Anti-Cancer Drug Design 13:243-277; Pettit, G. R., et al. Synthesis, 1996, 719-725;

Pettit et al (1996) J. Chem. Soc. Perkin Trans. 15:859-863; and Doronina (2003) Nat. Biotechnol. 21(7)778-784.

Amatoxins In some embodiments, the cytotoxin of the antibody-drug conjugate (ADC) is an RNA polymerase inhibitor. In some embodiments, the RNA polymerase inhibitor is an amatoxin or derivative thereof. In some embodiments, the cytotoxin is an amatoxin or derivative thereof, such as a-amanitin, b-amanitin, y-amanitin, e-amanitin, amanin, amaninamide, amanullin, amanullinic acid, and proamanullin. Amatoxins useful in conjunction with the compositions and methods described herein include compounds according to, but are not limited to, formula (I) (SEQ ID NO: 291),

wherein:

Ri is H, OH, or OR_A; R₂ is H, OH, or OR_B;

R_Aand R_B, when present, together with the oxygen atoms to which they are bound, combine to form an optionally substituted 5-membered heterocycloalkyl group;

R₃ is H or R_d; R4 is H, OH, ORD, or R_D;

R₅ is H, OH, ORD, or R_D;

R₆ is H, OH, ORD, or R_D;

R7 is H, OH, ORD, or R_D;

Rs is OH, NH₂, or ORD; Rg is H, OH, or ORD;

X is -S-, -S(O)-, or -SO₂-; and

R_D is optionally substituted alkyl (e.g., C₁-C₆ alkyl), optionally substituted heteroalkyl (e.g., C₁-C₆ heteroalkyl), optionally substituted alkenyl (e.g., C₂-C₆ alkenyl), optionally substituted heteroalkenyl (e.g., C₂-C₆ heteroalkenyl), optionally substituted alkynyl (e.g., C₂- C& alkynyl), optionally substituted heteroalkynyl (e.g., C₂-C₆ heteroalkynyl), optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl.

For instance, in one embodiment, amatoxins useful in conjunction with the compositions and methods described herein include compounds according to formula (la) (SEQ ID NO: 292)

wherein R , R₅, X, and Rs are each as defined above.

For instance, in one embodiment, amatoxins useful in conjunction with the compositions and methods described herein include compounds according to formula (lb) (SEQ ID NO: 293), below:

wherein:

Ri is H, OH, or OR_A;

R₂ is H, OH, or ORB;

R_Aand RB, when present, together with the oxygen atoms to which they are bound, combine to form an optionally substituted 5-membered heterocycloalkyl group;

R₃ is H or R_d;

R4 is H, OH, ORD, or R_D;

R₅ is H, OH, ORD, or R_D;

R₆ is H, OH, ORD, or R_D;

R7 is H, OH, ORD, or R_D;

Rs is OH, IMH2, or ORD;

Rg is H, OH, or ORD;

X is -S-, -S(O)-, or -SO₂-; and

RD is optionally substituted alkyl (e.g., C₁-C₆ alkyl), optionally substituted heteroalkyl (e.g., C₁-C₆ heteroalkyl), optionally substituted alkenyl (e.g., C₂-C₆ alkenyl), optionally substituted heteroalkenyl (e.g., C₂-C₆ heteroalkenyl), optionally substituted alkynyl (e.g., C₂- C& alkynyl), optionally substituted heteroalkynyl (e.g., C₂-C₆ heteroalkynyl), optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl.

In one embodiment, amatoxins useful in conjunction with the compositions and methods described herein also include compounds according to formula (lc) (SEQ ID NO: 294), below:

wherein:

Ri is H, OH, or OR_A;

R₂ is H, OH, or OR_B;

R_Aand R_B, when present, together with the oxygen atoms to which they are bound, combine to form an optionally substituted 5-membered heterocycloalkyl group;

R₃ is H or R_d;

R4 is H, OH, ORD, or R_D;

R₅ is H, OH, ORD, or R_D;

R₆ is H, OH, ORD, or R_D;

R7 is H, OH, ORD, or R_D;

Rs is OH, IMH2, or ORD;

Rg is H, OH, or OR_D;

X is -S-, -S(O)-, or -SO₂-; and

R_D is optionally substituted alkyl (e.g., C₁-C₆ alkyl), optionally substituted heteroalkyl (e.g., C₁-C₆ heteroalkyl), optionally substituted alkenyl (e.g., C₂-C₆ alkenyl), optionally substituted heteroalkenyl (e.g., C₂-C₆ heteroalkenyl), optionally substituted alkynyl (e.g., C₂- C& alkynyl), optionally substituted heteroalkynyl (e.g., C₂-C₆ heteroalkynyl), optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl, or optionally substituted heteroaryl.

Synthetic methods of making amatoxin are described in U.S. Patent No. 9,676,702, which is incorporated by reference herein.

Many positions on amatoxins or derivatives thereof can serve as the position to covalently bond the linking moiety L, and, hence the antibodies or antigen-binding fragments thereof. In some embodiments, the cytotoxin in the ADC is an amatoxin or derivative thereof according to formula (I, la, lb, or lc). In one embodiment, the ADC is represented by the general formula Ab-Z-L-Am, wherein Ab is an antibody or antigen-binding fragment thereof that binds CD117, L is a linker, Z is a chemical moiety, and Am is an amatoxin. In certain embodiments, the ADC having the general formula Ab-Z-L-Am, is represented by formula (II) (SEQ ID NO: 295):

wherein: Ri is H, OH, ORA, or ORc;

R2 is H, OH, ORB, or ORc;

R_Aand R_B, when present, together with the oxygen atoms to which they are bound, combine to form a 5-membered heterocycloalkyl group;

R₃ is H, Rc, or R_D; R4 is H, OH, ORc, ORD, R_C; or RD;

R₅ is H, OH, ORc, ORD, R_C, or RD;

Re is H, OH, ORc, ORD, R_C, or RD;

R7 is H, OH, ORc, ORD, R_C, or RD;

R₈ is OH, IMH2, ORc, ORD, NHR_c, or NR_CR_D; Rg is H, OH, ORc, or ORD;

X is -S-, -S(O)-, or -SO2-;

Rc is-L-Z-Ab,

R_D is C₁-C₆ alkyl, C₁-C₆ heteroalkyl, C₂-C₆ alkenyl, C₂-C₆ heteroalkenyl, C₂-C₆ alkynyl, C₂-C₆ heteroalkynyl, cycloalkyl, heterocycloalkyl, aryl, heteroaryl, or a combination thereof, wherein each C₁-C₆ alkyl, C₁-C₆ heteroalkyl, C₂-C₆ alkenyl, C₂-C₆ heteroalkenyl, C₂-C₆ alkynyl, C₂-C₆ heteroalkynyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl is optionally substituted with from 1 to 5 substituents independently selected for each occasion from the group consisting of alkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, alkaryl, alkyl heteroaryl, amino, ammonium, acyl, acyloxy, acylamino, aminocarbonyl, alkoxycarbonyl, ureido, carbamate, aryl, heteroaryl, sulfinyl, sulfonyl, hydroxyl, alkoxy, sulfanyl, halogen, carboxy, trihalomethyl, cyano, hydroxy, mercapto, and nitro.

L is a linker, such as optionally substituted C1-C6 alkyl, optionally substituted C1-C6 heteroalkyl, optionally substituted C2-C6 alkenyl, optionally substituted C2-C6 heteroalkenyl, optionally substituted C2-C6 alkynyl, optionally substituted C2-C6 heteroalkynyl, optionally substituted cycloalkyl, optionally substituted heterocycloalkyl, optionally substituted aryl, (C=0); or comprises a peptide or a dipeptide; or comprises -((CH2)_mO)n(CH2)_m-, where m and n are each independently selected from 1, 2, 3, 4, 5, 6, 7, 8, 9, and 10; or a combination of any thereof; and

Z is a chemical moiety formed from a coupling reaction between a reactive substituent 71 present on L and a reactive substituent present within an antibody, or antigen binding fragment thereof, that binds CD117 (such as GNNK+ CD117).

In some embodiments, Am contains exactly one Rc substituent.

In some embodiments, the cytotoxin is an amatoxin or derivative thereof and the ADC Ab-Z-L-Am is represented by formula (II), wherein:

Ri and R2are each independently H or OH;

R3 is R_c;

R4, R₆, and R are each H;

R₅ is H, OH, or OC1-C6 alkyl;

Rs is OH or NH₂;

R₉ is H or OH;

X is -S-, -S(O)-, or -SO2-; and

Rcand RD are as defined above.

Such amatoxin-linker conjugates are described, for example, in U.S. Patent Application Publication No. 2014/0294865, the disclosure of which is incorporated herein by reference in its entirety.

In some embodiments, the cytotoxin is an amatoxin or derivative thereof and the ADC Ab-Z-L-Am is represented by formula (II), wherein:

Ri and R2 are each independently H or OH;

R₃, R₆, and R are each H;

R4 and R₅ are each independently H, OH, ORc, or R_c;

Rs is OH or NH₂;

R₉ is H or OH; X is -S-, -S(O)-, or -SO2-; and

Rc and RD are as defined above.

Such amatoxin-linker conjugates are described, for example, in U.S. Patent Application Publication No. 2015/0218220, the disclosure of which is incorporated herein by 5 reference in its entirety.

In some embodiments, the cytotoxin is an amatoxin or derivative thereof and the ADC Ab-Z-L-Am is represented by formula (II), wherein:

Ri and R2 are each independently H or OH;

R₃, R6, and R7 are each H; 0 R4 and R₅ are each independently H or OH;

R₈ is OH, NH₂, OR_C, or NHR_C;

R₉ is H or OH;

X is -S-, -S(O)-, or -SO2-; and

Rc and RD are as defined above. 5 Such amatoxin conjugates are described, for example, in U.S. Patent Nos. 9,233,173 and 9,399,681 , the disclosures of each of which are incorporated herein by reference in their entirety.

In some embodiments, the ADC Ab-Z-L-Am is represented by formula (IIA) (SEQ ID NO: 296):

wherein each of Ri, R2, RA, RB, R3, R4, Rs, R6, R7, Rs, R9, Rc, RD, X, L, and Z are as defined above with respect to Formula (III).

In some embodiments, the ADC Ab-Z-L-Am is represented by formula (MB) (SEQ ID NO: 297):

wherein each of Ri, R2, RA, RB, R3, R4, Rs, R6, R7, Rs, R9, Rc, RD, X, L, and Z are as defined above with respect to Formula (III). Anti-CD117: Linkers

A variety of linkers can be used to conjugate antibodies, or antigen-binding fragments, as described herein (e.g., antibodies, or antigen-binding fragments thereof, that recognize and bind CD117 (such as GNNK+ CD117) with a cytotoxic molecule.

The term “Linker" as used herein means a divalent chemical moiety comprising a covalent bond or a chain of atoms that covalently attaches an anti-CD117 antibody or fragment thereof (Ab) to a drug moiety (D) to form antibody-drug conjugates (ADC) of formula II. Suitable linkers have two reactive termini, one for conjugation to an antibody and the other for conjugation to a cytotoxin. The antibody conjugation reactive terminus of the linker (reactive moiety, Z') is typically a site that is capable of conjugation to the antibody through a cysteine thiol or lysine amine group on the antibody, and so is typically a thiol- reactive group such as a double bond (as in maleimide) or a leaving group such as a chloro, bromo, iodo, or an R-sulfanyl group, or an amine-reactive group such as a carboxyl group; while the cytotoxin conjugation reactive terminus of the linker is typically a site that is capable of conjugation to the cytotoxin. Non-limiting examples for linker-cytotoxin conjugation include, for example, formation of an amide bond with a basic amine or carboxyl group on the cytotoxin, via a carboxyl or basic amine group on the linker, respectively, or formation of an ether or the like, via alkylation of an OH group on the cytotoxin, via e.g., a leaving group on the linker. In some embodiments, cytotoxin-linker conjugation is through formation of an amide bond with a basic amine or carboxyl group on the cytotoxin, and so the reactive substituent on the linker is respectively a carboxyl or basic amine group. When the term "linker" is used in describing the linker in conjugated form, one or both of the reactive termini will be absent (such as reactive moiety Z', having been converted to chemical moiety Z) or incomplete (such as being only the carbonyl of the carboxylic acid) because of the formation of the bonds between the linker and/or the cytotoxin, and between the linker and/or the antibody or antigen-binding fragment thereof. Such conjugation reactions are described further herein below.

In some embodiments, the linker is cleavable under intracellular conditions, such that cleavage of the linker releases the drug unit from the antibody in the intracellular environment. In yet other embodiments, the linker unit is not cleavable and the drug is released, for example, by antibody degradation. The linkers useful for the present ADCs are preferably stable extracellularly, prevent aggregation of ADC molecules and keep the ADC freely soluble in aqueous media and in a monomeric state. Before transport or delivery into a cell, the ADC is preferably stable and remains intact, i.e. the antibody remains linked to the drug moiety. The linkers are stable outside the target cell and may be cleaved at some efficacious rate inside the cell. An effective linker will: (i) maintain the specific binding properties of the antibody; (ii) allow intracellular delivery of the conjugate or drug moiety; (iii) remain stable and intact, i.e. not cleaved, until the conjugate has been delivered or transported to its targeted site; and (iv) maintain a cytotoxic, cell-killing effect or a cytostatic effect of the cytotoxic moiety. Stability of the ADC may be measured by standard analytical techniques such as mass spectroscopy, HPLC, and the separation/analysis technique LC/MS. Covalent attachment of the antibody and the drug moiety requires the linker to have two reactive functional groups, i.e. bivalency in a reactive sense. Bivalent linker reagents which are useful to attach two or more functional or biologically active moieties, such as peptides, nucleic acids, drugs, toxins, antibodies, haptens, and reporter groups are known, and methods have been described their resulting conjugates (Hermanson, G. T. (1996) Bioconjugate Techniques; Academic Press: New York, p. 234-242).

Suitable cleavable linkers include those that may be cleaved, for instance, by enzymatic hydrolysis, photolysis, hydrolysis under acidic conditions, hydrolysis under basic conditions, oxidation, disulfide reduction, nucleophilic cleavage, or organometallic cleavage (see, for example, Leriche et al., Bioorg. Med. Chem., 20:571-582, 2012, the disclosure of which is incorporated herein by reference as it pertains to linkers suitable for covalent conjugation). Suitable cleavable linkers may include, for example, chemical moieties such as a hydrazine, a disulfide, a thioether or a dipeptide.

Linkers hydrolyzable under acidic conditions include, for example, hydrazones, semicarbazones, thiosemicarbazones, cis-aconitic amides, orthoesters, acetals, ketals, or the like. (See, e.g., U.S. Pat. Nos. 5,122,368; 5,824,805; 5,622,929; Dubowchik and Walker, 1999, Pharm. Therapeutics 83:67-123; Neville et al., 1989, Biol. Chem. 264:14653-14661 , the disclosure of each of which is incorporated herein by reference in its entirety as it pertains to linkers suitable for covalent conjugation. Such linkers are relatively stable under neutral pH conditions, such as those in the blood, but are unstable at below pH 5.5 or 5.0, the approximate pH of the lysosome.

Linkers cleavable under reducing conditions include, for example, a disulfide. A variety of disulfide linkers are known in the art, including, for example, those that can be formed using SATA (N-succinimidyl-S-acetylthioacetate), SPDP (N-succinimidyl-3-(2- pyridyldithiojpropionate), SPDB (N-succinimidyl-3-(2-pyridyldithio)butyrate) and SMPT (N- succinimidyl-oxycarbonyl-alpha-methyl-alpha-(2-pyridyl-dithio)toluene), SPDB and SMPT (See, e.g., Thorpe et al., 1987, Cancer Res. 47:5924-5931 ; Wawrzynczak et al., In Immunoconjugates: Antibody Conjugates in Radioimagery and Therapy of Cancer (C. W. Vogel ed., Oxford U. Press, 1987. See also U.S. Pat. No. 4,880,935, the disclosure of each of which is incorporated herein by reference in its entirety as it pertains to linkers suitable for covalent conjugation.

Additional linkers suitable for the synthesis of drug-antibody conjugates conjugates as described herein include those capable of releasing a cytotoxin by a 1 ,6-elimination process (a "self-immolative" group), such as p-aminobenzyl alcohol (PABC), p-aminobenzyl (PAB), 6-maleimidohexanoic acid, pH-sensitive carbonates, and other reagents described in Jain et al., Pharm. Res. 32:3526-3540, 2015, the disclosure of which is incorporated herein by reference in its entirety.

In some embodiments, the linker includes a self-immolative group such as the afore mentioned PAB or PABC (para-aminobenzyloxycarbonyl), which are disclosed in, for example, Carl et al., J. Med. Chem. (1981) 24:479-480; Chakravarty et al (1983) J. Med. Chem. 26:638-644; US 6214345; US20030130189; US20030096743; US6759509; US20040052793; US6218519; US6835807; US6268488; US20040018194; W098/13059; US20040052793; US6677435; US5621002; US20040121940; W02004/032828). Other such chemical moieties capable of this process (“self-immolative linkers”) include methylene carbamates and heteroaryl groups such as aminothiazoles, aminoimidazoles, aminopyrimidines, and the like. Linkers containing such heterocyclic self-immolative groups are disclosed in, for example, U.S. Patent Publication Nos. 20160303254 and 20150079114, and U.S. Patent No. 7,754,681 ; Hay et al. (1999) Bioorg. Med. Chem. Lett. 9:2237; US 2005/0256030; de Groot et al (2001) J. Org. Chem. 66:8815-8830; and US 7223837.

Linkers susceptible to enzymatic hydrolysis can be, e.g., a peptide-containing linker that is cleaved by an intracellular peptidase or protease enzyme, including, but not limited to, a lysosomal or endosomal protease. One advantage of using intracellular proteolytic release of the therapeutic agent is that the agent is typically attenuated when conjugated and the serum stabilities of the conjugates are typically high. In some embodiments, the peptidyl linker is at least two amino acids long or at least three amino acids long. Exemplary amino acid linkers include a dipeptide, a tripeptide, a tetrapeptide or a pentapeptide. Examples of suitable peptides include those containing amino acids such as Valine, Alanine, Citrulline (Cit), Phenylalanine, Lysine, Leucine, and Glycine. Amino acid residues which comprise an amino acid linker component include those occurring naturally, as well as minor amino acids and non-naturally occurring amino acid analogs, such as citrulline. Exemplary dipeptides include valine-citrulline (vc or val-cit) and alanine-phenylalanine (af or ala-phe). Exemplary tripeptides include glycine-valine-citrulline (gly-val-cit) and glycine-glycine-glycine (gly-gly- gly). In some embodiments, the linker includes a dipeptide such as Val-Cit, Ala-Val, or Phe- Lys, Val-Lys, Ala-Lys, Phe-Cit, Leu-Cit, lle-Cit, Phe-Arg, or Trp-Cit. Linkers containing dipeptides such as Val-Cit or Phe-Lys are disclosed in, for example, U.S. Pat. No.

6,214,345, the disclosure of which is incorporated herein by reference in its entirety as it pertains to linkers suitable for covalent conjugation. In some embodiments, the linker includes a dipeptide selected from Val-Ala and Val-Cit. In some embodiments, a dipeptide is used in combination with a self-immolative linker.

Linkers suitable for use herein further may include one or more groups selected from Ci-C₆ alkylene, C1-C₆ heteroalkylene, C2-C₆ alkenylene, C2-C₆ heteroalkenylene, C2-C₆ alkynylene, C₂-C₆ heteroalkynylene, C₃-C₆cycloalkylene, heterocycloalkylene, arylene, heteroarylene, and combinations thereof, each of which may be optionally substituted. Non limiting examples of such groups include (CH₂)_n, (CH2CH₂0)_n, and -(C=0)(CH₂)_n- units, wherein n is an integer from 1-6, independently selected for each occasion.

In some embodiments, each C₁-C₆ alkyl, C₁-C₆ heteroalkyl, C₂-C₆ alkenyl, C₂-C₆ heteroalkenyl, C₂-C₆ alkynyl, C₂-C₆heteroalkynyl, C₃-C₆ cycloalkyl, heterocycloalkyl, aryl, or heteroaryl group may be optionally substituted with from 1 to 5 substituents independently selected for each occasion from the group consisting of alkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, alkaryl, alkyl heteroaryl, amino, ammonium, acyl, acyloxy, acylamino, aminocarbonyl, alkoxycarbonyl, ureido, carbamate, aryl, heteroaryl, sulfinyl, sulfonyl, hydroxyl, alkoxy, sulfanyl, halogen, carboxy, trihalomethyl, cyano, hydroxy, mercapto, and nitro.

In some embodiments, each C₁-C₆ alkyl, C₁-C₆ heteroalkyl, C₂-C₆ alkenyl, C₂-C₆ heteroalkenyl, C₂-C₆ alkynyl, C₂-C₆heteroalkynyl, C₃-C₆ cycloalkyl, heterocycloalkyl, aryl, or heteroaryl group may optionally be interrupted by one or more heteroatoms selected from O, S and N.

In some embodiments, each C₁-C₆ alkyl, C₁-C₆ heteroalkyl, C₂-C₆ alkenyl, C₂-C₆ heteroalkenyl, C₂-C₆ alkynyl, C₂-C₆heteroalkynyl, C₃-C₆ cycloalkyl, heterocycloalkyl, aryl, or heteroaryl group may optionally be interrupted by one or more heteroatoms selected from O, S and N and may be optionally substituted with from 1 to 5 substituents independently selected for each occasion from the group consisting of alkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, alkaryl, alkyl heteroaryl, amino, ammonium, acyl, acyloxy, acylamino, aminocarbonyl, alkoxycarbonyl, ureido, carbamate, aryl, heteroaryl, sulfinyl, sulfonyl, hydroxyl, alkoxy, sulfanyl, halogen, carboxy, trihalomethyl, cyano, hydroxy, mercapto, and nitro.

Suitable linkers may contain groups having solubility enhancing properties. Linkers including the (CH₂CH₂0)p unit (polyethylene glycol, PEG), for example, can enhance solubility, as can alkyl chains substituted with amino, sulfonic acid, phosphonic acid or phosphoric acid residues. Linkers including such moieties are disclosed in, for example,

U.S. Patent Nos. 8,236,319 and 9,504,756, the disclosure of each of which is incorporated herein by reference in its entirety as it pertains to linkers suitable for covalent conjugation.

Further solubility enhancing groups include, for example, acyl and carbamoyl sulfamide groups, having the structure:

wherein a is 0 or 1 ; and

R¹⁰ is selected from the group consisting of hydrogen, Ci-C₂₄ alkyl groups, C₃-C₂₄ cycloalkyl groups, Ci-C₂₄ (hetero)aryl groups, Ci-C₂₄ alkyl(hetero)aryl groups and Ci-C₂₄ (hetero)arylalkyl groups, the Ci-C₂₄ alkyl groups, C₃-C₂₄ cycloalkyl groups, C₂-C₂₄ (hetero)aryl groups, C₃-C₂₄ alkyl(hetero)aryl groups and C₃-C₂₄ (hetero)arylalkyl groups, each of which may be optionally substituted and/or optionally interrupted by one or more heteroatoms selected from O, S and NR¹¹R¹², wherein R¹¹ and R¹² are independently selected from the group consisting of hydrogen and C1 -C4 alkyl groups; or R¹⁰ is a cytotoxin, wherein the cytotoxin is optionally connected to N via a spacer moiety. Linkers containing such groups are described, for example, in U.S. Patent No. 9,636,421 and U.S. Patent Application Publication No. 2017/0298145, the disclosures of which are incorporated herein by reference in their entirety as they pertain to linkers suitable for covalent conjugation to cytotoxins and antibodies or antigen-binding fragments thereof.

In some embodiments, the linker comprises a ((CH₂)_mO) _n(CH₂)_m- group where n and m are each independently selected from 1, 2, 3, 4, 5, 6, 7, 8, 9, and 10; and a heteroaryl group, wherein the heteroaryl group is a triazole. In some embodiments, the ((CH₂)_mO) _n(CH₂)_m- group and triazole together comprise

where n is from 1 to 10, and the wavy lines indicate attachment points to additional linker components, the chemical moiety Z, or the amatoxin.

Other linkers that may be used in the methods and compositions described herein are described in US 2019/0144504, which is incorporated by reference herein.

In some embodiments, the linker may include one or more of a hydrazine, a disulfide, a thioether, a dipeptide, a p-aminobenzyl (PAB) group, a heterocyclic self-immolative group, an optionally substituted C1-C6 alkyl, an optionally substituted C1-C6 heteroalkyl, an optionally substituted C₂-C₆ alkenyl, an optionally substituted C₂-C₆ heteroalkenyl, an optionally substituted C₂-C₆alkynyl, an optionally substituted C₂-C₆heteroalkynyl, an optionally substituted C3-C6 cycloalkyl, an optionally substituted heterocycloalkyl, an optionally substituted aryl, an optionally substituted heteroaryl, acyl, -(C=0)-, or -(CH₂CH₂0)_n- group, wherein n is an integer from 1-6. One of skill in the art will recognize that one or more of the groups listed may be present in the form of a bivalent (diradical) species, e.g., C1-C6 alkylene and the like.

In some embodiments, the linker L comprises the moiety ^*-l_il_₂-^**, wherein:

l_2 is absent or is -(CH₂)_m-, -NR¹³(CH₂)_m-, -(CH₂)_mNR¹³C(=0)(CH₂)_m-, -X₄, - (CH₂)_mNR¹³C(=0)X₄, - (CH₂)_mNR¹³C(=0)-, -((CH₂)_mO)_n(CH₂)_m-, -((CH₂)_mO)_n(CH₂)_mX₃(CH₂)_m-,

- NR¹³((CH₂)_mO)_nX₃(CH₂)_m-, -NR¹³((CH₂)_mO)_n(CH₂)_mX₃(CH₂)_m-, -XiX₂C(=0)(CH₂)_m-, - (CH₂)_m(0(CH₂)_m)_n-, -(CH₂)_mNR¹³(CH₂)_m-, -(CH₂)_mNR¹³C(=0)(CH₂)_mX₃(CH₂)_m-, - (CH₂)_mC(=0)NR¹³(CH₂)_mNR¹³C(=0)(CH₂)_m-, -(CH₂)_mC(=0)-, - (CH₂)_mNR¹³(CH₂)_mC(=0)X₂XiC(=0)-, -(CH₂)_mX₃(CH₂)_mC(=0)X₂XiC(=0)-, - (CH₂)_mC(=0)NR¹³(CH₂)_m-, -(CH₂)_mC(=0)NR¹³(CH₂)_mX₃(CH₂)_m-, - (CH₂)_mX₃(CH₂)_mNR¹³C(=0)(CH₂)_m-, -(CH₂)_mX₃(CH₂)_mC(=0)NR¹³(CH₂)_m-, - (CH₂)_m0)_n(CH₂)_mNR¹³C(=0)(CH₂)_m-, -(CH₂)_mC(=0)NR¹³(CH₂)_m(0(CH₂)_m)_n-, - (CH₂)_m(0(CH₂)_m)_nC(=0)-, -(CH₂)_mNR¹³(CH₂)_mC(=0)-, -(CH₂)_mC(=0)NR¹³(CH₂)_mNR¹³C(=0)-, -(CH₂)_m(0(CH₂)_m)_nX₃(CH₂)_m-, - (CH₂)_mX₃((CH₂)_mO)_n(CH₂)_m-, -(CH₂)_mX₃(CH₂)_mC(=0)-, - (CH₂)_mC(=0)NR¹³(CH₂)_m0)_n(CH₂)_mX₃(CH₂)_m-, - (CH₂)_mX₃(CH₂)_m(0(CH₂)_m)_nNR¹³C(=0)(CH₂)_m- , -(CH₂)_mX₃(CH₂)_m(0(CH₂)m)nC(=0)-, -(CH₂)_mX₃(CH₂)_m(0(CH₂)m)n-, - (CH₂)_mC(=0)NR¹³(CH₂)_mC(=0)-, -(CH₂)_mC(=0)NR¹³(CH₂)_m(0(CH₂)_m)_nC(=0)-, - ((CH₂)_m0)_n(CH₂)_mNR¹³C(=0)(CH₂)_m-, -(CH₂)_mC(=0)NR¹³(CH₂)_mC(=0)NR¹³(CH₂)_m-, - (CH₂)_mNR¹³C(=0)(CH₂)_mNR¹³C(=0)(CH₂) -(CH₂)_mX₃(CH₂)_mC(=0)NR¹³-, -(CH₂)_mC(=0)NR¹³-, -(CH₂)_mX₃-, -C(R¹³)₂(CH₂)_m-, -(CH₂)_mC(R¹³)₂NR¹³-, -(CH₂)_mC(=0)NR¹³(CH₂)_mNR¹³-, - (CH₂)_mC(=0)NR¹³(CH₂)_mNR¹³C(=0)NR¹³-, -(CH₂)_mC(=0)X₂XiC(=0)-, - C(R¹³)₂(CH₂)_mNR¹³C(=0)(CH₂)_m-, -(CH₂)_mC(=0)NR¹³(CH₂)_mC(R¹³)₂NR¹³-, - C(R¹³)₂(CH₂)_mX₃(CH₂)_m-, -(CH₂)_mX₃(CH₂)_mC(R¹³)₂NR¹³-, -C(R¹³)₂(CH₂)_m0C(=0)NR¹³(CH₂)_m-, - (CH₂)_mNR¹³C(=0)0(CH₂)_mC(R¹³)₂NR¹³-, -(CH₂)_mX₃(CH₂)_mNR¹³-, -

(CH₂)_mX₃(CH₂)_m(0(CH₂)_m)_nNR¹³-, -(CH₂)_mNR¹³-, -(CH₂)_mC(=0)NR¹³(CH₂)_m(0(CH₂)_m)_nNR¹³ -

(CH₂)_m(0(CH₂)_m)_nNR¹³-, -(CH₂CH₂0)_n(CH₂)_m-, -(CH₂)_m(OCH₂CH₂)_n; -(CH₂)_mO(CH₂)_m-, - (CH₂)_mS(=0)₂-, - (CH₂)_mC(=0)NR¹³(CH₂)_mS(=0)₂-, -(CH₂)_mX₃(CH₂)_mS(=0)₂-, - (CH₂)_mX₂XiC(=0)-, -(CH₂)_m(0(CH₂)_m)_nC(=0)X₂XiC(=0)-, -(CH₂)_m(0(CH₂)_m)_nX₂XiC(=0)-, - (CH₂)_mX₃(CH₂)_mX₂XiC(=0)-, -(CH₂)_mX₃(CH₂)_m(0(CH₂)_m)_nX₂Xi C(=0)-, - (CH₂)_mX₃(CH₂)_mC(=0)NR¹³(CH₂)_mNR¹³C(=0)-, -(CH₂)_mX₃(CH₂)_mC(=0)NR¹³(CH₂)_mC(=0)-, - (CH₂)_mX₃(CH₂)_mC(=0)NR¹³(CH₂)_m(0(CH₂)_m)_nC(=0)-, -(CH₂)_mC(=0)X₂XiC(=0)NR¹³(CH₂)_m-, - (CH₂)_mX₃(0(CH₂)_m)_nC(=0)-, -(CH₂)_mNR¹³C(=0)((CH₂)_m0)_n(CH₂)_m-, - (CH₂)_m(0(CH₂)_m)_nC(=0)NR¹³(CH₂)_m-, -(CH₂)_mNR¹³C(=0)NR¹³(CH₂)_m- or - (CH₂)_mX₃(CH₂)_mNR¹³C(=0)-; wherein

Xi is

wherein

R¹³ is independently selected for each occasion from H and C1-C6 alkyl; m is independently selected for each occasion from 1, 2, 3, 4, 5, 6, 7, 8, 9 and 10; n is independently selected for each occasion from 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 and 14; and wherein the single asterisk (^*) indicates the attachment point to the cytotoxin (e.g., an amatoxin), and the double asterisk (^**) indicates the attachment point to the reactive substituent Z or chemical moiety Z, with the proviso that Li and l_₂ are not both absent.

In some embodiments, the linker includes a p-aminobenzyl group (PAB). In one embodiment, the p-aminobenzyl group is disposed between the cytotoxic drug and a protease cleavage site in the linker. In one embodiment, the p-aminobenzyl group is part of a p-aminobenzyloxycarbonyl unit. In one embodiment, the p-aminobenzyl group is part of a p- aminobenzylamido unit.

In some embodiments, the linker comprises PAB, Val-Cit-PAB, Val-Ala- PAB, Val-Lys(Ac)-PAB, Phe-Lys-PAB, Phe-Lys(Ac)-PAB, D-Val-Leu-Lys, Gly-Gly-Arg, Ala- Ala-Asn-PAB, or Ala-PAB.

In some embodiments, the linker comprises a combination of one or more of a peptide, oligosaccharide, -(CH₂)_n-, -(CH₂CH₂0)_n-, PAB, Val-Cit-PAB, Val-Ala-PAB, Val- Lys(Ac)-PAB, Phe-Lys-PAB, Phe-Lys(Ac)-PAB, D-Val-Leu-Lys, Gly-Gly-Arg, Ala-Ala-Asn- PAB, or Ala-PAB.

In one specific embodiment, the linker comprises PAB-Ala-Val-propionyl, represented by the structure

wherein the wavy lines indicate attachment points to the cytotoxin and the reactive moiety Z'. In another specific embodiment, the linker comprises PAB-Cit-Val-propionyl, represented by the structure

wherein the wavy lines indicate attachment points to the cytotoxin and the reactive moiety Z'. Such PAB-dipeptide-propionyl linkers are disclosed in, e.g., Patent Application Publication No. WO2017/149077, which is incorporated by reference herein in its entirety.

In certain embodiments, the linker of the ADC is maleimidocaproyl-Val-Ala-para- aminobenzyl (mc-Val-Ala-PAB). In certain embodiments, the linker of the ADC is maleimidocaproyl-Val-Cit-para- aminobenzyl (mc-vc-PAB).

In some embodiments, the linker comprises

In some embodiments, the linker comprises MCC (4-[N- maleimidomethyl]cyclohexane-1 -carboxylate).

In some embodiments, the linker comprises a -(CH2)_n- unit, wherein n is an integer from 2 to 6.

In some embodiments, the linker comprises a -(C=0)(CH₂)_n- unit, wherein n is an integer from 1-6. Linkers that can be used to conjugate an antibody, or antigen-binding fragment thereof, to a cytotoxic agent include those that are covalently bound to the cytotoxic agent on one end of the linker and, on the other end of the linker, contain a chemical moiety formed from a coupling reaction between a reactive substituent present on the linker and a reactive substituent present within the antibody, or antigen-binding fragment thereof, that binds CD117 (such as GNNK+ CD117). Reactive substituents that may be present within an antibody, or antigen-binding fragment thereof, that binds CD117 (such as GNNK+ CD117) include, without limitation, hydroxyl moieties of serine, threonine, and tyrosine residues; amino moieties of lysine residues; carboxyl moieties of aspartic acid and glutamic acid residues; and thiol moieties of cysteine residues, as well as propargyl, azido, haloaryl (e.g., fluoroaryl), haloheteroaryl (e.g., fluoroheteroaryl), haloalkyl, and haloheteroalkyl moieties of non-naturally occurring amino acids.

Examples of linkers useful for the synthesis of drug-antibody conjugates conjugates include those that contain electrophiles, such as Michael acceptors (e.g., maleimides), activated esters, electron-deficient carbonyl compounds, and aldehydes, among others, suitable for reaction with nucleophilic substituents present within antibodies or antigen binding fragments, such as amine and thiol moieties. For instance, linkers suitable for the synthesis of drug-antibody conjugates include, without limitation, succinimidyl 4-(N- maleimidomethyl)-cyclohexane-L-carboxylate (SMCC), N- succinimidyl iodoacetate (SIA), sulfo-SMCC, m-maleimidobenzoyl-/V-hydroxysuccinimidyl ester (MBS), sulfo-MBS, and succinimidyl iodoacetate, among others described, for instance, Liu et al., 18:690-697, 1979, the disclosure of which is incorporated herein by reference as it pertains to linkers for chemical conjugation. Additional linkers include the non-cleavable maleimidocaproyl linkers, which are particularly useful for the conjugation of microtubule-disrupting agents such as auristatins, are described by Doronina et al., Bioconjugate Chem. 17:14-24, 2006, the disclosure of which is incorporated herein by reference as it pertains to linkers for chemical conjugation.

It will be recognized by one of skill in the art that any one or more of the chemical groups, moieties and features disclosed herein may be combined in multiple ways to form linkers useful for conjugation of the antibodies and cytotoxins as disclosed herein. Further linkers useful in conjunction with the compositions and methods described herein, are described, for example, in U.S. Patent Application Publication No. 2015/0218220, the disclosure of which is incorporated herein by reference in its entirety.

Linkers useful in conjunction with the antibody-drug described herein include, without limitation, linkers containing chemical moieties formed by coupling reactions as depicted in Table 3, below. Curved lines designate points of attachment to the antibody, or antigen binding fragment, and the cytotoxic molecule, respectively.

Table 3. Exemplary chemical moieties Z formed by coupling reactions in the formation of antibody-drug

One of skill in the art will recognize that a reactive substituent Z' attached to the linker and a reactive substituent on the antibody or antigen-binding fragment thereof, are engaged in the covalent coupling reaction to produce the chemical moiety Z, and will recognize the reactive substituent Z'. Therefore, antibody-drug conjugates useful in conjunction with the methods described herein may be formed by the reaction of an antibody, or antigen-binding fragment thereof, with a linker or cytotoxin-linker conjugate, as described herein, the linker or cytotoxin-linker conjugate including a reactive substituent Z', suitable for reaction with a reactive substituent on the antibody, or antigen-binding fragment thereof, to form the chemical moiety Z.

In some embodiments, Z ' is -NR¹³C(=0)CH=CH₂, -N₃, -SH, -S(=0)₂(CH=CH₂), - (CH₂)₂S(=0)₂(CH=CH₂), -NR¹³S(=0)₂(CH=CH₂), -NR¹³C(=0)CH₂R¹⁴, -NR¹³C(=0)CH₂Br, - NR¹³C(=0)CH₂l, -NHC(=0)CH₂Br, -NHC(=0)CH₂l, -ONH₂, -C(0)NHNH₂, -C0₂H, -NH₂, - NH(C=0), -NC(=S),

wherein

R¹³ is independently selected for each occasion from H and C₁-C₆ alkyl; R¹⁴ is -S(CH₂)_nCHR¹⁵NHC(=0)R¹³;

R¹⁵ is R¹³ or -C(=0)0R¹³;

R¹⁶ is independently selected for each occasion from H, C₁-C₆ alkyl, F, Cl, and -OH; R¹⁷ is independently selected for each occasion from H, C₁-C₆ alkyl, F, Cl, -NH₂, - OCH₃, -OCH₂CH₃, -N(CH₃)₂, -CN, -N0₂ and-OH; and R¹⁸ is independently selected for each occasion from H, C1-C6 alkyl, F, benzyloxy substituted with -C(=0)0H, benzyl substituted with -C(=0)0H, C1-C4 alkoxy substituted with -C(=0)0H, and C1-C4 alkyl substituted with -C(=0)0H.

As depicted in Table 3, examples of suitably reactive substituents on the linker and antibody or antigen-binding fragment thereof include a nucleophile/electrophile pair (e.g., a thiol/haloalkyl pair, an amine/carbonyl pair, or a thiol/ a,b -unsaturated carbonyl pair, and the like), a diene/dienophile pair (e.g., an azide/alkyne pair, or a diene/ a,b-unsaturated carbonyl pair, among others), and the like. Coupling reactions between the reactive substitutents to form the chemical moiety Z include, without limitation, thiol alkylation, hydroxyl alkylation, amine alkylation, amine or hydroxylamine condensation, hydrazine formation, amidation, esterification, disulfide formation, cycloaddition (e.g., [4+2] Diels-Alder cycloaddition, [3+2] Huisgen cycloaddition, among others), nucleophilic aromatic substitution, electrophilic aromatic substitution, and other reactive modalities known in the art or described herein. Preferably, the linker contains an electrophilic functional group for reaction with a nucleophilic functional group on the antibody, or antigen-binding fragment thereof.

Reactive substituents that may be present within an antibody, or antigen-binding fragment thereof, as disclosed herein include, without limitation, nucleophilic groups such as (i) N-terminal amine groups, (ii) side chain amine groups, e.g. lysine, (iii) side chain thiol groups, e.g. cysteine, and (iv) sugar hydroxyl or amino groups where the antibody is glycosylated. Reactive substituents that may be present within an antibody, or antigen binding fragment thereof, as disclosed herein include, without limitation, hydroxyl moieties of serine, threonine, and tyrosine residues; amino moieties of lysine residues; carboxyl moieties of aspartic acid and glutamic acid residues; and thiol moieties of cysteine residues, as well as propargyl, azido, haloaryl (e.g., fluoroaryl), haloheteroaryl (e.g., fluoroheteroaryl), haloalkyl, and haloheteroalkyl moieties of non-naturally occurring amino acids. In some embodiments, the reactive substituents present within an antibody, or antigen-binding fragment thereof as disclosed herein include, are amine or thiol moieties. Certain antibodies have reducible interchain disulfides, i.e. cysteine bridges. Antibodies may be made reactive for conjugation with linker reagents by treatment with a reducing agent such as DTT (dithiothreitol). Each cysteine bridge will thus form, theoretically, two reactive thiol nucleophiles. Additional nucleophilic groups can be introduced into antibodies through the reaction of lysines with 2-iminothiolane (Traut's reagent) resulting in conversion of an amine into a thiol. Reactive thiol groups may be introduced into the antibody (or fragment thereof) by introducing one, two, three, four, or more cysteine residues (e.g., preparing mutant antibodies comprising one or more non-native cysteine amino acid residues). U.S. Pat. No. 7,521 ,541 teaches engineering antibodies by introduction of reactive cysteine amino acids. In some embodiments, the reactive moiety Z' attached to the linker is a nucleophilic group which is reactive with an electrophilic group present on an antibody. Useful electrophilic groups on an antibody include, but are not limited to, aldehyde and ketone carbonyl groups. The heteroatom of a nucleophilic group can react with an electrophilic group on an antibody and form a covalent bond to the antibody. Useful nucleophilic groups include, but are not limited to, hydrazide, oxime, amino, hydroxyl, hydrazine, thiosemicarbazone, hydrazine carboxylate, and arylhydrazide.

In some embodiments, Z is the product of a reaction between reactive nucleophilic substituents present within the antibodies, or antigen-binding fragments thereof, such as amine and thiol moieties, and a reactive electrophilic substituent Z'. For instance, Z' may be a Michael acceptor (e.g., maleimide), activated ester, electron-deficient carbonyl compound, or an aldehyde, among others.

Several representative and non-limiting examples of reactive substituents Z' and the resulting chemical moieties Z are provided in Table 4.

Table 4. Complementary reactive substituents and chemical moieties

For instance, linkers suitable for the synthesis of ADCs of the disclosure include, without limitation, reactive substituents Z' such as maleimide or haloalkyl groups. These may be attached to the linker by reagents such as succinimidyl 4-(N-maleimidomethyl)- cyclohexane-L-carboxylate (SMCC), N- succinimidyl iodoacetate (SIA), sulfo-SMCC, m- maleimidobenzoyl-/V-hydroxysuccinimidyl ester (MBS), sulfo-MBS, and succinimidyl iodoacetate, among others described, in for instance, Liu et al., 18:690-697, 1979, the disclosure of which is incorporated herein by reference as it pertains to linkers for chemical conjugation.

In some embodiments, the reactive substituent Z' attached to linker L is a maleimide, azide, or alkyne. An example of a maleimide-containing linker is the non-cleavable maleimidocaproyl-based linker.

In some embodiments, the reactive substituent Z' is -(C=0)- or -NH(C=0)-, such that the linker may be joined to the antibody, or antigen-binding fragment thereof, by an amide or urea moiety, respectively, resulting from reaction of the -(C=0)- or -NH(C=0)- group with an amino group of the antibody or antigen-binding fragment thereof.

In some embodiments, the reactive substituent is an N-maleimidyl group, halogenated N-alkylamido group, sulfonyloxy N-alkylamido group, carbonate group, sulfonyl halide group, thiol group or derivative thereof, alkynyl group comprising an internal carbon- carbon triple bond, (het-ero)cycloalkynyl group, bicyclo[6.1 0]non-4-yn-9-yl group, alkenyl group comprising an internal carbon-carbon double bond, cycloalkenyl group, tetrazinyl group, azido group, phosphine group, nitrile oxide group, nitrone group, nitrile imine group, diazo group, ketone group, (O-alkyl)hydroxylamino group, hydrazine group, halogenated N- maleimidyl group, 1,1 -bis (sulfonylmethyl)methylcarbonyl group or elimination derivatives thereof, carbonyl halide group, or an allenamide group, each of which may be optionally substituted. In some embodiments, the reactive substituent comprises a cycloalkene group, a cycloalkyne group, or an optionally substituted (hetero)cycloalkynyl group.

In some embodiments, the anti-CD117 ADC comprises an anti-CD117 antibody conjugated to an amatoxin of formula I as disclosed herein, via a linker and a chemical moiety Z. In some embodiments, the linker includes a hydrazine, a disulfide, a thioether or a dipeptide. In some embodiments, the linker includes a dipeptide selected from Val-Ala and Val-Cit. In some embodiments, the linker includes a para-aminobenzyl group (PAB). In some embodiments, the linker includes the moiety PAB-Cit-Val. In some embodiments, the linker includes the moiety PAB-Ala-Val. In some embodiments, the linker includes a -((C=0)(CH₂)_n - unit, wherein n is an integer from 1-6. In some embodiments, the linker is -PAB-Cit-Val- ((C=0)(CH₂)n-. In some embodiments, the linker includes a -(CH2)_n- unit, where n is an integer from 2-6. In some embodiments, the linker is -PAB-Cit-Val-((C=0)(CH2)_n- In some embodiments, the linker is -PAB-Ala-Val-((C=0)(CH2)_n- In some embodiments, the linker is -(CH2)n- In some embodiments, the linker is -((CH2)_n-, wherein n is 6. In some embodiments, the chemical moiety Z is selected from Table 3 or Table 4. In some embodiments, the chemical moiety Z is

where S is a sulfur atom which represents the reactive substituent present within an antibody, or antigen-binding fragment thereof, that binds CD117 (e.g., from the -SH group of a cysteine residue).

In some embodiments, an amatoxin as disclosed herein is conjugated to a linker- reactive moiety -L-Z' having the following formula:

where the wavy line indicates the point of attachment to a substituent on the cytotoxin (e.g., an amatoxin). This linker-reactive substituent group L-Z' may alternatively be referred to as N-beta-maleimidopropionyl-Val-Ala-para-aminobenzyl (BMP-Val-Ala-PAB).

In some embodiments, an amatoxin as disclosed herein is conjugated to a linker- reactive moiety -L-Z' having the following formula:

where the wavy line indicates the point of attachment to a substituent on the cytotoxin (e.g., an amatoxin). This linker-reactive substituent group L-Z' may alternatively be referred to as N-beta-maleimidopropyl-Val-Cit-para-aminobenzyl (BMP-Val-Cit-PAB).

In some embodiments, the linker-reactive substituent group structure L-Z', prior to conjugation with the antibody or antigen binding fragment thereof, is:

In some embodiments, the linker L and the chemical moiety Z, taken together as L-Z, is

where S is a sulfur atom which represents the reactive substituent present within an antibody, or antigen-binding fragment thereof, such as an anti-CD117 antibody (e.g., from the -SH group of a cysteine residue). The wavy line at the linker terminus indicates the point of attachment to the amatoxin.

In some embodiments, the linker L and the chemical moiety Z, after conjugation to the antibody, taken together as L-Z-Ab, has the structure:

where S is a sulfur atom which represents the reactive substituent present within an antibody, or antigen-binding fragment thereof, such as an anti-CD-117 antibody. The wavy line at the linker terminus indicates the point of attachment to the amatoxin.

One of skill in the art will recognize the linker- reactive substituent group structure, prior to conjugation with the antibody or antigen binding fragment thereof, includes a maleimide as the group Z'. The foregoing linker moieties and amatoxin-linker conjugates, among others useful in conjunction with the compositions and methods described herein, are described, for example, in U.S. Patent Application Publication No. 2015/0218220 and Patent Application Publication No. WO2017/149077, the disclosure of each of which is incorporated herein by reference in its entirety.

Preparation of Antibody-Drug Conjugates In the ADCs as disclosed herein, an ant-CD117 antibody or antigen binding fragment thereof is conjugated to one or more cytotoxic drug moieties (D), e.g. about 1 to about 20 drug moieties per antibody, through a linker L and a chemical moiety Z as disclosed herein. The ADCs of the present disclosure may be prepared by several routes, employing organic chemistry reactions, conditions, and reagents known to those skilled in the art, including: (1) reaction of a reactive substituent of an antibody or antigen binding fragment thereof with a bivalent linker reagent to form Ab-Z-L as described herein above, followed by reaction with a drug moiety D; or (2) reaction of a reactive substituent of a drug moiety with a bivalent linker reagent to form D-L-Z, followed by reaction with a reactive substituent of an antibody or antigen binding fragment thereof as described herein above to form an ADC of formula D-L- Z-Ab, such as Am-Z-L-Ab. Additional methods for preparing ADC are described herein.

In another aspect, the antibody or antigen binding fragment thereof has one or more lysine residues that can be chemically modified to introduce one or more sulfhydryl groups. The ADC is then formed by conjugation through the sulfhydryl group's sulfur atom as described herein above. The reagents that can be used to modify lysine include, but are not limited to, N-succinimidyl S-acetylthioacetate (SATA) and 2-lminothiolane hydrochloride (Traut's Reagent).

In another aspect, the antibody or antigen binding fragment thereof can have one or more carbohydrate groups that can be chemically modified to have one or more sulfhydryl groups. The ADC is then formed by conjugation through the sulfhydryl group's sulfur atom as described herein above.

In yet another aspect, the antibody can have one or more carbohydrate groups that can be oxidized to provide an aldehyde (-CHO) group (see, for e.g., Laguzza, et al., J. Med. Chem. 1989, 32(3), 548-55). The ADC is then formed by conjugation through the corresponding aldehyde as described herein above. Other protocols for the modification of proteins for the attachment or association of cytotoxins are described in Coligan et al., Current Protocols in Protein Science, vol. 2, John Wiley & Sons (2002), incorporated herein by reference.

Methods for the conjugation of linker-drug moieties to cell-targeted proteins such as antibodies, immunoglobulins or fragments thereof are found, for example, in U.S. Pat. No. 5,208,020; U.S. Pat. No. 6,441 ,163; W02005037992; W02005081711 ; and W02006/034488, all of which are hereby expressly incorporated by reference in their entirety.

The foregoing linker moieties and amatoxin-linker conjugates, among others useful in conjunction with the compositions and methods described herein, are described, for example, in U.S. Patent Application Publication No. 2015/0218220 and Patent Application Publication No. WO2017/149077, the disclosure of each of which is incorporated herein by reference in its entirety. The foregoing linker moieties and amatoxin-linker conjugates, among others useful in conjunction with the compositions and methods described herein, are described, for example, in U.S. Patent Application Publication No. 2015/0218220 and Patent Application Publication No. WO2017/149077, the disclosure of each of which is incorporated herein by reference in its entirety.

In one embodiment, the CD117 antibodies, or antigen-binding fragments, described herein may be bound to an amatoxin so as to form an ADC represented by the formula Ab- Z-L-Am, wherein Ab is the CD117 antibody, or antigen-binding fragment thereof, L is a linker, Z is a chemical moiety and Am is an amatoxin, each as described herein.

In some embodiments, Am-L-Z-Ab is one of (SEQ ID NOS 298, 298, and 298):

In some embodiments, Am-L-Z-Ab is (SEQ ID NO: 299):

In some instances, the anti-CD117 ADC has the structure of formula (III) (SEQ ID NO: 285):

wherein:

X is S or-S(O)-;

L is a linker;

Z is a chemical moiety formed by a coupling reaction between a reactive substituent present on L and a reactive substituent present within the anti-CD117 antibody; and Ab is the anti-CD117 antibody. In some embodiments, L is a non-cleavable linker;

In some embodiments, an anti-CD117 ADC described herein has the structure of formula (Ilia) (SEQ ID NO: 286):

(Ilia). or formula (lllb) (SEQ ID NO: 287):

In some instances, the anti-CD117 ADC has the structure of formula (IV) (SEQ ID NO: 288):

a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein Ab is the anti-CD117 antibody.

In some instances, the anti-CD117 ADC has the structure of formula (IVa) (SEQ ID NO: 289):

a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein Ab is the anti-CD117 antibody.

In some instances, the anti-CD117 ADC has the structure of formula (IVb) (SEQ ID NO: 29):

a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein Ab is the anti-CD117 antibody. Amatoxins that may be used in the ADCs described herein are also provided in WO

2020/216947, which is incorporated by reference herein.

Example

The following examples are put forth so as to provide those of ordinary skill in the art with a description of how the compositions and methods described herein may be used, made, and evaluated, and are intended to be purely exemplary of the present disclosure and are not intended to limit the scope of what the inventors regard as their invention.

In the following examples, the therapeutic antibody is anti-CD117 antibody Ab85. Example 1 : Preparation of Antibody Cocktail

Antibody cocktails used in Example 2 (below) were prepared as follows. LiveDead Aqua (ThermoFisher, Cat # L34957) supplied as lyophilized stock. As needed, dye reconstituted in 50 pl_ DMSO and aliquoted into 5 mI_ aliquots, was stored at -20°C. For each experiment, one 5mI_ aliquot thawed to room temperature and 45 mI_ 1x PBS added. 5 mI_ of this stock is used per sample. Six 5 ml. falcon tubes labeled for unstained and five panel conditions for each sample as described below:

A master mix of common markers for all tubes was prepared as follows:

47.5 mI_ mix added to appropriate tubes. Panel-specific antibodies (see below) were added to appropriate tubes:

Samples were mixed by briefly vortexing and incubated at room temperature for 20 minutes. 3 ml. 1x BD Lyse (BD Biosciences, Cat # 349202) were added to each tube. Samples were mixed by inverting and incubated at room temperature for 10 minutes. All tubes were centrifuged at 540 g for 4 minutes at room temperature, and the supernatant was removed by decanting and the cells were resuspended in residual buffer by briefly vortexing. The tubes washed with 2 mL cold FCM buffer and centrifuged at 540 g for 4 minutes at room temperature. Supernatant removed by decanting and cells resuspended in residual volume buffer by briefly vortexing. Tubes transferred into 5 mL falcon flow tubes, 350 pL cold FCM (fixation) was buffer added and the tubes were placed on ice or refrigerated at 2-8 °C until acquisition on the Canto A.

Example 2: Reagent Selection for Receptor Occupancy (RO) assay

CD117 receptor occupancy by a therapeutic antibody can be determined in an in vitro or ex vivo assay based on flow cytometric analysis of CD117-expressing cells in whole blood. Since receptor occupancy is typically measured in whole blood system, the assay is dependent on the target expression levels of circulating cells. While high expression levels of the target receptor (i.e. the CD117 receptor) and an abundant population of circulating cells is ideal, in practice however, this is not always the case. As described in more detail below, it has been demonstrated that non-ideal conditions can be solved using a high affinity detection antibody (both a competing antibody (i.e., to measure free receptor) and a non competing antibody (i.e., to measure total receptor)) and a strong fluorophore signal.

In order to assess appropriate competing and non-competing anti-CD117 antiboides for the receptor occupancy assay, octet binding studies were performed with a number of different anti-CD117 antibodies to determine their ability to bind competitively or non- competitively with therapeutic antibody Ab85.

The results of the binding assays showed that the anti-CD117 antibody SR-1 (BioXcell (West Lebanon, NFI)) and Ab85 demonstrated competitive binding with the therapeutic antibody, while the anti-CD117 antibody YB5.B8 (Invitrogen), anti-CD117 antibody 104D2 (BioLegend) and Ab67 demonstrated non-competitive binding with the therapeutic antibody (data not shown).

In order to assess the signal to background range of various fluorophore-labeled anti- CD117 antibodies, an assay was performed to measure the geometric mean fluorescence intensity (gMFI) of the aforementioned competing and non-competing antibodies labeled with a variety of detectable agents (Fig. 1). The antibodies were titrated in the presence of CD117+ cells (Kasumi-1 cells; Fig. 2A) and a negative control (Kasumi-1 KO cells; Fig. 2B), and analyzed by flow cytometry. The data are summarized in Fig. 3 and demonstrated that the gMFI for Alexa Fluor 647 (AF647) conjugates were superior to the other fluorophores tested, independent of antibody backbone. Flowever, the data suggested that the AF647 signal was non-specfic at concentrations higher than 1 nM (Fig. 3).

In order to assess the appropriate detectable agents for use in a blood sample taken from a human patient who does not have a high CD117 expression level in blood, a whole blood spike-in assay was developed (Fig. 4). Briefly, a sample of whole blood from a healthy human subject was spiked with either hematopoietic stem cells (FISCs) or a CD117+ cell line (e.g., Kasumi-1 cells) at 10% of whole blood cell count (WBC) and stained with the fluorophore-labeled anti-CD117 antibodies Fig. 4). After cell lysis and washing steps, the resulting samples were analyzed using a flow cytometer to measure the gMFI. Representative data for the anti-CD117 antibody 104D2-labeled with phycoerythrin (i.e.,

“104D2-PE”) are provided in Fig. 5 and show the readout for single color whole blood spike- in assay using a spike of Kasumi cells (Fig. 5B) was significantly higher in comparison to the readout for single color whole blood (Fig. 5A). In order to determine the preferred fluorophore and the appropriate concentration where the preferred fluorophore is saturating (1.25 per 200uL for Ab85-PE and 10uL per 200uL for 104D2 BV421 (data not shown)), a series of whole blood spike-in assay were performed by staining with 3 different antibody cocktails, each having a different CD117 fluorophore (Figs. 6A-6C; the “fluors” (i.e., fluorophores) were purchased from Biolegend; catalog numbers 303432, 301720, 317330, 343610, 303504, 304014, 302242, 420404 and 313204) and performing a dose titration of the CD117 fluorophore and analyzed using flow cytometry (Fig. 7). The data show that the phycoerythrin (PE; red color channel) had better dynamic range (~ 290) compared to Brilliant Violet™ 421 (BV421 ; blue color channel) (Figs. 8A, 8B and 8D). In addition, Alexa Fluor 647 (AF647; red color channel) had a lower dynamic range (~ 21) due to high background (Figs. 8C and 8D).

An assay was then performed to determine CD117 receptor occupancy based on the previously described whole blood spike-in assay format. Briefly, a sample of whole blood from a healthy human subject was spiked with either hematopoietic stem cells (FISCs) or a CD117+ cell line (e.g., Kasumi-1 cells) at 10% of whole blood cell count (WBC) and incubated with the therapeutic antibody (up to 1 nM) and increasing concentrations of Ab85 conjugated to either fluorophore PE (i.e., Ab85-PE (a competing antibody)) or fluorophore AF647 (i.e., Ab85-AF647 (a competing antibody)) in the presence of increasing levels of antibody 104D2 conjugated to BV421 (i.e., a non-competing antibody). Occupancy was measured on CD117 expressing cells using flow cytometry. The results of the assay are provided in Fig. 9 and show that in the presence of bound therapeutic antibody, Ab85-PE is blocked from binding CD117 in a concentration dependent manner, providing a measure of CD117 receptor occupancy for healthy human subjects. Under these conditions, the assay is capable of detecting saturation of receptor binding by the therapeutic antibody (i.e. 100%

RO) in a concentration dependent manner.

Based on the results of the whole blood spike-in assays provided above, the data showed that the AF647 fluorophore had a significantly high background, and therefore, an insufficient dynamic range. The data for the PE and BV421 fluorophores, however, demonstrated significantly higher (and relatively similar) dynamic ranges. Accordingly, the competing anti-CD117 antibody and non-competing anti-CD117 antibody for the receptor occupancy assay were the Ab85 labeled with the fluorophore PE and anti-CD117 antibody 104D2 conjugated with the fluorophore BV421 , respectively.

Example 3: Dose determination using receptor occupancy (RO) assay

Receptor occupancy will be determined using a pre-dose, 2h, 4h, 8h, 24h, 36h and 48h post-dose peripheral blood samples from the human patient. The dosing schedule is typically designed to achieve exposures that result in sustained receptor occupancy (RO) based on typical pharmacokinetic properties of a therapeutic antibody. The blood samples will be fixed immediately post collection to chemically preserve the sample and shipped for subsequent analysis using quantitative flow cytometry. To determine receptor occupancy, each sample will be split for analysis with two detection monoclonal antibodies (MAbs), one competing with the drug (antibody) to determine the number of free (unbound) CD117 receptors, and one non-competing MAb binding to a different epitope on the receptor to determine the total number of CD117 receptors on the cell surface. By using detection MAbs conjugated to Brilliant Violet™ 421 (BV421) with a defined antibody: BV421 ratio, the absolute receptor numbers will be determined. By using detection MAbs conjugated to phycoerythin (PE) fluorescent protein with a defined antibody: PE ratio, the free receptor numbers will be determined using a standard curve generated with quantibrite beads with defined and varying numbers of PE molecules. The percentage receptor occupancy at each time point will be derived from the free and total CD117 receptor copy numbers using the formula % RO = 100 x (1- (free receptors/total receptors). In certain embodiments, the % RO free receptors can be determined using the following formula:

In other embodiments, the % RO total receptors can be determined using the following formula:

Analysis of the pre-dose, 2h, 4h, 8h, 24h, 36h, and 48h samples will allow measurement of receptor occupancy as well as duration of target engagement to guide dose escalation. If sustained occupancy (>90% occupancy at 24h post-dose) is achieved in subjects at a given dose level, further dose escalation will be stopped.

Other Embodiments

All publications, patents, and patent applications mentioned in this specification are incorporated herein by reference to the same extent as if each independent publication or patent application was specifically and individually indicated to be incorporated by reference.

While the invention has been described in connection with specific embodiments thereof, it will be understood that it is capable of further modifications and this application is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the invention that come within known or customary practice within the art to which the invention pertains and may be applied to the essential features hereinbefore set forth, and follows in the scope of the claims.

Other embodiments are within the claims.

Claims

CLAIMS What is claimed is:

1. A method for treating a human subject in need thereof, comprising: determining CD117 receptor occupancy of a therapeutic anti-CD117 antibody on

CD117 expressing cells from a human subject, said method comprising performing a receptor occupancy (RO) assay on a sample from the human subject, and determining the percent receptor occupancy of the therapeutic anti-CD117 antibody on CD117 expressing cells from the sample; and administering to the human subject an amount of the therapeutic anti-CD117 antibody that is less than 100 times an amount of the therapeutic anti-CD117 antibody sufficient to result in about 100% CD117 receptor occupancy as determined by the RO assay, wherein the therapeutic anti-CD117 antibody depletes CD117+ cells in the human subject thereby treating the human subject.

2. The method of claim 1 , wherein the therapeutic anti-CD117 antibody comprises a heavy chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 105, 106, and 107, respectively, and comprises a light chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 108, 109, and 110, respectively.

3. The method of claim 1 , wherein the therapeutic anti-CD117 antibody, or antigen binding fragment thereof, comprises a light chain variable region comprising the amino acid sequence set forth as SEQ ID NO: 104, and a heavy chain variable region comprising the amino acid sequence set forth as SEQ ID NO: 103.

4. The method of claim 1 , wherein the therapeutic anti-CD117 antibody comprises a heavy chain having the amino acid sequence as set forth as SEQ ID NO: 138, and a light chain having an amino acid sequence set forth as SEQ ID NO: 144.

5. The method of any one of claims 1 -4, wherein the therapeutic anti-CD117 antibody is an lgG1 isotype.

6. The method of any one of claims 1-5, wherein the human subject is administered an amount of the therapeutic anti-CD117 antibody that is less than an amount of the therapeutic anti-CD117 antibody sufficient to result in about 100% CD117 receptor occupancy as determined by the RO assay.

7. The method of any one of claims 1-5, wherein the human subject is administered an amount of the therapeutic anti-CD117 antibody that is less than an amount of the therapeutic anti-CD117 antibody sufficient to result in about 80% CD117 receptor occupancy as determined by the RO assay.

8. The method of any one of claims 1-5, wherein the RO assay comprises contacting the sample with an anti-CD117 antibody, or an antigen binding fragment thereof, that cross blocks the therapeutic anti-CD117 antibody.

9. The method of any one of claims 1 -8, wherein the therapeutic anti-CD117 antibody that is administered to the human subject as an anti-CD117 antibody drug conjugate (ADC) comprising the therapeutic anti-CD117 antibody conjugated via a linker to an amatoxin.

10. The method of claim 9, wherein the ADC has the structure of formula (III):

or a stereoisomer thereof; wherein:

X is S or S(O); L is a linker;

Z is a chemical moiety formed by a coupling reaction between a reactive substituent Z' present on L and a reactive substituent present within the anti-CD117 antibody; and Ab is the anti-CD117 antibody.

11. The method of claim 10, wherein the ADC has the structure of formula (Ilia):

(Ilia). or formula (lllb):

(lllb).

12. The method of claim 10 or 11 , wherein L comprises one or more moieties selected from a bond, -(C=0)-, a -C(0)NH- group, an -OC(0)NH- group, C₁-C₆ alkylene, C₁-C₆ heteroalkylene, C2-C₆ alkenylene, C2-C₆ heteroalkenylene, C2-C₆ alkynylene, C2-C₆ heteroalkynylene, C₃-C₆ cycloalkylene, heterocycloalkylene, arylene, heteroarylene, a - (CH₂CH₂0)p- group where p is an integer from 1-6; a solubility enhancing group, and a peptide; wherein each C1-C₆ alkylene, C1-C₆ heteroalkylene, C2-C₆ alkenylene, C2-C₆ heteroalkenylene, C2-C₆ alkynylene, C2-C₆ heteroalkynylene, C₃-C₆ cycloalkylene, heterocycloalkylene, arylene, or heteroarylene may optionally be substituted with from 1 to 5 substituents independently selected for each occasion from the group consisting of alkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, alkaryl, alkyl heteroaryl, amino, ammonium, acyl, acyloxy, acylamino, aminocarbonyl, alkoxycarbonyl, ureido, carbamate, aryl, heteroaryl, sulfinyl, sulfonyl, hydroxyl, alkoxy, sulfanyl, halogen, carboxy, trihalomethyl, cyano, hydroxy, mercapto, and nitro; or each C1-C6 alkylene, C1-C6 heteroalkylene, C2-C6 alkenylene, C2-C6 heteroalkenylene, C2-C6 alkynylene, C2-C6 heteroalkynylene, C3-C6 cycloalkylene, heterocycloalkylene, arylene, or heteroarylene may optionally be interrupted by one or more heteroatoms selected from O, S and N.

13. The method of claim 10, wherein the ADC has the structure of formula (IV):

a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein Ab is the anti- CD117 antibody.

14. The method of claim 13, wherein the ADC has the structure of formula (IVa):

a stereoisomer thereof, or a pharmaceutically acceptable salt thereof.

15. The method of claim 13, wherein the ADC has the structure of formula (IVb):

a stereoisomer thereof, or a pharmaceutically acceptable salt thereof.

16. A method for determining receptor occupancy of a therapeutic anti-CD117 antibody on a CD117 expressing cell from a human subject, said method comprising performing a receptor occupancy (RO) assay on a sample obtained from a human subject, and determining the percent receptor occupancy of the therapeutic anti-CD117 antibody on the CD117 expressing cell from the sample, wherein the therapeutic anti-CD117 antibody comprises a heavy chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 105, 106, and 107, respectively, and comprises a light chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 108, 109, and 110, respectively.

17. The method of claim 16, wherein the RO assay comprises the steps of:

(a) contacting the sample with an amount of the anti-CD117 therapeutic antibody,

(b) contacting the sample with an amount of a second anti-CD117 antibody, or an antigen-binding fragment thereof, that competes with the anti-CD117 therapeutic antibody for binding to CD117 on the CD117 expressing cell, wherein the second anti-CD117 antibody, or an antigen-binding fragment thereof, is labelled with a first detectable agent;

(c) detecting the amount of the second antibody bound to the CD117 on the cell surface on the CD117 expressing cell in the sample, and

(d) calculating the percentage of CD117 bound by the anti-CD117 therapeutic antibody, thereby determining receptor occupancy of the therapeutic anti-CD117 antibody.

18. A method for determining receptor occupancy of a therapeutic anti-CD117 antibody on a CD117 expressing cell from a human subject who has been administered the therapeutic antibody, said method comprising performing a receptor occupancy (RO) assay on a sample from a human subject, and determining the percent receptor occupancy of the therapeutic anti-CD117 antibody on the CD117 expressing cell from the sample, and wherein therapeutic anti-CD117 antibody comprises a heavy chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 105, 106, and 107, respectively, and comprises a light chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 108, 109, and 110, respectively.

19. The method of claim 18, wherein the RO assay comprises the steps of:

(a) obtaining a sample from the human subject administered the therapeutic antibody;

(b) contacting the sample with an amount of a second anti-CD117 antibody, or an antigen-binding fragment thereof, that competes with the anti-CD117 therapeutic antibody for binding to a CD117 receptor, wherein the second anti-CD117 antibody, or an antigen binding fragment thereof, is labelled with a first detectable agent;

(c) detecting the amount of the second antibody bound to the CD117 receptor on the CD117 expressing cell in the sample, and

(d) calculating the percentage of CD117 bound by the anti-CD117 therapeutic antibody, thereby determining receptor occupancy of the therapeutic anti-CD117 antibody.

20. The method of claim 17 or19, wherein calculating the percentage of CD117 bound by the anti-CD117 therapeutic antibody further comprises the steps contacting the sample (or an equivalent sample) with an amount of a third anti- CD117 antibody, or an antigen-binding fragment thereof, that does not compete with the anti-CD117 therapeutic antibody for binding to a CD117 receptor, wherein the third anti- CD117 antibody, or an antigen-binding fragment thereof, is labelled with a second detectable agent, and detecting the amount of the third anti-CD117 antibody, or an antigen-binding fragment thereof, bound to the CD117 receptor on the CD117 expressing cell in the sample, thereby determining the total amount of the CD117 receptor on the CD117 expressing cell in the sample.

21. The method of claim 20, wherein the second detectable agent is detected at a different emission wavelength than the first detectable agent.

22. The method of any one of claims 17-21, wherein the receptor occupancy of the therapeutic anti-CD117 antibody is determined by detecting a signal from the first detectable agent, detecting a signal from the second detectable agent, and comparing the signals in order to determine the percent receptor occupancy.

23. The method of any one of claims 17-22, wherein the detecting is determined using flow cytometry.

24. The method of any one of claims 17-23, wherein the second anti-CD117 antibody, or an antigen-binding fragment thereof, is an antigen binding fragment of the therapeutic antibody, a competitive anti-CD117 antibody that cross blocks the therapeutic antibody, or an antigen-binding fragment of a competitive anti-CD117 antibody that cross blocks the therapeutic antibody.

25. The method of any one of claims 17-23, wherein the detectable agent is selected from the group consisting of a fluorescent label, a luminescent label, a bioluminescent label, a magnetic label, a radiolabel, and an enzyme.

26. The method of claim 25, wherein the detectable agent is a fluorescent label selected from the group consisting of phycoerythrin (PE), allophycocyanin (APC), BD Horizon Brilliant™ Violet 421 (BV421), BD Horizon Brilliant™ Violet 510 (BV510), BD Horizon Brilliant™ Violet 785 (BV785), fluorescein (FITC), PerCP-Cy5.5, and Alexa Fluor® 647 (AF647).

27. The method of claim 26, wherein the PE is phycoerythrin (PE)-Dazzle 594, PE/Cy5, PE/Cy5.5 and PE/Cy7.

28. The method of claim 26, wherein the APC is allophycocyanin-Cy7.

29. The method of claim 20, wherein the third anti-CD117 antibody comprises antibody 104D2 conjugated to BV421.

30. The method of claim 18 or 29, wherein the second antibody is the anti-CD117 therapeutic antibody conjugated to phycoerythrin.

31. The method of claim 19, wherein the sample is obtained from the human subject immediately following administration of the anti-CD117 therapeutic antibody to the human subject.

32. The method of claim 19, wherein the sample is obtained from the human subject at about 2 hours after administration of the anti-CD117 therapeutic antibody to the human subject.

33. The method of claim 19, wherein the sample is obtained from the human subject at about 4 hours after administration of the anti-CD117 therapeutic antibody to the human subject.

34. The method of claim 19, wherein the sample is obtained from the human subject at about 8 hours after administration of the anti-CD117 therapeutic antibody to the human subject.

35. The method of claim 19, wherein the sample is obtained from the human subject at about 24 hours after administration of the anti-CD117 therapeutic antibody to the human subject.

36. The method of claim 19, wherein the sample is obtained from the human subject at about 36 hours after administration of the anti-CD117 therapeutic antibody to the human subject.

37. The method of claim 19, wherein the sample is obtained from the human subject at about 48 hours after administration of the anti-CD117 therapeutic antibody to the human subject.

38. The method of any one of claims 16-37, wherein the sample comprises a CD117+ cell.

39. The method of any one of claims 16-37, wherein the sample comprises a leukemic blast cell, a hematopoietic stem cell (HSC), a hematopoietic stem and progenitor cell (HSPCs).

40. The method of any one of claims 16-39, wherein the sample is whole blood or bone marrow from the human subject.

41. The method of any one of claims 16-40, wherein the second anti-CD117 antibody, or the antigen binding fragment thereof, binds to the same epitope as the therapeutic antibody.

42. The method of claim 16, wherein the RO assay comprises contacting the sample with a) the anti-CD117 therapeutic antibody, the antigen binding fragment thereof, and b) a second antibody, or an antigen-binding fragment thereof, which is labelled and specifically binds to the therapeutic anti-CD117 antibody, or an antigen binding fragment thereof, and contacting the sample (or an equivalent sample) with a third anti-CD117 antibody, or an antigen-binding fragment thereof, which does not compete with the therapeutic anti- CD117 antibody for binding to human CD117, wherein the second antibody, or antigen-binding fragment thereof, does not cross react with the third anti-CD117 antibody, or an antigen-binding fragment thereof, and wherein the second anti-CD117 antibody, or antigen binding fragment thereof, is labelled with a first detectable agent and the third antibody, or an antigen-binding fragment thereof, is labeled with a second detectable agent.

43. The method of any one of claims 16-42, wherein the therapeutic anti-CD117 antibody, or antigen binding fragment thereof, comprises a light chain variable region comprising the amino acid sequence set forth as SEQ ID NO: 104, and a heavy chain variable region comprising the amino acid sequence set forth as SEQ ID NO: 103.

44. The method of any one of claims 16-43, wherein the therapeutic anti-CD117 antibody comprises a heavy chain having the amino acid sequence as set forth as SEQ ID NO: 138, and a light chain having an amino acid sequence set forth as SEQ ID NO: 144.

45. The method of any one of claims 16-44, wherein the therapeutic anti-CD117 antibody is an lgG1 isotype.

46. The method of any one of claims 16-45, further comprising determining a dose of the therapeutic antibody for treating a human subject in need based on the percent receptor occupancy.

47. A method of depleting CD117 expressing cells in a human subject, comprising administering an dose of an anti-CD117 antibody drug conjugate (ADC) comprising an anti- CD117 antibody conjugated to an amatoxin via a linker, to the human subject, wherein the dose is determined using the method of any one of claims 16-45, and wherein the anti- CD117 antibody comprises a heavy chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 105, 106, and 107, respectively, and comprises a light chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 108, 109, and 110, respectively.

48. A method of treating a human subject in need thereof, comprising administering an dose of an anti-CD117 antibody drug conjugate (ADC) comprising an anti-CD117 antibody conjugated to an amatoxin to the human subject, wherein the dose is determined using the method of any one of claims 16-45, and wherein the anti-CD117 antibody comprises a heavy chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 105, 106, and 107, respectively, and comprises a light chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 108, 109, and 110, respectively.

49. A method of conditioning a human subject, comprising administering an dose of an anti-CD117 antibody drug conjugate (ADC) comprising an anti-CD117 antibody conjugated to an amatoxin to the human subject, wherein the dose is determined using the method of any one of claims 16-45, and wherein the anti-CD117 antibody comprises a heavy chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 105, 106, and 107, respectively, and comprises a light chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 108, 109, and 110, respectively.

50. The method of any one of claims 47-49, wherein the sample is from the same human subject.

51. The method of any one of claims 47-49, wherein the amount administered to the human subject is less than 1.1 times an amount of the therapeutic anti-CD117 antibody sufficient to result in about 100% CD117 receptor occupancy as determined by the RO assay.

52. The method of any one of claims 47-49, wherein the dose resulted in at least about 80% receptor occupancy in the RO assay.

53. The method of any one of claims 47-49, wherein the dose resulted in at least about 85% receptor occupancy in the RO assay.

54. The method of any one of claims 47-49, wherein the dose resulted in at least about 90% receptor occupancy in the RO assay.

55. The method of any one of claims 47-49, wherein the dose resulted in at least about 95% receptor occupancy in the RO assay.

56. The method of any one of claims 47-49, wherein the dose resulted in at least about 99% receptor occupancy in the RO assay.

57. A method of conditioning a human subject in need thereof, the method comprising administering to the human subject an amount of an anti-CD117 ADC sufficient to achieve and/or maintain a receptor occupancy of at least about 80% as determined according to any one of the methods of claims 16-30, wherein the anti-CD117 ADC comprises an anti-CD117 antibody conjugated to an amatoxin, and wherein the anti-CD117 antibody comprises a heavy chain variable region comprising CDR1 , CDR2 and CDR3 as set forth in SEQ ID NO: 105, 106, and 107, respectively, and a light chain variable region comprising CDR1, CDR2 and CDR3 as set forth in SEQ ID NO: 108, 109, and 110, respectively.

58. The method of claim 57, wherein the receptor occupancy achieved and/or maintained is at least about 85%.

59. The method of claim 57, wherein the receptor occupancy achieved and/or maintained is at least about 90%.

60. The method of claim 57, wherein the receptor occupancy achieved and/or maintained is at least about 95%.

61 . The method of claim 57, wherein the receptor occupancy achieved and/or maintained is at least about 99%.

62. The method of claim 57, wherein the receptor occupancy achieved and/or maintained is about 100%.

63. The method of any one of claims 47-62, wherein the ADC has the structure of formula (III):

or a stereoisomer thereof; wherein:

X is S or S(O);

L is a linker;

Z is a chemical moiety formed by a coupling reaction between a reactive substituent Z' present on L and a reactive substituent present within the anti-CD117 antibody; and

Ab is the anti-CD117 antibody.

64. The method of any one of claims 47-62, wherein the ADC has the structure of formula (Ilia):

(Ilia). or formula (lllb):

65. The method of claim 64, wherein L comprises one or more moieties selected from a bond, -(C=0)-, a -C(0)NH- group, an -0C(0)NH- group, C₁-C₆ alkylene, C₁-C₆ heteroalkylene, C2-C₆ alkenylene, C2-C₆ heteroalkenylene, C2-C₆ alkynylene, C2-C₆ heteroalkynylene, C₃-C₆ cycloalkylene, heterocycloalkylene, arylene, heteroarylene, a - (CH₂CH₂0)p- group where p is an integer from 1-6, a solubility enhancing group, and a peptide; wherein each C1-C₆ alkylene, C1-C₆ heteroalkylene, C2-C₆ alkenylene, C2-C₆ heteroalkenylene, C2-C₆ alkynylene, C2-C₆ heteroalkynylene, C₃-C₆ cycloalkylene, heterocycloalkylene, arylene, or heteroarylene may optionally be substituted with from 1 to 5 substituents independently selected for each occasion from the group consisting of alkyl, alkenyl, alkynyl, cycloalkyl, heterocycloalkyl, alkaryl, alkyl heteroaryl, amino, ammonium, acyl, acyloxy, acylamino, aminocarbonyl, alkoxycarbonyl, ureido, carbamate, aryl, heteroaryl, sulfinyl, sulfonyl, hydroxyl, alkoxy, sulfanyl, halogen, carboxy, trihalomethyl, cyano, hydroxy, mercapto, and nitro; or each C1-C₆ alkylene, C1-C₆ heteroalkylene, C2-C₆ alkenylene, C2-C₆ heteroalkenylene, C2-C₆ alkynylene, C2-C₆ heteroalkynylene, C₃-C₆ cycloalkylene, heterocycloalkylene, arylene, or heteroarylene may optionally be interrupted by one or more heteroatoms selected from O, S and N.

66. The method of any one of claims 47-62, wherein the ADC has the structure of formula (IV):

a stereoisomer thereof, or a pharmaceutically acceptable salt thereof, wherein Ab is the anti- CD117 antibody.

67. The method of any one of claims 47-62, wherein the ADC has the structure of formula (IVa):

a stereoisomer thereof, or a pharmaceutically acceptable salt thereof.

68. The method of any one of claims 47-62, wherein the ADC has the structure of formula (IVb):

a stereoisomer thereof, or a pharmaceutically acceptable salt thereof.

69. The method of any one of claims 47-68, further comprising administering a stem cell transplant to the human subject.

70. The method of claim 69, wherein the stem cell transplant comprises HSCs.

71. The method of claim 69, wherein the stem cell transplant consists essentially of

HSCs.

72. The method of claim 70 or 71 , wherein the HSCs are allogeneic.

73. The method of any one of claims 1-72, wherein the human subject has a disorder that would benefit from CD117+ cell depletion.

74. The method of any one of claims 1-72, wherein the human subject is in need of a cell transplant.

75. The method of any one of claims 1-72, wherein the human subject has a stem cell disorder.

76. The method of any one of claims 1-69, wherein the human subject has cancer or an autoimmune disease.

77. The method of claim 76, wherein the cancer is a hematological cancer.

78. The method of claim 77, wherein the hematological cancer is leukemia.

79. The method of claim 78, wherein the leukemia is acute myeloid leukemia.

80. The method of claim 78, wherein the leukemia is acute lymphoblastic leukemia or chronic lymphocytic leukemia.

81. The method of claim 77, wherein the hematological cancer is myelodysplastic syndrome.

82. A method for determining receptor occupancy of a therapeutic anti-CD117 antibody on CD117 expressing cells from a human subject, said method comprising performing a receptor occupancy (RO) assay on a sample from a human subject, and determining the percent receptor occupancy of the therapeutic anti-CD117 antibody on CD117 expressing cells from the sample, wherein the therapeutic anti-CD117 antibody comprises a heavy chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 105, 106, and 107, respectively, and comprises a light chain variable region comprising a CDR1 , CDR2 and CDR3 having an amino acid sequence as set forth as SEQ ID NO: 108, 109, and 110, respectively.