Compositions and methods for the depletion of cd117+ cells

Abstract

The invention provides compositions and methods useful for the depletion of CD117+ cells and for the treatment of various hematopoietic diseases, metabolic disorders, cancers, and autoimmune diseases, among others. Described herein are antibodies, antigen-binding fragments, ligands, and conjugates thereof that can be applied to effect the treatment of these conditions, for instance, by depleting a population of CD117+ cells in a patient, such as a human. The compositions and methods described herein can be used to treat a disorder directly, for instance, by depleting a population of CD117+ cancer cells or autoimmune cells. The compositions and methods described herein can also be used to prepare a patient for hematopoietic stem cell transplant therapy and to improve the engraftment of hematopoietic stem cell transplants by selectively depleting endogenous hematopoietic stem cells prior to the transplant procedure.

1 . A method of depleting a population of CD117+ cells in a human patient, the method comprising administering to the patient an effective amount of an antibody or antigen-binding fragment thereof capable of binding CD117, wherein the antibody or antigen-binding fragment thereof is conjugated to a cytotoxin selected from the group consisting of an amatoxin, pseudomonas exotoxin A, deBouganin, diphtheria toxin, saporin, maytansine, a maytansinoid, an auristatin, an anthracycline, a calicheamicin, irinotecan, SN-38, a duocarmycin, a pyrrolobenzodiazepine, a pyrrolobenzodiazepine dimer, an indolinobenzodiazepine, and an indolinobenzodiazepine dimer, or a variant thereof. 
     
     
         2 .- 8 . (canceled) 
     
     
         9 . A method comprising:
 a. administering to a human patient an antibody or antigen-binding fragment thereof capable of binding CD117 in an amount sufficient to deplete a population of CD117+ cells in the patient; and   b. subsequently administering to the patient a transplant comprising hematopoietic stem cells.   
     
     
         10 . The method of  claim 9 , wherein the antibody or antigen-binding fragment thereof is conjugated to a cytotoxin. 
     
     
         11 . The method of  claim 1 , wherein the antibody or antigen-binding fragment thereof conjugated to a cytotoxin is represented by the formula Ab-Am, wherein Ab is the antibody or antigen-binding fragment thereof and Am an amatoxin represented by formula (I) 
       
         
           
           
               
               
           
         
         wherein R 1  is H, OH, OR A , or OR C ; 
         R 2  is H, OH, OR B , or OR C ;
 R A  and R B , together with the oxygen atoms to which they are bound, combine to form an optionally substituted 5-membered heterocyclolalkyl group; 
 
         R 3  is H, R C , or R D ; 
         R 4 , R 5 , R 6 , and R 7  are each independently H, OH, OR C , OR D , R C , or R D ; 
         R 8  is OH, NH 2 , OR C , OR D , NHR C , or NR C R D ; 
         R 9  is H, OH, OR C , or OR D ; 
         X is —S—, —S(O)—, or —SO 2 —;
 R C  is -L-Z; 
 R D  is substituted C 1 -C 6  alkyl, substituted C 1 -C 6  heteroalkyl, substituted C 2 -C 6  alkenyl, substituted C 2 -C 6  heteroalkenyl, substituted C 2 -C 6  alkynyl, substituted C 2 -C 6  heteroalkynyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl; 
 L is a peptide containing linker; and 
 Z is a chemical moiety formed from a coupling reaction between a reactive substituent present on L and a reactive substituent present within the antibody or antigen-binding fragment thereof. 
 
       
     
     
         12 .- 24 . (canceled) 
     
     
         25 . The method of  claim 1 , wherein the antibody has an isotype selected from the group consisting of IgG, IgA, IgM, IgD, and IgE. 
     
     
         26 . The method of  claim 1 , wherein the antibody or antigen-binding fragment thereof is internalized by a cancer cell, autoimmune cell, or hematopoietic stem cell following administration to the patient. 
     
     
         27 . The method of  claim 1 , wherein the antibody or antigen-binding fragment thereof is capable of promoting necrosis of a cancer cell, autoimmune cell, or hematopoietic stem cell. 
     
     
         28 . (canceled) 
     
     
         29 . The method of  claim 9 , wherein the transplant comprising hematopoietic stem cells is administered to the patient after the concentration of the antibody or antigen-binding fragment thereof has substantially cleared from the blood of the patient. 
     
     
         30 .- 32 . (canceled) 
     
     
         33 . The method of  claim 9 , wherein the patient is suffering from a disorder selected from the group consisting of a stem cell disorder, a hemoglobinopathy disorder, a myelodysplastic disorder, an immunodeficiency disorder, a metabolic disorder and cancer. 
     
     
         34 .- 47 . (canceled) 
     
     
         48 . The method of  claim 33 , wherein the cancer is selected from the group consisting of leukemia, lymphoma, multiple myeloma, and neuroblastoma. 
     
     
         49 .- 82 . (canceled) 
     
     
         83 . A conjugate represented by the formula Ab-Am, wherein Ab is an antibody or antigen-binding fragment thereof that binds CD117 and Am is an amatoxin. 
     
     
         84 . The conjugate of  claim 83 , wherein Am is represented by formula (I) 
       
         
           
           
               
               
           
         
         wherein R 1  is H, OH, OR A , or OR C ; 
         R 2  is H, OH, OR B , or OR C ; 
         R A  and R B , together with the oxygen atoms to which they are bound, combine to form an optionally substituted 5-membered heterocyclolalkyl group; 
         R 3  is H, R C , or R D ; 
         R 4 , R 5 , R 6 , and R 7  are each independently H, OH, OR C , OR D , R C , or R D ; 
         R 8  is OH, NH 2 , OR C , OR D , NHR C , or NR C R D ; 
         R 9  is H, OH, OR C , or OR D ; 
         X is —S—, —S(O)—, or —SO 2 —; 
         R C  is -L-Z; 
         R D  is substituted C 1 -C 6  alkyl, substituted C 1 -C 6  heteroalkyl, substituted C 2 -C 6  alkenyl, substituted C 2 -C 6  heteroalkenyl, substituted C 2 -C 6  alkynyl, substituted C 2 -C 6  heteroalkynyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl; 
         L is a peptide containing linker; and 
         Z is a chemical moiety formed from a coupling reaction between a reactive substituent present on L and a reactive substituent present within the antibody or antigen-binding fragment thereof. 
       
     
     
         85 . The conjugate of  claim 83 , wherein Am is represented by formula (IB) 
       
         
           
           
               
               
           
         
         wherein R 1  is H, OH, OR A , or OR C ; 
         R 2  is H, OH, OR B , or OR C ;
 R A  and R B , together with the oxygen atoms to which they are bound, combine to form an optionally substituted 5-membered heterocyclolalkyl group; 
 
         R 3  is H, R C , or R D ; 
         R 4 , R 5 , R 6 , and R 7  are each independently H, OH, OR C , OR D , R C , or R D ; 
         R 8  is OH, NH 2 , OR C , OR D , NHR C , or NR C R D ; 
         R 9  is H, OH, OR C , or OR D ; 
         X is —S—, —S(O)—, or —SO 2 —;
 R C  is -L-Z; 
 R D  is substituted C 1 -C 6  alkyl, substituted C 1 -C 6  heteroalkyl, substituted C 2 -C 6  alkenyl, substituted C 2 -C 6  heteroalkenyl, substituted C 2 -C 6  alkynyl, substituted C 2 -C 6  heteroalkynyl, substituted cycloalkyl, substituted heterocycloalkyl, substituted aryl, or substituted heteroaryl; 
 L is a peptide containing a linker; and 
 Z is a chemical moiety formed from a coupling reaction between a reactive substituent present on L and a reactive substituent present within the antibody or antigen-binding fragment thereof. 
 
       
     
     
         86 . The conjugate of  claim 83 , wherein the wherein the antibody or antigen-binding fragment thereof is conjugated to the amatoxin by way of a cysteine residue in the Fc domain of the antibody or antigen-binding fragment thereof. 
     
     
         87 . The conjugate of  claim 86 , wherein the cysteine residue is introduced by way of a mutation in the Fc domain of the antibody or antigen-binding fragment thereof. 
     
     
         88 . (canceled) 
     
     
         89 . The conjugate of  claim 86 , wherein the cysteine residue is naturally occurring in the Fc domain of the antibody or antigen-binding fragment thereof. 
     
     
         90 .- 94 . (canceled) 
     
     
         95 . The conjugate of  claim 83 , wherein the antibody or antigen-binding fragment thereof is internalized by a CD117+ cell. 
     
     
         96 .- 99 . (canceled) 
     
     
         100 . A conjugate represented by the formula Ab-Cy, wherein Ab is an antibody or antigen-binding fragment thereof that binds CD117 and Cy is selected from the group consisting of pseudomonas exotoxin A, deBouganin, diphtheria toxin, saporin, maytansine, a maytansinoid, auristatin, an anthracycline, a calicheamicin, irinotecan, SN-38, a duocarmycin, a pyrrolobenzodiazepine, a pyrrolobenzodiazepine dimer, an indolinobenzodiazepine and an indolinobenzodiazepine dimer. 
     
     
         101 .- 112 . (canceled) 
     
     
         113 . The conjugate of  claim 83 , wherein the antibody or antigen-binding fragment thereof comprises the following complementarity determining regions (CDRs):
 a CDR-H1 having the amino acid sequence SYWIG (SEQ ID NO: 1);   a CDR-H2 having the amino acid sequence IIYPGDSDTRYSPSFQG (SEQ ID NO: 2);   a CDR-H3 having the amino acid sequence HGRGYNGYEGAFDI (SEQ ID NO: 3);   a CDR-L1 having the amino acid sequence RASQGISSALA (SEQ ID NO: 4);   a CDR-L2 having the amino acid sequence DASSLES (SEQ ID NO: 5); and   a CDR-L3 having the amino acid sequence CQQFNSYPLT (SEQ ID NO: 6).   
     
     
         114 . The conjugate of  claim 83 , wherein the amatoxin is selected from the group consisting of, α-amanitin, β-amanitin, γ-amanitin, ε-amanitin, amanin, amaninamide, amanullin, amanullinic acid, and proamanullin.