Compositions and methods for the depletion of CD117+ cells

Patent metadata

Field	Value
Publication number	US-10899843-B2
Application number	US-201816168823-A
Country	US
Kind code	B2
Filing date	Oct 23, 2018
Priority date	Oct 24, 2017
Publication date	Jan 26, 2021
Grant date	Jan 26, 2021

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, e.g., acute myeloid leukemia (AML) and autoimmune diseases, among others. Described herein are antibodies, antigen-binding fragments, 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.

First claim

What is claimed is:

1. An isolated anti-CD117 antibody, or antigen-binding fragment thereof, comprising
(i) a heavy chain variable region comprising a CDR1 domain comprising the amino acid sequence as set forth in SEQ ID NO: 145, a CDR2 domain comprising the amino acid sequence as set forth in SEQ ID NO:146, and a CDR3 domain comprising the amino acid sequence as set forth in SEQ ID NO: 147; and a light chain variable region comprising a CDR1 domain comprising the amino acid sequence as set forth in SEQ ID NO: 148, a CDR2 domain comprising the amino acid sequence as set forth in SEQ ID NO:149, and a CDR3 domain comprising the amino acid sequence as set forth in SEQ ID NO: 150; or
(ii) a heavy chain variable region comprising the amino acid sequence as set forth in SEQ ID NO: 143, and a light chain variable region comprising the amino acid sequence as set forth in SEQ ID NO: 144.

2. The anti-CD117 antibody, or antigen-binding fragment thereof, of claim 1 , wherein the antibody, or antigen-binding fragment thereof, binds CD117 with a K D of about 100 nM or less, about 90 nM or less, about 80 nM or less, about 70 nM or less, about 60 nM or less, about 50 nM or less, about 40 nM or less, about 30 nM or less, about 20 nM or less, about 10 nM or less, about 8 nM or less, about 6 nM or less, about 4 nM or less, about 2 nM or less, or about 1 nM or less as determined by a Bio-Layer Interferometry (BLI) assay.

3. The anti-CD117 antibody, or antigen-binding fragment thereof, of claim 1 , wherein the antibody, or antigen-binding fragment thereof, is human.

4. The anti-CD117 antibody, or antigen-binding fragment thereof, of claim 1 , wherein the antibody is an intact antibody.

5. The anti-CD117 antibody, or antigen-binding fragment thereof, of claim 1 , wherein the antibody is an IgG.

6. The anti-CD117 antibody, or antigen-binding fragment thereof, of claim 5 , wherein the IgG is an IgG1 or an IgG4.

7. The anti-CD117 antibody, or antigen-binding fragment thereof, of claim 1 , wherein the antibody, or antigen-binding fragment thereof, is a monoclonal antibody.

8. The anti-CD117 antibody, or antigen-binding fragment thereof, of claim 1 , comprising a heavy chain constant region having an amino acid sequence as set forth in SEQ ID NO: 169 and/or a light chain constant region comprising an amino acid sequence as set forth in SEQ ID NO: 183.

9. The anti-CD117 antibody, or antigen-binding fragment thereof, of claim 1 , comprising an Fc region comprising at least one amino acid substitution selected from the group consisting of D265C, H435A, L234A, and L235A (numbering according to the EU index).

10. The anti-CD117 antibody, or antigen-binding fragment thereof, of claim 1 , comprising an Fc region, wherein the Fc region comprises amino acid substitutions D265C, L234A, and L235A (numbering according to the EU index).

11. An intact anti-CD117 human antibody comprising a light chain comprising an amino acid sequence as set forth in SEQ ID NO: 184, and a heavy chain comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 175, SEQ ID NO: 176, SEQ ID NO: 177, and SEQ ID NO: 178.

12. An intact anti-CD117 human antibody comprising a light chain comprising an amino acid sequence as set forth in SEQ ID NO: 185, and a heavy chain comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 179, SEQ ID NO: 180, SEQ ID NO: 181, and SEQ ID NO: 182.

13. A pharmaceutical composition comprising the antibody, or antigen-binding fragment thereof, of claim 1 , and a pharmaceutically acceptable carrier.

14. An antibody drug conjugate comprising an anti-CD117 antibody conjugated to a cytotoxin via a linker, wherein the antibody comprises the antibody, or antigen-binding fragment thereof, of claim 1 , wherein the cytotoxin is selected from the group consisting of an amatoxin, a pseudomonas exotoxin A, deBouganin, a diphtheria toxin, saporin, a 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.

15. The antibody drug conjugate of claim 14 , 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.

16. An antibody drug conjugate (ADC) comprising an isolated anti-CD117 antibody, or antigen-binding fragment thereof, conjugated to a cytotoxin via a linker, wherein the antibody, or antigen-binding fragment therof, comprises
(i) a heavy chain variable region comprising a CDR1 domain comprising the amino acid sequence as set forth in SEQ ID NO: 145, a CDR2 domain comprising the amino acid sequence as set forth in SEQ ID NO:146, and a CDR3 domain comprising the amino acid sequence as set forth in SEQ ID NO: 147; and a light chain variable region comprising a CDR1 domain comprising the amino acid sequence as set forth in SEQ ID NO: 148, a CDR2 domain comprising the amino acid sequence as set forth in SEQ ID NO:149, and a CDR3 domain comprising the amino acid sequence as set forth in SEQ ID NO: 150; or
(ii) a heavy chain variable region comprising the amino acid sequence as set forth in SEQ ID NO: 143, and a light chain variable region comprising the amino acid sequence as set forth in SEQ ID NO: 144.

17. The ADC of claim 16 , wherein the cytotoxin is selected from the group consisting of an amatoxin, an auristatin, a maytansine, a maytansinoid, a pyrrolobenzodiazepine, and a pyrrolobenzodiazepine dimer.

18. An antibody drug conjugate (ADC) represented by the 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, wherein the antibody, or antigen-binding fragment thereof, comprises
(i) a heavy chain variable region comprising a CDR1 domain comprising the amino acid sequence as set forth in SEQ ID NO: 145, a CDR2 domain comprising the amino acid sequence as set forth in SEQ ID NO:146, and a CDR3 domain comprising the amino acid sequence as set forth in SEQ ID NO: 147; and a light chain variable region comprising a CDR1 domain comprising the amino acid sequence as set forth in SEQ ID NO: 148, a CDR2 domain comprising the amino acid sequence as set forth in SEQ ID NO:149, and a CDR3 domain comprising the amino acid sequence as set forth in SEQ ID NO: 150; or
(ii) a heavy chain variable region comprising the amino acid sequence as set forth in SEQ ID NO: 143, and a light chain variable region comprising the amino acid sequence as set forth in SEQ ID NO: 144.

19. The ADC of claim 18 , wherein the Am-L-Z 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 , when present, together with the oxygen atoms to which they are bound, combine to form an optionally substituted 5-membered heterocycloalkyl 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 optionally substituted C 1 -C 6 alkyl, optionally substituted C 1 -C 6 heteroalkyl, optionally substituted C 2 -C 6 alkenyl, optionally substituted C 2 -C 6 heteroalkenyl, optionally s

Assignees

• Magenta Therapeutics Inc

Inventors

• Pearse Bradley R
• Cooke Michael
• Boitano Anthony
• Palchaudhuri Rahul
• Mcdonough Sean
• Panwar Rajiv
• Glanville Jacob

Classifications

• A61K47/6831 Primary

  Fungal toxins, e.g. alpha sarcine, mitogillin, zinniol or restrictocin · CPC title

• C07K2317/71

  Decreased effector function due to an Fc-modification · CPC title

• C07K16/2803

  against the immunoglobulin superfamily · CPC title

• C07K2317/94

  Stability, e.g. half-life, pH, temperature or enzyme-resistance · CPC title

• C07K2317/52

  Constant or Fc region; Isotype · CPC title