CD38-binding proteins comprising de-immunized Shiga toxin A subunit effectors

Patent metadata

Field	Value
Publication number	US-12180262-B2
Application number	US-202318332366-A
Country	US
Kind code	B2
Filing date	Jun 9, 2023
Priority date	Jan 23, 2019
Publication date	Dec 31, 2024
Grant date	Dec 31, 2024

Abstract

The instant invention provides binding proteins (“CD38-binding proteins”) which each comprise (1) a CD38-binding region for cell-targeting and (2) a Shiga toxin A Subunit effector polypeptide (“Shiga toxin effector polypeptide”). The Shiga toxin effector polypeptide components of the CD38-binding proteins may comprise a combination of mutations relative to a wild-type Shiga toxin sequence providing (1) de-immunization and/or (2) a reduction in protease sensitivity; wherein each Shiga toxin effector polypeptide retains one or more Shiga toxin function, such as, e.g., stimulating cellular internalization, directing intracellular routing, catalytic activity, and/or potent cytotoxicity. The CD38-binding proteins may have one or multiple uses, e.g., the selective killing of a specific CD38-expressing cell-type; and more generally, for the diagnosis and treatment of cancers and disorders involving CD38-expressing cells, e.g., in CD38-positive hematopoietic cancers such as multiple myeloma.

First claim

What is claimed is:

1. A method of treating or slowing the progression of multiple myeloma in a subject in need thereof, the method comprising administering to the subject an effective amount of a pharmaceutical composition comprising a CD38-binding fusion protein, wherein the CD38-binding fusion protein comprises:
1) a Shiga toxin A subunit effector polypeptide; and
2) a CD38-binding domain, comprising:
a) a heavy chain variable domain (VH) comprising:
i) a vHCDR1 comprising the sequence of SEQ ID NO: 34;
ii) a vHCDR2 comprising the sequence of SEQ ID NO: 35; and
iii) a vHCDR3 comprising the sequence of SEQ ID NO: 36; and

b) a light chain variable domain (VL) comprising:
i) a vLCDR1 comprising the sequence of SEQ ID NO: 31;
ii) a vLCDR2 comprising the sequence of SEQ ID NO: 32; and
iii) a vLCDR3 comprising the sequence of SEQ ID NO: 33.

2. The method of claim 1 , wherein the VL comprises a sequence having at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid identity to the sequence of SEQ ID NO: 43, and the VH comprises a sequence having at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence identity to the sequence of SEQ ID NO: 44.

3. The method of claim 1 , wherein the VL comprises the sequence of SEQ ID NO: 43 and the VH comprises the sequence of SEQ ID NO: 44.

4. The method of claim 1 , wherein the CD38-binding fusion protein comprises a first linker between the Shiga toxin A subunit effector polypeptide and the CD38-binding domain.

5. The method of claim 4 , wherein the first linker is a proteinaceous linker.

6. The method of claim 5 , wherein the first linker comprises about 1 to about 50 amino acid residues.

7. The method of claim 4 , wherein the first linker comprises a sequence having at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% amino acid sequence identity to any one of SEQ ID NOs: 70-75.

8. The method of claim 4 , wherein the first linker comprises the sequence of SEQ ID NO: 70.

9. The method of claim 1 , wherein the CD38-binding fusion protein comprises a second linker between the VH and the VL.

10. The method of claim 9 , wherein the second linker comprises the sequence (Gly4Ser)n (SEQ ID NO: 195), wherein n is equal to 1, 2, 3, 4, or 5.

11. The method of claim 9 , wherein the second linker comprises the sequence (Gly4Ser)n (SEQ ID NO: 195), wherein n is equal to 1.

12. The method of claim 9 , wherein the CD38-binding fusion protein comprises, from its N- to C-terminus, the Shiga toxin A subunit effector polypeptide-first linker-VH-second linker-VL.

13. The method of claim 9 , wherein the fusion protein comprises, from its N- to C-terminus, the Shiga toxin A subunit effector polypeptide-first linker-VL-second linker-VH.

14. The CD38-binding fusion protein of claim 1 , wherein the Shiga toxin A subunit effector polypeptide comprises a sequence having at least 95%, at least 96%, at least 97%, at least 95%, at least 99%, or 100% amino acid sequence identity to any one of SEQ ID NOs: 45-69.

15. The method of claim 1 , wherein the Shiga toxin A subunit effector polypeptide comprises the sequence of SEQ ID NO: 46.

16. The method of claim 1 , wherein the Shiga toxin A subunit effector polypeptide comprises the sequence of SEQ ID NO: 46, the VL comprises the sequence of SEQ ID NO: 43, and the VH comprises the sequence of SEQ ID NO: 44.

17. The method of claim 1 , wherein the CD38-binding fusion protein has at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence identity amino acid sequence identity to SEQ ID NO: 79.

18. The method of claim 1 , wherein the CD38-binding protein comprises the sequence of SEQ ID NO: 79.

19. The composition of claim 18 , wherein at least about 90% of the CD38-binding fusion protein is in the form of a homodimer.

20. The method of claim 1 , wherein the CD38-binding fusion protein comprises two identical polypeptides, each polypeptide comprising a sequence at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% amino acid sequence identity to SEQ ID NO: 79.

21. The method of claim 1 , wherein the CD38-binding fusion protein comprises two identical polypeptides, each polypeptide comprising the sequence of SEQ ID NO: 79.

22. The method of claim 1 , wherein the composition comprises a pharmaceutically acceptable carrier or excipient.

23. The method of claim 1 , wherein the CD38-binding fusion protein is administered at a dose of about 1 μg/kg to about 1500 μg/kg of the subject's body weight.

24. The method of claim 1 , wherein the CD38-binding fusion protein is administered by intravenous infusion.

25. The method of claim 1 , wherein the CD38-binding fusion protein is administered once per week.

26. The method of claim 1 , wherein the CD38-binding fusion protein is administered once per week during a 28-day cycle.

27. The method of claim 26 , wherein the CD38-binding fusion protein is administered on days 1, 8, 15, and 22 of the 28-day cycle.

28. The method of claim 26 , wherein the CD38-binding fusion protein is administered for at least one additional 28-day cycle.

29. The method of claim 1 , wherein the multiple myeloma is relapsed or refractory to treatment with at least one additional anti-cancer therapy.

30. The method of claim 1 , wherein the multiple myeloma is relapsed or refractory to daratumumab, at least one proteasome inhibitor (PI)-based therapy, at least one immunomodulatory drug (IMiD)-based therapy, or at least one steroid-based therapy.

31. A method of treating or slowing the progression of multiple myeloma in a subject in need thereof, the method comprising administering to the subject an effective amount of a pharmaceutical composition comprising a CD38-binding fusion protein, wherein the CD38-binding fusion protein comprises a polypeptide having the sequence of SEQ ID NO: 79;
wherein the CD38-binding fusion protein is administered at a dose in the range of about 1 μg/kg to about 1500 μg/kg of the subject's body weight.

Assignees

• Millennium Pharm Inc
• Molecular Templates Inc

Inventors

• Chattopadhyay Nibedita
• Poma Eric
• Willert Erin

Classifications

• C12N15/63

  Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression · CPC title

• C07K2317/92

  Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value · CPC title

• C07K2317/565

  Complementarity determining region [CDR] · CPC title

• A61K38/00

  Medicinal preparations containing peptides (peptides containing beta-lactam rings A61K31/00; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, A61K31/00; ergot alkaloids of the cyclic peptide type A61K31/48; containing macromolecular compounds having statistically distributed amino acid units A61K31/74; medicinal preparations containing antigens or antibodies A61K39/00; medicinal preparations characterised by the non-active ingredients, e.g. peptides as drug carriers, A61K47/00) · CPC title

• A61P35/00

  Antineoplastic agents · CPC title