De novo design of potent and selective interleukin mimetics

Patent metadata

Field	Value
Publication number	US-12240880-B2
Application number	US-202217698553-A
Country	US
Kind code	B2
Filing date	Mar 18, 2022
Priority date	Jun 25, 2018
Publication date	Mar 4, 2025
Grant date	Mar 4, 2025

Abstract

De novo designed polypeptides that bind to IL-2 receptor β c heterodimer (IL-2Rβ c ), IL-4 receptor α c heterodimer (IL-4Rα c ), or IL-13 receptor α subunit (IL-13Rα) are disclosed, as are methods for using and designing the polypeptides.

First claim

We claim:

1. A method for treating cancer comprising administering to a subject having cancer a non-naturally occurring polypeptide comprising domains X1, X2, X3, and X4, wherein:
(a) X1 is a peptide comprising the amino acid sequence EHALYDAL (SEQ ID NO: 1);
(b) X2 is a helical-peptide of at least 8 amino acids in length;
(c) X3 is a peptide comprising the amino acid sequence YAFNFELI (SEQ ID NO:2);
(d) X4 is a peptide comprising the amino acid sequence ITILQSWIF (SEQ ID NO:3);
wherein X1, X2, X3, and X4 may be in any order in the polypeptide;
wherein amino acid linkers may be present between any of the domains; and
wherein the polypeptide binds to IL-2 receptor β c heterodimer (IL-2Rβ c ).

2. The method of claim 1 , wherein:
X1 is a peptide comprising an amino acid sequence at least 80% identical to the peptide PKKKIQLHAEHALYDALMILNI (SEQ ID NO: 4) provided that the amino acids at positions 10-17 relative to SEQ ID NO:4 are identical to SEQ ID NO:1;
X3 is a peptide comprising an amino acid sequence at least 80% identical to the peptide LEDYAFNFELILEEIARLFESG (SEQ ID NO:5) provided that the amino acids at positions 4-11 relative to SEQ ID NO:5 are identical to SEQ ID NO:2; and
X4 is a peptide comprising an amino acid sequence at least 80% identical to the peptide EDEQEEMANAIITILQSWIFS (SEQ ID NO:6) provided that the amino acids at positions 12-20 relative to SEQ ID NO:6 are identical to SEQ ID NO:3.

3. A method for treating cancer comprising administering to a subject having cancer a non-naturally occurring polypeptide comprising domains X1, X2, X3, and X4, wherein:
X1 is a peptide comprising an amino acid sequence at least 80% identical to the peptide

(SEQ ID NO: 4)

PKKKIQLHAEHALYDALMILNI;

X2 is a helical-peptide of at least 8 amino acids in length;
X3 is a peptide comprising an amino acid sequence at least 80% identical to the peptide LEDYAFNFELILEEIARLFESG (SEQ ID NO:5); and
X4 is a peptide comprising an amino acid sequence at least 80% identical to the peptide

(SEQ ID NO: 6)

EDEQEEMANAIITILQSWIFS;

wherein X1, X2, X3, and X4 may be in any order in the polypeptide;
wherein amino acid linkers may be present between any of the domains; and
wherein the polypeptide binds to IL-2 receptor β c heterodimer (IL-2Rβ c ).

4. The method of claim 3 , wherein:
X1 is a peptide comprising the amino acid sequence PKKKIQLHAEHALYDALMILNI (SEQ ID NO: 4);
X3 is a peptide comprising the amino acid sequence LEDYAFNFELILEEIARLFESG (SEQ ID NO:5); and
X4 is a peptide comprising the amino acid sequence EDEQEEMANAIITILQSWIFS (SEQ ID NO:6).

5. The method of claim 3 , wherein X2 is a peptide comprising an amino acid sequence at least 80% identical to the peptide KDEAEKAKRMKEWMKRIKT (SEQ ID NO:7).

6. The method of claim 4 , wherein X2 is a peptide comprising an amino acid sequence at least 90% identical to the peptide KDEAEKAKRMKEWMKRIKT (SEQ ID NO:7).

7. The method of claim 3 wherein the domains are arranged N-terminal to C-terminal in an arrangement selected from X1-X3-X2-X4.

8. The method of claim 6 wherein the domains are arranged N-terminal to C-terminal in an arrangement selected from X1-X3-X2-X4.

9. The method of claim 1 wherein the polypeptide comprises an amino acid sequence at least 80% identical to the amino acid sequence set forth in SEQ ID NO: 181.

10. The method of claim 9 wherein the polypeptide comprises an amino acid sequence at least 90% identical to the amino acid sequence set forth in SEQ ID NO: 181.

11. The method of claim 10 wherein the polypeptide comprises an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO: 181.

12. The method of claim 3 wherein the polypeptide comprises an amino acid sequence at least 80% identical to the amino acid sequence set forth in SEQ ID NO: 181.

13. The method of claim 12 wherein the polypeptide comprises an amino acid sequence at least 95% identical to the amino acid sequence set forth in SEQ ID NO: 181.

14. The method of claim 13 wherein the polypeptide comprises the amino acid sequence set forth in SEQ ID NO: 181.

15. The method of claim 13 wherein the polypeptide comprises an amino acid sequence that is 99% identical to the amino acid sequence set forth in SEQ ID NO:181 and comprises a cysteine at position 62.

16. The method of claim 2 wherein the polypeptide is linked to a stabilization compound.

17. The method of claim 3 wherein the polypeptide is linked to a stabilization compound.

18. The method of claim 15 wherein a polyethylene glycol containing moiety is linked to the cysteine residue at position 62.

19. The method of claim 18 wherein the polyethylene glycol is linked via a maleimide group to the cysteine residue.

20. The method of claim 19 wherein the subject has melanoma or renal cell cancer.

Assignees

• Univ Washington
• Univ Leland Stanford Junior

Inventors

• Silva Manzano Daniel Adriano
• Yu Shawn
• Ulge Umut
• Baker David
• Garcia Kenan Christopher
• Spangler Jamie
• Walkey Carl

Classifications

• C07K2319/74

  containing a fusion for binding to a cell surface receptor · CPC title

• C07K2319/33

  fusions for targeting to specific cell types, e.g. tissue specific targeting, targeting of a bacterial subspecies · CPC title

• C07K2319/30

  Non-immunoglobulin-derived peptide or protein having an immunoglobulin constant or Fc region, or a fragment thereof, attached thereto · CPC title

• C07K14/5443

  IL-15 · CPC title

• C07K14/5406

  IL-4 · CPC title