De novo design of potent and selective interleukin mimetics

Patent metadata

Field	Value
Publication number	US-11401313-B2
Application number	US-202016909210-A
Country	US
Kind code	B2
Filing date	Jun 23, 2020
Priority date	Jun 25, 2018
Publication date	Aug 2, 2022
Grant date	Aug 2, 2022

Abstract

De novo designed polypeptides that bind to IL-2 receptor βc heterodimer (IL-2Rβc), IL-4 receptor αcheterodimer (IL-4Rαc), 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 nucleic acid encoding 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 nucleic acid of claim 1 , wherein:
X1 is a peptide comprising an amino acid sequence at least 60% 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 60% 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 60% 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. The nucleic acid of claim 2 , wherein X2 is a peptide comprising an amino acid sequence at least 50% identical to the peptide KDEAEKAKRMKEWMKRIKT (SEQ ID NO:7).

4. The nucleic acid 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.

5. The nucleic acid of claim 4 , wherein X2 is a peptide comprising an amino acid sequence at least 80% identical to the peptide KDEAEKAKRMKEWMKRIKT (SEQ ID NO:7).

6. The nucleic acid of claim 4 wherein the domains are arranged N-terminal to C-terminal in an arrangement selected from X1-X3-X2-X4.

7. The nucleic acid of claim 1 , 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).

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

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

10. The nucleic acid of claim 1 wherein the domains are arranged N-terminal to C-terminal in an arrangement selected from X1-X3-X2-X4.

11. A nucleic acid encoding 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 PKKKIQLHAEHALYDALMILNI (SEQ ID NO: 4);
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 EDEQEEMANAIITILQSWIFS (SEQ ID NO:6);
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 ).

12. The nucleic acid of claim 11 , wherein:
X1 is a peptide comprising an amino acid sequence at least 80% identical to the peptide PKKKIQLHAEHALYDALMILNI (SEQ ID NO: 4), wherein the amino acid at position 1 is P or if substituted is A, F, I, L, M, Q, R, S, or W;
the amino acid at position 2 is K or if substituted is A, D, E, G, or V;
the amino acid at position 3 is K or if substituted is D, E, F, or W;
the amino acid at position 4 is K or if substituted is D, E, N, P, R, or W;
the amino acid at position 5 is I or if substituted is D, E, H, K, L, M, or S;
the amino acid at position 6 is Q or if substituted is A, D, E, G, L, P, S, or W;
the amino acid at position 7 is L or if substituted is D, E, Q, Y, or I;
the amino acid at position 8 is H or if substituted is A, F, W, Y, M, or T;
the amino acid at position 9 is A or if substituted is C, F, or P;
the amino acid at position 10 is E or if substituted is C, D, F, K, or P;
the amino acid at position 11 is H or if substituted is D, F, or E;
the amino acid at position 12 is A or if substituted is D, E, P, S, T, or V;
the amino acid at position 13 is L or if substituted is H, I, M, P, R, V, or W;
the amino acid at position 14 is Y or if substituted is F, R, W, or K;
the amino acid at position 15 is D or if substituted is E, N, or Y;
the amino acid at position 16 is A or if substituted is C, L, M, or S;
the amino acid at position 17 is L or if substituted is F, I, M, P, or R;
the amino acid at position 18 is M or if substituted is G, Q, Y, or S;
the amino acid at position 19 is I or if substituted is L, M, P, Q, or V;
the amino acid at position 20 is L or if substituted is A, K, M, Q, R, or S;
the amino acid at position 21 is N or if substituted is G, K, P, R, S, or W;
the amino acid at position 22 is I or if substituted is D, E, K, M, N, W, or Y, wherein the position numbering is relative to SEQ ID NO: 4;
X3 is a peptide comprising an amino acid sequence at least 80% identical to the peptide LEDYAFNFELILEEIARLFESG (SEQ ID NO:5); wherein the amino acid at position 1 is L or if substituted is A;
the amino acid at position 2 is E or if substituted is D, G, K, M, or T;
the amino acid at position 3 is D or if substituted is E, N, Y, or R;
the amino acid at position 4 is Y or if substituted is C, D, G, T, or F;
the amino acid at position 5 is A or if substituted is F, H, S, V, W, or Y;
the amino acid at position 6 is F or if substituted is A, I, M, T, V, Y, or K;
the amino acid at position 7 is N or if substituted is D, K, S, T, or R;
the amino acid at position 8 is F or if substituted is A, C, G, L, M, S, or V;
the amino acid at position 9 is E or if substituted is C, H, K, L, R, S, T, or V;
the amino acid at position 10 is L or if substituted is F, I, M, Y, or R;
the amino acid at position 11 is I or if substituted is L, N, T, or Y;
the amino acid at position 12 is L or if substituted is F, K, M, S, or V;
the amino acid at position 13 is E or if substituted is A, D, F, G, I, N, P,Q, S, T, or W;
the amino acid at position 14 is E or if substituted is A, F, G, H, S, or V;
the amino acid at position 15 is I or if substituted is C, L, M, V, or W;
the amino acid at position 16 is A or if substituted is D, G, S, T, or V;
the amino acid at position 17 is R or if substituted is H, K, L, or N;
the amino acid at position 18 is L or if substituted is C, D, G, I, Q, R, T, or W;
the amino acid at position 19 is F or if substituted is D, M, N, or W;
the amino acid at position 20 is E or if substituted is A, C, F, G, M, S, or Y;
the a

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

• C07K2319/30

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

• G01N33/6869

  Interleukin · CPC title

• C07K14/5443

  IL-15 · CPC title

• A61P35/00

  Antineoplastic agents · 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