Beta-catenin targeting peptides and uses thereof

Abstract

The invention relates to β-catenin targeting peptides comprising an α-helical segment that are optionally stapled or stitched, and pharmaceutical compositions thereof. Uses of the inventive β-catenin targeting polypeptides including methods for treatment of disease, such as diseases associated with aberrant Wnt signaling, including cancer, are also provided.

1 - 60 . (canceled) 
     
     
         61 . An isolated polypeptide comprising an α-helical segment, wherein the polypeptide binds β-catenin, and the α-helical segment comprises lactam and disulfide cross-links. 
     
     
         62 . The polypeptide of  claim 61 , wherein the polypeptide comprises a β-catenin binding sequence from Axin or T-cell factor 4 (TCF4). 
     
     
         63 . The polypeptide of  claim 62 , wherein the polypeptide inhibits the interaction of 3-catenin with a T-cell factor (TCF). 
     
     
         64 . The polypeptide of  claim 63 , wherein the polypeptide inhibits the interaction of 3-catenin with TCF4. 
     
     
         65 . The polypeptide of  claim 62 , wherein the polypeptide comprises a wild-type 3-catenin binding sequence from Axin. 
     
     
         66 . The polypeptide of  claim 65 , wherein the polypeptide comprises a modified 3-catenin binding sequence from Axin. 
     
     
         67 . The polypeptide of  claim 62 , wherein the polypeptide comprises a wild-type 3-catenin binding sequence from TCF. 
     
     
         68 . The polypeptide of  claim 67 , wherein the polypeptide comprises a modified 3-catenin binding sequence from TCF. 
     
     
         69 . The polypeptide of  claim 61 , wherein the polypeptide is further modified to induce and/or stabilize an α-helical conformation. 
     
     
         70 . The polypeptide of  claim 69 , wherein the modification is selected from the group consisting of a peptide staple, a peptide stitch, α-methylation, N-caps, and a hydrogen bond surrogate. 
     
     
         71 . The polypeptide of  claim 61 , wherein the β-catenin binding polypeptide comprises an amino acid sequence of any one of the sequences of SEQ ID NO: 28-58. 
     
     
         72 . The polypeptide of  claim 61  comprising a free N-terminus, an acetylated N-terminus, a linker molecule, a labeling moiety, an affinity tag, and/or a targeting moiety. 
     
     
         73 . A pharmaceutical composition comprising the polypeptide of  claim 61  and a pharmaceutically acceptable excipient. 
     
     
         74 . A method of modulating Wnt-mediated transcription, the method comprising contacting a cell with the polypeptide of  claim 61 . 
     
     
         75 . A method to inhibit cell proliferation that is dependent on aberrant Wnt-signaling, the method comprising contacting the cell with a polypeptide of  claim 61 . 
     
     
         76 . An isolated polypeptide comprising an α-helical segment, wherein the polypeptide is of Formula (I): 
       
         
           
           
               
               
           
         
         and/or Formula (II) 
       
       
         
           
           
               
               
           
         
       
       wherein
 each instance of [X AA ] s , [X AA ] y , [X AA ] z  and [X AA ] t  is independently derived from an amino acid sequence of axin-1, axin-2, or TCF4; 
 each instance of K, L 1 , L 2 , and M, is, independently, a bond; cyclic or acyclic, branched or unbranched, substituted or unsubstituted alkylene; cyclic or acyclic, branched or unbranched, substituted or unsubstituted alkenylene; cyclic or acyclic, branched or unbranched, substituted or unsubstituted alkynylene; cyclic or acyclic, branched or unbranched, substituted or unsubstituted heteroalkylene; cyclic or acyclic, branched or unbranched, substituted or unsubstituted heteroalkenylene; cyclic or acyclic, branched or unbranched, substituted or unsubstituted heteroalkynylene; substituted or unsubstituted arylene; substituted or unsubstituted heteroarylene; or substituted or unsubstituted acylene; 
 each instance of R a  is, independently, hydrogen; cyclic or acyclic, branched or unbranched, substituted or unsubstituted aliphatic; cyclic or acyclic, branched or unbranched, substituted or unsubstituted heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; cyclic or acyclic, substituted or unsubstituted acyl; or a suitable amino protecting group; 
 each instance of R b  is, independently, a suitable amino acid side chain; hydrogen; cyclic or acyclic, branched or unbranched, substituted or unsubstituted aliphatic; cyclic or acyclic, branched or unbranched, substituted or unsubstituted heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; cyclic or acyclic, substituted or unsubstituted acyl; substituted or unsubstituted hydroxyl; substituted or unsubstituted thiol; substituted or unsubstituted amino; cyano; isocyano; halo; or nitro; 
 each instance of R e  is, independently, a bond to the linker moiety, —R E , —OR E , —N(R E ) 2 , or —SR E , wherein each instance of R E  is, independently, hydrogen; cyclic or acyclic, branched or unbranched, substituted or unsubstituted aliphatic; cyclic or acyclic, branched or unbranched, substituted or unsubstituted heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; substituted or unsubstituted acyl; a resin; a suitable hydroxyl, amino, or thiol protecting group; or two R E  groups of —N(R E ) 2  together form a substituted or unsubstituted 5- to 6-membered heterocyclic or heteroaromatic ring; 
 each instance of R f  is, independently, a bond to the linker moiety; hydrogen; cyclic or acyclic, branched or unbranched, substituted or unsubstituted aliphatic; cyclic or acyclic, branched or unbranched, substituted or unsubstituted heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; substituted or unsubstituted acyl; a resin; a suitable amino protecting group; a label optionally joined by a tether, wherein the tether is selected from cyclic or acyclic, branched or unbranched, substituted or unsubstituted alkylene; cyclic or acyclic, branched or unbranched, substituted or unsubstituted alkenylene; cyclic or acyclic, branched or unbranched, substituted or unsubstituted alkynylene; cyclic or acyclic, branched or unbranched, substituted or unsubstituted heteroalkylene; cyclic or acyclic, branched or unbranched, substituted or unsubstituted heteroalkenylene; cyclic or acyclic, branched or unbranched, substituted or unsubstituted heteroalkynylene; substituted or unsubstituted arylene; substituted or unsubstituted heteroarylene; or substituted or unsubstituted acylene; or R f  and R a  together form a substituted or unsubstituted 5- to 6-membered heterocyclic or heteroaromatic ring; 
 each instance of R KL , R LL,  and R LM , is, independently, hydrogen; cyclic or acyclic, branched or unbranched, substituted or unsubstituted aliphatic; cyclic or acyclic, branched or unbranched, substituted or unsubstituted heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; substituted or unsubstituted acyl; substituted or unsubstituted hydroxyl; substituted or unsubstituted thiol; substituted or unsubstituted amino; azido; cyano; isocyano; halo; nitro; 
 or two adjacent R KL  groups are joined to form a substituted or unsubstituted 5- to 8-membered cycloaliphatic ring; substituted or unsubstituted 5- to 8-membered cycloheteroaliphatic ring; substituted or unsubstituted aryl ring; or substituted or unsubstituted heteroaryl ring; two adjacent R KL  groups are joined to form a substituted or unsubstituted 5- to 8-membered cycloaliphatic ring; substituted or unsubstituted 5- to 8-membered cycloheteroaliphatic ring; substituted or unsubstituted aryl ring; or substituted or unsubstituted heteroaryl ring; or two adjacent R LM  groups are joined to form a substituted or unsubstituted 5- to 8-membered cycloaliphatic ring; substituted or unsubstituted 5- to 8-membered cycloheteroaliphatic ring; substituted or unsubstituted aryl ring; or substituted or unsubstituted heteroaryl ring; 
 each instance of X AA  is, independently, a natural or unnatural amino acid; 
 each instance of y and z is, independently, an integer between 2 to 6; 
 each instance of j is, independently, an integer between 1 to 10; 
 each instance of p is, independently, an integer between 0 to 10; 
 each instance of s and t is, independently, an integer between 0 and 100; 
 each instance of u, v, and q, is, independently, an integer between 0 to 2; and 
    corresponds to a single or double bond. 
 
     
     
         77 . The polypeptide of  claim 76 , wherein each instance of [X AA ] s  is X 1 X 2 X 3 X 4 X 5 ; [X AA ] z  is X 6 X 7 X 8 ; and [X AA ] t  is X 9 X 10 X 11 X 12 X 13 X 14 X 15 ;
 X 1  is selected from the group consisting of R, K and no amino acid;   X 2  is selected from the group consisting of R, K, W and no amino acid;   X 3  is selected from the group consisting of W, Y and Q;   X 4  is selected from the group consisting of P, S, W, A, F and L;   X 5  is selected from the group consisting of E, Q, R and W;   X 6  is selected from the group consisting of I and L;   X 7  is selected from the group consisting of I and L;   X 8  is selected from the group consisting of D and N;   X 9  is selected from the group consisting of H and W;   X 10  is selected from the group consisting of V, W, L, M, F, and I;   X 11  is selected from the group consisting of Q, E, L, D, H, R, S, and V;   X 12  is selected from the group consisting of R, S, and K;   X 13  is selected from the group consisting of V, I, L, W, F, and H;   X 14  is selected from the group consisting of M, Norleucine, I, L, W, F, and H; and   X 15  is selected from the group consisting of R, G, P, E, H, K, Q, and no amino acid.   
     
     
         78 . The polypeptide of  claim 77 , wherein the amino acid of X 1,2,11,12,15  is a positively charged amino acid and/or the amino acid of X 3,4,5,6,7,9,10,13,14  is a bulky, hydrophobic amino acid 
     
     
         79 . The polypeptide of  claim 76 , wherein each instance of [X AA ] s  is X 1 X 2 X 3 X 4 X 5 ; [X AA ] z  is X 6 X 7 X 8 ; and [X AA ] t  is X 9 X 10 X 11 X 12 X 13 X 14 X 15 ;
 X 1  is selected from the group consisting of R, V, E, Q, T, K, W, and L;   X 2  is selected from the group consisting of W, S, L, N, Y, K, V, and Q:   X 3  is selected from the group consisting of P, L, S, W, A, and F;   X 4  is selected from the group consisting of E, Q, and W;   X 5  is S;   X 6  is I;   X 7  is L;   X 8  is D;   X 9  is selected from the group consisting of E and Q;   X 10  is H;   X 11  is selected from the group consisting of W, V, F, M, L, and I;   X 12  is selected from the group consisting of E, Q, H, D, V, and L;   X 13  is selected from the group consisting of R and K;   X 14  is selected from the group consisting of V and W;   X 15  is selected from the group consisting of M, W, F, and E; and   X 16  is selected from the group consisting of R, G, P, E, and Q.   
     
     
         80 . The polypeptide of  claim 76 , wherein [X AA ] s  is selected from the group consisting of: ENPE (SEQ ID NO:3), PE, PQ, RWPQ (SEQ ID NO:4), RWPR (SEQ ID NO:5), RRWPR (SEQ ID NO:6); [X AA ] z  is ILD (SEQ ID NO:7); and [X AA ] t  is selected from the group consisting of: HVQRVM (SEQ ID NO:8), HVRRVMR (SEQ ID NO:9), HVRRWMR (SEQ ID NO:10), HVRRVWR (SEQ ID NO:11), HVRRWNleR (SEQ ID NO:12), HVRRRWR (SEQ ID NO:13).