Ligand-directed covalent modification of protein

1. A protein-modifier-ligand conjugate of the Formula XIII,

wherein

Scaffold is an inhibitor of Protein,

Protein is X linked Inhibitor of Apoptosis Protein (XIAP); wherein Protein contains the lysine residue in, or in proximity to, the substrate-binding site or cofactor-binding site of Protein, and wherein a portion of the lysine residue is depicted in Formula XIII; and

Tether is a bond, a bivalent C 1 -C 15 saturated or unsaturated, straight, branched, or cyclic hydrocarbon moiety, an aryl moiety, or a heteroaryl moiety; wherein, optionally, one or more methylene units of the hydrocarbon chain are independently replaced by —NR 1 —, —O—, —C(O)—, —S—, —SO—, —SO 2 —, —C(═S)—, or —C(═NR 1 )—; and one or more methine groups of the C 1 -C 15 alkyl, when present, can be independently replaced by

x is 0 or 1;

y is 1;

R 1 is hydrogen or C 1 -C 8 alkyl; and

Y 1 is a moiety of Formula XV-a, XV-b, or XV-d,

wherein

each R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , and R 8 is independently hydrogen or C 1 -C 6 alkyl;

optionally when proper any two of R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , and R 8 can be linked together to form a 3- to 8-membered carbocyclic or heterocyclic ring;

one or more methylene groups of the C 1 -C 6 alkyl can be replaced by —NR 1 —, —O—, —C(O)—, —S—, —SO—, —SO 2 —, or —C(═S)—; one or more methine groups of the C 1 -C 6 alkyl, when present, can be independently replaced by

and

M is connected to the position labeled as “*”;

Tether is connected to the position of Yi labeled as “**”;

is a single bond;

M is —NH—, the nitrogen atom of M being a nitrogen from the side chain primary amine group of the lysine residue of Protein, and wherein M(CH 2 ) 4 -Protein is selected from the group consisting of K297-XIAP and K299-XIAP.

2. The conjugate of claim 1 , wherein the conjugate of Formula XIII is a conjugate of Formula XIII′:

3. The conjugate of claim 2 , wherein Scaffold is a radical resulting from the removal of one or more hydrogens of a compound of Formula VII, VIII, IX-a, or IX-b:

wherein

V and W are each independently —(CR 14 R 15 ) q X 3 (CR 16 R 17 ) r —;

q and r are each independently 0, 1, 2, 3, or 4;

X 3 is —CR 18 R 19 — or —NR 20 —;

R x , R y , R 12 , R 13 , R 14 , R 15 , R 16 , R 17 , R 18 , R 19 , and R 20 are each independently hydrogen or C 1 -C 6 alkyl; wherein one or more methylene groups of the C 1 -C 6 alkyl can be replaced by —NR 1 —, —O—, —C(O)—, —S—, —SO—, —SO 2 —, —C(═S)—, optionally substituted aryl or heteroaryl groups; one or more methine groups of the C 1 -C 6 alkyl, when present, can be independently replaced by

and

R 1 is hydrogen or C 1 -C 8 alkyl;

wherein

X 4 is —CR 33 — or —N—;

p and s are each independently 0, 1, 2, 3, or 4;

R 12 , R 13 , R 21 , R 22 , R 24 , R 25 , R 26 , R 27 , R 28 , R 29 , R 30 , R 31 , R 32 , and R 33 are each independently hydrogen or C 1 -C 6 alkyl;

R 23 is hydrogen, C 1 -C 6 alkyl, halogen, amino, or nitro; wherein one or more methylene groups of C 1 -C 6 alkyl can be optionally replaced by —NR 1 —, —O—, —C(O)—, —S—, —SO—, —SO 2 —, or —C(═S)—; one or more methine groups of the C 1 -C 6 alkyl, when present, can be independently replaced by

R 1 is hydrogen or C 1 -C 8 alkyl; and

optionally R 21 and R 23 taken together can form a 4- to 8-membered carbocyclic or heterocyclic ring;

wherein

X 5 is —O—, —CR 42 R 43 — or —NR 42 —;

R 12 , R 13 , R 27 , R 28 , R 29 , R 30 , R 31 , R 32 , R 33 , R 34 , R 35 , R 36 , R 37 , R 38 , R 39 , R 40 , R 41 , R 42 , and R 43 are each independently hydrogen or C 1 -C 6 alkyl; wherein one or more methylene groups of C 1 -C 6 alkyl can be optionally replaced by —NR 1 —, —O—, —C(O)—, —S—, —SO—, —SO 2 —, or —C(═S)—; one or more methine groups of the C 1 -C 6 alkyl, when present, can be independently replaced by

R 1 is hydrogen or C 1 -C 8 alkyl; and

D, E, F, G, and H are each independently optionally substituted aryl or heteroaryl;

wherein F and G are fused together to form a bicyclic optionally substituted aryl or heteroaryl.

4. The conjugate of claim 2 , wherein the bivalent moiety of Formula XV-a, XV-b, or XV-d is a bivalent moiety of Formula XV-h, XV-i, or XV- 1 ;

wherein

M is connected to the position of Y 1 labeled as “*”; and

Tether is connected to the position of Y 1 labeled as “**”.

5. The conjugate of claim 2 , wherein Y 1 is a moiety of Formula XV-a:

6. The conjugate of claim 2 , wherein Y 1 is a moiety of Formula XV-b:

7. The conjugate of claim 2 , wherein Y 1 is a moiety of Formula XV-d: