Chemical linkers and cleavable substrates and conjugates thereof

1. A compound of the formula

wherein

L 1 is a self-immolative linker;

m is an integer 0, 1, 2, 3, 4, 5, or 6;

F is a linker comprising the structure:

wherein

AA 1 is one or more members independently selected from the group consisting of natural amino acids and unnatural α-amino acids;

c is an integer from 1 to 20;

L 2 is a self-immolative linker;

o is 0 or 1;

L 4 is a linker member;

p is 0 or 1;

X 4 is a member selected from the group consisting of protected reactive functional groups, unprotected reactive functional groups, detectable labels, and targeting agents; and

D has the structure:

wherein

Z is a member selected from O, S and NR 23

wherein

R 23 is a member selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, and acyl;

R 1 is H, substituted or unsubstituted lower alkyl, C(O)R 8 , or CO 2 R 8 , wherein R 8 is a member selected from group consisting of substituted alkyl, unsubstituted alkyl, NR 9 R 10 , NR 9 NHR 10 , and OR 9

in which R 9 and R 10 are members independently selected from H, substituted or unsubstituted alkyl and substituted or unsubstituted heteroalkyl; and

R 2 is H, substituted alkyl or unsubstituted lower alkyl,

X is a member selected from O, S and NR 23 ;

R 3 is a member selected from the group consisting of (═O), SR 11 , NHR 11 and OR 11 ,

wherein R 11 is a member selected from the group consisting of H, substituted alkyl, unsubstituted alkyl, substituted heteroalkyl, unsubstituted heteroalkyl, monophosphates, diphosphates, triphosphates, sulfonates, acyl, C(O)R 12 R 13 , C(O)OR 12 , C(O)NR 12 R 13 , P(O)(OR 12 ) 2 , C(O)CHR 12 R 13 , SR 12 and SiR 12 R 13 R 14 ,

in which R 12 , R 13 , and R 14 are members independently selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl and substituted or unsubstituted aryl, wherein R 12 and R 13 together with the nitrogen or carbon atom to which they are attached are optionally joined to form a substituted or unsubstituted heterocycloalkyl ring system having from 4 to 6 members, optionally containing two or more heteroatoms;

R 4 , R 4′ , R 5 and R 5′ are members independently selected from the group consisting of H, substituted alkyl, unsubstituted alkyl, substituted aryl, unsubstituted aryl, substituted heteroaryl, unsubstituted heteroaryl, substituted heterocycloalkyl, unsubstituted heterocycloalkyl, halogen, NO 2 , NR 15 R 16 , NHC(O)R 15 , OC(O)NR 15 R 16 , OC(O)OR 15 , C(O)R 15 , SR 15 , OR 15 , CR 15 =NR 16 , and O(CH 2 ) n N(CH 3 ) 2 , or any adjacent pair of R 4 , R 4′ , R 5 and R 5′ , together with the carbon atoms to which they are attached, are joined to form a substituted or unsubstituted cycloalkyl or heterocycloalkyl ring system having from 4 to 6 members,

wherein

n is an integer from 1 to 20;

R 15 and R 16 are independently selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted heterocycloalkyl, and substituted or unsubstituted peptidyl, wherein R 15 and R 16 together with the nitrogen atom to which they are attached are optionally joined to form a substituted or unsubstituted heterocycloalkyl ring system having from 4 to 6 members, optionally containing two or more heteroatoms;

wherein at least one of R 4 , R 4′ , R 5 and R 5′ links said drug to L 1 , if present, or to F, and comprises

wherein v is an integer from 1 to 6; and

each R 27 , R 27′ , R 28 , and R 28′ is independently selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, and substituted or unsubstituted heterocycloalkyl;

R 6 is a single bond which is either present or absent and when present R 6 and R 7 are joined to form a cyclopropyl ring; and

R 7 is CH 2 —X 1 or —CH 2 — joined in said cyclopropyl ring with R 6 , wherein

X 1 is a leaving group;

or a pharmaceutically acceptable salt thereof.

2. A compound of the formula

wherein

L 1 is a self-immolative linker;

m is an integer 0, 1, 2, 3, 4, 5, or 6;

F is a linker comprising the structure:

wherein

AA 1 is one or more members independently selected from the group consisting of natural amino acids and unnatural α-amino acids;

c is an integer from 1 to 20;

L 3 is a spacer group comprising a primary or secondary amine or a carboxyl functional group; wherein if L 3 is present, m is 0 and either the amine of L 3 forms an amide bond with a pendant carboxyl functional group of D or the carboxyl of L 3 forms an amide bond with a pendant amine functional group of D;

o is 0 or 1;

L 4 is a linker member, wherein L 4 comprises

directly attached to the N-terminus of (AA 1 ) c , wherein

R 20 is a member selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, and acyl,

each R 25 , R 25′ , R 26 , and R 26 ′ is independently selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, and substituted or unsubstituted heterocycloalkyl;

and s and t are independently integers from 1 to 6;

p is 1;

X 4 is a member selected from the group consisting of protected reactive functional groups, unprotected reactive functional groups, detectable labels, and targeting agents; and

D comprises a structure:

wherein the ring system A is a member selected from substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl and substituted or unsubstituted heterocycloalkyl groups;

E and G are members independently selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, a heteroatom, a single bond, or E and G are joined to form a ring system selected from substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl and substituted or unsubstituted heterocycloalkyl;

X is a member selected from O, S and NR 23 ;

R 23 is a member selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, and acyl;

R 3 is a member selected from the group consisting of (═O), SR 11 , NHR 11 and OR 11 ,

wherein

R 11 is a member selected from the group consisting of H, substituted alkyl, unsubstituted alkyl, substituted heteroalkyl, unsubstituted heteroalkyl, monophosphates, diphosphates, triphosphates, sulfonates, acyl, C(O)R 12 R 13 ,C(O)OR 12 , C(O)NR 12 R 13 , P(O)(OR 12 ) 2 , C(O)CHR 12 R 13 , SR 12 and SiR 12 R 13 R 14 ,

in which

R 12 , R 13 and R 14 are members independently selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl and substituted or unsubstituted aryl, wherein R 12 and R 13 together with the nitrogen or carbon atom to which they are attached are optionally joined to form a substituted or unsubstituted heterocycloalkyl ring system having from 4 to 6 members, optionally containing two or more heteroatoms;

R 4 , R 4′ , R 5 and R 5′ are members independently selected from the group consisting of H, substituted alkyl, unsubstituted alkyl, substituted aryl, unsubstituted aryl, substituted heteroaryl, unsubstituted heteroaryl, substituted heterocycloalkyl, unsubstituted heterocycloalkyl, halogen, NO 2 , NR 15 R 16 , NHC(O)R 15 , OC(O)NR 15 R 16 , OC(O)OR 15 , C(O)R 15 , SR 15 , OR 15 , CR 15 =NR 16 , and O(CH 2 ) n N(CH 3 ) 2 , or any adjacent pair of R 4 , R 4′ , R 5 and R 5′ , together with the carbon atoms to which they are attached, are joined to form a substituted or unsubstituted cycloalkyl or heterocycloalkyl ring system having from 4 to 6 members,

wherein

n is an integer from 1 to 20;

R 15 and R 16 are independently selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted heterocycloalkyl, and substituted or unsubstituted peptidyl, wherein R 15 and R 16 together with the nitrogen atom to which they are attached are optionally joined to form a substituted or unsubstituted heterocycloalkyl ring system having from 4 to 6 members, optionally containing two or more heteroatoms;

R 6 is a single bond which is either present or absent and when present R 6 and R 7 are joined to form a cyclopropyl ring; and

R 7 is CH 2 —X 1 or —CH 2 — joined in said cyclopropyl ring with R 6 , wherein

X 1 is a leaving group,

wherein at least one of R 4 , R 4′ , R 5 , R 5′ , R 15 , R 16 links said drug to L 1 , if present, or to F;

or a pharmaceutically acceptable salt thereof.

3. The compound of claim 2 , wherein the compound is

wherein r is an integer in the range from 0 to 24.

4. The compound of claim 2 , wherein D has the structure:

wherein

Z is a member selected from O, S and NR 23

wherein

R 23 is a member selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, and acyl;

R 1 is H, substituted or unsubstituted lower alkyl, C(O)R 8 , or CO 2 R 8 , wherein R 8 is a member selected from the group consisting of substituted alkyl, unsubstituted alkyl, NR 9 R 10 , NR 9 NHR 10 , and OR 9

in which R 9 and R 10 are members independently selected from H, substituted or unsubstituted alkyl and substituted or unsubstituted heteroalkyl; and

R 2 is H, substituted alkyl or unsubstituted lower alkyl.

5. The compound of claim 2 , wherein D has the structure:

wherein

Z is a member selected from O, S and NR 23

wherein

R 23 is a member selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, and acyl;

R 1 is H, substituted or unsubstituted lower alkyl, C(O)R 8 , or CO 2 R 8 , wherein R 8 is a member selected from NR 9 R 10 and OR 9 ,

in which

R 9 and R 10 are members independently selected from H, substituted or unsubstituted alkyl and substituted or unsubstituted heteroalkyl;

R 1 is H, substituted or unsubstituted lower alkyl, or C(O)R 8 , wherein R 8 is a member selected from NR 9 R 10 and OR 9 ,

in which

R 9 and R 10 are members independently selected from H, substituted or unsubstituted alkyl and substituted or unsubstituted heteroalkyl;

R 2 is H, or substituted or unsubstituted lower alkyl or unsubstituted heteroalkyl or cyano or alkoxy; and

R 2 ′ is H, or substituted or unsubstituted lower alkyl or unsubstituted heteroalkyl.

6. The compound of claim 2 , wherein (AA 1 ) c , is a peptide sequence selected from the group consisting of Val-Cit, Val-Lys, Phe-Lys, Lys-Lys, Ala-Lys, Phe-Cit, Leu-Cit, Ile-Cit, Trp, Cit, Phe-Ala, Phe-N 9 -tosyl-Arg, Phe-N 9 -nitro-Arg, Phe-Phe-Lys, D-Phe-Phe-Lys, Gly-Phe-Lys, Leu-Ala-Leu, Ile-Ala-Leu, Val-Ala-Val, Ala-Leu-Ala-Leu (SEQ. ID NO: 1), β-Ala-Leu-Ala-Leu (SEQ. ID NO: 2) and Gly-Phe-Leu-Gly (SEQ. ID NO: 3).

7. The compound of claim 2 , wherein (AA 1 ) c , is Val-Cit or Val-Lys.

8. The compound of claim 2 , wherein s and t are independently 1 or 2.

9. The compound of claim 2 , wherein R 20 is H or lower alkyl.