Peptidyl prodrugs and linkers and stabilizers useful therefor
View Patent ↗The present invention provides analogues of duocarmycins that are potent cytotoxins. Also provided are peptidyl and disulfide linkers that are cleaved in vivo. The linkers are of use in forming prodrugs and conjugates of the cytotoxins of the invention as well as other diagnostic and therapeutic moieties. The invention provides prodrugs and conjugates of the duocarmycin analogues with the linker arms of the invention.
1. A compound having the structure:
wherein
A is a member selected from substituted or unsubstituted phenyl and substituted or unsubstituted pyrrole;
Z is a member selected from O, S and NR 23 ;
X is a member selected from O, S and NR 23
wherein
each R 23 is independently 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, diphosphates, triphosphates, acyl, C(O)R 12 , 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 and R 5 are members independently selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted heterocycloalkyl, halogen, NO 2 , NR 15 R 16 , NC(O)R 15 , OC(O)NR 15 R 16 , OC(O)OR 15 , C(O)R 15 , SR 15 , and OR 15
wherein
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; and
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 the compound comprises at least one member selected from R 15 or R 16 having the structure:
wherein
X 4 is member selected from protected or unprotected reactive functional groups, detectable labels and targeting agents;
L 3 is a linker selected from substituted or unsubstituted alkyl and substituted or unsubstituted heteroalkyl groups;
AA 1 , AA C and AA c+1 are members independently selected from natural and unnatural α-amino acids;
L 4 is a linker selected from substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl groups, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, and substituted or unsubstituted cycloalkyl;
p and t are integers independently selected from 0 and 1; and
c is an integer from 0 to 20;
or a pharmaceutically acceptable salt thereof.
2. The compound of claim 1 , wherein R 11 is C(O)NR 12 R 13 wherein R 12 and R 13 are members independently selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl and substituted or unsubstituted aryl.
3. The compound of claim 1 , wherein A is a substituted or unsubstituted phenyl ring.
4. The compound of claim 3 , wherein the phenyl ring is substituted with CN.
5. The compound of claim 3 , wherein A is an unsubstituted phenyl ring.
6. The compound of claim 1 , wherein A is a pyrrole ring system.
7. The compound of claim 1 , wherein said targeting agent is a biomolecule.
8. The compound of claim 7 , wherein said biomolecule is a member selected from antibodies, receptors, peptides, lectins, saccharides, nucleic acids and combinations thereof.
9. The compound of claim 1 , wherein X is O and Z is O or NH.
10. The compound of claim 1 , wherein R 3 is —OC(O)NR 12 R 13 .
11. The compound of claim 10 , wherein one of R 4 or R 5 is
wherein p and t=1 and c=0 or 1.
12. The compound of claim 11 , wherein AA 1 is valine.
13. The compound of claim 11 , wherein L 3 is a substituted heteroalkyl.
14. The compound of claim 11 , wherein L 4 is a substituted aryl or heteroaryl.
15. The compound of claim 10 , wherein X 4 is an antibody.
16. The compound of claim 10 , wherein the reactive functional group is a N-hydroxysuccinimide ester, N-hydroxybenztriazole ester, acid halide, acyl imidazole, thioester, p-nitrophenyl ester, alkyl, alkenyl, alkynyl, aromatic ester, hydroxy, haloalkyl, dienophile, aldehydes, ketone, sulfonyl halide, amine, sulfhydryl group, alkene, or an epoxide, or
wherein the reactive functional group is prepared from an ester, thioesters, carbonate, carbamate, amide, urea, thiourea, acetal, ketal, acyloxyalkyl derivative, enol ester, N-sulfonylimidate, anhydrids, N-acylamide N-Mannich based hydroxymethyl ketone ester, disulfide, phosphonate ester, or phosphonamidate.
17. The compound of claim 10 , wherein X 4 is a reactive functional group having the structure:
where . . . is a single or double bond.
18. The compound of claim 1 , wherein R 6 is a single bond and R 7 is CH 2 -halogen.
19. The compound of claim 1 , wherein one of R 4 or R 5 is NR 15 R 16 .
20. The compound of claim 19 , wherein one of R 4 or R 5 is
wherein p and t=1 and c=0 or 1.
21. The compound of claim 20 , wherein X 4 is an antibody.
22. The compound of claim 20 , wherein X 4 is a reactive functional group having the structure:
where . . . is a single or double bond.
23. The compound of claim 20 , wherein AA 1 is valine.
24. The compound of claim 20 , wherein L 3 is a substituted heteroalkyl.
25. The compound of claim 20 , wherein L 4 is a substituted aryl or heteroaryl.
26. The compound of claim 1 , wherein X 4 is an antibody.
27. The compound of claim 1 , wherein the reactive functional group is a N-hydroxysuccinimide ester, N-hydroxybenztriazole ester, acid halide, acyl imidazole, thioester, p-nitrophenyl ester, alkyl, alkenyl, alkynyl, aromatic ester, hydroxy, haloalkyl, dienophile, aldehydes, ketone, sulfonyl halide, amine, sulfhydryl group, alkene, or an epoxide, or
wherein the reactive functional group is prepared from an ester, thioesters, carbonate, carbamate, amide, urea, thiourca, acetal, ketal, acyloxyalkyl derivative, enol ester, N-sulfonylimidate, anhydrids, N-acylamide N-Mannich based hydroxymethyl ketone ester, disulfide, phosphonate ester, or phosphonamidate.
28. The compound of claim 1 , wherein X 4 is a reactive functional group having the structure:
where . . . is a single or double bond.
29. The compound of claim 1 , wherein:
the targeting agent is a selected from saccharides, lectins, receptors, ligand for receptors, BSA, antibodies, polyamino acids, polysaccharides, peptides, nucleic acids, cyclodextrins, aptamers, antisense compounds, nucleic acids that form triple helices, and nucleotide analogs,
the detectable label is selected from magnetic beads, fluorescent labels, radiolabels, and colorimeteric labels, and
the reactive functional group selected from olefins, acetylenes, alcohols, phenols, ethers, oxides, halides, aldehydes, ketones, carboxylic acids, esters, amides, cyanates, isocyanates, thiocyanates, isothiocyanates, amines, hydrazines, hydrazones, hydrazides, diazo, diazoniurn, nitro, nitriles, mercaptans, sulfides, disulfides, sulfoxides, sulfones, sulfonic acids, sulfinic acids, acetals, ketals, anhydrides, sulfates, sulfenic acids isonitriles, amidines, imides, imidates, nitrones, hydroxylamines, oximes, hydroxamic acids thiohydroxamic acids, allenes, ortho esters, sulfites, enamines, ynammes, ureas, pseudoureas, semicarbazides, carbodiimides, carbamates, imines, azides, azo groups, azoxy groups, and nitroso groups.
30. The compound of claim 29 , wherein X 1 is a halogen.
31. A compound having the structure:
wherein
A is a member selected from substituted or unsubstituted phenyl, and substituted or unsubstituted pyrrole;
X is a member selected from O, S and NR 23
wherein
each R 23 is independently 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 (= 0 ), 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, diphosphates, triphosphates, acyl, C(O)R 12 , 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 and R 5 are members independently selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted heterocycloalkyl, halogen, NO 2 , NR 15 R 16 , NC(O)R 15 , OC(O)NR 15 R 16 , OC(O)OR 5 , C(O)R 15 , SR 15 ,and OR 15
wherein
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; and
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 is a halogen;
wherein the compound comprises at least one member selected from R 15 or R 16 having the structure:
wherein
X 4 is member selected from an antibody or
where . . . is a single or double bond;
L 3 is a linker selected from substituted or unsubstituted alkyl and substituted or unsubstituted heteroalkyl groups;
AA 1 , AA C and AA C+1 are members independently selected from natural and unnatural α-amino acids;
L 4 is a linker selected from substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl groups, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, and substituted or unsubstituted cycloalkyl;
p and t are integers independently selected from 0 and 1;and
c is an integer from 0 to 20; or a pharmaceutically acceptable salt thereof.
32. A compound having the structure:
wherein
X is a member selected from O, S and NR 23
wherein
each R 23 is independently 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, diphosphates, triphosphates, acyl, C(O)R 12 , 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 and R 5 are members independently selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted heterocycloalkyl, halogen, NO 2 , NR 15 R 16 , NC(O)R 15 , OC(O)NR 15 R 6 , OC(O)OR 15 , C(O)R 15 , SR 15 , and OR 15
wherein
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; and
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 halogen;
wherein the compound comprises at least one member selected from R 15 or having the structure:
wherein
X 4 is member selected from an antibody or
where . . . is a single or double bond;
L 3 is a linker selected from substituted or unsubstituted alkyl and substituted or unsubstituted heteroalkyl groups;
AA 1 , AA C and AA C+1 are members independently selected from natural α-amino acids;
L 4 is a linker selected from substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl;
p and t are integers independently selected from 0 and 1;and
c is 0 or 1; or a pharmaceutically acceptable salt thereof.