Hydrazinyl-pyrrolo compounds and methods for producing a conjugate

1. A conjugate comprising at least one modified amino acid residue of formula (III):

wherein

m is 0 or 1;

R 1 is selected from hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, aryl, substituted aryl, heteroaryl, substituted heteroaryl, cycloalkyl, substituted cycloalkyl, heterocyclyl, and substituted heterocyclyl;

R 2 and R 3 are each independently selected from hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, alkoxy, substituted alkoxy, amino, substituted amino, carboxyl, carboxyl ester, acyl, acyloxy, acyl amino, amino acyl, alkylamide, substituted alkylamide, sulfonyl, thioalkoxy, substituted thioalkoxy, aryl, substituted aryl, heteroaryl, substituted heteroaryl, cycloalkyl, substituted cycloalkyl, heterocyclyl, and substituted heterocyclyl, or R 2 and R 3 are optionally cyclically linked to form a 5 or 6-membered heterocyclyl;

X 1 is C or N;

X 2 , X 3 and X 4 are each C;

X 5 is C;

Y 1 , Y 2 , Y 3 , Y 4 and Y 5 , if present, are each independently selected from hydrogen, halogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, alkoxy, substituted alkoxy, amino, substituted amino, carboxyl, carboxyl ester, acyl, acyloxy, acyl amino, amino acyl, alkylamide, substituted alkylamide, sulfonyl, thioalkoxy, substituted thioalkoxy, aryl, substituted aryl, heteroaryl, substituted heteroaryl, cycloalkyl, substituted cycloalkyl, heterocyclyl, and substituted heterocyclyl, wherein Y 1 and Y 2 , Y 2 and Y 3 , or Y 3 and Y 4 are optionally cyclically linked;

Q 1 is a bond to either X 4 or X 5 , wherein if Q 1 is a bond to X 4 , then Y 4 is absent, or if Q 1 is a bond to X 5 , then Y 5 is absent;

L is a linker of the formula -(T 1 -V 1 ) a -(T 2 -V 2 ) b -(T 3 -V 3 ) c -(T 4 -V 4 ) d -(T 5 -V 5 ) e —, wherein a, b, c, d and e are each independently 0 or 1, where the sum of a, b, c, d and e is 1 to 5;

T 1 , T 2 , and T 3 are each independently selected from (C 1 -C 12 )alkyl, substituted (C 1 -C 12 )alkyl, (EDA) w , (PEG) n , (AA) p , —(CR 13 OH) h —, piperidin-4-amino (P4A), para-amino-benzyloxycarbonyl (PABC), meta-amino-benzyloxycarbonyl (MABC), para-amino-benzyloxy (PABO), meta-amino-benzyloxy (MABO), para-aminobenzyl, an acetal group, a disulfide, a hydrazine, a carbohydrate, a beta-lactam, an ester, (AA) p -MABC-(AA) p , (AA) p -MABO-(AA) p , (AA) p -PABO-(AA) p and (AA) p -PABC-(AA) p ;

T 4 is selected from (C 1 -C 12 )alkyl, substituted (C 1 -C 12 )alkyl, (EDA) w , (PEG) n , (AA) p , —(CR 13 OH) h —, piperidin-4-amino (P4A), para-amino-benzyloxycarbonyl (PABC), meta-amino-benzyloxycarbonyl (MABC), para-amino-benzyloxy (PABO), meta-amino-benzyloxy (MABO), para-aminobenzyl, an acetal group, a disulfide, a hydrazine, a carbohydrate, a beta-lactam, an ester, (AA) p -MABC-(AA) p , (AA) p -MABO-(AA) p , (AA) p -PABO)-(AA) p , (AA) p -PABC-(AA) p , PABC-(AA) p , (AA) p -PABO, and MABC-(AA) p ;

T 5 is selected from (C 1 -C 12 )alkyl, substituted (C 1 -C 12 )alkyl, (EDA) w , (PEG) n , (AA) p , —(CR 13 OH) h —, piperidin-4-amino (P4A), para-amino-benzyloxycarbonyl (PABC), meta-amino-benzyloxycarbonyl (MABC), para-amino-benzyloxy (PABO), meta-amino-benzyloxy (MABO), para-aminobenzyl, an acetal group, a disulfide, a hydrazine, a carbohydrate, a beta-lactam, an ester, (AA) p -MABC-(AA) p , (AA) p -MABO-(AA) p , (AA) p -PABO-(AA) p , (AA) p -PABC-(AA) p , and PABC-(AA) p ;

wherein:

EDA is an ethylene diamine having the following structure:

where q is an integer from 1 to 6 and r is 0 or 1;

piperidin-4-amino (P4A) is

PEG is a polyethylene glycol;

AA is an amino acid residue;

w is an integer from 1 to 20;

n is an integer from 1 to 30;

p is an integer from 1 to 20;

h is an integer from 1 to 12;

V 1 , V 2 , V 3 , V 4 and V 5 are each independently selected from the group consisting of a covalent bond, —CO—, —CONR 11 —, —NR 11 CO—, —C(O)O—, —OC(O)—, —O—, —S—, —S(O)—, —SO 2 —, —SO 2 NR 11 —, —NR 11 SO 2 — and —P(O)OH—, and

each R 11 and R 13 are independently selected from hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, alkoxy, substituted alkoxy, amino, substituted amino, carboxyl, carboxyl ester, acyl, acyloxy, acyl amino, amino acyl, alkylamide, substituted alkylamide, sulfonyl, thioalkoxy, substituted thioalkoxy, aryl, substituted aryl, heteroaryl, substituted heteroaryl, cycloalkyl, substituted cycloalkyl, heterocyclyl, and substituted heterocyclyl;

each R 12 of the EDA is independently selected from hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, alkoxy, substituted alkoxy, amino, substituted amino, carboxyl, carboxyl ester, acyl, acyloxy, acyl amino, amino acyl, alkylamide, substituted alkylamide, sulfonyl, thioalkoxy, substituted thioalkoxy, aryl, substituted aryl, heteroaryl, substituted heteroaryl, cycloalkyl, substituted cycloalkyl, heterocyclyl, and substituted heterocyclyl, wherein any two adjacent R 12 groups may be cyclically linked to form a piperazinyl ring;

each R 12 of the P4A is independently selected from hydrogen, alkyl, substituted alkyl, polyethylene glycol, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, alkoxy, substituted alkoxy, amino, substituted amino, carboxyl, carboxyl ester, acyl, acyloxy, acyl amino, amino acyl, alkylamide, substituted alkylamide, sulfonyl, thioalkoxy, substituted thioalkoxy, aryl, substituted aryl, heteroaryl, substituted heteroaryl, cycloalkyl, substituted cycloalkyl, heterocyclyl, and substituted heterocyclyl;

wherein one of W 1 and W 2 is a polypeptide and the other is a chemical entity selected from the group consisting of a drug and a detectable label, and

wherein when the sum of a, b, c, d and e is 2 and one of T 1 -V 1 , T 2 -V 2 , T 3 -V 3 , T 4 -V 4 or T 5 -V 5 is (PEG) n —CO, then n is not 6.

2. The conjugate of claim 1 , wherein Y 1 and Y 2 , Y 2 and Y 3 , or Y 3 and Y 4 are cyclically linked to form a fused benzo ring.

3. The conjugate of claim 1 , wherein:

T 1 is selected from a (C 1 -C 12 )alkyl and a substituted (C 1 -C 12 )alkyl;

T 2 , T 3 , T 4 and T 5 are each independently selected from (EDA) w , (PEG) n , (C 1 -C 12 )alkyl, substituted (C 1 -C 12 )alkyl, (AA) p , —(CR 13 OH) h —, piperidin-4-amino, MABC, MABO, PABO, PABC, para-aminobenzyl, an acetal group, a disulfide, a hydrazine, a carbohydrate, a beta-lactam, an ester, (AA) p -MABC-(AA) p , (AA) p -MABO-(AA) p , (AA) p -PABO-(AA) p and (AA) p -PABC-(AA) p ; and

V 1 , V 2 , V 3 , V 4 and V 5 are each independently selected from the group consisting of: a covalent bond, —CO—, —NR 11 —, —CONR 11 —, —NR 11 CO—, —C(O)O—, —OC(O)—, —O—, —S—, —S(O)—, —SO 2 —, —SO 2 NR 11 —, —NR 11 SO 2 —, and —P(O)OH—;

wherein:

(PEG) n is

where n is an integer from 1 to 30;

EDA is an ethylene diamine having the following structure:

where q is an integer from 1 to 6 and r is 0 or 1;

piperidin-4-amino is

each R 11 and R 12 is independently selected from hydrogen, an alkyl, a substituted alkyl, a polyethylene glycol, an aryl and a substituted aryl, wherein any two adjacent R 12 groups may be cyclically linked to form a piperazinyl ring; and

R 13 is selected from hydrogen, an alkyl, a substituted alkyl, an aryl, and a substituted aryl.

4. The conjugate of claim 1 , wherein:

a, b, c and d are each 1, and e is 0; or

a, b and c are each 1, and d and e are each 0; or

a and b are each 1, and c, d and e are each 0.

5. The conjugate of claim 1 , wherein T 1 , T 2 , T 3 , T 4 and T 5 and V 1 , V 2 , V 3 , V 4 and V 5 are selected from the following table:

T 1

V 1

T 2

V 2

T 3

V 3

T 4

V 4

T 5

V 5

(C 1 -C 12 )alkyl

—CONR 11 —

(PEG) n

—CO—

—

—

—

—

—

—

(C 1 -C 12 )alkyl

—CO—

(AA) p

—NR 11 —

(PEG) n

—CO—

—

—

—

—

(C 1 -C 12 )alkyl

—CO—

(AA) p

—

—

—

—

—

—

—

(C 1 -C 12 )alkyl

—CONR 11 —

(PEG) n

—NR 11 —

—

—

—

—

—

—

(C 1 -C 12 )alkyl

—CO—

(AA) p

—NR 11 —

(PEG) n

—NR 11 —

—

—

—

—

(C 1 -C 12 )alkyl

—CO—

(EDA) w

—CO—

—

—

—

—

—

—

(C 1 -C 12 )alkyl

—CONR 11 —

(C 1 -C 12 )alkyl

—NR 11 —

—

—

—

—

—

—

(C 1 -C 12 )alkyl

—CONR 11 —

(PEG) n

—CO—

(EDA) w

—

—

—

—

—

(C 1 -C 12 )alkyl

—CO—

(EDA) w

—

—

—

—

—

—

—

(C 1 -C 12 )alkyl

—CO—

(EDA) w

—CO—

(CR 13 OH) h

—CONR 11 —

(C 1 -C 12 )alkyl

—CO—

—

—

(C 1 -C 12 )alkyl

—CO—

(AA) p

—NR 11 —

(C 1 -C 12 )alkyl

—CO—

—

—

—

—

(C 1 -C 12 )alkyl

—CONR 11 —

(PEG) n

—CO—

(AA) p

—

—

—

—

—

(C 1 -C 12 )alkyl

—CONR 11 —

(PEG) n

—CO—

(AA) p

—

MABO

—

—

—

(C 1 -C 12 )alkyl

—CONR 11 —

(PEG) n

—CO—

(AA) p

—

PABO

—

—

—

(C 1 -C 12 )alkyl

—CONR 11 —

(PEG) n

—CO—

(AA) p

—

PABC

—

—

—

(C 1 -C 12 )alkyl

—CO—

(EDA) w

—CO—

(CR 13 OH) h

—CO—

(AA) p

—

—

—

(C 1 -C 12 )alkyl

—CO—

(AA) p

—NR 11 —

(C 1 -C 12 )alkyl

—CO—

(AA) p

—

—

—

(C 1 -C 12 )alkyl

—CO—

(AA) p

—NR 11 —

(PEG) n

—CO—

(AA) p

—

—

—

(C 1 -C 12 )alkyl

—CO—

(AA) p

—NR 11 —

(C 1 -C 12 )alkyl

—CO—

(AA) p

—

—

—

(C 1 -C 12 )alkyl

—CO—

(AA) p

—NR 11 —

(PEG) n

—CO—

(AA) p -

—

—

—

PABC-

(AA) p

(C 1 -C 12 )alkyl

—CO—

(AA) p

—NR 11 —

(PEG) n

—CO—

(AA) p -

—

PABC-

—

(AA) p

(C 1 -C 12 )alkyl

—CO—

(AA) p

—NR 11 —

(PEG) n

—CO—

(AA) p -

—

—

—

PABO

(C 1 -C 12 )alkyl

—CO—

(AA) p

—NR 11 —

(PEG) n

—CO—

(AA) p

—

PABO

—

(C 1 -C 12 )alkyl

—CO—

(AA) p

—NR 11 —

(PEG) n

—SO 2 —

(AA) p

—

—

—

(C 1 -C 12 )alkyl

—CONR 11 —

(PEG) n

—CO—

(AA) p

—

PABC-

—

—

—

(AA) p

(C 1 -C 12 )alkyl

—CONR 11 —

(PEG) n

—CO—

(AA) p

—

PABC

—

(AA) p

—

(C 1 -C 12 )alkyl

—CO—

(EDA) w

—CO—

(CR 13 OH) h

—CONR 11 —

(PEG) n

—CO—

—

—

(C 1 -C 12 )alkyl

—CO—

(AA) p

—NR 11 —

(PEG) n

—CO—

MABC-

—

—

—

(AA) p -

(C 1 -C 12 )alkyl

—CO—

(AA) p

—NR 11 —

(PEG) n

—CO—

MABC

—

(AA) p

—

(C 1 -C 12 )alkyl

—CONR 11 —

(PEG) n

—CO—

MABO

—

—

—

—

—

(C 1 -C 12 )alkyl

—CO—

(AA) p

—NR 11 —

(PEG) n

—CO—

MABO

—

—

—

(C 1 -C 12 )alkyl

—CO—

(AA) p

—NR 11 —

(PEG) n

—CO—

PABO

—

—

—

(C 1 -C 12 )alkyl

—CO—

(AA) p

—NR 11 —

(PEG) n

—CO—

PABC

—

—

—

(C 1 -C 12 )alkyl

—CONR 11 —

(PEG) n

—CO—

MABC

—

(AA) p

—

—

—

(C 1 -C 12 )alkyl

—CO—

(CR 13 OH) h

—CO—

—

—

—

—

—

—

(C 1 -C 12 )alkyl

—CONR 11 —

substituted

—NR 11 —

(PEG) n

—CO—

—

—

—

—

(C 1 -C 12 )alkyl

(C 1 -C 12 )alkyl

—SO 2 —

(C 1 -C 12 )alkyl

—CO—

—

—

—

—

—

—

(C 1 -C 12 )alkyl

—CONR 11 —

(PEG) n

—CO—

(AA) p

—

PABC

—NR 11 —

—

—

(C 1 -C 12 )alkyl

—CONR 11 —

(C 1 -C 12 )alkyl

—

(CR 13 OH) h

—CONR 11 —

—

—

—

—

(C 1 -C 12 )alkyl

—CO—

P4A

—CO—

(C 1 -C 12 )alkyl

—CO—

(AA) p

—

PABO

—CO—

(C 1 -C 12 )alkyl

—CO—

P4A

—CO—

(C 1 -C 12 )alkyl

—CO—

(AA) p

—

PABO

—

(C 1 -C 12 )alkyl

—CO—

P4A

—CO—

(C 1 -C 12 )alkyl

—CO—

(AA) p

—

PABC-

—

(AA) p

(C 1 -C 12 )alkyl

—CO—

P4A

—CO—

(C 1 -C 12 )alkyl

—CO—

(AA) p

—

—

—.

6. The conjugate of claim 1 , wherein L is selected from the group consisting of the following structures:

wherein:

each f is independently 0 or an integer from 1 to 12;

each w is independently 0 or an integer from 1 to 20;

each n is independently 0 or an integer from 1 to 30;

each p is independently 0 or an integer from 1 to 20;

each h is independently 0 or an integer from 1 to 12;

each R is independently hydrogen, alkyl, substituted alkyl, a polyethylene glycol, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, alkoxy, substituted alkoxy, amino, substituted amino, carboxyl, carboxyl ester, acyl, acyloxy, acyl amino, amino acyl, alkylamide, substituted alkylamide, sulfonyl, thioalkoxy, substituted thioalkoxy, aryl, substituted aryl, heteroaryl, substituted heteroaryl, cycloalkyl, substituted cycloalkyl, heterocyclyl, and substituted heterocyclyl; and

each R′ is independently H, a sidechain group of an amino acid, alkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, alkoxy, substituted alkoxy, amino, substituted amino, carboxyl, carboxyl ester, acyl, acyloxy, acyl amino, amino acyl, alkylamide, substituted alkylamide, sulfonyl, thioalkoxy, substituted thioalkoxy, aryl, substituted aryl, heteroaryl, substituted heteroaryl, cycloalkyl, substituted cycloalkyl, heterocyclyl, and substituted heterocyclyl.

7. The conjugate of claim 1 , wherein Q 1 is a bond to X 5 and Y 5 is absent.

8. The conjugate of claim 1 , wherein m is 1.

9. The conjugate of claim 1 , wherein R 2 and R 3 are each independently selected from alkyl and substituted alkyl.

10. The conjugate of claim 1 , wherein X 1 , X 2 , X 3 and X 4 are each C.

11. The conjugate of claim 1 , wherein Y 1 , Y 2 and Y 3 are each H, and one of either Y 4 or Y 5 is H.

12. The conjugate of claim 1 , wherein the conjugate comprises at least one modified amino acid residue of formula (IIIa):

13. The conjugate of claim 1 , wherein the conjugate comprises at least one modified amino acid residue of formula (IIId):

14. The conjugate of claim 1 , wherein the chemical entity is a drug.

15. The conjugate of claim 1 , wherein W 1 is the chemical entity, and W 2 is the polypeptide; or wherein W 1 is the polypeptide, and W 2 is the chemical entity.

16. A pharmaceutical composition comprising:

a conjugate of claim 1 ; and

a pharmaceutically acceptable excipient.

17. A method of delivering a conjugate to a subject, the method comprising: administering to the subject an effective amount of a conjugate of claim 1 .