Drug-conjugates, conjugation methods, and uses thereof

1. A compound having the structure of Formula II:

or a pharmaceutically acceptable salt thereof, wherein:

Y is CH 2 ;

R 9 is selected from the group consisting of H (hydrogen), optionally substituted C 1 -C 8 alkyl, optionally substituted C 3 -C 8 cycloalkyl, optionally substituted aryl, and optionally substituted heteroaryl;

optionally R 1 and R 2 , R 1 and R 3 , R 7 and R 8 , R 8 and R 9 , or R 7 and R 9 together with the atoms to which they are attached form an optionally substituted cyclic 5- to 7-membered ring;

X is selected from the group consisting of —OR 10 and —SO 2 —R 10 ;

R 10 is R C ;

R 1 is H (hydrogen), optionally substituted C 1 -C 6 alkyl, R 1A , or R 1B ;

R 1A is a monoclonal antibody or an antibody fragment;

R 1B is -L 1 (CH 2 ) n R C , -L 1 O(CH 2 ) n R C or —(CH 2 ) n R C ;

R 2 -R 7 are each independently selected from the group consisting of H (hydrogen), optionally substituted C 1 -C 8 alkyl, optionally substituted C 3 -C 8 cycloalkyl, optionally substituted aryl, and optionally substituted heteroaryl;

R 8 is selected from the group consisting of H (hydrogen), —(CH 2 ) n R C , optionally substituted C 1 -C 8 alkyl, optionally substituted C 3 -C 8 cycloalkyl, optionally, substituted aryl, and optionally substituted heterocyclyl;

R C is C 1 -C 8 alkyl, C 3 -C 8 cycloalkyl, aryl, heteroaryl, and heterocyclyl, each optionally substituted with one or more R D , or R C is a monoclonal antibody or an antibody fragment;

each R D is independently selected from the group consisting of —OH, —N 3 , halo, cyano, nitro, —(CH 2 ) n NR E R F , —(CH 2 ) n C(═O)NR E R F , —O(CH 2 ) n NR E R F , —O(CH 2 ) n C(═O)NR E R F , —O(CH 2 ) m OC(═O)NR E R F , —NR G C(═O)R H , —NR G S(O) z R H , —O(CH 2 ) m O(CH 2 ) m R J , —O(CH 2 ) n C(═O)R J , —O(CH 2 ) n R J , optionally substituted C 1 -C 8 alkyl, optionally substituted C 3 -C 8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, and optionally substituted —O—(C 1 -C 8 alkyl);

R E and R F are each independently selected from hydrogen, -[(L 1 ) s (C(R 2A ) 2 ) r (NR 2A ) s (C(R 2A ) 2 ) r ]-[L 1 (C(R 2A ) 2 ) r (NR 2A ) s (C(R 2A ) 2 ) r ] s - (L 1 ) s -R J , -[(L 1 ) s (C(R 2A ) 2 ) r (NR 2A ) s (C(R 2A ) 2 ) r ]-(L 1 ) s [(C(R 2A ) 2 ) r O(C(R 2A ) 2 ) r (L 2 ) s ] s -(L 1 ) s -R J , optionally substituted C 1-8 alkyl, optionally substituted C 3-8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl;

each R G is independently hydrogen, optionally substituted C 1 -C 8 alkyl, optionally substituted C 3 -C 8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, or optionally substituted heterocyclyl;

each R H is independently hydrogen, optionally substituted C 1 -C 8 alkyl, optionally substituted C 3 -C 8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, or —NR E R F ;

each R J is independently selected from the group consisting of hydrogen, optionally substituted C 1 -C 8 alkyl, optionally substituted —O—(C 1 -C 8 alkyl), optionally substituted C 3 -C 8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, —(CH 2 ) n OR 2B , —O(CH 2 ) n OR 2B , —(CH 2 ) n NR 2B R 2B , —C(R 2A ) 2 NR 2B R 2B , —(CH 2 ) n C(═O)OR 2B , and —C(═O)NHR 2B ;

each R 2A is independently selected, wherein R 2A is selected from the group consisting of hydrogen, halo, —OH, optionally substituted C 1 -C 8 alkyl, optionally substituted —O—(C 1 -C 8 alkyl), optionally substituted C 3 -C 8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, —(CH 2 ) n OR 2B , —(CH 2 ) n NR 2C R 2C , —C(═O)OR 2B , and —C(═O)NR 2C R 2C , or optionally two geminal R 2A and the carbon to which they are attached form an optionally substituted three- to six-membered carbocyclic ring;

each R 2B is independently selected from the group consisting of hydrogen, —OH, —(CH 2 ) n C(═O)OH, —C(═O)(C(R 2D ) 2 ) n L 3 R 2E , optionally substituted C 1 -C 8 alkyl, optionally substituted C 3 -C 8 cycloalkyl, optionally substituted —O—(C 1 -C 8 alkyl), optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl;

each R 2C is independently selected from the group consisting of hydrogen, —OH, optionally substituted C 1 -C 8 alkyl, optionally substituted C 3 -C 8 cycloalkyl, optionally substituted —O—(C 1 -C 8 alkyl), optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl, or optionally both R 2C together with the nitrogen to which they are attached form a optionally substituted heterocyclyl;

each R 2D is independently selected from the group consisting of hydrogen, optionally substituted C 1 -C 8 alkyl, optionally substituted C 3 -C 8 cycloalkyl, optionally substituted —O—(C 1 -C 8 alkyl), optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl;

each R 2E is independently selected from the group consisting of optionally substituted C 1 -C 8 alkyl, optionally substituted C 3 -C 8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl, and —(CH 2 ) n C(═O)OR 2F ;

each R 2F is independently selected from the group consisting hydrogen, optionally substituted C 1 -C 8 alkyl, optionally substituted C 3 -C 8 cycloalkyl, optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl;

each L 1 is independently selected from the group consisting of —C(═O)—, —S(═O)—, —C(═S)—, —S(═O) 2 —, —C(═O)O—, —C(═O)NR 2A —, —S(═O)NR 2A —, —S(═O) 2 NR 2A —, —C(═O)NR 2A C(═O)—, and —C(CF 3 ) 2 NR 2A —;

each L 2 is independently selected from the group consisting of optionally substituted aryl, optionally substituted heteroaryl, and optionally substituted heterocyclyl;

each L 3 is independently selected from the group consisting of —C(═O)—, —S(═O)—, —C(═S)—, —S(═O) 2 —, —C(═O)O—, —C(═O)NR 2A —, —S(═O)NR 2A —, —S(═O) 2 NR 2A —, —C(═O)NR 2A C(═O)—, and —C(CF 3 ) 2 NR 2A —;

each m independently is 1 or 2;

each n independently is 0, 1, 2, 3, 4, 5, or 6;

each r independently is 0, 1, 2, 3, 4, 5, or 6;

each s independently is 0 or 1; and

each z independently is 1 or 2.

2. The compound of claim 1 , wherein

R 9 is selected from the group consisting of H (hydrogen), C 1 -C 8 alkyl, C 3 -C 8 cycloalkyl, substituted C 1 -C 8 alkyl, aryl, and heteroaryl;

R 1 is H (hydrogen), or unsubstituted C 1 -C 6 alkyl, R 1A , or R 1B ;

R 2 -R 7 are each independently selected from the group consisting of H (hydrogen), C 1 -C 8 alkyl, C 3 -C 8 cycloalkyl, aryl, and heteroaryl, or R 1 and R 2 together with the nitrogen to which they are attached form a cyclic 5- to 7-membered ring;

R 8 is selected from is selected from the group consisting of H (hydrogen), —(CH 2 ) n R c , C 1 -C 8 alkyl, C 3 -C 8 cycloalkyl, aryl, and heterocyclyl;

R C is C 1 -C 8 alkyl, C 3 -C 8 cycloalkyl, aryl, heteroaryl, and heterocyclyl, each optionally substituted with one or more R D , or R C is a monoclonal antibody or an antibody fragment;

each R D is independently selected from the group consisting of —OH, —N 3 , halo, cyano, nitro, —(CH 2 ) n NR E R F , —(CH 2 ) n C(═O)NR E R F , —O(CH 2 ) n NR E R F , —O(CH 2 ) n C(═O)NR E R F , —O(CH 2 ) m OC(═O)NR E R F , —NR G C(═O)R H , —NR G S(O) z R H , —O(CH 2 ) m O(CH 2 ) m R J , —O(CH 2 ) n C(═O)R J , —O(CH 2 ) n R J , C 1 -C 8 alkyl, C 3 -C 8 cycloalkyl, aryl, heteroaryl, heterocyclyl, and —O—(C 1 -C 8 alkyl);

R E and R F are each independently selected from hydrogen, -[(L 1 ) s (C(R 2A ) 2 ) r (NR 2A ) s (C(R 2A ) 2 ) r ]-[L 1 (C(R 2A ) 2 ) r (NR 2A ) s (C(R 2A ) 2 ) r ] s - (L 1 ) s -R J , -[(L 1 ) s (C(R 2A ) 2 ) r (NR 2A ) s (C(R 2A ) 2 ) r ]-(L 1 ) s [(C(R 2A ) 2 ) r O(C(R 2A ) 2 ) r (L 2 ) s ] s -(L 1 ) s -R J , C 1-8 alkyl, C 3-8 cycloalkyl, aryl, heteroaryl, and heterocyclyl;

each R G is independently hydrogen, C 1 -C 8 alkyl, C 3 -C 8 cycloalkyl, aryl, heteroaryl, or heterocyclyl;

each R H is independently hydrogen, C 1 -C 8 alkyl, C 3 -C 8 cycloalkyl, aryl, heteroaryl, heterocyclyl, or —NR E R F ;

each R J is independently selected from the group consisting of hydrogen, C 1 -C 8 alkyl, —O—(C 1 -C 8 alkyl), C 3 -C 8 cycloalkyl, aryl, heteroaryl, heterocyclyl, —(CH 2 ) n OR 2B , —O(CH 2 ) n OR 2B , —(CH 2 ) n NR 2B R 2B , —C(R 2A ) 2 NR 2B R 2B , —(CH 2 ) n C(═O)OR 2B , and —C(═O)NHR 2B ;

each R 2A is independently selected, wherein R 2A is selected from the group consisting of hydrogen, halo, —OH, C 1 -C 8 alkyl, —O—(C 1 -C 8 alkyl), C 3 -C 8 cycloalkyl, aryl, heteroaryl, heterocyclyl, —(CH 2 ) n OR 2B , —(CH 2 ) n NR 2C R 2C , —C(═O)OR 2B , and —C(═O)NR 2C R 2C , or optionally two geminal R 2A and the carbon to which they are attached form a three- to six-membered carbocyclic ring;

each R 2B is independently selected from the group consisting of hydrogen, —OH, —(CH 2 ) n C(═O)OH, —C(═O)(C(R 2D ) 2 ) n L 3 R 2E , C 1 -C 8 alkyl, C 3 -C 8 cycloalkyl, —O—(C 1 -C 8 alkyl), aryl, heteroaryl, and unsubstituted heterocyclyl;

each R 2C is independently selected from the group consisting of hydrogen, —OH, C 1 -C 8 alkyl, C 3 -C 8 cycloalkyl, —O—(C 1 -C 8 alkyl), aryl, heteroaryl, and heterocyclyl, or optionally both R 2C together with the nitrogen to which they are attached form a heterocyclyl;

each R 2D is independently selected from the group consisting of hydrogen, C 1 -C 8 alkyl, C 3 -C 8 cycloalkyl, —O—(C 1 -C 8 alkyl), aryl, heteroaryl, and heterocyclyl;

each R 2E is independently selected from the group consisting of C 1 -C 8 alkyl, C 3 -C 8 cycloalkyl, aryl, heteroaryl, and heterocyclyl, and —(CH 2 ) n C(═O)OR 2F ;

each R 2F is independently selected from the group consisting hydrogen, C 1 -C 8 alkyl, C 3 -C 8 cycloalkyl, aryl, heteroaryl, and heterocyclyl; and

each L 2 is independently selected from the group consisting of aryl, heteroaryl, and heterocyclyl.

3. The compound of claim 1 , wherein

R 1B is —C(═O)(CH 2 ) n R C or R C ;

R C is C 1 -C 8 alkyl substituted with one or more R D ;

R D is —O(CH 2 ) m O(═O)NR E R F , —O(CH 2 ) m O(CH 2 ) m R J , or optionally substituted heterocyclyl;

R J is —C(═O)OR 2B ; and

R 2B is —OH.

4. The compound of claim 1 , wherein R 1B is —C(═O)O(CH 2 ) n R C .

5. The compound of claim 4 , wherein

R C is aryl substituted with one or more R D ;

R D is —(CH 2 ) n NR E R F ;

R E is hydrogen; and

R F is -[(L 1 ) s (C(R 2A ) 2 ) r (NR 2A ) s (C(R 2A ) 2 ) r ]-[L 1 (C(R 2A ) 2 ) r (NR 2A ) s (C(R 2A ) 2 ) r ] s -(L 1 ) s -R J .

6. The compound of claim 5 , wherein

R F is —[C(═O)(C(R 2A ) 2 )(NR 2A )]-[L 1 (C(R 2A ) 2 ) r ]-R J or —[C(═O)(C(R 2A ) 2 )(NR 2A )]-L 1 [(C(R 2A ) 2 ) r O(C(R 2A ) 2 ) r ]-R J ;

R J is —(CH 2 ) n OR 2B or —C(═O)OR 2B ; and

R 2B is hydrogen or —(CH 2 ) n C(═O)OH.

7. The compound of claim 1 , wherein R C is aryl substituted with one or more R D .

8. The compound of claim 7 , wherein

R D is —(CH 2 ) n NR E R F ;

R E is hydrogen; and

R F is -[(L 1 ) s (C(R 2A ) 2 ) r (NR 2A ) s (C(R 2A ) 2 ) r ]-[L 1 (C(R 2A ) 2 ) r (NR 2A ) s (C(R 2A ) 2 ) r ] s -(L 1 ) s -R J .

9. The compound of claim 8 , wherein R F is —[C(═O)(C(R 2A ) 2 )(NR 2A )]—[C(═O)(C(R 2A ) 2 ) r (NR 2A )]—C(═O)—R J .

10. The compound of claim 7 , wherein

R D is —(CH 2 ) n NR E R F ;

R E is hydrogen; and

R F is -[(L 1 ) s (C(R 2A ) 2 ) r (NR 2A ) s (C(R 2A ) 2 ) r ]-(L 1 ) s -R J .

11. The compound of claim 10 , wherein R F is —[C(═O)(C(R 2A ) 2 ) r (NR 2A )]—C(═O)—R J .

12. The compound of claim 11 , wherein R J is —(CH 2 ) n C(═O)OR 2B ; and R 2B is hydrogen.

13. The compound of claim 8 , wherein

R F is —[C(═O)(C(R 2A ) 2 )(NR 2A )]—C(═O)[(C(R 2A ) 2 ) r O(C(R 2A ) 2 ) r ]—R J ;

R J is —O(CH 2 ) n C(═O)OR 2B ; and

R 2B is hydrogen.

14. The compound of claim 1 , wherein R 8 is —(CH 2 ) n R C .

15. The compound of claim 14 , wherein

R C is aryl substituted with one or more R D ;

R D is —O(CH 2 ) n R J or —O(CH 2 ) n C(═O)NR E R F ;

R J is —(CH 2 ) n C(═O)OR 2B ; and

R 2B is hydrogen.

16. The compound of claim 15 , wherein

R D is —O(CH 2 ) n C(═O)NR E R F ;

R E is hydrogen; and

R F is -[(L 1 ) s (C(R 2A ) 2 ) r (NR 2A ) s (C(R 2A ) 2 ) r ]-(L 1 ) s [(C(R 2A ) 2 ) r O(C(R 2A ) 2 ) r (L 2 ) s ] s -(L 1 ) s R J .

17. A pharmaceutical composition comprising the compound of claim 1 , or a pharmaceutically acceptable salt thereof; and a pharmaceutically acceptable carrier.

18. A pharmaceutical composition comprising the compound of claim 2 , or a pharmaceutically acceptable salt thereof; and a pharmaceutically acceptable carrier.