Novel linkers for antibody-drug conjugates and related compounds, compositions, and methods of use

Abstract

Provided herein are antibody-cytotoxin antibody-drug conjugates and related compounds, such as linker-cytotoxin conjugates and the linkers used to make them, and intermediates in their synthesis; compositions; and methods, including methods of treating cancers

1 . A linker of the following formula (I): 
       
         
           
           
               
               
           
         
         or an enantiomer, diasteriomer, or mixtures thereof, 
         wherein:
 each X and X′ is independently O, S, NH or NR 1  wherein R 1  is C 1-3  alkyl; 
 each Y and Y′ is independently hydrogen or an electrophilic leaving group that reacts selectively with thiols, provided if one of Y and Y′ is hydrogen, the other is the electrophilic leaving group; 
 W is —NH—, —N(R 1 )—, —CH 2 —, —CH 2 —NH—, —CH 2 —N(R 1 )—, —CH 2 CH 2 —, —CH(R 2 )—, or —CH 2 CH(R 2 )—; wherein R 1  and R 2  are independently C 1-3  alkyl; 
 Z is —CO 2 H, —NH 2 , —OH, —NH—R 3a , or —CO 2 R 3b ; wherein R 3a  is an amino protecting group, and R 3b  is a carboxyl protecting group; 
 R is any chemical group; or R is absent; 
 each L 1 , L 2  and L 3  is independently a linker selected from the group consisting of —O—, —C(O)—, —S—, —S(O)—, —S(O) 2 —, —NH—, —NCH 3 —, —(CH 2 ) q —, —NH(CH 2 ) 2 NH—, —OC(O)—, —CO 2 —, —NHCH 2 CH 2 C(O)—, —C(O)NHCH 2 CH 2 NH—, —NHCH 2 C(O)—, —NHC(O)—, —C(O)NH—, —NCH 3 C(O)—, —C(O)NCH 3 —, —(CH 2 CH 2 O) p , —(CH 2 CH 2 O) p CH 2 CH 2 —, —CH 2 CH 2 —(CH 2 CH 2 O) p —, —OCH(CH 2 O—) 2 , -(AA) r -, cyclopentanyl, cyclohexanyl, unsubstituted phenylenyl, and phenylenyl substituted by 1 or 2 substituents selected from the group consisting of halo, CF 3 —, CF 3 O—, CH 3 O—, —C(O)OH, —C(O)OC 1-3  alkyl, —C(O)CH 3 , —CN, —NH—, —NH 2 , —O—, —OH, —NHCH 3 , —N(CH 3 ) 2 , and C 1-3  alkyl; 
 a, b and c are each independently an integer of 0, 1, 2 or 3, provided that at least one of a, b or c is 1; 
 each k and k′ is independently an integer of 0 or 1; 
 each p is independently an integer of 1 to 14; 
 each q is independently an integer or 1 to 12; 
 each AA is independently an amino acid; 
 each r is 1 to 12; and 
 the   bond represents a single or a double bond. 
 
       
     
     
         2 . The linker of  claim 1 , wherein the   bond represents a single bond. 
     
     
         3 . The linker of  claim 1 , wherein each Y and Y′ is independently selected from the group consisting of a halo, a substituted thiol, and a substituted sulfonate. 
     
     
         4 . (canceled) 
     
     
         5 . (canceled) 
     
     
         6 . The linker of  claim 3 , wherein each Y and Y′ is independently selected from the group consisting of: 
       
         
           
           
               
               
           
         
         wherein R A  is selected from the group consisting of hydroxyl, amino, nitro, cyano, chloro, bromo, fluoro, iodo, oxo, carboxyl, C 1-6  alkoxycarbonyl, C 1-6  alkyl, C 2-6  alkenyl, and C 1-6  alkoxy; or 
         wherein each Y and Y′ is independently selected from the group consisting of: 
       
       
         
           
           
               
               
           
         
       
     
     
         7 . (canceled) 
     
     
         8 . The linker of  claim 1 , wherein:
 each L 1 , L 2  and L 3  is independently selected from the group consisting of —(CH 2 ) q —, —NH(CH 2 ) 2 NH—, —OC(O)—, —CO 2 —, —NHCH 2 CH 2 C(O)—, —C(O)NHCH 2 CH 2 NH—, —NHCH 2 C(O)—, —NHC(O)—, —C(O)NH—, —NCH 3 C(O)—, —C(O)NCH 3 —, —(CH 2 CH 2 O) p , —(CH 2 CH 2 O) p CH 2 CH 2 —, —CH 2 CH 2 —(CH 2 CH 2 O) p —, and -(AA) r -;   a, b and c are each independently 0, 1 or 2; and   each p, q and r is independently 1, 2, 3 or 4; or   wherein each AA is an amino acid selected from the group consisting of Ala, Arg, Asn, Asp, Cys, Glu, Gln, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr and Val; or   wherein each AA is an amino acid selected from the group consisting of Gly, Arg, Val, Ala, Cys, Gln, Leu, Ile, Leu, Lys and Ser or their N-methylated analogues.   
     
     
         9 . (canceled) 
     
     
         10 . (canceled) 
     
     
         11 . The linker of  claim 1 , wherein R 3a  is selected from the group consisting of 9-fluorenylmethyloxycarbamate (FMOC), t-butyl carbamate (BOC), benzyl carbamate (Cbz), acetamide, trifluroacetamide, phthalimide, benzylamine, triphenylmethylamine, benzylideneamine, and p-toluenesulfonamide (p-TOS); or
 wherein R 3b  is selected from the group consisting of a methyl ester, a t-butyl ester, a benzyl ester, an S-t-butyl ester, and 2-alkyl-1,3-oxazoline; or   wherein R is selected from the group consisting of W, (L 1 ) a , (L 2 ) b , (L 3 ) c , Z, W-(L 1 ) a -(L 2 ) b -(L 3 ) c , (L 1 ) a -(L 2 ) b -(L 3 ) c -Z, and W-(L 1 ) a -(L 2 ) b -(L 3 ) c -Z, as defined in  claim 1 ; or   wherein R is a detectable probe.   
     
     
         12 . (canceled) 
     
     
         13 . (canceled) 
     
     
         14 . (canceled) 
     
     
         15 . The linker of  claim 1 , wherein k and k′ are both 1. 
     
     
         16 . A linker-cytotoxin conjugate of the following formula (II): 
       
         
           
           
               
               
           
         
         or an enantiomer, diasteriomer, or mixtures thereof; 
         wherein:
 each X and X′ is independently O, S, NH or NR 1  wherein R 1  is C 1-3  alkyl; 
 each Y and Y′ is independently hydrogen or an electrophilic leaving group that reacts selectively with thiols, provided if one of Y and Y′ is hydrogen, the other is the electrophilic leaving group; 
 W is —NH—, —N(R 1 )—, —CH 2 —, —CH 2 —NH—, —CH 2 —N(R 1 )—, —CH 2 CH 2 —, —CH(R 2 )—, or —CH 2 CH(R 2 )—; wherein R 1  and R 2  are independently C 1-3  alkyl; 
 CTX is a cytotoxin; 
 R is any chemical group; or R is absent; 
 each L 1 , L 2  and L 3  is independently a linker selected from the group consisting of —O—, —C(O)—, —S—, —S(O)—, —S(O) 2 —, —NH—, —NCH 3 —, —(CH 2 ) q —, —NH(CH 2 ) 2 NH—, —OC(O)—, —CO 2 —, —NHCH 2 CH 2 C(O)—, —C(O)NHCH 2 CH 2 NH—, —NHCH 2 C(O)—, —NHC(O)—, —C(O)NH—, —NCH 3 C(O)—, —C(O)NCH 3 —, —(CH 2 CH 2 O) p , —(CH 2 CH 2 O) p CH 2 CH 2 —, —CH 2 CH 2 —(CH 2 CH 2 O) p —, —OCH(CH 2 O—) 2 , -(AA) r -, cyclopentanyl, cyclohexanyl, unsubstituted phenylenyl, and phenylenyl substituted by 1 or 2 substituents selected from the group consisting of halo, CF 3 —, CF 3 O—, CH 3 O—, —C(O)OH, —C(O)OC 1-3  alkyl, —C(O)CH 3 , —CN, —NH—, —NH 2 , —O—, —OH, —NHCH 3 , —N(CH 3 ) 2 , and C 1-3  alkyl; 
 a, b and c are each independently an integer of 0, 1, 2 or 3, provided that at least one of a, b or c is 1; 
 each k and k′ is independently an integer of 0 or 1; 
 each p is independently an integer of 1 to 14; 
 each q is independently an integer or 1 to 12; 
 m is an integer of 1 to 4; 
 each AA is independently an amino acid; 
 each r is 1 to 12; and 
 the   bond represents a single or a double bond. 
 
       
     
     
         17 . The linker-cytotoxin conjugate of  claim 16 , wherein the   bond represents a single bond. 
     
     
         18 . The linker-cytotoxin conjugate of  claim 16 , wherein CTX is bonded to (L 1 ) a -(L 2 ) b -(L 3 ) c  via an amide, an N—(C 1-6  alkyl)amide, a carbamate, an N—(C 1-6  alkyl)carbamate, an amine, an N—(C 1-6  alkyl)amine, an ether, a thioether, an urea, an N—(C 1-6  alkyl)urea, or an N,N-di(C 1-6  alkyl)urea bond; or
 CTX is bonded to (L 1 ) a -(L 2 ) b -(L 3 ) c  via a bond selected from the group consisting of: 
 
       
         
           
           
               
               
           
         
          wherein each R B  is independently branched or unbranched C 1-6  alkyl. 
       
     
     
         19 . (canceled) 
     
     
         20 . The linker-cytotoxin conjugate of  claim 16 , wherein the CTX is selected from a from the group consisting of a tubulin stabilizer, a tubulin destabilizer, a DNA alkylator, a DNA minor groove binder, a DNA intercalator, a topoisomerase I inhibitor, a topoisomerase II inhibitor, a gyrase inhibitor, a protein synthesis inhibitor, a proteosome inhibitor, and an anti-metabolite; or
 wherein the CTX is selected from the group consisting of Actinomycin-D, Amonafide, an auristatin, benzophenone, benzothiazole, a calicheamicin, Camptothecin, CC-1065 (NSC 298223), Cemadotin, Colchicine, Combretastatin A4, Dolastatin, Doxorubicin, Elinafide, Emtansine (DM1), Etoposide, KF-12347 (Leinamycin), a maytansinoid, Methotrexate, Mitoxantrone, Nocodazole, Proteosome Inhibitor 1 (PSI 1), Roridin A, T-2 Toxin (trichothecene analog), Taxol, a tubulysin, Velcade®, and Vincristine.   
     
     
         21 . (canceled) 
     
     
         22 . The linker-cytotoxin conjugate of  claim 16 , wherein R is selected from the group consisting of W, (L 1 ) a , (L 2 ) b , (L 3 ) c , Z, W-(L 1 ) a -(L 2 ) b -(L 3 ) c , (L 1 ) a -(L 2 ) b -(L 3 ) c -Z, W-(L 1 ) a -(L 2 ) b -(L 3 ) c -Z, and W-(L 1 ) a -(L 2 ) b -(L 3 ) c -CTX, as defined in  claim 16 ; or
 wherein R is a detectable probe.   
     
     
         23 . (canceled) 
     
     
         24 . The linker-cytotoxin conjugate of  claim 16 , wherein k and k′ are both 1. 
     
     
         25 . An antibody-drug conjugate of the following formula (III): 
       
         
           
           
               
               
           
         
         or a pharmaceutically acceptable salt thereof, 
         wherein:
 A is an antibody or antibody fragment; 
 the two depicted cysteine residues are from an opened cysteine-cysteine disulfide bond in A; 
 each X and X′ is independently O, S, NH or NR 1  wherein R 1  is C 1-3  alkyl; 
 W is —NH—, —N(R 1 )—, —CH 2 —, —CH 2 —NH—, —CH 2 —N(R 1 )—, —CH 2 CH 2 —, —CH(R 2 )—, or —CH 2 CH(R 2 )—; wherein R 1  and R 2  are independently C 1-3  alkyl; 
 CTX is a cytotoxin; 
 R is any chemical group; or R is absent; 
 each L 1 , L 2  and L 3  is independently a linker selected from the group consisting of —O—, —C(O)—, —S—, —S(O)—, —S(O) 2 —, —NH—, —NCH 3 —, —(CH 2 ) q —, —NH(CH 2 ) 2 NH—, —OC(O)—, —CO 2 —, —NHCH 2 CH 2 C(O)—, —C(O)NHCH 2 CH 2 NH—, —NHCH 2 C(O)—, —NHC(O)—, —C(O)NH—, —NCH 3 C(O)—, —C(O)NCH 3 —, —(CH 2 CH 2 O) p , —(CH 2 CH 2 O) p CH 2 CH 2 —, —CH 2 CH 2 —(CH 2 CH 2 O) p —, —OCH(CH 2 O—) 2 , -(AA) r -, cyclopentanyl, cyclohexanyl, unsubstituted phenylenyl, and phenylenyl substituted by 1 or 2 substituents selected from the group consisting of halo, CF 3 —, CF 3 O—, CH 3 O—, —C(O)OH, —C(O)OC 1-3  alkyl, —C(O)CH 3 , —CN, —NH—, —NH 2 , —O—, —OH, —NHCH 3 , —N(CH 3 ) 2 , and C 1-3  alkyl; 
 a, b and c are each independently an integer of 0, 1, 2 or 3, provided that at least one of a, b or c is 1; 
 each k and k′ is independently an integer of 0 or 1; 
 each p is independently an integer of 1 to 14; 
 each q is independently an integer or 1 to 12; 
 each AA is independently an amino acid; 
 each r is 1 to 12; 
 m is an integer of 1 to 4; 
 n is an integer of 1 to 4; and 
 the   bond represents a single or a double bond. 
 
       
     
     
         26 . The antibody-drug conjugate or pharmaceutically acceptable salt of  claim 25 , wherein the   bond represents a single bond. 
     
     
         27 . The antibody-drug conjugate or pharmaceutically acceptable salt of  claim 25 , wherein A is an antibody that is specific to a cancer antigen; or
 wherein A is selected from the group consisting of alemtuzumab, anitumumab, bevacizumab, brentuximab, cetuximab, gemtuzumab, glembatumumab, inotuzumab, ipilimumab, lovortumumab, milatuzumab, ofatumumab, rituximab, tositumomab, and trastuzumab.   
     
     
         28 . (canceled) 
     
     
         29 . The antibody-drug conjugate or pharmaceutically acceptable salt of  claim 25 , wherein the CTX is selected from a from the group consisting of a tubulin stabilizer, a tubulin destabilizer, a DNA alkylator, a DNA minor groove binder, a DNA intercalator, a topoisomerase I inhibitor, a topoisomerase II inhibitor, a gyrase inhibitor, a protein synthesis inhibitor, a proteosome inhibitor, and an anti-metabolite; or
 wherein the CTX is selected from the group consisting of Actinomycin-D, Amonafide, an auristatin, benzophenone, benzothiazole, a calicheamicin, Camptothecin, CC-1065 (NSC 298223), Cemadotin, Colchicine, Combretastatin A4, Dolastatin, Doxorubicin, Elinafide, Emtansine (DM1), Etoposide, KF-12347 (Leinamycin), a maytansinoid, Methotrexate, Mitoxantrone, Nocodazole, Proteosome Inhibitor 1 (PSI 1), Roridin A, T-2 Toxin (trichothecene analog), Taxol, a tubulysin, Velcade®, and Vincristine.   
     
     
         30 . (canceled) 
     
     
         31 . The antibody-drug conjugate or pharmaceutically acceptable salt of  claim 30 , wherein the CTX is an auristatin, a calicheamicin, a maytansinoid, or a tubulysin; or
 wherein the CTX is monomethylauristatin E, monomethylauristatin F, calicheamicin Y, a pyrrolobenzodiazepine, mertansine, tubulysin T2, tubulysin T3, or tubulysin T4.   
     
     
         32 . (canceled) 
     
     
         33 . The antibody-drug conjugate or pharmaceutically acceptable salt of  claim 25 , wherein R is selected from the group consisting of W, (L 1 ) a , (L 2 ) b , (L 3 ) c , Z, W-(L 1 ) a -(L 2 ) b -(L 3 ) c , (L 1 ) a -(L 2 ) b -(L 3 ) c -Z, and W-(L 1 ) a -(L 2 ) b -(L 3 ) c -Z, as defined in  claim 22 ; or
 wherein R is a detectable probe.   
     
     
         34 . (canceled) 
     
     
         35 . The antibody-drug conjugate or pharmaceutically acceptable salt of  claim 25 , wherein k and k′ are both 1. 
     
     
         36 . A pharmaceutical composition comprising the antibody-drug conjugate or pharmaceutically acceptable salt of  claim 25 , and a pharmaceutically acceptable diluent, carrier or excipient. 
     
     
         37 . A method of treating a cancer by administering to a human suffering therefrom an effective amount of the antibody-drug conjugate of  claim 25  or the pharmaceutical composition of  claim 36 .