Rifamycin analogs and antibody-drug conjugates thereof

An antibody-drug conjugate comprising an antibody, or an antigen-binding fragment thereof, conjugated via a linker or through a linker-spacer to a rifamycin analog having the structure of Formula (XX):

• wherein:
• X is selected from —O—, —S—, and —NR*—;
• Za is selected from —OR1 and —RN;
• R1 is selected from a bond;
• an aliphatic C1-C20 hydrocarbon, an aromatic C1-C20 hydrocarbon, a heteroaromatic C1-C20 hydrocarbon, a cyclic aliphatic C1-C20 hydrocarbon, a heterocyclic C1-C20 hydrocarbon, and combinations thereof, each of which further comprises 0-8 heteroatoms selected from halogen, O, N, and S, and wherein R1 is optionally substituted with one or more of —F;
• —Cl;
• —Br;
• —I;
• —OH, —OR*;
• —NO;
• —NO2;
• —NO3;
• —O—NO;
• —N3;
• —NH2;
• —NHR*;
• —N(R*)2;
• —N(R*)3+;
• —N(R*)—OH;
• —O—N(R*)2;
• —N(R*)—O—R*;
• —CN;
• —NC;
• —(C═O)—R*;
• —CHO;
• —CO2H;
• —CO2R*;
• —(C═O)—S—R*;
• —O—(C═O)—H;
• —O—(C═O)—R*;
• —S—(C═O)—R*;
• —(C═O)—NH2;
• —(C═O)—N(R*)2;
• —(C═O)—NHNH2;
• —O—(C═O)—NHNH2;
• —(C═S)—NH2;
• —(C═S)—N(R*)2;
• —N(R*)—CHO;
• —N(R*)—(C═O)—R*;
• —SCN;
• —NCS;
• —NSO;
• —SSR*;
• —SO2R*;
• —SO2—N(R*)2;
• —S(═O)—OR*;
• —S(═O)—R*;
• —Si(R*)3;
• —CF3;
• —O—CF3 and combinations thereof;
• RN is selected from:
• wherein the symbol represents the point of attachment;
• and R′, R″ and R′″ are selected from a hydrogen, a C1-C6 aliphatic hydrocarbon, and a protecting group selected from FMOC and BOC, or wherein R′ and R″ together form an aliphatic monocyclic, an aliphatic bicyclic, or an aliphatic polycyclic structure;
• R2, R3, and R4 are independently selected from hydrogen, a straight chained, branched or cyclic aliphatic C1-C20 hydrocarbon, or —(C═O)—R*, each of which further comprises 0-8 heteroatoms selected from halogen, O, N, and S;
• Ra is independently at each occurrence selected from hydrogen, —F, —Cl, —Br, —I, —OH, OR*, —NH2, —NHR*, —N(R*)2, —N(R*)3+, —(C═O)—R*, —CHO, —CO2H, —CO2R*, —SR*, SO2R*, and an aliphatic C1-C20 hydrocarbon, which further comprises 0-8 heteroatoms selected from halogen, O, N, and S, and wherein Ra is optionally substituted with one or more of —F, —Cl, —Br, —I, —OH, —OR*;
• R* is independently at each occurrence selected from hydrogen, an aliphatic C1-C20 hydrocarbon, an aromatic C1-C20 hydrocarbon, a heteroaromatic C1-C20 hydrocarbon, a cyclic aliphatic C1-C20 hydrocarbon, a heterocyclic C1-C20 hydrocarbon, and combinations thereof, which further comprises 0-8 heteroatoms selected from halogen, O, N, and S and combinations thereof, and
• wherein the group Za is bonded to the linker.

An antibody-drug conjugate comprising an antibody, or an antigen-binding fragment thereof, conjugated via a linker or through a linker-spacer to a rifamycin analog having the structure of Formula (XXI):

• wherein:
• X is selected from —O—, —S—, and —NR*—;
• R5 is selected from a bond;
• an aliphatic C1-C20 hydrocarbon which further comprises 0-8 heteroatoms selected from halogen, O, N, and S;
• wherein Y is C or N;
• R2, R3, and R4 are independently selected from a hydrogen, a straight chained, branched or cyclic aliphatic C1-C20 hydrocarbon, or —(C═O)—R*, each of which further comprises 0-8 heteroatoms selected from halogen, O, N, and S;
• R* is independently at each occurrence selected from hydrogen, an aliphatic C1-C20 hydrocarbon, an aromatic C1-C20 hydrocarbon, a heteroaromatic C1-C20 hydrocarbon, a cyclic aliphatic C1-C20 hydrocarbon, a heterocyclic C1-C20 hydrocarbon, and combinations thereof, which further comprises 0-8 heteroatoms selected from halogen, O, N, and S and combinations thereof, and
• R5 is a bond or an aliphatic C1-C8 hydrocarbon;
• wherein the group R5 is bonded to the linker.

An antibody-drug conjugate having the structure of Formula (XXII):

• wherein:
• BA is an antibody, or an antigen-binding fragment thereof;
• L is a linker;
• SP is a spacer group selected from
• Y is C or N;
• wherein the symbol represents the point of attachment;
• and R′, R″ and
• R′″ are selected from a hydrogen, a C1-C6 aliphatic hydrocarbon, and a protecting group selected from Fluorenylmethyloxycarbonyl (FMOC) and tert-Butyloxycarbonyl (Boc), or wherein R′ and R″ together form an aliphatic monocyclic, an aliphatic bicyclic, or an aliphatic polycyclic structure;
• R* is independently at each occurrence selected from hydrogen, an aliphatic C1-C20 hydrocarbon, an aromatic C1-C20 hydrocarbon, a heteroaromatic C1-C20 hydrocarbon, a cyclic aliphatic C1-C20 hydrocarbon, a heterocyclic C1-C20 hydrocarbon, and combinations thereof, which further comprises 0-8 heteroatoms selected from halogen, O, N, and S and combinations thereof, and
• X is selected from —O—, —S—, and —NR*.

A compound having the structure of formula (A):

• or a pharmaceutically acceptable salt thereof, wherein:
• X is selected from —O— and —NR*—;
• Za and Zb are independently selected from a hydrogen, —Cl, —Br, —OR1 and —RN, with the proviso that at least one of Za or Zb is not a hydrogen, wherein:
• R1 is selected from a hydrogen, RN, an aliphatic C1-C20 hydrocarbon, an aromatic C1-C20 hydrocarbon, a heteroaromatic C1-C20 hydrocarbon;
• a cyclic aliphatic C1-C20 hydrocarbon, a heterocyclic C1-C20 hydrocarbon, and combinations thereof, each of which further comprises 0-8 heteroatoms selected from halogen, O, N, and S, and wherein R1 is optionally substituted with one or more of —F, —Cl, —Br, —I, —OH, —OR*, —NO, —NO2, —NO3, —O—NO, —N3, —NH2, —NHR*, —N(R*)2, —N(R*)3+, —N(R*)—OH, —O—N(R*)2, —N(R*)—O—R*, —CN, —NC, —(C═O)—R*, —CHO, —CO2H, —CO2R*, —(C═O)—S—R*, —O—(C═O)—H, —O—(C═O)—R*, —S—(C═O)—R*, —(C═O)—NH2, —(C═O)—N(R*)2, —(C═O)—NHNH2, —O—(C═O)—NHNH2, —(C═S)—NH2, —(C═S)—N(R*)2, —N(R*)—CHO, —N(R*)—(C═O)—R*, —SCN, —NCS, —NSO, —SSR*, —SO2R*, —SO2—N(R*)2, —S(═O)—OR*, —S(═O)—R*, —Si(R*)3, —CF3, —O—CF3 and combinations thereof, with the provisos that R1 is not an n-butyl group, and when X is —O— and Ra is hydrogen, R1 is not hydrogen;
• RN is selected from:
• wherein the symbol represents the point of attachment;
• and R′, R″ and R′″ are selected from a hydrogen, a C1-C6 aliphatic hydrocarbon, and a protecting group selected from Fluorenylmethyloxycarbonyl (FMOC) and tert-Butyloxycarbonyl (Boc), or wherein R′ and R″ together form an aliphatic monocyclic, an aliphatic bicyclic, or an aliphatic polycyclic structure;
• R2, R3, and R4 are independently selected from hydrogen, an aliphatic C1-C20 hydrocarbon, and —(C═O)—R*, each of which further comprises 0-8 heteroatoms selected from halogen, O, N, and S;
• Ra is selected from hydrogen, —F, —Cl, —Br, —I, —OH, —OR*, —NH2, —NHR*, —N(R*)2, —N(R*)3+, —(C═O)—R*, —CHO, —CO2H, —CO2R*, —SR*, —SO2R*, and an aliphatic C1-C20 hydrocarbon, which further comprises 0-8 heteroatoms selected from halogen, O, N, and S, and wherein
• Ra is optionally substituted with one or more of —F, —Cl, —Br, —I, —OH, —OR*;
• Rb is selected from hydrogen, —F, —Cl, —Br, —I, —OH, —OR*, —(C═O)—R*, —CHO, —CO2H, —CO2R* and an aliphatic C1-C20 hydrocarbon, which further comprises 0-3 heteroatoms selected from halogen, O, and S, and wherein Rb is optionally substituted with one or more of —F, —Cl, —Br, —I, —OH, —OR*, and
• R* is independently at each occurrence selected from hydrogen, an aliphatic C1-C20 hydrocarbon, an aromatic C1-C20 hydrocarbon, a heteroaromatic C1-C20 hydrocarbon, a cyclic aliphatic C1-C20 hydrocarbon, a heterocyclic C1-C20 hydrocarbon, and combinations thereof, which further comprises 0-8 heteroatoms selected from halogen, O, N, and S and combinations thereof.

A method of manufacturing a compound having the structure of formula (V):

• wherein X is selected from —O— and NR*—;
• R6 is selected from a hydrogen, RN, an aliphatic C1-C20 hydrocarbon, an aromatic C1-C20 hydrocarbon, a heteroaromatic C1-C20 hydrocarbon, a cyclic aliphatic C1-C20 hydrocarbon, a heterocyclic C1-C20 hydrocarbon, and combinations thereof;
• RN is selected from:
• wherein the symbol represents the point of attachment;
• and R′, R″ and R′″ are selected from a hydrogen, a C1-C6 aliphatic hydrocarbon, and a protecting group selected from FMOC and BOC, or wherein R′ and R″ together form an aliphatic monocyclic, an aliphatic bicyclic, or an aliphatic polycyclic structure;
• and
• R* is independently at each occurrence selected from hydrogen, an aliphatic C1-C20 hydrocarbon, an aromatic C1-C20 hydrocarbon, a heteroaromatic C1-C20 hydrocarbon, a cyclic aliphatic C1-C20 hydrocarbon, a heterocyclic C1-C20 hydrocarbon, and combinations thereof, which further comprises 0-8 heteroatoms selected from halogen, O, N, and S and combinations thereof,
• comprising the steps of:
• (a) contacting Rifamycin S having the structure:
• with a compound having the structure of formula (VI):
• wherein X′ is selected from —OH and —NHR*, and
• (b) treating the product of step (a) with an oxidizing agent.