Substituted silaxanthenium red to near-infrared fluorochromes for in vitro and in vivo imaging and detection

A conjugate compound that is a compound of Formula I substituted with 1, 2, or 3 groups defined by -L-BM;

• wherein L is a bond or a linker, -BM is a radical of a biological molecule, and Formula I is represented by:
• or a salt thereof, wherein:
• A1 is phenyl substituted with 1, 2, or 3 substituents independently selected from the group consisting of hydroxyl, —CO2-(optionally substituted heterocycloalkyl), —N(R6)C(O)(R7), alkylene-(optionally substituted heterocyclyl), nitro, alkylene-O-alkylene-CO2H, alkylene-O-alkylene-CO2−, —SO2—N(R6)-alkylene-CO2H, —SO2—N(R6)-alkylene-CO2−, —N(R6)—SO2-alkylene-CO2H, —N(R6)—SO2-alkylene-CO2−, —SO2—N(R6)-(optionally substituted heterocycloalkyl), —SO2—N(R6)2, —SO2—N(R6)-alkylene-(optionally substituted heterocyclyl);
• or
• A1 is a 5-6 membered heteroaryl, optionally substituted with 1, 2, or 3 substituents independently selected from the group consisting of alkyl, haloalkyl, halogen, hydroxyl, alkoxy, —CO2H, —CO2−, —CO2-(optionally substituted heterocycloalkyl), —C(O)N(R6)(R7), —N(R6)C(O)(R7), alkylene-(optionally substituted heterocyclyl), nitro, alkylene-O-alkylene-CO2H, alkylene-O-alkylene-CO2−, —SO2—N(R6)-alkylene-CO2H, —SO2—N(R6)-alkylene-CO2−, —N(R6)—SO2-alkylene-CO2H, —N(R6)—SO2-alkylene-CO2−, —SO2—N(R6)-(optionally substituted heterocycloalkyl), —SO2—N(R6)2, —SO2—N(R6)-alkylene-(optionally substituted heterocyclyl), X1, and alkylene-X1;
• X1 represents independently for each occurrence a maleimide, a succinimidyl ester, a carboxamide, propargyl, azidoalkyl, isothiocyanate, —NH2—OH, —SH, —SO3H, carboxyl, —C(O)Cl, —(CO)O(CO)R8, —CON(H)NH2, an acetoxymethyl ester, a substituted or unsubstituted N-hydroxysuccinimidyl ester, a substituted or unsubstituted N-hydroxysulfosuccinimido ester, a nitro-phenol ester, a fluoro-phenol ester, azide, —NCS, —CHO, —COCH2I, a phosphoramidite, or a phthalamido;
• R1 and R2 each represent independently hydrogen, alkyl, cycloalkyl, heterocycloalkyl, or —C(O)N(R6)(optionally substituted alkyl);
• or R1 and R2 are taken together with the nitrogen atom to which they are attached to form a monocyclic or bicyclic ring;
• R3 and R4 each represent independently hydrogen, alkyl, cycloalkyl, heterocycloalkyl, or —C(O)N(R6)(optionally substituted alkyl);
• or R3 and R4 are taken together with the nitrogen atom to which they are attached to form a monocyclic or bicyclic ring;
• R5 represents independently for each occurrence C1-6 alkyl;
• R6 represents independently for each occurrence hydrogen or alkyl;
• R7 represents independently for each occurrence hydrogen, alkyl, alkylene-CO2H, alkylene-C(O)N(R6)2, alkylene-(optionally substituted heterocyclyl), optionally substituted heterocyclyl, alkylene-(optionally substituted heteroaryl), or hydroxyl alkylene-(optionally substituted heterocyclyl);
• and
• R8 represents independently for each occurrence hydrogen, alkyl, or aryl.

A conjugate compound represented by Formula II:

• or a salt thereof;
• wherein:
• A1 is phenyl substituted with 1, 2, or 3 substituents independently selected from the group consisting of —C(O)-ψ, alkylene-C(O)-ψ, alkylene-C(O)N(R6)-ψ, —N(R6)C(O)-ψ, alkylene-C(O)-ψ, alkylene-N(R6)C(O)-ψ, hydroxyl, —CO2-(optionally substituted heterocycloalkyl), —N(R6)C(O)(R7), alkylene-(optionally substituted heterocyclyl), nitro, alkylene-O-alkylene-CO2H, alkylene-O-alkylene-CO2−, —SO2—N(R6)-alkylene-CO2H, —SO2—N(R6)-alkylene-CO2−, —N(R6)—SO2-alkylene-CO2H, N(R6)—SO2-alkylene-CO2−, —SO2—N(R6)-(optionally substituted heterocycloalkyl), —SO2—N(R6)2, and —SO2—N(R6)-(alkylene-(optionally substituted heterocyclyl);
• or
• A1 is a 5-6 membered heteroaryl, optionally substituted with 1, 2, or 3 substituents independently selected from the group consisting of —C(O)-ψ, —C(O)N(R6)-ψ, alkylene-C(O)-ψ, alkylene-C(O)N(R6)-ψ, —N(R6)C(O)-ψ, alkylene-C(O)-ψ, alkylene-N(R6)C(O)-ψ, alkyl, haloalkyl, halogen, hydroxyl, alkoxy, —CO2H, —CO2−, —CO2-(optionally substituted heterocycloalkyl), —C(O)N(R6)(R7), —N(R6)C(O)(R7), alkylene-(optionally substituted heterocyclyl), nitro, alkylene-O-alkylene-CO2H, alkylene-O-alkylene-CO2−, —SO2—N(R6)-alkylene-CO2H, —SO2N(R6)-alkylene-CO2−, —N(R6)—SO2-alkylene-CO2H, N(R6)—SO2-alkylene-CO2−, —SO2—N(R6)-(optionally substituted heterocycloalkyl), —SO2—N(R6)2, and —SO2—N(R6)alkylene-optionally substituted heterocyclyl);
• Ψ is a radical of a biological molecule;
• R1 and R2 each represent independently hydrogen, alkyl, cycloalkyl, heterocycloalkyl, or —C(O)N(R6)(optionally substituted alkyl);
• or R1 and R2 are taken together with the nitrogen atom to which they are attached to form a monocyclic or bicyclic ring;
• R3 and R4 each represent independently hydrogen, alkyl, cycloalkyl, heterocycloalkyl, or —C(O)N(R6)(optionally substituted alkyl);
• or R3 and R4 are taken together with the nitrogen atom to which they are attached to form a monocyclic or bicyclic ring;
• R5 represents independently for each occurrence C1-6 alkyl;
• R6 represents independently for each occurrence hydrogen or alkyl;
• and
• R7 represents independently for each occurrence hydrogen, alkyl, alkylene-CO2H, alkylene-C(O)N(R6)2, alkylene-(optionally substituted heterocyclyl) optionally substituted heterocyclyl, alkylene-(optionally substituted heteroaryl), or hydroxyl alkylene-(optionally substituted heterocyclyl).

A compound represented by Formula III:

• or a salt thereof, wherein:
• X, Y and Z are, independently, O, S, N, Si, C or (C═C);
• L is absent or is a linker moiety, optionally bearing a functional group or reactive group selected from a carboxylate, carboxyalkyl, maleimide, succinimidyl ester, carboxamide, propargyl, azidoalkyl, isothiocyanate, —NH2—OH, —SH, —SO3H, carboxyl, —COCl, —(CO)O(CO)R7—CONHNH2, acetoxymethyl ester, substituted and unsubstituted N-hydroxysuccinimidyl ester, substituted and unsubstituted N-hydroxysulfosuccinimido ester, nitro- or fluoro or phenol ester, azide, —NCS, —CHO, —COCH2I, phosphoramidite, phthalamido, or maleimide, wherein R7 is selected from the group consisting of H, alkyl and aryl;
• R1, R2, R3 and R4 are, independently, H, methyl, ethyl, alkyl, or cyclic alkyl, aryl, substituted aryl, heteroaryl, or heterocyclic alkynyl, carboxyalkyl, aminoalkyl, haloalkyl, azidoalkyl, amide, amino acid, or peptide;
• R5 is absent or is H, C1-20 alkyl, carboxyl, carboxyalkyl, sulfonate, sulfonamide, halogen, hydroxy, amine, amide, nitro, cyano, O-alkyl, S-alkyl, silyl, O-silyl methyl, ethyl, isopropyl, carboxyalkyl, haloalkyl, alkylsulfhydryl, trifluoromethyl, hydrazide;
• and
• W1 and W2 are, independently, absent or cyclic groups containing aliphatic carbon, nitrogen, oxygen, sulfur, or silicon forming a 4 to 9 membered ring with R1 and R2 or R3 and R4, optionally with further substituents.

A fluorescent biomolecule represented by Formula IV:

• or a salt thereof;
• wherein;
• X, Y and Z are, independently, O, S, N, Si, C or (C═C);
• L is a linking group optionally comprising a reactive group selected from a carboxylate, carboxyalkyl, maleimide, succinimidyl ester, carboxamide, propargyl, azidoalkyl, or isothiocyanate;
• BM is a biomolecule, wherein the fluorescent biomolecule comprises at least one BM;
• R1, R2, R3 and R4 are, independently, H, methyl, ethyl, alkyl, or cyclic alkyl, aryl, substituted aryl, heteroaryl, or heterocyclic;
• R5 is absent or is H, C1-20 alkyl, carboxyl, carboxyalkyl, sulfonate, sulfonamide, halogen, hydroxy, amine, amide, nitro, cyano, O-alkyl, S-alkyl, silyl, -silyl methyl, ethyl, isopropyl, carboxyalkyl;
• and
• W1 and W2 are, independently, absent or cyclic groups containing aliphatic carbon, nitrogen, oxygen, sulfur, or silicon forming a 4 to 9 membered ring with R1 and R2 or R3 and R4, optionally with further substituents.