Polynucleotide constructs having disulfide groups

A polynucleotide construct comprising one or more components (i) comprising a disulfide linkage, wherein each of said one or more components (i) is attached to an internucleotide bridging group or a terminal group of said polynucleotide construct, and each of said one or more components (i) comprises at least 4 atoms in a chain between said disulfide linkage and the phosphorus atom of said internucleotide bridging group or said terminal group;

• and
• wherein said chain does not comprise a phosphate, an amide, an ester, or an alkenylene;
• and
• wherein when said chain comprises an alkylene group, the number of atoms between said terminal group and said disulfide group is 4 or 5.

A polynucleotide construct having the structure of Formula I:

• or a salt thereof,
• wherein n is a number from 0 to 150;
• each B1 is independently a nucleobase;
• each X is independently selected from the group consisting of O, S, and optionally substituted N;
• each Y is independently selected from the group consisting of hydrogen, hydroxyl, halo, optionally substituted C1-6 alkoxy, and a protected hydroxyl group;
• each Y1 is independently H or optionally substituted C1-6 alkyl;
• each Z is independently O or S;
• R1 is selected from the group consisting of H, hydroxyl, optionally substituted C1-6 alkoxy, a protected hydroxyl group, a monophosphate, a diphosphate, a triphosphate, a tetraphosphate, a pentaphosphate, a 5′ cap, phosphothiol, an optionally substituted C1-6 alkyl, an amino containing group, a biotin containing group, a digoxigenin containing group, a cholesterol containing group, a dye containing group, a quencher containing group, a polypeptide, a carbohydrate, a neutral organic polymer, a positively charged polymer, a therapeutic agent, a targeting moiety, an endosomal escape moiety, and any combination thereof, or R1 is
• or a salt thereof;
• R2 is selected from the group consisting of H, hydroxyl, optionally substituted C1-6 alkoxy, a protected hydroxyl group, a monophosphate, a diphosphate, a triphosphate, a tetraphosphate, a pentaphosphate, an optionally substituted C1-6 alkyl, an amino containing group, a biotin containing group, a digoxigenin containing group, a cholesterol containing group, a quencher containing group, a phosphothiol, a polypeptide, a carbohydrate, a neutral organic polymer, a positively charged polymer, a therapeutic agent, a targeting moiety, an endosomal escape moiety, and any combination thereof, or R2 is
• or a salt thereof;
• and
• each R3 is independently absent, a hydrogen, optionally substituted C1-6 alkyl, or a group having the structure of Formula II:
• wherein each A1 is independently a bond or a linker comprising one or more of optionally substituted N;
• O;
• S;
• optionally substituted C1-6 alkylene;
• optionally substituted C2-6 alkenylene;
• optionally substituted C2-6 alkynylene;
• optionally substituted C3-8 cycloalkylene;
• optionally substituted C3-8 cycloalkenylene;
• optionally substituted (C3-8 cycloalkyl)-C1-4-alkylene;
• optionally substituted (C3-8 cycloalkenyl)-C1-4-alkylene;
• optionally substituted C6-14 arylene;
• optionally substituted (C6-14 aryl)-C1-4-alkylene;
• optionally substituted C1-9 heteroarylene having 1 to 4 heteroatoms selected from N, O, and S;
• optionally substituted (C1-9 heteroaryl)-C1-4-alkylene having 1 to 4 heteroatoms selected from N, O, and S;
• optionally substituted C1-9 heterocyclylene having 1 to 4 heteroatoms selected from N, O, and S;
• and optionally substituted (C1-9 heterocyclyl)-C1-4-alkylene having 1 to 4 heteroatoms selected from N, O, and S, provided that when A1 comprises one or more of optionally substituted N, O, and S, said optionally substituted N, O, or S is not directly bonded to the disulfide;
• and each A2 is selected from the group consisting of optionally substituted C1-6 alkylene;
• optionally substituted C3-8 cycloalkylene;
• optionally substituted C3-8 cycloalkenylene;
• optionally substituted C6-14 arylene;
• optionally substituted C1-9 heteroarylene having 1 to 4 heteroatoms selected from N, O, and S;
• and optionally substituted C1-9 heterocyclylene having 1 to 4 heteroatoms selected from N, O, and S;
• or A1 and A2, together with —S—S—, join to form an optionally substituted 5 to 16 membered ring;
• each A3 is independently selected from the group consisting of a bond, optionally substituted C1-6 alkylene;
• optionally substituted C3-8 cycloalkylene;
• optionally substituted C3-8 cycloalkenylene;
• optionally substituted C6-14 arylene, optionally substituted C1-9 heteroarylene having 1 to 4 heteroatoms selected from N, O, and S;
• optionally substituted C1-9 heterocyclylene having 1 to 4 heteroatoms selected from N, O, and S;
• O;
• optionally substituted N;
• and S;
• each A4 is independently selected from the group consisting of optionally substituted C1-6 alkylene;
• optionally substituted C3-8 cycloalkylene;
• and optionally substituted C1-9 heterocyclylene having 1 to 4 heteroatoms selected from N, O, and S;
• each L is independently absent or a conjugating group comprising one or more conjugating moieties;
• each R4 is independently hydrogen, optionally substituted C1-6 alkyl, a hydrophilic functional group, or a group comprising an auxiliary moiety selected from the group consisting of a small molecule, a polypeptide, a carbohydrate, a neutral organic polymer, a positively charged polymer, a therapeutic agent, a targeting moiety, an endosomal escape moiety, and any combination thereof;
• each r is independently an integer from 1 to 10;
• wherein, in at least one of R1, R2, and R3, A2, A3, and A4 combine to form a group having at least three atoms in the shortest chain connecting —S—S— and X;
• wherein at least one R3 has the structure of formula (II) or at least one of R1 and R2 is
• or a salt thereof;
• and
• wherein,
• when R1 or R2 is
• or a salt thereof in which A2, A3, and A4 combine to form an alkylene group, said alkylene group is C4-5 alkylene;
• or
• when R1 or R2 is
• or a salt thereof, the group -A2-A3-A4-X— does not comprise an amide, an ester, or an alkenylene.

A polynucleotide construct comprising one or more groups of Formula (V) attached to one or more internucleotide bridging groups or terminal nucleotide groups of said polynucleotide:

• or a salt thereof,
• wherein
• each L is independently a bond or a conjugating group comprising one or more conjugating moieties;
• each R4 is independently hydrogen, optionally substituted C1-6 alkyl, a hydrophilic functional group, or a group comprising an auxiliary moiety selected from the group consisting of a small molecule, a polypeptide, a carbohydrate, a neutral organic polymer, a positively charged polymer, a therapeutic agent, a targeting moiety, an endosomal escape moiety, and combination thereof;
• each r is independently an integer from 1 to 10;
• and
• each A5 is independently selected from the group consisting of:
• wherein,
• each R9 is, independently, halo, optionally substituted C1-6 alkyl;
• optionally substituted C2-6 alkenyl;
• optionally substituted C2-6 alkynyl;
• optionally substituted C3-8 cycloalkyl;
• optionally substituted C3-8 cycloalkenyl;
• optionally substituted (C3-8 cycloalkyl)-C1-4-alkyl;
• optionally substituted (C3-8 cycloalkenyl)-C1-4-alkyl;
• optionally substituted C6-14 aryl;
• optionally substituted (C6-14 aryl)-C1-4-alkyl;
• optionally substituted C1-9 heteroaryl having 1 to 4 heteroatoms selected from N, O, and S;
• optionally substituted (C1-9 heteroaryl)-C1-4-alkyl having 1 to 4 heteroatoms selected from N, O;
• optionally substituted C1-9 heterocyclyl having 1 to 4 heteroatoms selected from N, O, and S;
• optionally substituted (C1-9 heterocyclyl)-C1-4-alkyl having 1 to 4 heteroatoms selected from N, O, and S;
• amino;
• or optionally substituted C1-6 alkoxy;
• or two adjacent R9 groups, together with the atoms to which each said R9 is attached, combine to form a cyclic group selected from the group consisting of C6 aryl, C2-5 heterocyclyl, or C2-5 heteroaryl, wherein said cyclic group is optionally substituted with 1, 2, or 3 substituents selected from the group consisting of C2-7 alkanoyl;
• C1-6 alkyl;
• C2-6 alkenyl;
• C2-6 alkynyl;
• C1-6 alkylsulfinyl;
• C6-10 aryl;
• amino;
• (C6-10 aryl)-C1-4-alkyl;
• C3-8 cycloalkyl;
• (C3-8 cycloalkyl)-C1-4-alkyl;
• C3-8 cycloalkenyl;
• (C3-8 cycloalkenyl)-C1-4-alkyl;
• halo;
• C1-9 heterocyclyl;
• C1-9 heteroaryl;
• (C1-9 heterocyclyl)oxy;
• (C1-9 heterocyclyl)aza;
• hydroxy;
• C1-6 thioalkoxy;
• —(CH2)qCO2RA, where q is an integer from zero to four, and RA is selected from the group consisting of C1-6 alkyl, C6-10 aryl, and (C6-10 aryl)-C1-4-alkyl;
• —(CH2)qCONRBRC, where q is an integer from zero to four and where RB and RC are independently selected from the group consisting of hydrogen, C1-6 alkyl, C6-10 aryl, and (C6-10 aryl)-C1-4-alkyl;
• —(CH2)qSO2RD, where q is an integer from zero to four and where RD is selected from the group consisting of C1-6 alkyl, C6-10 aryl, and (C6-10 aryl)-C1-4-alkyl;
• —(CH2)qSO2NRERF, where q is an integer from zero to four and where each of RE and RF is, independently, selected from the group consisting of hydrogen;
• C1-6 alkyl;
• C6-10 aryl;
• (C6-10 aryl)-C1-4-alkyl;
• thiol;
• C6-10 aryloxy;
• C3-8 cycloalkoxy;
• (C6-10 aryl)-C1-4-alkoxy;
• (C1-9 heterocyclyl)-C1-4-alkyl;
• (C1-9 heteroaryl)-C1-4-alkyl;
• C3-12 silyl;
• cyano;
• and —S(O)RH where RH is selected from the group consisting of hydrogen, C1-C6 alkyl, C6-10 aryl, and (C6-10 aryl)-C1-4-alkyl;
• each q is independently 0, 1, 2, 3, or 4;
• each s is independently 0, 1, or 2;
• and
• wherein, when group of Formula (III) is attached at 5′ or 3′ end of said polynucleotide, A5 is not (i), (xviii), (xxv), (xxvi), (xxvii), or (xxviii).

A compound having a structure of Formula (VII):

• or a salt thereof,
• wherein
• B1 is a nucleobase;
• X is selected from the group consisting of O, S, and NR4;
• Y is selected from the group consisting of hydrogen, hydroxyl, halo, optionally substituted C1-6 alkoxy, and a protected hydroxyl group;
• Y1 is H or optionally substituted C1-6 alkyl;
• Z is absent, O, or S;
• R1 is selected from the group consisting of hydroxyl, optionally substituted C1-6 alkoxy, a protected hydroxyl group, a monophosphate, a diphosphate, a triphosphate, a tetraphosphate, and a pentaphosphate, a 5′ cap, phosphothiol, an optionally substituted C1-6 alkyl, an amino containing group, a biotin containing group, a digoxigenin containing group, a cholesterol containing group, a dye containing group, a quencher containing group, a polypeptide, a carbohydrate, a neutral organic polymer, a positively charged polymer, a therapeutic agent, a targeting moiety, an endosomal escape moiety, and any combination thereof;
• R2 is selected from the group consisting of H, hydroxyl, optionally substituted C1-6 alkoxy, a protected hydroxyl group, a monophosphate, a diphosphate, a triphosphate, a tetraphosphate, a pentaphosphate, an amino, a 5′ cap, phosphothiol, an optionally substituted C1-6 alkyl, an amino containing group, a biotin containing group, a digoxigenin containing group, a cholesterol containing group, a dye containing group, a quencher containing group, a polypeptide, a carbohydrate, a neutral organic polymer, a positively charged polymer, a therapeutic agent, a targeting moiety, an endosomal escape moiety, and a combination thereof;
• and
• R3 is a group having the structure of Formula (VIII):
• wherein A1 is selected from the group consisting of a bond, optionally substituted C1-6 alkylene;
• optionally substituted C2-6 alkenylene;
• optionally substituted C2-6 alkynylene;
• optionally substituted C3-8 cycloalkylene;
• optionally substituted C3-8 cycloalkenylene;
• optionally substituted (C3-8 cycloalkyl)-C1-4-alkylene;
• optionally substituted (C3-8 cycloalkenyl)-C1-4-alkylene;
• optionally substituted C6-14 arylene;
• optionally substituted (C6-14 aryl)-C1-4-alkylene;
• optionally substituted C1-9 heteroarylene having 1 to 4 heteroatoms selected from N, O, and S;
• optionally substituted (C1-9 heteroaryl)-C1-4-alkylene having 1 to 4 heteroatoms selected from N, O, and S;
• optionally substituted C1-9 heterocyclylene having 1 to 4 heteroatoms selected from N, O, and S;
• and optionally substituted (C1-9 heterocyclyl)-C1-4-alkylene having 1 to 4 heteroatoms selected from N, O, and S;
• and A2 is selected from the group consisting of optionally substituted C1-6 alkylene;
• optionally substituted C3-8 cycloalkylene;
• optionally substituted C3-8 cycloalkenylene;
• optionally substituted C6-14 arylene;
• optionally substituted C1-9 heteroarylene having 1 to 4 heteroatoms selected from N, O, and S;
• and optionally substituted C1-9 heterocyclylene having 1 to 4 heteroatoms selected from N, O, and S;
• or A1 and A2, together with —S—S—, join to form an optionally substituted 5 to 16 membered ring;
• A3 is selected from the group consisting of a bond, optionally substituted C1-6 alkylene;
• optionally substituted C3-8 cycloalkylene;
• optionally substituted C3-8 cycloalkenylene;
• optionally substituted C6-14 arylene, optionally substituted C1-9 heteroarylene having 1 to 4 heteroatoms selected from N, O, and S;
• optionally substituted C1-9 heterocyclylene having 1 to 4 heteroatoms selected from N, O, and S;
• O;
• optionally substituted N;
• and S;
• A4 is selected from the group consisting of optionally substituted C1-6 alkylene;
• optionally substituted C3-8 cycloalkylene;
• and optionally substituted C1-9 heterocyclylene having 1 to 4 heteroatoms selected from N, O, and S;
• L is a bond or a conjugating group comprising one or more conjugating moieties;
• R4 is absent, hydrogen, optionally substituted C1-6 alkyl, a hydrophilic functional group, or a group comprising an auxiliary moiety selected from the group consisting of a small molecule, a polypeptide, a carbohydrate, a neutral organic polymer, a positively charged polymer, a therapeutic agent, a targeting moiety, an endosomal escape moiety, and any combination thereof;
• r is an integer from 1 to 10;
• wherein A2, A3, and A4 combine to form a group having at least three atoms in the shortest chain connecting —S—S— and X.