DNA glycosylase inhibitors, and uses related thereto
First Claim
Patent Images
1. A compound represented by the formula, or a pharmaceutically acceptable salt thereof:
-
whereinB is a nucleoside purine or pyrimidine base, or a heterocyclic analog thereof;
X is O, N, S or CH2;
R1, independently for each occurrence, is absent or is a hydrogen, or an amino protecting group;
R2 is a hydrogen, a nucleotide or oligonucleotide, a phosphoryl, a phosphonate, a phosphoramidate, a carbarnate, a phosphorothioate, a phosphorodithioate, a hydroxyl blocking group, or as valence and stability permit, a halogen, a lower alkyl, a lower alkenyl, a lower alkynyl, a carbonyl, a thiocarbonyl, a ketyl, an aldehyde, an amino, an acylamino, an amido, an amidino, a cyano, a nitro, an azido, a sulfonyl, a sulfoxido, a sulfate, a sulfonate, a sulfamoyl, a sulfonamido, a phosphoryl, a phosphonate, a phosphinate, —
(CH2)m—
R8, —
(CH2)m—
OH, —
(CH2)m—
O-lower alkyl, —
(CH2)m—
O-lower alkenyl, —
(CH2)m—
O—
(CH2)n—
R8, —
(CH2)m—
SH, —
(CH2)m—
S-lower alkyl, —
(CH2)m—
S-lower alkenyl, —
(CH2)m—
S—
(CH2)n—
R8, or a solid or polymeric support;
R3 is a hydrogen, a nucleotide or oligonucleotide, a phosphoryl, a phosphonate, a phosphoramidate, a carbamate, a phosphorothioate, a phosphorodithioate, a hydroxyl blocking group, or as valence and stability permit, a halogen, a lower alkyl, a lower alkenyl, a lower alkynyl, a carbonyl, a thiocarbonyl, a ketyl, an aldehyde, an amino, an acylamino, an amido, an amidino, a cyano, a nitro, an azido, a sulfonyl, a sulfoxido, a sulfate, a sulfonate, a sulfamoyl, a sulfonamido, a phosphoryl, a phosphonate, a phosphinate, —
(CH2)m—
R8, —
(CH2)m—
OH, —
(CH2)m—
O-lower alkyl, —
(CH2)m—
O-lower alkenyl, —
(CH2)m—
O—
(CH2)n—
R8, —
(CH2)m—
SH, —
(CH2)m—
S-lower alkyl, —
(CH2)m—
S-lower alkenyl, —
(CH2)m—
S—
(CH2)n—
R8, or a solid or polymeric support;
R4, R5, R6 and R7 are each, independently, as valence and stability permit, hydrogen, a halogen, a lower alkyl, a lower alkenyl, a lower alkynyl, a carbonyl, a thiocarbonyl, a ketyl, an aldehyde, an amino, an acylamino, an amido, an amidino, a cyano, a nitro, an azido, a sulfonyl, a sulfoxido, a sulfate, a sulfonate, a sulfamoyl, a sulfonamido, a phosphoryl, a phosphonate, a phosphinate, —
(CH2)m—
R8, —
(CH2)m—
OH, —
(CH2)m—
O-lower alkyl, —
(CH2)m—
O-lower alkenyl, —
(CH2)m—
O—
(CH2)n—
R8, —
(CH2)m—
SH, —
(CH2)m—
S-lower alkyl, —
(CH2)m—
S-lower alkenyl, —
(CH2)m—
S—
(CH2)n—
R8;
R8 is, independently for each occurrence, a substituted or unsubstituted aryl, aralkyl, cycloalkyl, cycloalkenyl or heterocycle, a carbonyl, a sulfonyl or a phosphoryl; and
p is 1 or 2, and n and m are independently for each occurrence zero or an integer in the range of 1 to 6, which compound inhibits an N-glycosidic activity of a DNA glycosylase.
2 Assignments
0 Petitions
Accused Products
Abstract
The present invention pertains to novel inhibitors of DNA glycosylases. The invention is based at least in part on the observation that specific substituted pyrrolidines, and analogs thereof, are capable of specifically inhibiting DNA glycosylases, e.g., as transition state analogs, and consequently are useful for modulation of DNA repair. Such compounds can, for example, be used for treating subjects having a disorder associated with excessive cell proliferation, such as in the treatment of various cancers. Furthermore, these glycosylase inhibitors can be used as anti-bacterial, anti-viral and anti-fungal agents.
30 Citations
25 Claims
-
1. A compound represented by the formula, or a pharmaceutically acceptable salt thereof:
-
wherein B is a nucleoside purine or pyrimidine base, or a heterocyclic analog thereof;
X is O, N, S or CH2;
R1, independently for each occurrence, is absent or is a hydrogen, or an amino protecting group;
R2 is a hydrogen, a nucleotide or oligonucleotide, a phosphoryl, a phosphonate, a phosphoramidate, a carbarnate, a phosphorothioate, a phosphorodithioate, a hydroxyl blocking group, or as valence and stability permit, a halogen, a lower alkyl, a lower alkenyl, a lower alkynyl, a carbonyl, a thiocarbonyl, a ketyl, an aldehyde, an amino, an acylamino, an amido, an amidino, a cyano, a nitro, an azido, a sulfonyl, a sulfoxido, a sulfate, a sulfonate, a sulfamoyl, a sulfonamido, a phosphoryl, a phosphonate, a phosphinate, —
(CH2)m—
R8, —
(CH2)m—
OH, —
(CH2)m—
O-lower alkyl, —
(CH2)m—
O-lower alkenyl, —
(CH2)m—
O—
(CH2)n—
R8, —
(CH2)m—
SH, —
(CH2)m—
S-lower alkyl, —
(CH2)m—
S-lower alkenyl, —
(CH2)m—
S—
(CH2)n—
R8, or a solid or polymeric support;
R3 is a hydrogen, a nucleotide or oligonucleotide, a phosphoryl, a phosphonate, a phosphoramidate, a carbamate, a phosphorothioate, a phosphorodithioate, a hydroxyl blocking group, or as valence and stability permit, a halogen, a lower alkyl, a lower alkenyl, a lower alkynyl, a carbonyl, a thiocarbonyl, a ketyl, an aldehyde, an amino, an acylamino, an amido, an amidino, a cyano, a nitro, an azido, a sulfonyl, a sulfoxido, a sulfate, a sulfonate, a sulfamoyl, a sulfonamido, a phosphoryl, a phosphonate, a phosphinate, —
(CH2)m—
R8, —
(CH2)m—
OH, —
(CH2)m—
O-lower alkyl, —
(CH2)m—
O-lower alkenyl, —
(CH2)m—
O—
(CH2)n—
R8, —
(CH2)m—
SH, —
(CH2)m—
S-lower alkyl, —
(CH2)m—
S-lower alkenyl, —
(CH2)m—
S—
(CH2)n—
R8, or a solid or polymeric support;
R4, R5, R6 and R7 are each, independently, as valence and stability permit, hydrogen, a halogen, a lower alkyl, a lower alkenyl, a lower alkynyl, a carbonyl, a thiocarbonyl, a ketyl, an aldehyde, an amino, an acylamino, an amido, an amidino, a cyano, a nitro, an azido, a sulfonyl, a sulfoxido, a sulfate, a sulfonate, a sulfamoyl, a sulfonamido, a phosphoryl, a phosphonate, a phosphinate, —
(CH2)m—
R8, —
(CH2)m—
OH, —
(CH2)m—
O-lower alkyl, —
(CH2)m—
O-lower alkenyl, —
(CH2)m—
O—
(CH2)n—
R8, —
(CH2)m—
SH, —
(CH2)m—
S-lower alkyl, —
(CH2)m—
S-lower alkenyl, —
(CH2)m—
S—
(CH2)n—
R8;
R8 is, independently for each occurrence, a substituted or unsubstituted aryl, aralkyl, cycloalkyl, cycloalkenyl or heterocycle, a carbonyl, a sulfonyl or a phosphoryl; and
p is 1 or 2, and n and m are independently for each occurrence zero or an integer in the range of 1 to 6, which compound inhibits an N-glycosidic activity of a DNA glycosylase. - View Dependent Claims (6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23)
-
-
2. A compound represented by the formula, or a pharmaceutically acceptable salt thereof:
-
wherein B is a nucleoside purine or pyrimidine base, or a heterocyclic analog thereof;
X is O, N, S or CH2;
R1, independently for each occurrence, is absent or is a hydrogen, or an amino protecting group;
R2 is a hydrogen, a nucleotide or oligonucleotide, a phosphoryl, a phosphonate, a phosphoramidate, a carbamate, a phosphorothioate, a phosphorodithioate, a hydroxyl blocking group, or as valence and stability permit, a halogen, a lower alkyl, a lower alkenyl, a lower alkynyl, a carbonyl, a thiocarbonyl, a ketyl, an aldehyde, an amino, an acylamino, an amido, an amidino, a cyano, a nitro, an azido, a sulfonyl, a sulfoxido, a sulfate, a sulfonate, a sulfamoyl, a sulfonamido, a phosphoryl, a phosphonate, a phosphinate, —
(CH2)m—
R8, —
(CH2)m—
OH, —
(CH2)m—
O-lower alkyl, —
(CH2)m—
O-lower alkenyl, —
(CH2)m—
O—
(CH2)n—
R8, —
(CH2)m—
SH, —
(CH2)m—
S-lower alkyl, —
(CH2)m—
S-lower alkenyl, —
(CH2)m—
S—
(CH2)n—
R8, or a solid or polymeric support;
R3 is a hydrogen, a nucleotide or oligonucleotide, a phosphoryl, a phosphonate, a phosphoramidate, a carbamate, a phosphorothioate, a phosphorodithioate, a hydroxyl blocking group, or as valence and stability permit, a halogen, a lower alkyl, a lower alkenyl, a lower alkynyl, a carbonyl, a thiocarbonyl, a ketyl, an aldehyde, an amino, an acylamino, an amido, an amidino, a cyano, a nitro, an azido, a sulfonyl, a sulfoxido, a sulfate, a sulfonate, a sulfamoyl, a sulfonamido, a phosphoryl, a phosphonate, a phosphinate, —
(CH2)m—
R8, —
(CH2)m—
OH, —
(CH2)m—
O-lower alkyl, —
(CH2)m—
O-lower alkenyl, —
(CH2)m—
O—
(CH2)n—
R8, —
(CH2)m—
SH, —
(CH2)m—
S-lower alkyl, —
(CH2)m—
S-lower alkenyl, —
(CH2)m—
S—
(CH2)n—
R8, or a solid or polymeric support;
R4, R5, R6 and R7 are each, independently, as valence and stability permit, hydrogen, a halogen, a lower alkyl, a lower alkenyl, a lower alkynyl, a carbonyl, a thiocarbonyl, a ketyl, an aldehyde, an amino, an acylamino, an amido, an amidino, a cyano, a nitro, an azido, a sulfonyl, a sulfoxido, a sulfate, a sulfonate, a sulfamoyl, a sulfonamido, a phosphoryl, a phosphonate, a phosphinate, —
(CH2)m—
R8, —
(CH2)m—
OH, —
(CH2)m—
O-lower alkyl, —
(CH2)m—
O-lower alkenyl, —
(CH2)m—
O—
(CH2)n—
R8, —
(CH2)m—
SH, —
(CH2)m—
S-lower alkyl, —
(CH2)m—
S-lower alkenyl, —
(CH2)m—
S—
(CH2)n—
R8;
R8 is, independently for each occurrence, a substituted or unsubstituted aryl, aralkyl, cycloalkyl, cycloalkenyl or heterocycle, a carbonyl, a sulfonyl or a phosphoryl; and
p is 1 or 2, and n and m are independently for each occurrence zero or an integer in the range of 1 to 6, which compound inhibits an N-glycosidic activity of a DNA glycosylase.
-
-
3. A nucleic acid comprising at least one analog represented by the formula:
-
wherein B is a nucleoside purine or pyrimidine base, or a heterocyclic analog thereof;
X is O, N, S or CH2;
R1, independently for each occurrence, is absent or is a hydrogen, or an amino protecting group;
R2 is a hydrogen, a nucleotide or oligonucleotide, a phosphoryl, a phosphonate, a phosphoramidate, a carbamate, a phosphorothioate, a phosphorodithioate, a hydroxyl blocking group, or as valence and stability permit, a halogen, a lower alkyl, a lower alkenyl, a lower alkynyl, a carbonyl, a thiocarbonyl, a ketyl, an aldehyde, an amino, an acylamino, an amido, an amidino, a cyano, a nitro, an azido, a sulfonyl, a sulfoxido, a sulfate, a sulfonate, a sulfamoyl, a sulfonamido, a phosphoryl, a phosphonate, a phosphinate, —
(CH2)m—
R8, —
(CH2)m—
OH, —
(CH2)m—
O-lower alkyl, —
(CH2)m—
O-lower alkenyl, —
(CH2)m—
O—
(CH2)n—
R8, —
(CH2)m—
SH, —
(CH2)m—
S-lower alkyl, —
(CH2)m—
S-lower alkenyl, —
(CH2)m—
S—
(CH2)n—
R8, or a solid or polymeric support;
R3 is a hydrogen, a nucleotide or oligonucleotide, a phosphoryl, a phosphonate, a phosphoramidate, a carbamate, a phosphorothioate, a phosphorodithioate, a hydroxyl blocking group, or as valence and stability permit, a halogen, a lower alkyl, a lower alkenyl, a lower alkynyl, a carbonyl, a thiocarbonyl, a ketyl, an aldehyde, an amino, an acylamino, an amido, an amidino, a cyano, a nitro, an azido, a sulfonyl, a sulfoxido, a sulfate, a sulfonate, a sulfamoyl, a sulfonamido, a phosphoryl, a phosphonate, a phosphinate, —
(CH2)m—
R8, —
(CH2)m—
OH, —
(CH2)m—
O-lower alkyl, —
(CH2)m—
O-lower alkenyl, —
(CH2)m—
O—
(CH2)n—
R8, —
(CH2)m—
SH, —
(CH2)m—
S-lower alkyl, —
(CH2)m—
S-lower alkenyl, —
(CH2)m—
S—
(CH2)n—
R8, or a solid or polymeric support;
R4, R5, R6 and R7 are each, independently, as valence and stability permit, hydrogen, a halogen, a lower alkyl, a lower alkenyl, a lower alkynyl, a carbonyl, a thiocarbonyl, a ketyl, an aldehyde, an amino, an acylamino, an amido, an amidino, a cyano, a nitro, an azido, a sulfonyl, a sulfoxido, a sulfate, a sulfonate, a sulfamoyl, a sulfonamido, a phosphoryl, a phosphonate, a phosphinate, —
(CH2)m—
R8, —
(CH2)m—
OH, —
(CH2)m—
O-lower alkyl, —
(CH2)m—
O-lower alkenyl, —
(CH2)m—
O—
(CH2)n—
R8, —
(CH2)m—
SH, —
(CH2)m—
S-lower alkyl, —
(CH2)m—
S-lower alkenyl, —
(CH2)m—
S—
(CH2)n—
R8;
R8 is, independently for each occurrence, a substituted or unsubstituted aryl, aralkyl, cycloalkyl, cycloalkenyl or heterocycle, a carbonyl, a sulfonyl or a phosphoryl; and
p is 1 or 2, and n and m are independently for each occurrence zero or an integer in the range of 1 to 6, which nucleic acid inhibits an N-glycosidic activity of a DNA glycosylase. - View Dependent Claims (19, 20, 21, 24)
-
-
4. A nucleic acid comprising at least one analog represented by the formula:
-
wherein B is a nucleoside purine or pyrimidine base, or a heterocyclic analog thereof;
X is O, N, S or CH2;
R1, independently for each occurrence, is absent or is a hydrogen, or an amino protecting group;
R2 is a hydrogen, a nucleotide or oligonucleotide, a phosphoryl, a phosphonate, a phosphoramidate, a carbamate, a phosphorothioate, a phosphorodithioate, a hydroxyl blocking group, or as valence and stability permit, a halogen, a lower alkyl, a lower alkenyl, a lower alkynyl, a carbonyl, a thiocarbonyl, a ketyl, an aldehyde, an amino, an acylamino, an amido, an amidino, a cyano, a nitro, an azido, a sulfonyl, a sulfoxido, a sulfate, a sulfonate, a sulfamoyl, a sulfonarnido, a phosphoryl, a phosphonate, a phosphinate, —
(CH2)m—
R8, —
(CH2)m—
OH, —
(CH2)m—
O-lower alkyl, —
(CH2)m—
O-lower alkenyl, —
(CH2)m—
O—
(CH2)n—
R8, —
(CH2)m—
SH, —
(CH2)m—
S-lower alkyl, —
(CH2)m—
S-lower alkenyl, —
(CH2)m—
S—
(CH2)n—
R8, or a solid or polymeric support;
R3 is a hydrogen, a nucleotide or oligonucleotide, a phosphoryl, a phosphonate, a phosphoramidate, a carbamate, a phosphorothioate, a phosphorodithioate, a hydroxyl blocking group, or as valence and stability permit, a halogen, a lower alkyl, a lower alkenyl, a lower alkynyl, a carbonyl, a thiocarbonyl, a ketyl, an aldehyde, an amino, an acylamino, an amido, an amidino, a cyano, a nitro, an azido, a sulfonyl, a sulfoxido, a sulfate, a sulfonate, a sulfamoyl, a sulfonamido, a phosphoryl, a phosphonate, a phosphinate, —
(CH2)m—
R8, —
(CH2)m—
OH, —
(CH2)m—
O-lower alkyl, —
(CH2)m—
O-lower alkenyl, —
(CH2)m—
O—
(CH2)n—
R8, —
(CH2)m—
SH, —
(CH2)m—
S-lower alkyl, —
(CH2)m—
S-lower alkenyl, —
(CH2)m—
S—
(CH2)n—
R8, or a solid or polymeric support;
R4, R5, R6 and R7 are each, independently, as valence and stability permit, hydrogen, a halogen, a lower alkyl, a lower alkenyl, a lower alkynyl, a carbonyl, a thiocarbonyl, a ketyl, an aldehyde, an amino, an acylamino, an amido, an amidino, a cyano, a nitro, an azido, a sulfonyl, a sulfoxido, a sulfate, a sulfonate, a sulfamoyl, a sulfonamido, a phosphoryl, a phosphonate, a phosphinate, —
(CH2)m—
R8, —
(CH2)m—
OH, —
(CH2)m—
O-lower alkyl, —
(CH2)m—
O-lower alkenyl, —
(CH2)m—
O—
(CH2)n—
R8, —
(CH2)m—
SH, —
(CH2)m—
S-lower alkyl, —
(CH2)m—
S-lower alkenyl, —
(CH2)m—
S—
(CH2)n—
R8;
R8 is, independently for each occurrence, a substituted or unsubstituted aryl, aralkyl, cycloalkyl, cycloalkenyl or heterocycle, a carbonyl, a sulfonyl or a phosphoryl; and
p is 1 or 2, and n and m are independently for each occurrence zero or an integer in the range of 1 to 6, which nucleic acid inhibits an N-glycosidic activity of a DNA glycosylase.
-
-
5. A glycosylase inhibitor comprising a analog represented by the formula:
-
wherein B is a nucleoside purine or pyrimidine base, or a heterocyclic analog thereof;
X is O, N, S or CH2;
R1, independently for each occurrence, is absent or is a hydrogen, or an amino protecting group;
R2 is a hydrogen, a nucleotide or oligonucleotide, a phosphoryl, a phosphonate, a phosphoramidate, a carbamate, a phosphorothioate, a phosphorodithioate, a hydroxyl blocking group, or as valence and stability permit, a halogen, a lower alkyl, a lower alkenyl, a lower alkynyl, a carbonyl, a thiocarbonyl, a ketyl, an aldehyde, an amino, an acylamino, an amido, an amidino, a cyano, a nitro, an azido, a sulfonyl, a sulfoxido, a sulfate, a sulfonate, a sulfamoyl, a sulfonamido, a phosphoryl, a phosphonate, a phosphinate, —
(CH2)m—
R8, —
(CH2)m—
OH, —
(CH2)m—
O-lower alkyl, —
(CH2)m—
O-lower alkenyl, —
(CH2)m—
O—
(CH2)n—
R8, —
(CH2)m—
SH, —
(CH2)m—
S-lower alkyl, —
(CH2)m—
S-lower alkenyl, —
(CH2)m—
S—
(CH2)n—
R8, or a solid or polymeric support;
R3 is a hydrogen, a nucleotide or oligonucleotide, a phosphoryl, a phosphonate, a phosphoramidate, a carbamate, a phosphorothioate, a phosphorodithioate, a hydroxyl blocking group, or as valence and stability permit, a halogen, a lower alkyl, a lower alkenyl, a lower alkynyl, a carbonyl, a thiocarbonyl, a ketyl, an aldehyde, an amino, an acylarmino, an amido, an amidino, a cyano, a nitro, an azido, a sulfonyl, a sulfoxido, a sulfate, a sulfonate, a sulfamoyl, a sulfonamido, a phosphoryl, a phosphonate, a phosphinate, —
(CH2)m—
R8, —
(CH2)m—
OH, —
(CH2)m—
O-lower alkyl, —
(CH2)m—
O-lower alkenyl, —
(CH2)m—
O—
(CH2)n—
R8, —
(CH2)m—
SH, —
(CH2)m—
S-lower alkyl, —
(CH2)m—
S-lower alkenyl, —
(CH2)m—
S—
(CH2)n—
R8, or a solid or polymeric support;
R4, R5, R6 and R7 are each, independently, as valence and stability permit, hydrogen, a halogen, a lower alkyl, a lower alkenyl, a lower alkynyl, a carbonyl, a thiocarbonyl, a ketyl, an aldehyde, an amino, an acylamino, an amido, an amidino, a cyano, a nitro, an azido, a sulfonyl, a sulfoxido, a sulfate, a sulfonate, a sulfamoyl, a sulfonamido, a phosphoryl, a phosphonate, a phosphinate, —
(CH2)m—
R8, —
(CH2)m—
OH, —
(CH2)m—
O-lower alkyl, —
(CH2)m—
O-lower alkenyl, —
(CH2)m—
O—
(CH2)n—
R8, —
(CH2)m—
SH, —
(CH2)m—
S-lower alkyl, —
(CH2)m—
S-lower alkenyl, —
(CH2)m—
S—
(CH2)n—
R8;
R8 is, independently for each occurrence, a substituted or unsubstituted aryl, aralkyl, cycloalkyl, cycloalkenyl or heterocycle, a carbonyl, a sulfonyl or a phosphoryl; and
p is 1 or 2, and n and m are independently for each occurrence zero or an integer in the range of 1 to 6, which inhibitor inhibits an N-glycosidic activity of a DNA glycosylase. - View Dependent Claims (25)
-
Specification