Oligonucleotide Analogues Incorporating 5-Aza-Cytosine Therein

• US 20130236536A1
• Filed: 05/14/2013
• Published: 09/12/2013
• Est. Priority Date: 09/29/2005
• Status: Active Grant

• Current Assignee: Astex Pharmaceuticals, Inc. (Otsuka Holdings Company Limited)
• Original Assignee: Astex Pharmaceuticals, Inc. (Otsuka Holdings Company Limited)
• Inventors: Phiasivongsa, Pasit, Redkar, Sanjeev
• Granted Patent: US 9,358,248 B2
• Time in Patent Office: Days
• US Class Current: 424/450
• CPC Class Codes: A61K 31/282 Platinum compounds
• CPC Class Codes: A61K 31/337 having four-membered rings, e.g. taxol
• CPC Class Codes: A61K 31/4406 only substituted in position 3, e.g. zimeldine nicotinic acid A61K31/455
• CPC Class Codes: A61K 31/7084 Compounds having two nucleosides or nucleotides, e.g. nicotinamide-adenine dinucleotide, flavine-adenine dinucleotide
• CPC Class Codes: A61K 33/243 Platinum; Compounds thereof
• CPC Class Codes: A61K 45/06 Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
• CPC Class Codes: A61K 9/0019 Injectable compositions; Intramuscular, intravenous, arterial, subcutaneous administration; Compositions to be administered through the skin in an invasive manner non-active ingredients are additionally classified in A61K47/00
• CPC Class Codes: A61K 9/0053 Mouth and digestive tract, i.e. intraoral and peroral administration rectal administration A61K9/0031
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 35/02 specific for leukemia
• CPC Class Codes: A61P 35/04 specific for metastasis
• CPC Class Codes: A61P 7/00 Drugs for disorders of the blood or the extracellular fluid
• CPC Class Codes: A61P 7/06 Antianaemics
• CPC Class Codes: C07H 19/20 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C12N 15/111 General methods applicable to biologically active non-coding nucleic acids
• CPC Class Codes: C12N 2310/11 Antisense
• CPC Class Codes: C12N 2310/317 with an inverted bond, e.g. a cap structure
• CPC Class Codes: C12N 2310/334 Modified C
• CPC Class Codes: C12N 2310/336 Modified G
• CPC Class Codes: C12N 2320/30 : Special therapeutic applications
• CPC Class Codes: C12N 2330/30 : chemically synthesised

Abstract

Oligonucleotide analogues are provided that incorporate 5-aza-cytosine in the oligonucleotide sequence, e.g., in the form of 5-aza-2′-deoxycytidine (decitabine) or 5-aza-cytidine. In particular, oligonucleotide analogues rich in decitabine-deoxyguanosine islets (DpG and GpD) are provided to target the CpG islets in the human genome, especially in the promoter regions of genes susceptible to aberrant hypermethylation. Such analogues can be used for modulation of DNA methylation, such as effective inhibition of methylation of cytosine at the C-5 position. Methods for synthesizing these oligonucleotide analogues and for modulating nucleic acid methylation are provided. Also provided are phosphoramidite building blocks for synthesizing the oligonucleotide analogues, methods for synthesizing, formulating and administering these compounds or compositions to treat conditions, such as cancer and hematological disorders.

Claims

1-114. -114. (canceled)

115. A pharmaceutical combination comprising:

1) a first therapeutic agent that is an isolated or synthetic dinucleotide analogue, or its salt or ester, comprising one 5-aza-cytosine as a base residue in the sequence of the dinucleotide analogue, wherein the dinucleotide analogue has a general formula of;

5′

-DpG-3′

or 5′

GpD-3′

, wherein D is decitabine;

p is a phospholinker wherein the number of phosphorus atoms in the phospholinker is one; and

G is deoxyguanosine; and

2) a second therapeutic agent.

116. The pharmaceutical combination of claim 115, wherein the dinucleotide analogue has the general formula of 5′

-DpG-3′

.

117. The pharmaceutical combination of claim 115, wherein the dinucleotide analogue has the general formula of 5′

GpD-3′

.

118. The pharmaceutical combination of claim 115, wherein p is a phosphorodiester linker

119. The pharmaceutical combination of claim 115, wherein the salt is a sodium, calcium, lithium, potassium, ammonium, or trialkylammonium salt.

120. The pharmaceutical combination of claim 115, wherein the salt is a sodium salt.

121. The pharmaceutical combination of claim 115, wherein the dinucleotide analogue is a compound of the formula:

122. The pharmaceutical combination of claim 121, wherein the counter ion is a sodium ion.

123. The pharmaceutical combination of claim 115, wherein the second therapeutic agent is an alkylating agent, an agent that is a member of the retinoids superfamily, an antibiotic agent, a hormonal agent, a plant-derived agent, a biologic agent, an interleukin, an interferon, a cytokine, an inhibitor of histone deacetylase, a platinum compound, a taxane, an anti-neoplastic agent, an immune-modulating agent, or a monoclonal antibody.

124. The pharmaceutical combination of claim 115, wherein the second therapeutic agent is an inhibitor of histone deacetylase.

125. The pharmaceutical combination of claim 124, wherein the inhibitor of histone deacetylase is a hydroxamic acid, a cyclic peptide, a benzamide, a short-chain fatty acid, trichostatin A, suberoylanilide hydroxamic acid, oxamflatin, suberic bishydroxamic acid, m-carboxy-cinnamic acid bishydroxamic acid, pyroxamide, trapoxin A, apicidin, FR901228, MS-27-275, butyric acid, arginine butyrate, or phenylbutyrate.

126. The pharmaceutical combination of claim 124, wherein the inhibitor of histone deacetylase is MS-27-275.

127. The pharmaceutical combination of claim 115, wherein the second therapeutic agent is a platinum compound.

128. The pharmaceutical combination of claim 127, wherein the platinum compound is cisplatin.

129. The pharmaceutical combination of claim 127, wherein the platinum compound is carboplatin.

130. The pharmaceutical combination of claim 115, wherein the second therapeutic agent is a taxane.

131. The pharmaceutical combination of claim 130, wherein the taxane is paclitaxel.

132. The pharmaceutical combination of claim 130, wherein the taxane is docetaxel.

133. The pharmaceutical combination of claim 115, wherein the second therapeutic agent is an anti-neoplastic agent.

134. The pharmaceutical combination of claim 115, wherein the second therapeutic agent is an immune-modulating agent.

135. The pharmaceutical combination of claim 115, wherein the dinucleotide analogue is provided in a dosage form, wherein the dosage form comprises a pharmaceutically-acceptable carrier.

136. The pharmaceutical combination of claim 135, wherein the pharmaceutically-acceptable carrier is a solution.

137. The pharmaceutical combination of claim 135, wherein the pharmaceutically-acceptable carrier is an aqueous solution.

138. The pharmaceutical combination of claim 135, wherein the pharmaceutically-acceptable carrier has less than 40% water.

139. The pharmaceutical combination of claim 135, wherein the pharmaceutically-acceptable carrier has less than 5% water.

140. The pharmaceutical combination of claim 135, wherein the pharmaceutically-acceptable carrier has less than 1% water.

141. The pharmaceutical combination of claim 135, wherein the pharmaceutically-acceptable carrier is substantially anhydrous.

142. The pharmaceutical combination of claim 135, wherein the pharmaceutically-acceptable carrier comprises a solvent selected from the group consisting of ethanol, glycerin, propylene glycol, polyethylene glycol, and combinations thereof.

143. The pharmaceutical combination of claim 135, wherein the pharmaceutically-acceptable carrier is a solution comprising ethanol, glycerin, propylene glycol, polyethylene glycol, or a combination thereof.

144. The pharmaceutical combination of claim 135, wherein the pharmaceutically-acceptable carrier comprises a concentration of propylene glycol and a concentration of glycerine.

145. The pharmaceutical combination of claim 144, wherein the concentration of propylene glycol in the pharmaceutically-acceptable carrier is between 10-80%.

146. The pharmaceutical combination of claim 144, wherein the concentration of propylene glycol in the pharmaceutically-acceptable carrier is between 50-70%.

147. The pharmaceutical combination of claim 135, wherein the dosage form is formulated for administration by injection.

148. The pharmaceutical combination of claim 135, wherein the dosage form is formulated for administration by subcutaneous injection.

149. The pharmaceutical combination of claim 135, wherein the dosage form comprises between 0.1 and 200 mg of the dinucleotide analogue per mL of the pharmaceutically-acceptable carrier.

150. The pharmaceutical combination of claim 135, wherein the dosage form comprises between 0.1 and 100 mg of the dinucleotide analogue per mL of the pharmaceutically-acceptable carrier.

151. A method for treating a disease in a patient in need of relief thereof, the method comprising administering to the patient:

1) a therapeutically-effective amount of a first therapeutic agent that is an isolated or synthetic dinucleotide analogue, or its salt or ester, comprising one 5-aza-cytosine as a base residue in the sequence of the dinucleotide analogue, wherein the dinucleotide analogue has a general formula of;

5′

-DpG-3′

or 5′

GpD-3′

, wherein D is decitabine;

p is a phospholinker wherein the number of phosphorus atoms in the phospholinker is one; and

G is deoxyguanosine; and

2) a therapeutically-effective amount of a second therapeutic agent.

152. The method of claim 151, wherein the dinucleotide analogue has the general formula of 5′

-DpG-3′

.

153. The method of claim 151, wherein the dinucleotide analogue has the general formula of 5′

GpD-3′

.

154. The method of claim 151, wherein p is a phosphorodiester linker.

155. The method of claim 151, wherein the salt is a sodium, calcium, lithium, potassium, ammonium, or trialkylammonium salt.

156. The method of claim 151, wherein the salt is a sodium salt.

157. The method of claim 151, wherein the dinucleotide analogue is a compound of the formula:

158. The method of claim 157, wherein the counter ion is a sodium ion.

159. The method of claim 151, wherein the second therapeutic agent is an alkylating agent, an agent that is a member of the retinoids superfamily, an antibiotic agent, a hormonal agent, a plant-derived agent, a biologic agent, an interleukin, an interferon, a cytokine, an inhibitor of histone deacetylase, a platinum compound, a taxane, an anti-neoplastic agent, an immune-modulating agent, or a monoclonal antibody.

160. The method of claim 151, wherein the second therapeutic agent is an inhibitor of histone deacetylase.

161. The method of claim 160, wherein the inhibitor of histone deacetylase is a hydroxamic acid, a cyclic peptide, a benzamide, a short-chain fatty acid, trichostatin A, suberoylanilide hydroxamic acid, oxamflatin, suberic bishydroxamic acid, m-carboxy-cinnamic acid bishydroxamic acid, pyroxamide, trapoxin A, apicidin, FR901228, MS-27-275, butyric acid, arginine butyrate, or phenylbutyrate.

162. The method of claim 160, wherein the inhibitor of histone deacetylase is MS-27-275.

163. The method of claim 151, wherein the second therapeutic agent is a platinum compound.

164. The method of claim 163, wherein the platinum compound is cisplatin.

165. The method of claim 163, wherein the platinum compound is carboplatin.

166. The method of claim 151, wherein the second therapeutic agent is a taxane.

167. The method of claim 166, wherein the taxane is paclitaxel.

168. The method of claim 166, wherein the taxane is docetaxel.

169. The method of claim 151, wherein the second therapeutic agent is an anti-neoplastic agent.

170. The method of claim 151, wherein the second therapeutic agent is an immune-modulating agent.

171. The method of claim 151, wherein the dinucleotide analogue is administered orally, parenterally, topically, intraperitoneally, intravenously, intraarterially, transdermally, sublingually, intramuscularly, rectally, transbuccally, intranasally, liposomally, via inhalation, vaginally, intraoccularly, via local delivery, subcutaneously, intraadiposally, intraarticularly, or intrathecally.

172. The method of claim 151, wherein the dinucleotide analogue is administered intravenously.

173. The method of claim 151, wherein the dinucleotide analogue is administered subcutaneously.

174. The method of claim 151, wherein the disease is a hematological disorder.

175. The method of claim 174, wherein the hematological disorder is acute promyelocytic leukemia.

176. The method of claim 174, wherein the hematological disorder is acute lymphoblastic leukemia.

177. The method of claim 174, wherein the hematological disorder is myelodysplastic syndrome.

178. The method of claim 174, wherein the hematological disorder is acute myeloid leukemia.

179. The method of claim 174, wherein the hematological disorder is chronic myelogenous leukemia.

180. The method of claim 151, wherein the disease is a solid tumor.

181. The method of claim 151, wherein the disease is a benign tumor.

182. The method of claim 181, wherein the benign tumor is hepatocellular adenoma.

183. The method of claim 181, wherein the benign tumor is hepatocarcinoma.

184. The method of claim 151, wherein the disease is cancer.

185. The method of claim 184 wherein the cancer is breast cancer, skin cancer, bone cancer, prostate cancer, liver cancer, lung cancer, non-small cell lung cancer, brain cancer, cancer of the larynx, cancer of the gall bladder, cancer of the pancreas, cancer of the rectum, cancer of the parathyroid, cancer of the thyroid, cancer of the adrenal, cancer of the neural tissue, cancer of the head and neck, colon cancer, stomach cancer, cancer of the bronchi, kidney cancer, basal cell carcinoma, squamous cell carcinoma of both ulcerating and papillary type, metastatic skin carcinoma, osteo sarcoma, Ewing'"'"'s sarcoma, veticulum cell sarcoma, myeloma, giant cell tumor, small-cell lung tumor, gallstones, islet cell tumor, primary brain tumor, acute and chronic lymphocytic and granulocytic tumors, hairy-cell tumor, adenoma, hyperplasia, medullary carcinoma, pheochromocytoma, mucosal neuronms, intestinal ganglloneuromas, hyperplastic corneal nerve tumor, marfanoid habitus tumor, Wilm'"'"'s tumor, seminoma, ovarian tumor, leiomyomater tumor, cervical dysplasia and in situ carcinoma, neuroblastoma, retinoblastoma, soft tissue sarcoma, malignant carcinoid, topical skin lesion, mycosis fungoide, rhabdomyosarcoma, Kaposi'"'"'s sarcoma, osteogenic sarcoma, malignant hypercalcemia, renal cell tumor, polycythermia vera, adenocarcinoma, glioblastoma multiforma, leukemias, lymphoma, malignant melanoma, or epidermoid carcinoma.

186. The method of claim 184, wherein the cancer is ovarian tumor.

187. The method of claim 184, wherein the cancer is liver cancer.

188. The method of claim 184, wherein the cancer is lung cancer.

189. The method of claim 184, wherein the cancer is non-small cell lung cancer.

190. The method of claim 184, wherein the cancer is colon cancer.

191. The method of claim 184, wherein the cancer is cancer of the pancreas.

192. The method of claim 184, wherein the cancer is malignant melanoma.

193. The method of claim 151, wherein the disease is associated with abnormal hemoglobin synthesis.

194. The method of claim 193, wherein the disease associated with abnormal hemoglobin synthesis is sickle cell anemia.

195. The method of claim 193, wherein the disease associated with abnormal hemoglobin synthesis is β

-thalassemia.

196. The method of claim 151, wherein the dinucleotide analogue and the second therapeutic agent are administered simultaneously.

197. The method of claim 151, wherein the dinucleotide analogue and the second therapeutic agent are administered sequentially.

198. A kit comprising:

1) a first vessel containing a first therapeutic agent that is an isolated or synthetic dinucleotide analogue, or its salt or ester, comprising one 5-aza-cytosine as a base residue in the sequence of the dinucleotide analogue, wherein the dinucleotide analogue has a general formula of;

5′

-DpG-3′

or 5′

GpD-3′

, wherein D is decitabine;

p is a phospholinker wherein the number of phosphorus atoms in the phospholinker is one; and

G is deoxyguanosine;

2) a second vessel containing a second therapeutic agent; and

3) a third vessel containing a pharmaceutically-acceptable carrier.

199. The kit of claim 198, wherein the dinucleotide analogue has the general formula of 5′

-DpG-3′

.

200. The kit of claim 198, wherein the dinucleotide analogue has the general formula of 5′

GpD-3′

.

201. The kit of claim 198, wherein p is a phosphorodiester linker.

202. The kit of claim 198, wherein the salt is a sodium, calcium, lithium, potassium, ammonium, or trialkylammonium salt.

203. The kit of claim 198, wherein the salt is a sodium salt.

204. The kit of claim 198, wherein the dinucleotide analogue is a compound of the formula:

205. The kit of claim 204, wherein the counter ion is a sodium ion.

206. The kit of claim 198, wherein the dinucleotide analogue or its salt or ester is in solid form.

207. The kit of claim 198, wherein the second therapeutic agent is an alkylating agent, an agent that is a member of the retinoids superfamily, an antibiotic agent, a hormonal agent, a plant-derived agent, a biologic agent, an interleukin, an interferon, a cytokine, an inhibitor of histone deacetylase, a platinum compound, a taxane, an anti-neoplastic agent, an immune-modulating agent, or a monoclonal antibody.

208. The kit of claim 198, wherein the second therapeutic agent is an inhibitor of histone deacetylase.

209. The kit of claim 208, wherein the inhibitor of histone deacetylase is a hydroxamic acid, a cyclic peptide, a benzamide, a short-chain fatty acid, trichostatin A, suberoylanilide hydroxamic acid, oxamflatin, suberic bishydroxamic acid, m-carboxy-cinnamic acid bishydroxamic acid, pyroxamide, trapoxin A, apicidin, FR901228, MS-27-275, butyric acid, arginine butyrate, or phenylbutyrate.

210. The kit of claim 208, wherein the inhibitor of histone deacetylase is MS-27-275.

211. The kit of claim 198, wherein the second therapeutic agent is a platinum compound.

212. The kit of claim 211, wherein the platinum compound is cisplatin.

213. The kit of claim 211, wherein the platinum compound is carboplatin.

214. The kit of claim 198, wherein the second therapeutic agent is a taxane.

215. The kit of claim 214, wherein the taxane is paclitaxel.

216. The kit of claim 214, wherein the taxane is docetaxel.

217. The kit of claim 198, wherein the second therapeutic agent is an anti-neoplastic agent.

218. The kit of claim 198, wherein the second therapeutic agent is an immune-modulating agent.

219. The kit of claim 198, wherein the pharmaceutically-acceptable carrier is a solution.

220. The kit of claim 198, wherein the pharmaceutically-acceptable carrier is an aqueous solution.

221. The kit of claim 198, wherein the pharmaceutically-acceptable carrier has less than 40% water.

222. The kit of claim 198, wherein the pharmaceutically-acceptable carrier has less than 5% water.

223. The kit of claim 198, wherein the pharmaceutically-acceptable carrier has less than 1% water.

224. The kit of claim 198, wherein the pharmaceutically-acceptable carrier is substantially anhydrous.

225. The kit of claim 198, wherein the pharmaceutically-acceptable carrier comprises a solvent selected from the group consisting of ethanol, glycerin, propylene glycol, polyethylene glycol, and combinations thereof.

226. The kit of claim 198, wherein the pharmaceutically-acceptable carrier is a solution comprising ethanol, glycerin, propylene glycol, polyethylene glycol, or a combination thereof.

227. The kit of claim 198, wherein the pharmaceutically-acceptable carrier comprises a concentration of propylene glycol and a concentration of glycerine.

228. The kit of claim 227, wherein the concentration of propylene glycol in the pharmaceutically-acceptable carrier is between 10-80%.

229. The kit of claim 227, wherein the concentration of propylene glycol in the pharmaceutically-acceptable carrier is between 50-70%.

230. The kit of claim 198, further comprising instructions for administration by injection.

231. The kit of claim 198, further comprising instructions for administration by subcutaneous injection.