# US 9,040,490 B2 · Cytosine analogue, a method of preparation of a cytosine analogue, a DNA methyltransferase 1 inhibitor, a method for DNA methylation inhibition, the use of the analogue in the treatment of diseases associated with deviations from normal DNA methylation

> Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt

- Number: US 9,040,490 B2
- Document ID: US9040490B2
- Status: Granted
- Kind: B2
- Application number: 13/576,709
- Filed: 2011-03-17
- Published: 2012-12-20
- Granted: 2015-05-26
- Earliest claimed: 2010-03-19
- Assignees: Instytut Chemii Bioorganicznej Pan
- Applicants: Jan Barciszewski; Wojciech T. Markiewicz; Ewelina Adamska; Beata Plitta; Malgorzata Giel-Pietraszuk; Eliza Wyszko; Maria Markiewicz; Agnieszka Fedoruk-Wyszomirska; Tadeusz Kulinski; Marcin Chmielewski
- Inventors: Jan Barciszewski; Wojciech T. Markiewicz; Ewelina Adamska; Beata Plitta; Malgorzata Giel-Pietraszuk; Eliza Wyszko; Maria Markiewicz; Agnieszka Fedoruk-Wyszomirska; Tadeusz Kulinski; Marcin Chmielewski
- Web page: https://patentgrep.com/patent/US9040490B2

## CPC

- C07H 19/073: with 2-deoxyribosyl as the saccharide radical
- A61P 35/00: Antineoplastic agents
- A61P 43/00: Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
- C07D 239/47: One nitrogen atom and one oxygen or sulfur atom, e.g. cytosine
- C07D 401/12: linked by a chain containing hetero atoms as chain links
- C07D 405/12: linked by a chain containing hetero atoms as chain links
- C07H: SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS (derivatives of aldonic or saccharic acids C07C, C07D; aldonic acids, saccharic acids C07C59/105, C07C59/285; cyanohydrins C07C255/16; glycals C07D; compounds of unknown constitution C07G; polysaccharides, derivatives thereof C08B; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification C12N15/00; sugar industry C13)
- A61P: SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- C07D: HETEROCYCLIC COMPOUNDS (macromolecular compounds C08)

## Abstract

A cytosine analog, a method of preparation of a cytosine analog, a DNA methyltransferase 1 inhibitor, and a method for DNA methylation inhibition, is provided for the treatment of diseases associated with deviations from normal DNA methylation. The analog of cytosine may be comprised of 1, N4, 5 and 6-substituted derivatives of cytosine or 5,6-dihydrocytosine, wherein the analog can be described by the chemical formula where R1 is H, R3, R4, 2′-deoxyribosyl, R4 is alkyl or aryl, X is N or C, wherein if X in the analog of formula I is N, then R5 is no substituent and if X in the analog of formula I and/or II is C or if X in the analog of formula II is N, then R5 and R6 are independently alkyl, aryl, hydroxyalkyl, aminoalkyl, hydroxyl, carboxyl, amino group, alkoxyl, aryloxyl, aminoalkyl, aminoaryl, thio group, sulfonyl, sulfinyl or halogen.

## Claims

### Claim 1

A method of preparation of an analogue of cytosine or a physiologically acceptable salt or a prodrug thereof, selected from the group consisting of 1, N4, 5 and 6 substituted derivatives of cytosine, 5-azacytosine, or 5,6-dihydrocytosine, wherein said analogue is described by the chemical formulas
where
R1 is H, R4, or 2′-deoxyribosyl,
R4 is alkyl or aralkyl,
X is N in formula I or II, or X is C in formula I,
wherein with the proviso that if X in the analogue of formula I is N,
then R5 is no substituent and,
wherein with the proviso that if X in the analogue of formula I is C or if X in the analogue of formula II is N,
then R5 and R6 are independently alkyl, aryl, hydroxyalkyl, aminoalkyl, hydroxyl, carboxyl, amino group, alkoxyl, aryloxyl, aminoalkyl, aminoaryl, thio group, sulfonyl, sulfinyl or halogen,
wherein the method comprises:
a) adding an N4-unsubstituted cytosine or an analogue thereof as defined above and an aromatic or an alkyl aldehyde in the quantity of 4-6 eq to anhydrous methanol or ethanol,
b) introducing NaBH4 or BH3×SMe2 to the mixture in the amount of at least 1.1 eq relative to the aldehyde in order to reduce the obtained imine,
c) neutralizing the reducing agent with hydrochloric acid,
d) evaporating the mixture,
e) pouring the mixture into water,
f) extracting the mixture with ethyl acetate or butanol to obtain a mixture of alcohol and an N4-modified cytosine or an analogue thereof as defined above in ethyl acetate or butanol,
g) obtaining a pure product by:
evaporating the separated organic layer to dryness to obtain the pure product or;
extracting the separated organic layer with aqueous solution of an inorganic acid to obtain an aqueous solution of cytosine hydrochloride or other modified said N4-modified cytosine salt, depending on the acid added, where the resulting salt is free of alcohol, further comprising
1) neutralizing the solution with a hydroxide or other hydroxyl group donor,
2) extracting the solution with ethyl acetate or butanol,
3) at least one of freeze drying, evaporating, or a combination thereof the organic layer to obtain the pure product.

### Claim 2 (depends on 1)

The method according to claim 1, further comprising wherein before an aromatic aldehyde is added, excess magnesium metal is added generate an anhydrous methanol or ethanol solvent in the amount of at least 4 eq relative to the N4-modified cytosine coreactant and heated until complete dissolution of magnesium filings; next, at least 2 mmol of the N4-modified cytosine coreactant is added, followed by the aromatic aldehyde in the amount of 4-6 eq, minimum of 4 eq relative to said N4-modified cytosine coreactant; next, the reaction mixture is placed in temperature in the range of 45-65° C. for at least 3 hours, and later, a reducing agent, comprising NaBH4 is added to the cooled mixture in the amount of at least 1 eq relative to aldehyde; the mixture is then kept at room temperature for at least 15 minutes, followed by addition of inorganic acid solution; next, the mixture is evaporated, water is added again and the mixture is extracted with ethyl acetate to isolate the product; the separated organic layer containing the product and the aromatic alcohol is evaporated to obtain pure product or extracted with an aqueous solution of inorganic acid to obtain an aqueous solution of the N4-modified cytosine hydrochloride or other N4-modified cytosine salt, depending on the acid added, where the resulting salt is free of alcohol; the solution is then neutralized with a hydroxide or other hydroxyl group donor and again extracted with ethyl acetate; the organic layer is evaporated to obtain pure product.

### Claim 3 (depends on 2)

The method according to claim 2, wherein the aromatic aldehyde is furfuryl aldehyde or benzaldehyde.

### Claim 4 (depends on 2)

The method according to claim 2, wherein the synthetic yield after purification is at least 50% and is dependent on the aldehyde.

### Claim 5 (depends on 1)

An alternative to the imine generating process steps according to claim 1, further comprising adding, 3-5 eq of acetic acid, at least 0.75 eq of an N4-unsubstituted cytosine or analogue thereof and at least 3 eq of an aldehyde to anhydrous methanol, n-propanol or ethanol, and the entire mixture is boiled for at least 2 hours; the resulting imine is isolated by extraction with water or methanol and hexane, where the excess aldehyde is transferred to the hexane layer and the imine with the remaining unreacted substrate remains in the water or methanol layer; next, the aqueous layer is extracted with butanol/ethyl acetate to isolate the imine from the aqueous layer, the solvent is evaporated and the resulting intermediate imine product is subjected to freeze drying.

### Claim 6 (depends on 1)

An alternative to the method according to claim 1 beginning at step b), further comprising the solvent of the reaction mixture from step a) is evaporated and methylene chloride and a solution of BH3×SMe2 in tetrahydrofuran are added; the reaction is conducted at room temperature for at least 9 hours, and when reduction is completed, the reaction mixture is treated with aqueous solution of an inorganic acid for at least 10 hours; afterwards, the reaction mixture is evaporated and extracted with water and ethyl acetate or butanol to obtain the pure product or extracted with aqueous solution of an inorganic acid to obtain an aqueous solution of the N4-modified cytosine hydrochloride; next, after neutralization of the aqueous solution of the N4-modified cytosine hydrochloride, the solution is extracted with ethyl acetate or butanol; the organic layer is at least one of evaporated, freeze dried, or a combination thereof to obtain the pure product.

### Claim 7 (depends on 5)

The method according to claim 5, further comprising the reaction of an N4-unmodified cytosine, 5-azacytosine or 5,6-dihydrocytosine derivative with propanal or acetaldehyde, the product is purified on a water/acetone reverse phase chromatographic column.

### Claim 8

An analogue of cytosine or a physiologically acceptable salt or a prodrug thereof, selected from the group consisting of 1, N4, 5 and 6 substituted derivatives of cytosine, 5-azacytosine, or 5,6-dihydrocytosine, wherein said analogue is described by the chemical formulas
where R1 is H, R4, or 2′-deoxyribosyl,
R4 is alkyl or aralkyl,
X is N in formula I or II, or X is C in formula I,
wherein with the proviso that if X in the analogue of formula I is N,
then R5 is no substituent, and
wherein with the proviso that if X in the analogue of formula I is C or if X in the analogue of formula II is N,
then R5 and R6 are independently alkyl, aryl, hydroxyalkyl, aminoalkyl, hydroxyl, carboxyl, amino group, alkoxyl, aryloxyl, aminoalkyl, aminoaryl, thio group, sulfonyl, sulfinyl or halogen.

### Claim 9 (depends on 8)

The analogue according to claim 8, wherein the physiologically acceptable salt is a sodium, a calcium, a potassium or an ammonium salt.

### Claim 10 (depends on 8, 9)

A method for inhibiting DNA methylation in a cell in need thereof comprising administrating to the cell an effective amount of the compound or a physiologically acceptable salt or a prodrug thereof according to claim 8 or 9.

### Claim 11 (depends on 10)

The method according to claim 10, wherein activity of DNA methyltransferase within the cell is inhibited by degradation of DNA methyltransferase 1 (DNMT1).