Urea nucleosides as therapeutic and diagnostic agents

• US 6,441,161 B1
• Filed: 11/06/2000
• Issued: 08/27/2002
• Est. Priority Date: 03/27/1996
• Status: Expired due to Term

• Current Assignee: Gilead Sciences Inc.
• Original Assignee: Gilead Sciences Inc.
• Inventors: Kirschenheuter, Gary P., Eaton, Bruce
• Primary Examiner(s): Wilson, James O.
• Application Number:
  US09/707,253
• Time in Patent Office: 659 Days
• Field of Search: 536/27.1, 536/27.11, 536/27.3, 536/27.8, 536/27.81, 536/28.1, 536/28.5
• US Class Current: 536/27.1
• CPC Class Codes: C07H 11/02 Nitrates; Nitrites
• CPC Class Codes: C07H 19/06 Pyrimidine radicals
• CPC Class Codes: C07H 19/16 Purine radicals

Abstract

Modified nucleosides and methods of making and using the nucleosides are disclosed. The compounds can be prepared by reacting nucleoside starting materials that contain a suitable leaving group at one or more of the carbon atoms in the purine or pyrimidine ring, with a vinylstannane, carbon monoxide, and a palladium catalyst to provide 1-ene-3-one intermediates. These intermediates are then reacted with suitably functionalized primary or secondary amines via a Michael reaction. When the intermediate is a 5-position modified pyrimidine ring, and the amine contains a second hydrogen, it can do a second Michael reaction with the ene-one or the ene-imine in the pyrimidine ring. Appropriate modification of the amine reactant can yield products with various bioactivities. The nucleosides can be used therapeutically as anti-cancer, anti-bacterial or anti-viral drugs. The nucleosides can also be used for diagnostic applications, for example, by incorporating a radiolabel or fluorescent label into the molecule. The nucleosides can be used to prepare oligonucleotides for use in various applications, either alone or in combination with other modified nucleosides and/or naturally occurring nucleosides.

Claims

1. A method for preparing modified nucleosides, comprising:

a) reacting a nucleoside starting material having the following formula;

with a vinylstannane of the formula (alkyl₃Sn)(R⁸)C═

C(R⁸)₂ and carbon monoxide in the presence of a palladium catalyst to form an ene-one intermediate;

b) reacting the ene-one intermediate with an amine of the formula HNR¹R² wherein;

Lg is independently selected from the group consisting of H or a leaving group;

R¹ and R² function to modulate, modify and/or control the biological activity of the compound and are independently selected from the group consisting of H, C₁-C₁₈ alkyl, alkenyl or alkynyl, phenyl, aralkyl, alkaryl, an alkanoic acid or its ester and amide derivatives, a peptide fragment, an HIV aspartyl protease inhibitor, groups that are cleaved intracellularly, and groups that increase the hydrophilicity, hydrophobicity, electrostatic capacity or hydrogen bonding capacity of the compound;

R³, R⁴ and R⁵ are independently selected from the group consisting of H, —

OH, protected oxy-, —

NH₂, F, —

N₃, —

CN, —

NC, —

OAc, —

SAc, —

OBz, and —

OSiR⁷₃, wherein R⁷ is C1-C4 alkyl or phenyl;

R⁶ is selected from the group consisting of—

OH, protected oxy-, phosphate, diphosphate, triphosphate, phosphate esters, phosphoramidites, phosphorothionates, and phosphorodithionates;

R⁸ is independently selected from the group consisting of H, aryl, aralkyl, alkyl, alkaryl, alkenyl, alkynyl, alkoxy, and —

C(O)—

R⁹, where R⁹ is selected from the group consisting of H, alkyl, aryl, aralkyl, alkaryl and alkoxy;

the protected oxy- groups of R⁴ and R⁵ taken together can represent an isopropylidene group (—

OC(CH₃)₂O—

) or an orthoformate group (—

OCH(OR⁷)O—

); and

the protected oxy- groups of R⁵ and R⁶ taken together can represent a 3′

,-5′

-tetraalkyldisiloxane group (—

OSi(alkyl)₂OSi(alkyl)₂O—

); and

c) isolating said modified nucleoside.

2. A method for preparing modified nucleosides, comprising:

a) reacting a nucleoside starting material having the following formula;

b) reacting the ene-one intermediate with an amine of the formula HNR¹ R² wherein;

Lg is independently selected from the group consisting of H or a leaving group;

R¹ and R 2are independently selected from the group consisting of H, C₁-C₁₈ alkyl, alkenyl or alkynyl, phenyl, aralkyl, alkaryl, an alkanoic acid or its ester and amide derivatives, a peptide fragment, an HIV aspartyl protease inhibitor, groups that are cleaved intracellularly, and groups that increase the hydrophilicity, hydrophobicity, electrostatic capacity or hydrogen bonding capacity of the compound;

R³, R⁴ and R⁵ are independently selected from the group consisting of H, —

OH, protected oxy-, —

NH₂, F, —

N₃, —

CN, —

NC, —

OAc, —

SAc, —

OBz, and —

OSiR⁷₃, wherein R⁷ is C₁-C₄ alkyl or phenyl;

R⁶ is selected from the group consisting of—

OH, protected oxy-, phosphate, diphosphate, triphosphate, phosphate esters, phosphoramidites, phosphorothionates, and phosphorodithionates;

R⁸ is independently selected from the group consisting of H, aryl, aralkyl, alkyl, alkaryl, alkenyl, alkynyl, alkoxy, and —

C(O)-R⁹, where R⁹ is selected from the group consisting of H, alkyl, aryl, aralkyl, alkaryl and alkoxy;

the protected oxy- groups of R⁴ and R⁵ taken together can represent an isopropylidene group (—

OC(CH₃)₂O—

) or an orthoformate group (—

OCH(OR⁷)O—

); and

the protected oxy- groups of R⁵ and R⁶ taken together can represent a 3′

,-5′

-tetraalkyldisiloxane group (—

OSi(alkyl)₂OSi(alkyl)₂O—

); and

wherein

R³-R⁶ function to impart a first biological activity and R¹ or R² function to impart a second biological activity to the compound; and

c) isolating said modified nucleoside.

3. A method for preparing modified nucleosides, comprising:

a) reacting a nucleoside starting material having the following formula;

with a vinylstannane of the formula (alkyl₃Sn)(R⁸)C═

C(R⁸)₂ and carbon monoxide in the presence of a palladium catalyst to form an ene-one intermediate;

b) reacting the ene-one intermediate with an amine of the formula HNR¹ R² wherein;

Lg is independently selected from the group consisting of H or a leaving group;

R¹ and R² function to enhance the efficacy, bioavailability, potency, specificity and/or limits the toxicity of the compound and are independently selected from the group consisting of H, C₁-C₁₈ alkyl, alkenyl or alkynyl, phenyl, aralkyl, alkaryl, an alkanoic acid or its ester and amide derivatives, a peptide fragment, an HIV aspartyl protease inhibitor, groups that are cleaved intracellularly, and groups that increase the hydrophilicity, hydrophobicity, electrostatic capacity or hydrogen bonding capacity of the compound;

R³, R⁴ and R⁵ are independently selected from the group consisting of H, —

OH, protected oxy-, —

NH₂, F, —

N₃, —

CN, —

NC, —

OAc, —

SAc, —

OBz, and —

OSiR⁷₃, wherein R⁷ is C₁-C4 alkyl or phenyl;

R⁶ is selected from the group consisting of —

OH, protected oxy-, phosphates diphosphate, triphosphate, phosphate esters, phosphoramidites, phosphorothionates, and phosphorodithionates;

R⁸ is independently selected from the group consisting of H, aryl, aralkyl, alkyl, alkaryl, alkenyl, alkynyl, alkoxy, and —

C(O)—

R⁹, where R⁹ is selected from the group consisting of H, alkyl, aryl, aralkyl, alkaryl and alkoxy;

the protected oxy- groups of R⁴ and R⁵ taken together can represent an isopropylidene group (—

OC(CH₃)₂O—

) or an orthoformate group (—

OCH(OR⁷)O—

); and

the protected oxy- groups of R⁵ and R⁶ taken together can represent a 3′

,-5′

-tetraalkyldisiloxane group (—

OSi(alkyl)₂OSi(alkyl)₂O—

); and

c)i isolating said modified nucleoside.