Title:
PHOSPHONATES WITH REDUCED TOXICITY FOR TREATMENT OF VIRAL INFECTIONS
Kind Code:
A1


Abstract:
There are provided, inter alia, acyclic nucleoside phosphonate compounds having reduced toxicity and enhanced antiviral activity, and pharmaceutically accepted salts and solvates thereof. There are also provided methods of using the disclosed compounds for inhibiting viral RNA-dependent RNA polymerase, inhibiting viral reverse transcriptase, inhibiting replication of virus, including hepatitis C virus or a human retrovirus, and treating a subject infected with a virus, including hepatitis C virus or a human retrovirus.



Inventors:
Hostetler, Karl Y. (Del Mar, CA, US)
Beadle, James R. (San Diego, CA, US)
Valiaeva, Nadejda (San Diego, CA, US)
Application Number:
15/261477
Publication Date:
04/06/2017
Filing Date:
09/09/2016
Assignee:
The Regents of the University of California (Oakland, CA, US)
Primary Class:
International Classes:
C07F9/6561; C07F9/6512
View Patent Images:



Other References:
“Nucleotides, Nucleosides, and Nucleobases (Molecular Biology).” © 2016. Available from: < http://what-when-how.com/molecular-biology/nucleotides-nucleosides-and-nucleobases-molecular-biology/ >.
American Chemical Society. STN Database. RN 123156-16-1. © October 13, 1989.
American Chemical Society. STN Database. RN 123155-83-9. © October 13, 1989.
American Chemical Society. STN Database. RN 183107-05-3. © November 14, 1996.
American Chemical Society. STN Database. RN 278611-52-2. © July 19, 2000.
American Chemical Society. STN Database. RN 278611-19-1. © July 19, 2000.
American Chemical Society. STN Database. RN 1022982-83-7. © May 27, 2008.
American Chemical Society. STN Database. RN 913356-63-5. © November 16, 2006.
American Chemical Society. STN Database. RN 1204478-95-4. © February 3, 2010.
American Chemical Society. STN Database. RN 1204478-93-2. © February 3, 2010.
Biochemical Pharmacology. (1992), Vol. 44 (10), pp. 2067-2077.
Proc. Natl. Acad. Sci. (1991), Vol. 88, pp. 4961-4965.
Nucleic Acids Symposium Series. (2008), 52(1), pp. 657-658.
Primary Examiner:
KENYON, JOHN S
Attorney, Agent or Firm:
Mintz Levin/San Diego Office (One Financial Center Boston MA 02111)
Claims:
What is claimed is:

1. A compound having the structure of Formula (I): embedded image wherein BN is a substituted or unsubstituted nucleobase; L1 is a bond or —O—; R1 is halogen, —CF3, substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted aryl; provided that, if L1 is a bond, then R1 is halogen, and if L1 is —O—, then R1 is —CF3, substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted aryl; and R2 is a permeability enhancing moiety, a phosphate, or a diphosphate; or pharmaceutically accepted salt or solvate thereof.

2. The compound of claim 1, wherein BN is unsubstituted adenine, substituted adenine, unsubstituted thymine, substituted thymine, unsubstituted guanine, substituted guanine, unsubstituted cytosine, substituted cytosine, unsubstituted uracil, substituted uracil, 2,6-diaminopurine, 6-methoxypurine, or 6-O-methylguanine.

3. The compound of claim 1, with structure of Formula (Ia): embedded image wherein L1 is —O—, and R1 is —CF3, substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted aryl.

4. The compound of claim 1, wherein R1 is unsubstituted alkyl, unsubstituted cycloalkyl, or unsubstituted aryl.

5. The compound of claim 1, wherein R1 is unsubstituted C1-C10 alkyl.

6. The compound of claim 5, wherein R1 is methyl, ethyl or isopropyl.

7. The compound of claim 1, wherein R1 is unsubstituted cycloalkyl.

8. The compound of claim 1, wherein R1 is unsubstituted aryl.

9. The compound of claim 8, wherein R1 is phenyl.

10. The compound of claim 1, wherein R1 is substituted alkyl, substituted cycloalkyl, or substituted aryl.

11. The compound of claim 1, with structure of Formula (Ib): embedded image wherein L1 is a bond, and R1 is halogen.

12. The compound of claim 11, wherein R1 is fluoro.

13. The compound of claim 1, wherein R2 has the structure of Formula (II):
-L2-O—R3 (II) wherein L2 is a substituted or unsubstituted alkylene, substituted or unsubstituted cycloalkylene, or substituted or unsubstituted arylene; and R3 is substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted aryl.

14. The compound of claim 13, with the structure of Formulae (Ia1S) to (Ia7S): embedded image embedded image

15. The compound of claim 1, wherein R2 is octadecyloxyethyl, hexadecyloxyethyl, hexadecyloxypropyl, 15-methyl-hexadecyloxypropyl, 15-methyl-hexadecyloxyethyl, 13-methyl-tetradecyloxypropyl, 13-methyl-tetradecyloxyethyl, 14-cyclopropyl-tetradecyloxypropyl, 14-cyclopropyl-tetradecyloxyethyl, or 1-O-octadecyl-2-O-benzyl-sn-glyceryl.

16. The compound of claim 1 with structure: embedded image embedded image embedded image embedded image embedded image

17. A pharmaceutical composition comprising a compound of claim 1 and a pharmaceutically acceptable excipient.

18. A method of inhibiting a viral reverse transcriptase comprising contacting a cell comprising a viral reverse transcriptase with an effective amount of a compound of claim 1, thereby inhibiting said viral reverse transcriptase.

19. The method according to claim 18, wherein said viral reverse transcriptase is from hepatitis C virus or a human retrovirus.

20. The method according to claim 19 wherein said human retrovirus is HIV.

Description:

CROSS-REFERENCES TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No. 14/499,865, filed Sep. 29, 2014, which is a continuation of U.S. application Ser. No. 13/649,671, filed Oct. 11, 2012, now issued as U.S. Pat. No. 8,846,643, which in turn is a continuation of PCT/US2011/032558, filed Apr. 14, 2011, which claims the benefit of U.S. Provisional Application No. 61/324,224, filed Apr. 14, 2010, each of which is incorporated herein in its entirety and for all purposes.

STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with government support under grant numbers AI-071803, AI-076558 and AI-074057 awarded by the National Institutes of Health. The Government has certain rights in the invention.

BACKGROUND OF THE INVENTION

The hepatitis C virus (HCV) is the leading cause of chronic liver disease worldwide, infecting an estimated 170 million persons. Antiviral research directed toward the development of improved treatment methods for chronic HCV infections has focused mainly on inhibitors of the NS5B polymerase. See e.g., Brown, N. A., 2009, Expert Opin. Investig. Drugs 18:709-725. Indeed, treatment of hepatitis C virus (HCV) infection remains an important unmet medical need due to the inadequacies of current interferon-based therapy. See e.g., Falck-Ytter, Y., et al., 2003, Ann. Intern. Med., 136:288-292. In the United States there are 3 to 4 million persons with chronic HCV infection. See e.g., Armstrong, G. L., et al., 2006, Ann. Intern. Med., 144:705-714. A number of agents are currently in clinical development for HCV including NS3 protease inhibitors and NS5B antiviral nucleosides and non-nucleoside polymerase inhibitors. See e.g., Sarrazin, C. & Zeuzem, S., 2010, Gastroenterology, 138:447-462. Clinical and in vitro data indicate that resistance develops readily with protease and non-nucleoside polymerase inhibitors. See e.g., Sarrazin, C, et al., 2007, Gastroenterology, 132:1767-1777; McCown, M. F., et al., 2009, Antimicrob. Agents Chemother., 53:2129-2132; Howe, A. Y. M, et al., 2008, Antimicrob. Agents Chemother., 52:3327-3338. Nucleoside inhibitors which target the catalytic site of the NS5B RNA dependent RNA polymerase have been shown to be active across different HCV genotypes. See e.g., McCown M. F., et al., 2008, Antimicrob. Agents Chemother., 52:1604-1612.

A current therapy for chronic hepatitis C includes combination treatment with weekly injections of pegylated alpha-IFN (pegIFN) and daily oral ribavirin (RBV) administration. PegIFN/RBV treatment is effective in >75% of patients infected with HCV genotype-2 (HCV-2) and genotype-3 (HCV-3), but most patients in North America, Europe and Japan are infected with HCV genotype-1 (HCV-1) and only about 40-50% of HCV-1 patients respond to therapy with pegIFN/RBV.

There are currently only a few anti-HCV nucleosides in clinical studies. See Table A.

TABLE A
Selected HCV polymerase and protease inhibitors in development
taken from (Brown, N. A., Expert Opin. Investig. Drugs 18: 709-725
(2009)).
Development
CompoundSponsorphaseComment
Nucleoside
HCV NS5B
Polymerase
Inhibitors (NIs)
NM283Idenix-NovartisIIbDevelopment
(valopicitabine)discontinued 2007
R1626RocheIIaProdrug of R1479;
development
discontinued 2008
R7128Pharmasset-RocheIIaProdrug of PSI-6130
IDX184IdenixIbPhase Ia data in
healthy volunteers
MK-0608MerckLate
preclinical
PSI-7851PharmassetIaPreclinical data
≧3 othersVarious sponsorsPreclinicalNo data available

Some acyclic nucleoside phosphonates (ANPs) are antiviral agents with activity against double stranded DNA (dsDNA) viruses, or viruses which rely on reverse transcription such as HBV and HIV-1. See e.g., Hostetler K. Y., 2009, Antiviral Res., 82:A84-98; Money, J. D. 2009, Antimicrob. Agents Chemother., 53:2865-2870; Hostetler, K. Y., et al., 2006, Antimicrob. Agents Chemother., 50:2857-2859. We previously reported that octadecyloxyethyl 9-(S)-[3-hydroxy-2-(phosphonomethoxy)propyl]adenine (ODE-(S)-HPMPA, 1) exhibited antiviral activity against genotype 1b and 2a HCV replicons. See e.g., Wyles, D. L., et al., 2009, Antimicrob. Agents Chemother., 53:2660-2662. Some acyclic nucleoside phosphonates of this class (i.e., HPMP series) are broad spectrum anti-DNA virus agents. See e.g., De Clercq, E., 2007, Biochem. Pharmacol. 73:911-922. Some compounds of this class have been reported to be inactive against RNA viruses, including HCV. See e.g., Holy, A., 2006, Antiviral Res. 71:248-253. ODE-(S)-HPMPA has shown cytotoxicity. See e.g., Wyles et al., 2009, Id.; Beadle, J. R., et al., 2006, 1 Med. Chem., 49:2010-2015.

Koh et al. prepared 2′-C-methyl phosphonate analogs of adenosine (Koh, Y., et al., 2005, J. Med. Chem. 48:2867). Others have reported phosphonates with weak anti-HCV activity. See e.g., Mackman, “Synthesis and antiviral activity of 4′-modified carbocyclic nucleoside phosphonates (CNPs),” Collection Symposium Series 10:191 (2008); Sheng, X. C. et al., 2009, Bioorg. Med. Chem. Lett. 19:3453-3457.

There is a need for improved anti-HCV therapeutic agents, i.e. drugs having improved antiviral and pharmacokinetic properties with enhanced activity against development of HCV resistance, improved oral bioavailability, greater efficacy and fewer undesirable side effects. The present invention provides solutions for these and other needs in the art. For example, we have found, inter alia, that derivatives of ODE-(S)-HPMPA modified by alkylation of the acyclic side chain hydroxyl are surprisingly potent inhibitors of HCV replication in vitro and importantly are much less toxic than ODE-(S)-HPMPA both in vitro and in vivo in mice.

BRIEF SUMMARY OF THE INVENTION

There are provided, inter alia, phosphonate ester compounds having biological activity, e.g., antiviral activity. There are also provided, inter alia, compounds having inhibitory activity for viruses, e.g., inhibition of hepatitis C virus replication. In some embodiments, the compounds are substantially less toxic than previously known antiviral phosphonates, e.g., anti-HCV phosphonates, while retaining excellent antiviral inhibitory activity, e.g., inhibition of HCV. There are also provided, inter alia, improved anti-HCV therapeutic agents.

In a first aspect, there is provided a compound having the structure of Formula (I), or pharmaceutically accepted salt or solvate thereof:

embedded image

With reference to Formula (I), BN is a substituted or unsubstituted nucleobase. L1 is a bond or —O—. R1 is halogen, —CF3, substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted aryl. In some embodiments, if L1 is a bond, then R1 is halogen. In certain embodiments, if L1 is —O—, then R1 is —CF3, substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted aryl. R2 is a permeability enhancing moiety, a phosphate, or a diphosphate.

In another aspect, there is provided a pharmaceutical composition which includes a compound of Formula (I) and a pharmaceutically acceptable excipient.

In another aspect, there is provided a method of inhibiting a viral RNA-dependent RNA polymerase. The method includes contacting a cell which includes a viral RNA-dependent RNA polymerase with an effective amount of a compound of Formula (I) thereby inhibiting the viral RNA-dependent RNA polymerase.

In another aspect, there is provided a method of inhibiting a viral RNA-dependent RNA polymerase. The method includes contacting a viral RNA-dependent RNA polymerase with an effective amount of a compound of Formula (I) thereby inhibiting the viral RNA-dependent RNA polymerase.

In another aspect, there is provided a method of inhibiting a viral reverse transcriptase. The method includes contacting a cell comprising a viral reverse transcriptase with an effective amount of a compound of Formula (I) thereby inhibiting the viral RNA-dependent RNA polymerase.

In another aspect, there is provided a method of inhibiting a viral reverse transcriptase. The method includes contacting a viral reverse transcriptase with an effective amount of a compound of Formula (I) thereby inhibiting the viral RNA-dependent RNA polymerase.

In another aspect, there is provided a method of inhibiting replication of an RNA virus (e.g. a hepatitis C virus or a human retrovirus). The method includes contacting a compound of Formula (I) with a cell infected with an RNA virus thereby inhibiting replication of the RNA virus.

In another aspect, there is provided a method of treating a subject infected with an RNA virus (e.g. a hepatitis C virus or a human retrovirus). The method includes administering to a subject in need thereof an effective amount of a compound of Formula (I) thereby treating the subject.

BRIEF DESCRIPTION OF THE DRAWINGS

Not applicable.

DETAILED DESCRIPTION OF THE INVENTION

I. Definitions

The abbreviations used herein have their conventional meaning within the chemical and biological arts.

Where moieties are specified by their conventional chemical formulae, written from left to right, they equally encompass the chemically identical moieties that would result from writing the structure from right to left, e.g., —CH2O— is equivalent to —OCH2—.

The term “alkyl,” by itself or as part of another substituent, means, unless otherwise stated, a straight (i.e. unbranched) or branched chain, or cyclic hydrocarbon radical, or combination thereof, which may be fully saturated, mono- or polyunsaturated and can include di- and multivalent radicals, having the number of carbon atoms designated (i.e. C1-C10 means one to ten carbons). Examples of saturated hydrocarbon radicals include, but are not limited to, groups such as methyl, ethyl, n-propyl, isopropyl, n-butyl, t-butyl, isobutyl, sec-butyl, cyclohexyl, (cyclohexyl)methyl, cyclopropylmethyl, homologs and isomers of, for example, n-pentyl, n-hexyl, n-heptyl, n-octyl, and the like. An unsaturated alkyl group is one having one or more double bonds or triple bonds. Examples of unsaturated alkyl groups include, but are not limited to, vinyl, 2-propenyl, crotyl, 2-isopentenyl, 2-(butadienyl), 2,4-pentadienyl, 3-(1,4-pentadienyl), ethynyl, 1- and 3-propynyl, 3-butynyl, and the higher homologs and isomers.

The term “alkylene” by itself or as part of another substituent means a divalent radical derived from an alkyl, as exemplified, but not limited, by —CH2CH2CH2CH2—. Typically, an alkyl (or alkylene) group will have from 1 to 24 carbon atoms, including those groups having 10 or fewer carbon atoms. A “lower alkyl” or “lower alkylene” is a shorter chain alkyl or alkylene group, generally having eight or fewer carbon atoms.

The terms “alkoxy,” “alkylamino,” and “alkylthio” (or thioalkoxy) are used in their conventional sense, and refer to those alkyl groups attached to the remainder of the molecule via an oxygen atom, an amino group, or a sulfur atom, respectively.

The term “heteroalkyl,” by itself or in combination with another term, means, unless otherwise stated, a stable straight or branched chain, or cyclic hydrocarbon radical, or combinations thereof, consisting of the stated number of carbon atoms and a heteroatom selected from the group consisting of O, N, P, Si and S, and wherein the nitrogen and sulfur atoms may optionally be oxidized and the nitrogen heteroatom may optionally be quaternized. The heteroatom(s) 0, N, P and S and Si may be placed at any interior position of the heteroalkyl group or at the position at which the alkyl group is attached to the remainder of the molecule. Examples include, but are not limited to, —CH2—CH2—O—CH3, —CH2—CH2—NH—CH3, —CH2—CH2—N(CH3)—CH3, —CH2—S—CH2—CH3, —CH2—CH2, —S(O)—CH3, —CH2—CH2—S(O)2—CH3, —CH═CH—O—CH3, —Si(CH3)3, —CH2—CH═N—OCH3, —CH═CH—N(CH3)—CH3, O—CH3, —O—CH2—CH3, and —CN. Up to two heteroatoms may be consecutive, such as, for example, —CH2—NH—OCH3 and —CH2—O—Si(CH3)3. Similarly, the term “heteroalkylene” by itself or as part of another substituent means a divalent radical derived from heteroalkyl, as exemplified, but not limited by, —CH2—CH2—S—CH2—CH2— and —CH2—S—CH2—CH2—NH—CH2—. For heteroalkylene groups, heteroatoms can also occupy either or both of the chain termini (e.g., alkyleneoxy, alkylenedioxy, alkyleneamino, alkylenediamino, and the like). Still further, for alkylene and heteroalkylene linking groups, no orientation of the linking group is implied by the direction in which the formula of the linking group is written. For example, the formula —C(O)2R′— represents both —C(O)2R′— and —R′C(O)2—. As described above, heteroalkyl groups, as used herein, include those groups that are attached to the remainder of the molecule through a heteroatom, such as —C(O)R′, —C(O)NR′, —NR′R″, —OR′, —SR′, and/or —SO2R′. Where “heteroalkyl” is recited, followed by recitations of specific heteroalkyl groups, such as —NR′R″ or the like, it will be understood that the terms heteroalkyl and —NR′R″ are not redundant or mutually exclusive. Rather, the specific heteroalkyl groups are recited to add clarity. Thus, the term “heteroalkyl” should not be interpreted herein as excluding specific heteroalkyl groups, such as —NR′R″ or the like.

The terms “cycloalkyl” and “heterocycloalkyl”, by themselves or in combination with other terms, represent, unless otherwise stated, cyclic versions of “alkyl” and “heteroalkyl”, respectively. Additionally, for heterocycloalkyl, a heteroatom can occupy the position at which the heterocycle is attached to the remainder of the molecule. Examples of cycloalkyl include, but are not limited to, cyclopentyl, cyclohexyl, 1-cyclohexenyl, 3-cyclohexenyl, cycloheptyl, and the like. Examples of heterocycloalkyl include, but are not limited to, 1-(1,2,5,6-tetrahydropyridyl), 1-piperidinyl, 2-piperidinyl, 3-piperidinyl, 4-morpholinyl, 3-morpholinyl, tetrahydrofuran-2-yl, tetrahydrofuran-3-yl, tetrahydrothien-2-yl, tetrahydrothien-3-yl, 1-piperazinyl, 2-piperazinyl, and the like.

The terms “halo” or “halogen,” by themselves or as part of another substituent, mean, unless otherwise stated, a fluorine, chlorine, bromine, or iodine atom. Additionally, terms such as “haloalkyl,” are meant to include monohaloalkyl and polyhaloalkyl. For example, the term “halo(C1-C4)alkyl” is meant to include, but not be limited to, trifluoromethyl, 2,2,2-trifluoroethyl, 4-chlorobutyl, 3-bromopropyl, and the like.

The term “aryl” means, unless otherwise stated, a polyunsaturated, aromatic, hydrocarbon substituent which can be a single ring or multiple rings (preferably from 1 to 3 rings) which are fused together or linked covalently. The term “heteroaryl” refers to aryl groups (or rings) that contain from one to four heteroatoms selected from N, O, and S, wherein the nitrogen and sulfur atoms are optionally oxidized, and the nitrogen atom(s) are optionally quaternized. A heteroaryl group can be attached to the remainder of the molecule through a carbon or heteroatom. Non-limiting examples of aryl and heteroaryl groups include phenyl, 1-naphthyl, 2-naphthyl, 4-biphenyl, 1-pyrrolyl, 2-pyrrolyl, 3-pyrrolyl, 3-pyrazolyl, 2-imidazolyl, 4-imidazolyl, pyrazinyl, 2-oxazolyl, 4-oxazolyl, 2-phenyl-4-oxazolyl, 5-oxazolyl, 3-isoxazolyl, 4-isoxazolyl, 5-isoxazolyl, 2-thiazolyl, 4-thiazolyl, 5-thiazolyl, 2-furyl, 3-furyl, 2-thienyl, 3-thienyl, 2-pyridyl, 3-pyridyl, 4-pyridyl, 2-pyrimidyl, 4-pyrimidyl, 5-benzothiazolyl, purinyl, 2-benzimidazolyl, 5-indolyl, 1-isoquinolyl, 5-isoquinolyl, 2-quinoxalinyl, 5-quinoxalinyl, 3-quinolyl, and 6-quinolyl. Substituent moieties for each of the above noted aryl and heteroaryl ring systems may be selected from the group of acceptable substituent moieties described below.

For brevity, the term “aryl” when used in combination with other terms (e.g., aryloxy, arylthioxy, arylalkyl) includes both aryl and heteroaryl rings as defined above. Thus, the term “arylalkyl” is meant to include those radicals in which an aryl group is attached to an alkyl group (e.g., benzyl, phenethyl, pyridylmethyl and the like) including those alkyl groups in which a carbon atom (e.g., a methylene group) has been replaced by, for example, an oxygen atom (e.g., phenoxymethyl, 2-pyridyloxymethyl, 3-(1-naphthyloxy)propyl, and the like).

The term “oxo” as used herein means an oxygen that is double bonded to a carbon atom.

Each of the above terms (e.g., “alkyl,” “heteroalkyl,” “aryl” and “heteroaryl”) are meant to include both substituted and unsubstituted forms of the indicated radical. Preferred substituent moieties for each type of radical are provided below.

Substituent moieties for the alkyl and heteroalkyl radicals (including those groups often referred to as alkylene, alkenyl, heteroalkylene, heteroalkenyl, alkynyl, cycloalkyl, heterocycloalkyl, cycloalkenyl, and heterocycloalkenyl) can be one or more of a variety of groups selected from, but not limited to: —OR′, ═O, ═NR′, —NR′R″, —SR′, -halogen, —SiR′R″R′″, —OC(O)R′, —C(O)R′, —CO2R′, —CONR′R″, —OC(O)NR′R″, —NR″C(O)R′, —NR′—C(O)NR″R′″, —NR″C(O)2R′, —NR—C(NR′R″R′″)═NR″″, —NR—C(NR′R″)═NR′″, —S(O)R′, —S(O)2R′, —S(O)2NR′R″, —NRSO2R′, —CN and —NO2 in a number ranging from zero to (2m′+1), where m′ is the total number of carbon atoms in such radical. R′, R″, R′″ and R″″ each preferably independently refer to hydrogen, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl (e.g., aryl substituted with 1-3 halogens), substituted or unsubstituted alkyl, alkoxy or thioalkoxy groups, or arylalkyl groups. When a compound of the invention includes more than one R group, for example, each of the R groups is independently selected as are each R′, R″, R″ and R″″ groups when more than one of these groups is present. When R′ and R″ are attached to the same nitrogen atom, they can be combined with the nitrogen atom to form a 4-, 5-, 6-, or 7-membered ring. For example, —NR′R″ is meant to include, but not be limited to, 1-pyrrolidinyl and 4-morpholinyl. From the above discussion of substituent moieties, one of skill in the art will understand that the term “alkyl” is meant to include groups including carbon atoms bound to groups other than hydrogen groups, such as haloalkyl (e.g., —CF3 and —CH2CF3) and acyl (e.g., —C(O)CH3, —C(O)CF3, —C(O)CH2OCH3, and the like).

Similar to the substituent moieties described for the alkyl radical, substituent moieties for the aryl and heteroaryl groups are varied and may be selected from, for example: halogen, —OR′, —NR′R″, —SR′, -halogen, —SiR′R″R′″, —OC(O)R′, —C(O)R′, —CO2R′, —CONR′R″, —OC(O)NR′R″, —NR″C(O)R′, —NR′—C(O)NR″R′″, —NR″C(O)2R′, —NR—C(NR′R″R′″)═NR″″, —NR—C(NR′R″)═NR′″, —S(O)R′, —S(O)2R′, —S(O)2NR′R″, —NRSO2R′, —CN and —NO2, —R′, —N3, —CH(Ph)2, fluoro(C1-C4)alkoxy, and fluoro(C1-C4)alkyl, in a number ranging from zero to the total number of open valences on the aromatic ring system; and where R′, R″, R′″ and R″″ are preferably independently selected from hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl and substituted or unsubstituted heteroaryl. When a compound of the invention includes more than one R group, for example, each of the R groups is independently selected as are each R′, R″, R″ and R″″ groups when more than one of these groups is present.

Two of the substituent moieties on adjacent atoms of the aryl or heteroaryl ring may optionally form a ring of the formula -Q′-C(O)—(CRR′)q-Q″-, wherein Q′ and Q″ are independently —NR—, —O—, —CRR′— or a single bond, and q is an integer of from 0 to 3. Alternatively, two of the substituent moieties on adjacent atoms of the aryl or heteroaryl ring may optionally be replaced with a substituent of the formula -A-(CH2)r—B—, wherein A and B are independently —CRR′—, —O—, —S—, —S(O)—, —S(O)2—, —S(O)2NR′— or a single bond, and r is an integer of from 1 to 4. One of the single bonds of the new ring so formed may optionally be replaced with a double bond. Alternatively, two of the substituent moieties on adjacent atoms of the aryl or heteroaryl ring may optionally be replaced with a substituent of the formula —(CRR′)s—X′—(C″R′″)d—, where s and d are independently integers of from 0 to 3, and X′ is —O—, —S—, —S(O)—, —S(O)2—, or —S(O)2NR′—. The substituent moieties R, R′, R″ and R″ are preferably independently selected from hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl.

As used herein, the term “heteroatom” or “ring heteroatom” is meant to include oxygen (O), nitrogen (N), sulfur (S), phosphorus (P), and silicon (Si).

The term “pharmaceutically acceptable salts” is meant to include salts of the active compounds which are prepared with relatively nontoxic acids or bases, depending on the particular substituent moieties found on the compounds described herein. When compounds of the present invention contain relatively acidic functionalities, base addition salts can be obtained by contacting the neutral form of such compounds with a sufficient amount of the desired base, either neat or in a suitable inert solvent. Examples of pharmaceutically acceptable base addition salts include sodium, potassium, calcium, ammonium, organic amino, or magnesium salt, or a similar salt. When compounds of the present invention contain relatively basic functionalities, acid addition salts can be obtained by contacting the neutral form of such compounds with a sufficient amount of the desired acid, either neat or in a suitable inert solvent. Examples of pharmaceutically acceptable acid addition salts include those derived from inorganic acids like hydrochloric, hydrobromic, nitric, carbonic, monohydrogencarbonic, phosphoric, monohydrogenphosphoric, dihydrogenphosphoric, sulfuric, monohydrogensulfuric, hydriodic, or phosphorous acids and the like, as well as the salts derived from relatively nontoxic organic acids like acetic, propionic, isobutyric, maleic, malonic, benzoic, succinic, suberic, fumaric, lactic, mandelic, phthalic, benzenesulfonic, p-tolylsulfonic, citric, tartaric, methanesulfonic, and the like. Also included are salts of amino acids such as arginate and the like, and salts of organic acids like glucuronic or galactunoric acids and the like (see, for example, Berge et al., “Pharmaceutical Salts”, Journal of Pharmaceutical Science, 1977, 66, 1-19). Certain specific compounds of the present invention contain both basic and acidic functionalities that allow the compounds to be converted into either base or acid addition salts.

The neutral forms of the compounds are preferably regenerated by contacting the salt with a base or acid and isolating the parent compound in the conventional manner. The parent form of the compound differs from the various salt forms in certain physical properties, such as solubility in polar solvents.

In addition to salt forms, the present invention provides compounds, which are in a prodrug form. Prodrugs of the compounds described herein are those compounds that readily undergo chemical changes under physiological conditions to provide the compounds of the present invention. Additionally, prodrugs can be converted to the compounds of the present invention by chemical or biochemical methods in an ex vivo environment. For example, prodrugs can be slowly converted to the compounds of the present invention when placed in a transdermal patch reservoir with a suitable enzyme or chemical reagent.

Certain compounds of the present invention can exist in unsolvated forms as well as solvated forms, including hydrated forms. In general, the solvated forms are equivalent to unsolvated forms and are encompassed within the scope of the present invention. Certain compounds of the present invention may exist in multiple crystalline or amorphous forms. In general, all physical forms are equivalent for the uses contemplated by the present invention and are intended to be within the scope of the present invention.

Certain compounds of the present invention possess asymmetric carbon atoms (optical centers) or double bonds; the racemates, diastereomers, tautomers, geometric isomers and individual isomers are encompassed within the scope of the present invention. The compounds of the present invention do not include those which are known in the art to be too unstable to synthesize and/or isolate.

The compounds of the present invention may also contain unnatural proportions of atomic isotopes at one or more of the atoms that constitute such compounds. For example, the compounds may be radiolabeled with radioactive isotopes, such as for example tritium (3H), iodine-125 (125I) or carbon-14 (14C). All isotopic variations of the compounds of the present invention, whether radioactive or not, are encompassed within the scope of the present invention.

In some embodiments, each substituted aryl and/or heterocycloalkyl is substituted with a substituent group, a size limited substituent group, or a lower substituent group. A “substituent group,” as used herein, means a group selected from the following moieties:

  • (A) —OH, —NH2, —SH, —CN, —CF3, oxo, halogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, unsubstituted heteroaryl, and
  • (B) alkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl, substituted with at least one substituent selected from:
    • (i) oxy, —OH, —SH, —CN, —CF3, halogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, unsubstituted heteroaryl, and
    • (ii) alkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl, substituted with at least one substituent selected from:
      • (a) oxy, —OH, —NH2, —SH, —CN, —CF3, halogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, unsubstituted heteroaryl, and
      • (b) alkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, or heteroaryl, substituted with at least one substituent selected from oxy, —OH, —NH2, —SH, —CN, —CF3, halogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, and unsubstituted heteroaryl.

A “size-limited substituent” or “size-limited substituent group,” as used herein means a group selected from all of the substituents described above for a “substituent group,” wherein each substituted or unsubstituted alkyl is a substituted or unsubstituted C1-C20 alkyl, each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 20 membered heteroalkyl, each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C4-C8 cycloalkyl, and each substituted or unsubstituted heterocycloalkyl is a substituted or unsubstituted 4 to 8 membered heterocycloalkyl.

A “lower substituent” or “lower substituent group,” as used herein means a group selected from all of the substituents described above for a “substituent group,” wherein each substituted or unsubstituted alkyl is a substituted or unsubstituted C1-C8 alkyl, each substituted or unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 8 membered heteroalkyl, each substituted or unsubstituted cycloalkyl is a substituted or unsubstituted C5-C7 cycloalkyl, and each substituted or unsubstituted heterocycloalkyl is a substituted or unsubstituted 5 to 7 membered heterocycloalkyl.

The term “treating” refers to any indicia of success in the treatment or amelioration of an injury, pathology or condition, including any objective or subjective parameter such as abatement; remission; diminishing of symptoms or making the injury, pathology or condition more tolerable to the patient; slowing in the rate of degeneration or decline; making the final point of degeneration less debilitating; improving a patient's physical or mental well-being, and the like. The treatment or amelioration of symptoms can be based on objective or subjective parameters; including the results of a physical examination, laboratory tests, and the like. For example, the methods described herein may be used to treat the symptoms of a viral infection.

As used herein, “nucleic acid” means single stranded DNA, RNA and derivative thereof. Modifications include, but are not limited to, those which provide other chemical groups that incorporate additional charge, polarizability, hydrogen bonding, electrostatic interaction, and functionality to the nucleic acid ligand bases or to the nucleic acid ligand as a whole. Such modifications include, but are not limited to, phosphodiester group modifications (e.g., phosphorothioates, methylphosphonates), 2′-position sugar modifications, 5-position pyrimidine modifications, 8-position purine modifications, modifications at exocyclic amines, substitution of 4-thiouridine, substitution of 5-bromo or 5-iodo-uracil; backbone modifications, methylations, unusual base-pairing combinations such as the isobases isocytidine and isoguanidine and the like. Modifications can also include 3′ and 5′ modifications such as capping moieties. A 2′-deoxy nucleic acid linker is a divalent nucleic acid compound of any appropriate length and/or internucleotide linkage wherein the nucleotides are 2′-deoxy nucleotides.

Solid and dashed wedge bonds indicate stereochemistry as customary in the art. A “squiggle” bond (i.e., “custom-character”) indicates either R- or S-stereochemistry.

II. Compositions

In a first aspect, there is provided a compound having the structure of Formula (I), or pharmaceutically accepted salt or solvate thereof:

embedded image

With reference to Formula (I), BN is a substituted or unsubstituted nucleobase. L1 is a bond or —O—. R1 is halogen, —CF3, substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted aryl. In some embodiments, if L1 is a bond, then R1 is halogen. In some embodiments, if L1 is —O—, then R1 is —CF3, substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted aryl. R2 is a permeability enhancing moiety, a phosphate, or a diphosphate.

As used herein, the term “nucleobase” refers to a moiety as generally known in the nucleic acid arts which can function as the base portion of a nucleic acid. A nucleobase is a portion of a nucleic acid involved in hybridization (base pairing), and includes, but is not limited to nitrogenous bases such as adenine, guanine, thymine, uracil, cytosine, 2,6-diaminopurine, and the like. The term “hybridization” is used herein in its conventional sense and refers generally to the pairing of complementary strands of nucleic acids, including triple-stranded nucleic acid hybridization.

In some embodiments, BN is substituted or unsubstituted thymine, substituted or unsubstituted guanine, substituted or unsubstituted cytosine, substituted or unsubstituted uracil, substituted or unsubstituted 2,6 diaminopurine, substituted or unsubstituted, substituted or unsubstituted methoxypurine, or substituted or unsubstituted 6-O-methylguanine. A person of ordinary skill in the art will immediately understand that, when referring to a nucleobase (BN), such as guanine, that the nucleobase is attached to the remainder of the molecule of Formula I (or embodiments thereof) and, therefore, exists as a monovalent moiety. In some embodiments, BN is unsubstituted adenine, unsubstituted thymine, unsubstituted guanine, unsubstituted cytosine, or unsubstituted uracil.

In some embodiments, BN is substituted adenine, substituted thymine, substituted guanine, substituted cytosine, or substituted uracil. In some embodiments, BN is 2,6-diaminopurine. In some embodiments, BN is 6-methoxypurine. In some embodiments, BN is 6-O-methylguanine.

In some embodiments, the compound of Formula (I) has the structure of Formula (Ia) following (wherein L1 is —O— according to Formula (I)). In some embodiments of Formula (Ia), R1 is —CF3, substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted aryl.

embedded image

In some embodiments of Formulae (I) or (Ia), R1 is unsubstituted alkyl. In some embodiments, R1 is R4-substituted alkyl. R4 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, R5-substituted or unsubstituted alkyl, R5-substituted or unsubstituted heteroalkyl, R5-substituted or unsubstituted cycloalkyl, R5-substituted or unsubstituted heterocycloalkyl, R5-substituted or unsubstituted aryl, or R5-substituted or unsubstituted heteroaryl. In some embodiments R4 is unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. In some embodiments R4 is R5-substituted alkyl, R5-substituted heteroalkyl, R5-substituted cycloalkyl, R5-substituted heterocycloalkyl, R5-substituted aryl, or R5-substituted heteroaryl. R5 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, R6-substituted or unsubstituted alkyl, R6-substituted or unsubstituted heteroalkyl, R6-substituted or unsubstituted cycloalkyl, R6-substituted or unsubstituted heterocycloalkyl, R6-substituted or unsubstituted aryl, or R6-substituted or unsubstituted heteroaryl. In some embodiments, R5 is unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. In some embodiments, R5 is R6-substituted alkyl, R6-substituted heteroalkyl, R6-substituted cycloalkyl, R6-substituted heterocycloalkyl, R6-substituted aryl, or R6-substituted heteroaryl. R6 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl.

In some embodiments, R1 is unsubstituted cycloalkyl. In some embodiments, R1 is R7-substituted cycloalkyl. R7 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, R8-substituted or unsubstituted alkyl, R8-substituted or unsubstituted heteroalkyl, R8-substituted or unsubstituted cycloalkyl, R8-substituted or unsubstituted heterocycloalkyl, R8-substituted or unsubstituted aryl, or R8-substituted or unsubstituted heteroaryl. In some embodiments R7 is unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. In some embodiments R7 is R8-substituted alkyl, R8-substituted heteroalkyl, R8-substituted cycloalkyl, R8-substituted heterocycloalkyl, R8-substituted aryl, or R8-substituted heteroaryl. R8 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, R9-substituted or unsubstituted alkyl, R9-substituted or unsubstituted heteroalkyl, R9-substituted or unsubstituted cycloalkyl, R9-substituted or unsubstituted heterocycloalkyl, R9-substituted or unsubstituted aryl, or R9-substituted or unsubstituted heteroaryl. In some embodiments, R8 is unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. In some embodiments, R8 is R9-substituted alkyl, R9-substituted heteroalkyl, R9-substituted cycloalkyl, R9-substituted heterocycloalkyl, R9-substituted aryl, or R9-substituted heteroaryl. R9 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl.

In some embodiments, R1 is unsubstituted aryl. In some embodiments, R1 is R10-substituted aryl. R10 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, R11-substituted or unsubstituted alkyl, R11-substituted or unsubstituted heteroalkyl, R11-substituted or unsubstituted cycloalkyl, R11-substituted or unsubstituted heterocycloalkyl, R11-substituted or unsubstituted aryl, or R11-substituted or unsubstituted heteroaryl. In some embodiments R10 is unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. In some embodiments R10 is R11-substituted alkyl, R11-substituted heteroalkyl, R11-substituted cycloalkyl, R11-substituted heterocycloalkyl, R11-substituted aryl, or R11-substituted heteroaryl. R11 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, R12-substituted or unsubstituted alkyl, R12-substituted or unsubstituted heteroalkyl, R12-substituted or unsubstituted cycloalkyl, R12-substituted or unsubstituted heterocycloalkyl, R12-substituted or unsubstituted aryl, or R12-substituted or unsubstituted heteroaryl. In some embodiments, R11 is unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. In some embodiments, R11 is R12-substituted alkyl, R12-substituted heteroalkyl, R12-substituted cycloalkyl, R12-substituted heterocycloalkyl, R12-substituted aryl, or R12-substituted heteroaryl. R12 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl.

Further to the compound of Formulae (I) or (Ia), in some embodiments, R1 is substituted (e.g., R4-substituted) or unsubstituted C1-C24 (e.g., C1-C10 or C1-C3) alkyl. In some embodiments, R1 is C1-C24 unsubstituted alkyl. In some embodiments, R1 is C1-C16 unsubstituted alkyl. In some embodiments, R1 is C1-C12 unsubstituted alkyl. In some embodiments, R1 is C1-C10 unsubstituted alkyl. In some embodiments, R1 is C1-C3 unsubstituted alkyl. In some embodiments, R1 is methyl, ethyl or isopropyl. In some embodiments, R1 is methyl. In some embodiments, R1 is ethyl. In some embodiments, R1 is isopropyl.

Further to the compound of Formulae (I) or (Ia), in some embodiments, R1 is substituted (e.g., R7-substituted) or unsubstituted C3-C8 cycloalkyl. In some embodiments, R1 is C3-C8 unsubstituted cycloalkyl.

Further to the compound of Formulae (I) or (Ia), in some embodiments, R1 is unsubstituted aryl. In some embodiments, R1 is substituted (e.g., R10-substituted) or unsubstituted phenyl.

Further to the compound of Formulae (I) or (Ia), in some embodiments, R1 is substituted alkyl. In some embodiments, R1 is substituted C1-C10 alkyl. In some embodiments, R1 is haloalkyl. In some embodiments, R1 is monohaloalkyl. In some embodiments, R1 is dihaloalkyl. In some embodiments, R1 is trihaloalkyl. In some embodiments, R1 is —CF3.

In some embodiments of the compound of Formulae (I) or (Ia) wherein R1 is substituted alkyl, substituted C1-C10 alkyl, substituted cycloalkyl, or substituted aryl, R1 is alkyl substituted with substituted or unsubstituted aryl. In some embodiments, R1 is benzyl.

In some embodiments of the compound of Formulae (I) or (Ia) wherein R1 is substituted alkyl, substituted cycloalkyl, or substituted aryl, R1 is substituted cycloalkyl. In some embodiments, R1 is substituted C3-C8 cycloalkyl.

In some embodiments of the compound of Formulae (I) or (Ia) wherein R1 is substituted alkyl, substituted cycloalkyl, or substituted aryl, R1 is substituted aryl. In some embodiments, R1 is substituted phenyl.

In some embodiments, the compound of Formula (I) has the structure of Formula (Ib) (i.e., where L1 is a bond). In some embodiments, R1 is halogen:

embedded image

In some embodiments of the compound of Formulae (I) or (Ib), R1 is fluoro. In Formula (Ib), BN and R2 are as defined above in Formulae (I) and (IA).

Further to the compound with the structure of any of Formulae (I), (Ia) or (Ib), in some embodiments, R2 has the structure of Formula (II) following,


-L2-O—R3 (II)

wherein L2 is a substituted or unsubstituted alkylene, substituted or unsubstituted cycloalkylene, or substituted or unsubstituted arylene. R3 is substituted or unsubstituted alkyl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted aryl.

In some embodiments, R3 is unsubstituted alkyl. In some embodiments, R3 is substituted (e.g., R13-substituted) or unsubstituted C1-C24 (e.g., C16-C24 or C8-C16) alkyl. In some embodiments, R3 is unsubstituted C1-C24 alkyl. In some embodiments, R3 is unsubstituted C8-C24 alkyl. In some embodiments, R3 is unsubstituted C16-C24 alkyl. In some embodiments, R3 is unsubstituted C8-C16 alkyl. In some embodiments, R3 is unsubstituted C8-C18 alkyl. In some embodiments, R3 is substituted (e.g., R13-substituted) or unsubstituted C1, C2, C3, C4, C5, C6, C7, C8, C9, C10, C11, C12, C13, C14, C15, C16, C17, C18, C19, C20, C21, C22, C23, or C24 alkyl.

In some embodiments, R3 is R13-substituted alkyl. R13 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, R14-substituted or unsubstituted alkyl, R14-substituted or unsubstituted heteroalkyl, R14-substituted or unsubstituted cycloalkyl, R14-substituted or unsubstituted heterocycloalkyl, R14-substituted or unsubstituted aryl, or R14-substituted or unsubstituted heteroaryl. In some embodiments, R13 is unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. In some embodiments, R13 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, R14-substituted alkyl, R14-substituted heteroalkyl, R14-substituted cycloalkyl, R14-substituted heterocycloalkyl, R14-substituted aryl, or R14 substituted heteroaryl. R14 is R15-substituted or unsubstituted alkyl, R15-substituted or unsubstituted heteroalkyl, R15-substituted or unsubstituted cycloalkyl, R15-substituted or unsubstituted heterocycloalkyl, R15-substituted or unsubstituted aryl, or R15-substituted or unsubstituted heteroaryl. In some embodiments, R14 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. In some embodiments, R14 is R15-substituted alkyl, R15-substituted heteroalkyl, R15-substituted cycloalkyl, R15-substituted heterocycloalkyl, R15-substituted aryl, or R15-substituted heteroaryl. R15 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl.

In some embodiments, R3 is R16-substituted cycloalkyl. R16 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, R17-substituted or unsubstituted alkyl, R17-substituted or unsubstituted heteroalkyl, R17-substituted or unsubstituted cycloalkyl, R17-substituted or unsubstituted heterocycloalkyl, R17-substituted or unsubstituted aryl, or R17-substituted or unsubstituted heteroaryl. In some embodiments, R16 is unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. In some embodiments, R16 is R17-substituted alkyl, R17-substituted heteroalkyl, R17-substituted cycloalkyl, R17-substituted heterocycloalkyl, R17-substituted aryl, or R17-substituted heteroaryl. R17 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, R18-substituted or unsubstituted alkyl, R18-substituted or unsubstituted heteroalkyl, R18-substituted or unsubstituted cycloalkyl, R18-substituted or unsubstituted heterocycloalkyl, R18-substituted or unsubstituted aryl, or R18-substituted or unsubstituted heteroaryl. In some embodiments, R17 is unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. In some embodiments, R17 is R18-substituted alkyl, R18-substituted heteroalkyl, R18-substituted cycloalkyl, R18-substituted heterocycloalkyl, R18-substituted aryl, or R18-substituted heteroaryl. R18 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl.

In some embodiments, R3 is R19-substituted aryl. R19 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, R20-substituted or unsubstituted alkyl, R20-substituted or unsubstituted heteroalkyl, R20-substituted or unsubstituted cycloalkyl, R20-substituted or unsubstituted heterocycloalkyl, R20-substituted or unsubstituted aryl, or R20-substituted or unsubstituted heteroaryl. In some embodiments, R19 is unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. In some embodiments, R19 is R20-substituted alkyl, R20-substituted heteroalkyl, R20-substituted cycloalkyl, R20-substituted heterocycloalkyl, R20-substituted aryl, or R20-substituted heteroaryl. R20 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, R21-substituted or unsubstituted alkyl, R21-substituted or unsubstituted heteroalkyl, R21-substituted or unsubstituted cycloalkyl, R21-substituted or unsubstituted heterocycloalkyl, R21-substituted or unsubstituted aryl, or R21-substituted or unsubstituted heteroaryl. In some embodiments, R20 is unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. In some embodiments, R20 is R21-substituted alkyl, R21-substituted heteroalkyl, R21-substituted cycloalkyl, R21-substituted heterocycloalkyl, R21-substituted aryl, or R21-substituted heteroaryl. R21 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl.

In some embodiments, L2 is substituted (e.g., R22-substituted) or unsubstituted C1-C8 alkylene. In some embodiments, L2 is substituted (e.g., R22-substituted) unsubstituted C1, C2, C3, C4, C5, C6, C7, or C8 alkylene.

In some embodiments, L2 is R22-substituted alkylene. R22 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, R23-substituted or unsubstituted alkyl, R23-substituted or unsubstituted heteroalkyl, R23-substituted or unsubstituted cycloalkyl, R23-substituted or unsubstituted heterocycloalkyl, 23-substituted or unsubstituted aryl, or 23-substituted or unsubstituted heteroaryl. In some embodiments, R22 is unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. In some embodiments, R22 is R23-substituted alkyl, R23-substituted heteroalkyl, R23-substituted cycloalkyl, R23-substituted heterocycloalkyl, R23-substituted aryl, or R23-substituted heteroaryl. R23 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, R24-substituted or unsubstituted alkyl, R24-substituted or unsubstituted heteroalkyl, R24-substituted or unsubstituted cycloalkyl, R24-substituted or unsubstituted heterocycloalkyl, R24-substituted or unsubstituted aryl, or R24-substituted or unsubstituted heteroaryl. In some embodiments, R23 is unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. In some embodiments, R23 is R24-substituted alkyl, R24-substituted heteroalkyl, R24-substituted cycloalkyl, R24-substituted heterocycloalkyl, R24-substituted aryl, or R24-substituted heteroaryl. R24 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl.

In some embodiments, L2 is R25-substituted cycloalkylene. R25 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, R26-substituted or unsubstituted alkyl, R26-substituted or unsubstituted heteroalkyl, R26-substituted or unsubstituted cycloalkyl, R26-substituted or unsubstituted heterocycloalkyl, R26-substituted or unsubstituted aryl, or R26-substituted or unsubstituted heteroaryl. In some embodiments, R25 is unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. In some embodiments, R25 is R26-substituted alkyl, R26-substituted heteroalkyl, R26-substituted cycloalkyl, R26-substituted heterocycloalkyl, R26-substituted aryl, or R26-substituted heteroaryl. R26 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, R27-substituted or unsubstituted alkyl, R27-substituted or unsubstituted heteroalkyl, R27-substituted or unsubstituted cycloalkyl, R27-substituted or unsubstituted heterocycloalkyl, R27-substituted or unsubstituted aryl, or R27-substituted or unsubstituted heteroaryl. In some embodiments, R26 is unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. In some embodiments, R26 is R27-substituted alkyl, R27-substituted heteroalkyl, R27-substituted cycloalkyl, R27-substituted heterocycloalkyl, R27-substituted aryl, or R27-substituted heteroaryl. R27 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl.

In some embodiments, L2 is R28-substituted arylene. R28 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, R29-substituted or unsubstituted alkyl, R29-substituted or unsubstituted heteroalkyl, R29-substituted or unsubstituted cycloalkyl, R29-substituted or unsubstituted heterocycloalkyl, R29-substituted or unsubstituted aryl, or R29-substituted or unsubstituted heteroaryl. In some embodiments, R28 is unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. In some embodiments, R28 is R29-substituted alkyl, R29-substituted heteroalkyl, R29-substituted cycloalkyl, R29-substituted heterocycloalkyl, R29-substituted aryl, or R29-substituted heteroaryl. R29 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, R30-substituted or unsubstituted alkyl, R30-substituted or unsubstituted heteroalkyl, R30-substituted or unsubstituted cycloalkyl, R30-substituted or unsubstituted heterocycloalkyl, R30-substituted or unsubstituted aryl, or R30-substituted or unsubstituted heteroaryl. In some embodiments, R29 is unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. In some embodiments, R29 is R30-substituted alkyl, R30-substituted heteroalkyl, R30-substituted cycloalkyl, R30-substituted heterocycloalkyl, R30-substituted aryl, or R30-substituted heteroaryl. R30 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl.

Further to the compound with the structure of any of Formulae (I), (Ia) or (Ib), or the compound wherein R2 has the structure of Formula (II), in some embodiments, R2 is octadecyloxyethyl, hexadecyloxyethyl, hexadecyloxypropyl, 15-methyl-hexadecyloxypropyl, 15-methyl-hexadecyloxyethyl, 13-methyl-tetradecyloxypropyl, 13-methyl-tetradecyloxyethyl, 14-cyclopropyl-tetradecyloxypropyl, 14-cyclopropyl-tetradecyloxyethyl, or 1-O-octadecyl-2-O-benzyl-sn-glyceryl. In some embodiments, L2 is C1, C2, C3, C4, C5, C6, C7, or C8 alkylene.

It is understood that some compounds described herein can exist as stereoisomeric forms including e.g., R-, S- and racemic (RS-) forms. Unless expressly indicated otherwise, all stereoisomer forms are contemplated herein. Accordingly, further to the compound with the structure of any of Formulae (I), (Ia) or (Ib), wherein R2 has the structure of Formula (II), in some embodiments, the compound has the structure of one of Formulae (Ia1S) to (Ia7S) following. R1 and R2 in Formulae (Ia1S) to (Ia7S) are as defined above.

embedded image embedded image

In some embodiments, the compound has the structure of one of Formulae (Ia1R) to (Ia7R) following. R1 and R2 in Formulae (Ia1R) to (Ia7R) are as defined above.

embedded image embedded image

In some embodiments, the compound has the structure of one of Formulae (Ia1RS) to (Ia7RS) following. R1 and R2 in Formulae (Ia1RS) to (Ia7RS) are as defined above.

embedded image embedded image

Further to the compound with the structure of Formulae (Ib), in some embodiments, the compound has the structure of one of Formulae (Ib1S) to (Ib7S) following. R1 and R2 in Formulae (Ib1S) to (Ib7S) are as defined above.

embedded image embedded image

In some embodiments, the compound has the structure of one of Formulae (Ib1R) to (Ib7R) following. R1 and R2 in Formulae (Ib1R) to (Ib7R) are as defined above.

embedded image embedded image

In some embodiments, the compound has the structure of one of Formulae (Ib1RS) to (Ib7RS) following. R1 and R2 in Formulae (Ib1RS) to (Ib7RS) are as defined above.

embedded image embedded image

In some embodiments of the compounds of Formulae I, Ia1S-Ia7S, Ia1R-Ia7R, or Ia1RS-Ia7RS, R1 is —CF3, substituted or unsubstituted C1-C10 alkyl, substituted or unsubstituted C3-C8 cycloalkyl (e.g. cyclopropyl) or substituted or unsubstituted aryl (e.g. benzyl or phenyl). In some embodiments, R1 is —CF3, unsubstituted C1-C10 alkyl, unsubstituted C3-C8 cycloalkyl (e.g. cyclopropyl) or unsubstituted aryl (e.g. benzyl or phenyl).

In some embodiments of the compounds of Formula I, R2 is a permeability enhancing moiety, a phosphate or a diphosphate. In some embodiments, R2 is a permeability enhancing moiety. A “permeability enhancing moiety” as used herein refers to a chemical moiety that forms an ester with the oxygen and phosphorus to which it is attached as shown in Formulae I, Ia1S-Ia7S, Ia1R-Ia7R, Ia1RS-Ia7RS, Ib1S-Ib7S, Ib1R-Ib7R, Ib1RS-Ib7RS, and which increases the cell permeability of the compound relative to compounds in which R2 is hydrogen. In some embodiments, permeability enhancers act to increase drug absorption through either the paracellular or transcellular pathways. See e.g., Ouyang, H., et al., 2002, J. Med. Chem., 45:2857-2866; Lane, M. E. & Corrigan, O. I., 2006, J. Pharm. Pharmacol., 58:271-275.

In some embodiments, R2 is substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. In some embodiments, R2 contains 3-24, 6-24, 9-24, 12-24, 15-24, 18-24, or 21-24 carbon atoms. In some embodiments, R2 is substituted or unsubstituted C3 or greater alkyl, or substituted or unsubstituted C3 or greater heteroalkyl. In some embodiments, R2 is unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. In some embodiments, R2 is unsubstituted C3 or greater alkyl, or unsubstituted C3 or greater heteroalkyl. In some embodiments, R2 is R31-substituted alkyl, R31-substituted heteroalkyl, R31-substituted cycloalkyl, R31-substituted heterocycloalkyl, R31-substituted aryl, or R31-substituted heteroaryl. R31 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, R32-substituted or unsubstituted alkyl, R32-substituted or unsubstituted heteroalkyl, R32-substituted or unsubstituted cycloalkyl, R32-substituted or unsubstituted heterocycloalkyl, R32-substituted or unsubstituted aryl, or R32-substituted or unsubstituted heteroaryl. In some embodiments R31 is unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. In some embodiments, R31 is R32-substituted alkyl, R32-substituted heteroalkyl, R32-substituted cycloalkyl, R32-substituted heterocycloalkyl, R32-substituted aryl, or R32-substituted heteroaryl. R32 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, R33-substituted or unsubstituted alkyl, R33-substituted or unsubstituted heteroalkyl, R33-substituted or unsubstituted cycloalkyl, R33-substituted or unsubstituted heterocycloalkyl, R33-substituted or unsubstituted aryl, or R33-substituted or unsubstituted heteroaryl. In some embodiments, R32 is unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl. In some embodiments, R32 is R33-substituted alkyl, R33-substituted heteroalkyl, R33-substituted cycloalkyl, R33-substituted heterocycloalkyl, R33-substituted aryl, or R33-substituted heteroaryl. R33 is —CN, —NH2, —COOH, —CF3, —OH, —SH, —CONH2, halogen, unsubstituted alkyl, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, or unsubstituted heteroaryl.

Without wishing to be bound by any theory, it is believed that the lipophilicity of a permeability enhancer can play a major role in permeability enhancement. In some embodiments, the permeability enhancing moiety has the structure of Formula (II),


-L2-O—R3. (II)

In some embodiments, L2 is a substituted or unsubstituted alkylene (e.g., substituted or unsubstituted C1-C8 alkylene), substituted or unsubstituted cycloalkylene (substituted or unsubstituted C3-C8 cycloalkylene), or substituted or unsubstituted arylene. In some embodiments, R3 is substituted or unsubstituted alkyl (e.g. substituted or unsubstituted C8-C24 alkyl), substituted or unsubstituted cycloalkyl (e.g. a substituted or unsubstituted C3-C8 cycloalkyl), or substituted or unsubstituted aryl. In some embodiments, -L2-O—R3 includes at least 16 atoms. In some embodiments, -L2-O—R3 has 18 to 24 atoms. In certain embodiments, the atoms are linked together in a linear arrangement. The permeability enhancing moiety may be octadecyloxyethyl, hexadecyloxyethyl, hexadecyloxypropyl, 15-methyl-hexadecyloxypropyl, 15-methyl-hexadecyloxyethyl, 13-methyl-tetradecyloxypropyl, 13-methyl-tetradecyloxyethyl, 14-cyclopropyl-tetradecyloxypropyl, 14-cyclopropyl-tetradecyloxyethyl, or 1-O-octadecyl-2-O-benzyl-sn-glyceryl. Additional exemplary permeability enhancing moieties useful in the compounds and methods described herein are described in U.S. Pat. No. 6,716,825 and U.S. Pat. No. 7,749,983, and US Patent Publication No. US2008-0221061, the contents of which are incorporated herein by reference in their entireties and for all purposes.

In some embodiments, the novel phosphonate compounds provided herein are less toxic, more active and selective than previously known candidates such as ODE-(S)-HPMPA (which includes a hydrogen at the corresponding R1 position) against a variety of viruses, including e.g., hepatitis C virus and HIV-1. The retention of antiviral efficacy against HIV and HCV with marked diminution of cellular toxicity caused by the addition of a methyl group to the side chain of HPMPA is quite unexpected and not obvious. Unmodified MPMPA had an EC50 of 20 μM and a CC50 of 40 μM suggesting no selective antiviral activity. “EC50” refers, in the customary sense, to the concentration required to achieve half-maximal effect of a compound. “CC50” refers, in the customary sense, to the concentration required to achieve half maximal cytotoxicity.

In some embodiments, each substituted group described above in the compounds of Formula I or embodiments thereof is substituted with at least one substituent group. More specifically, in some embodiments, each substituted alkyl, substituted cycloalkyl, substituted aryl, substituted alkylene substituted cycloalkylene, and/or substituted arylene, described above in the compounds of Formula I or embodiments thereof are substituted with at least one substituent group. In other embodiments, at least one or all of these groups are substituted with at least one size-limited substituent group. In some embodiments, no substituent of Formula I is further substituted.

In some embodiments, a compound is selected from Table 1 following.

TABLE 1
embedded image
embedded image
embedded image
embedded image
embedded image
embedded image
embedded image
embedded image
embedded image
embedded image
embedded image

In some embodiments, a compound is selected from Table 2 following.

TABLE 2
embedded image
embedded image
embedded image
embedded image
embedded image
embedded image
embedded image
embedded image
embedded image
embedded image
embedded image

In some embodiments, a compound is selected from Table 3 following.

TABLE 3
embedded image
embedded image
embedded image
embedded image
embedded image
embedded image
embedded image
embedded image
embedded image
embedded image
embedded image

Exemplary Syntheses

Synthesis of the new ANP analogs can be carried out using a synthon approach, e.g., the approach developed for alkoxyalkyl esters of (S)-9-[3-hydroxy-2-(phosphonomethoxy)-propyl]adenine [(S)-HPMPA]. See e.g., Beadle, J. R.; et al., 2006, Id. Exemplary of this approach is Scheme 1 (Example 1), wherein adenine can react with various alkyl glycidyl ethers under basic conditions to give a series of 9-(3-alkoxy-2-hydroxypropyl)adenines, e.g., Cmpds 2-5 (see Examples). After protection of the amino group with monomethoxytrityl, Cmpds 6-9 (see Examples) can be alkylated with octadecyloxyethyl or hexadecyloxypropyl p-toluenesulfonyloxymethyl-phosphonate, then deprotected to provide adenine derivatives Cmpds 15-19 (see Examples). As shown in Schemes 2 and 3 (see Examples), various 3-methoxy-2-phosphonomethoxypropyl (MPMP-) analogs of 2,6-diaminopurine (23-26) and guanine (34-37) can be prepared using similar methods. Additional schemes and experimental details for target Cmpds 40, 43 and 44 are provided in the Examples.

III. Methods of Use

The compounds provided herein are useful, inter alia, in inhibiting viral replication, including hepatitis C viruses. Examples below describe the synthesis of specific compounds of the invention. In particular the compound octadecyloxyethyl (S)-9-[(3-methoxy-2-phosphonomethoxy) propyl]adenine (ODE-(S)-MPMPA) has been tested and found to have potent inhibitory activity in HCV infected cells and in HIV-1 infected MT-2 cells. ODE-(S)-IPPMPA has been synthesized but has low activity against HCV. ODE-(S)-MPMPC has been synthesized and has antiviral activity against HIV-1 infected human peripheral blood mononuclear cells while hexadecyloxypropyl-(S)-MPMPG has submicromolar activity.

In another aspect, diphosphate metabolites of the compound of the invention may inhibit viral RNA-dependent RNA polymerases and thus inhibit the replication of the hepatitis C virus; they also inhibit replication of HIV-1 in vitro possibly due to inhibition of HIV reverse transcriptase.

Compounds described herein may be useful for treating human patients infected with an RNA virus, e.g., rotavirus, coronavirus, picornavirus, calicivirus, flavivirus, togavirus, or hepevirus; a DNA virus, e.g., herpesvirus, adenovirus, asfarvirus, polyomavirus, or poxvirus; or a retrovirus, e.g., alpharetrovirus, betaretrovirus, gammaretrovirus, deltaretrovirus, epsilonretrovus, lentivirus or spumavirus. In particular, compounds described herein may be useful for treating human patients infected with the hepatitis C virus or with a human retrovirus, such as HIV-1.

Compounds described herein may be useful for treating human patients infected with a disease caused by, or associated with, an RNA virus including a retrovirus, or a DNA virus.

In another aspect, the invention also provides processes and novel intermediates disclosed herein which are useful for preparing compounds of the invention. In other aspects, novel methods for synthesis, analysis, separation, isolation, purification, characterization, and testing of the compounds of this invention are provided.

In another aspect, a method of inhibiting a viral RNA-dependent RNA polymerase is provided. The method includes contacting a compound of Formula I or embodiment thereof wherein R2 is a permeability enhancing moiety, or embodiments thereof, with a cell including a viral RNA-dependent RNA polymerase thereby inhibiting said viral RNA-dependent RNA polymerase.

In another aspect, there is provided a method of inhibiting a viral RNA-dependent RNA polymerase. The method includes contacting a viral RNA-dependent RNA polymerase with an effective amount of a compound of Formula (I) thereby inhibiting the viral RNA-dependent RNA polymerase.

In another aspect, there is provided a method of inhibiting a viral reverse transcriptase. The method includes contacting a viral reverse transcriptase with an effective amount of a compound of Formula (I) thereby inhibiting the viral RNA-dependent RNA polymerase.

In another aspect, a method of inhibiting a viral reverse transcriptase is provided. The method includes contacting a compound of Formula I or embodiment thereof wherein R2 is a permeability enhancing moiety, or embodiments thereof, with a cell including a viral RNA-dependent RNA polymerase thereby inhibiting said viral RNA-dependent RNA polymerase.

In another aspect, a method of inhibiting replication of a hepatitis C virus or a human retrovirus is provided. The method includes contacting a compound of Formula I or embodiment thereof wherein R2 is a permeability enhancing moiety, or embodiments thereof, with a cell infected with a hepatitis C virus or a human retrovirus thereby inhibiting replication of said hepatitis C virus or human retrovirus.

In another aspect, a method of inhibiting viral RNA-dependent RNA polymerase is provided. The method includes contacting (e.g. in vitro) a compound of Formula I or embodiment thereof wherein R2 is a phosphate or diphosphate, or embodiments thereof, with a viral RNA-dependent RNA polymerase thereby inhibiting said viral RNA-dependent RNA polymerase.

In another aspect, a method of inhibiting viral reverse transcriptase is provided. The method includes contacting (e.g. in vitro) a compound of Formula I or embodiment thereof wherein R2 is a phosphate or diphosphate, or embodiments thereof, with a reverse transcriptase thereby inhibiting said reverse transcriptase.

IV. Methods of Treating Disease

In another aspect, a method of treating a subject infected with a hepatitis C virus or a human retrovirus is provided. The method includes administering to a subject in need thereof an effective amount of a compound of Formula I or embodiment thereof wherein R2 is a permeability enhancing moiety, or embodiments thereof. Diseases contemplated in the practice of the methods disclosed herein include diseases related to RNA viruses, e.g., SARS, poliomyelitis, the common cold, hepatitis A, yellow fever, West Nile Fever, West Nile meningitis, hepatitis C, Dengue fever, rubella, Ross River fever, sindbis fever, Chikungunya arthralgic disease, hepatitis E, Borna disease, Ebola hemorrhagic fever, Marburg hemorrhagic fever, measles, mumps, rabies, Lassa fever, Crimean-Congo hemorrhagic fever, and influenza. Additional diseases include those related to retroviruses, e.g., HIV, and diseases related to DNA viruses, e.g., herpes simplex, varicella zoster, African swine fever, cowpox, smallpox, hepatitis B, and progressive multifocal leukoencephalopathy,

V. Pharmaceutical Compositions

In another aspect, the present invention provides pharmaceutical compositions. The pharmaceutical composition includes a pharmaceutically acceptable excipient and a compound of the present invention (e.g. Formula I or embodiments thereof)).

The pharmaceutical compositions described herein are typically used to treat a disorder or condition using known methods of nucleic acid pharmaceutical antiviral therapies.

In an exemplary embodiment, the pharmaceutical composition includes from 1 μg to 2000 mg of a compound disclosed herein, e.g., 1 μg to 1 mg, 1 mg to 10 mg, 1 mg to 100 mg, 1 mg to 1000 mg, 1 mg to 1500 mg, or even 1 mg to 2000 mg.

A. Formulations

The compounds of the present invention can be prepared and administered in a wide variety of oral, parenteral and topical dosage forms. Oral preparations include tablets, pills, powder, dragees, capsules, liquids, lozenges, gels, syrups, slurries, suspensions, etc., suitable for ingestion by the patient. The compounds of the present invention can also be administered by injection, that is, intravenously, intramuscularly, intracutaneously, subcutaneously, intraduodenally, or intraperitoneally. Also, the compounds described herein can be administered by inhalation, for example, intranasally. Additionally, the compounds of the present invention can be administered transdermally. The compounds of the present invention can also be administered by in intraocular, intravaginal, and intrarectal routes including suppositories, insufflation, powders and aerosol formulations (for examples of steroid inhalants, see Rohatagi, J. Clin. Pharmacol. 35:1187-1193, 1995; Tjwa, Ann. Allergy Asthma Immunol. 75:107-111, 1995). Thus, the pharmaceutical compositions described herein may be adapted for oral administration. In some embodiments, the pharmaceutical composition is in the form of a tablet. Moreover, the present invention provides pharmaceutical compositions including a pharmaceutically acceptable carrier or excipient and either a compound of the present invention, or a pharmaceutically acceptable salt of a compound of the present invention.

For preparing pharmaceutical compositions from the compounds of the present invention, pharmaceutically acceptable carriers can be either solid or liquid. Solid form preparations include powders, tablets, pills, capsules, cachets, suppositories, and dispersible granules. A solid carrier can be one or more substances, which may also act as diluents, flavoring agents, binders, preservatives, tablet disintegrating agents, or an encapsulating material. Details on techniques for formulation and administration are well described in the scientific and patent literature, see, e.g., the latest edition of REMINGTON'S PHARMACEUTICAL SCIENCES, Maack Publishing Co, Easton Pa. (“Remington's”).

In powders, the carrier is a finely divided solid, which is in a mixture with the finely divided active component. In tablets, the active component is mixed with the carrier having the necessary binding properties in suitable proportions and compacted in the shape and size desired.

The powders and tablets preferably contain from 5% or 10% to 70% of the active compound. Suitable carriers are magnesium carbonate, magnesium stearate, talc, sugar, lactose, pectin, dextrin, starch, gelatin, tragacanth, methylcellulose, sodium carboxymethylcellulose, a low melting wax, cocoa butter, and the like. The term “preparation” is intended to include the formulation of the active compound with encapsulating material as a carrier providing a capsule in which the active component with or without other carriers, is surrounded by a carrier, which is thus in association with it. Similarly, cachets and lozenges are included. Tablets, powders, capsules, pills, cachets, and lozenges can be used as solid dosage forms suitable for oral administration.

Suitable solid excipients are carbohydrate or protein fillers include, but are not limited to sugars, including lactose, sucrose, mannitol, or sorbitol; starch from corn, wheat, rice, potato, or other plants; cellulose such as methyl cellulose, hydroxypropylmethyl-cellulose, or sodium carboxymethylcellulose; and gums including arabic and tragacanth; as well as proteins such as gelatin and collagen. If desired, disintegrating or solubilizing agents may be added, such as the cross-linked polyvinyl pyrrolidone, agar, alginic acid, or a salt thereof, such as sodium alginate.

Dragee cores are provided with suitable coatings such as concentrated sugar solutions, which may also contain gum arabic, talc, polyvinylpyrrolidone, carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures. Dyestuffs or pigments may be added to the tablets or dragee coatings for product identification or to characterize the quantity of active compound (i.e., dosage). Pharmaceutical preparations of the invention can also be used orally using, for example, push-fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin and a coating such as glycerol or sorbitol. Push-fit capsules can contain compounds of Formulae I or II mixed with a filler or binders such as lactose or starches, lubricants such as talc or magnesium stearate, and, optionally, stabilizers. In soft capsules, the compounds may be dissolved or suspended in suitable liquids, such as fatty oils, liquid paraffin, or liquid polyethylene glycol with or without stabilizers.

For preparing suppositories, a low melting wax, such as a mixture of fatty acid glycerides or cocoa butter, is first melted and the active component is dispersed homogeneously therein, as by stirring. The molten homogeneous mixture is then poured into convenient sized molds, allowed to cool, and thereby to solidify.

Liquid form preparations include solutions, suspensions, and emulsions, for example, water or water/propylene glycol solutions. For parenteral injection, liquid preparations can be formulated in solution in aqueous polyethylene glycol solution.

Aqueous solutions suitable for oral use can be prepared by dissolving the active component in water and adding suitable colorants, flavors, stabilizers, and thickening agents as desired. Aqueous suspensions suitable for oral use can be made by dispersing the finely divided active component in water with viscous material, such as natural or synthetic gums, resins, methylcellulose, sodium carboxymethylcellulose, hydroxypropylmethylcellulose, sodium alginate, polyvinylpyrrolidone, gum tragacanth and gum acacia, and dispersing or wetting agents such as a naturally occurring phosphatide (e.g., lecithin), a condensation product of an alkylene oxide with a fatty acid (e.g., polyoxyethylene stearate), a condensation product of ethylene oxide with a long chain aliphatic alcohol (e.g., heptadecaethylene oxycetanol), a condensation product of ethylene oxide with a partial ester derived from a fatty acid and a hexitol (e.g., polyoxyethylene sorbitol mono-oleate), or a condensation product of ethylene oxide with a partial ester derived from fatty acid and a hexitol anhydride (e.g., polyoxyethylene sorbitan mono-oleate). The aqueous suspension can also contain one or more preservatives such as ethyl or n-propyl p-hydroxybenzoate, one or more coloring agents, one or more flavoring agents and one or more sweetening agents, such as sucrose, aspartame or saccharin. Formulations can be adjusted for osmolarity.

Also included are solid form preparations, which are intended to be converted, shortly before use, to liquid form preparations for oral administration. Such liquid forms include solutions, suspensions, and emulsions. These preparations may contain, in addition to the active component, colorants, flavors, stabilizers, buffers, artificial and natural sweeteners, dispersants, thickeners, solubilizing agents, and the like.

Oil suspensions can be formulated by suspending a compound in a vegetable oil, such as arachis oil, olive oil, sesame oil or coconut oil, or in a mineral oil such as liquid paraffin; or a mixture of these. The oil suspensions can contain a thickening agent, such as beeswax, hard paraffin or cetyl alcohol. Sweetening agents can be added to provide a palatable oral preparation, such as glycerol, sorbitol or sucrose. These formulations can be preserved by the addition of an antioxidant such as ascorbic acid. As an example of an injectable oil vehicle, see Minto, J. Pharmacol. Exp. Ther. 281:93-102, 1997. The pharmaceutical formulations of the invention can also be in the form of oil-in-water emulsions. The oily phase can be a vegetable oil or a mineral oil, described above, or a mixture of these. Suitable emulsifying agents include naturally-occurring gums, such as gum acacia and gum tragacanth, naturally occurring phosphatides, such as soybean lecithin, esters or partial esters derived from fatty acids and hexitol anhydrides, such as sorbitan mono-oleate, and condensation products of these partial esters with ethylene oxide, such as polyoxyethylene sorbitan mono-oleate. The emulsion can also contain sweetening agents and flavoring agents, as in the formulation of syrups and elixirs. Such formulations can also contain a demulcent, a preservative, or a coloring agent.

The compounds can be delivered by transdermally, by a topical route, formulated as applicator sticks, solutions, suspensions, emulsions, gels, creams, ointments, pastes, jellies, paints, powders, and aerosols.

The compounds can also be delivered as microspheres for slow release in the body. For example, microspheres can be administered via intradermal injection of drug-containing microspheres, which slowly release subcutaneously (see Rao, J. Biomater Sci. Polym. Ed. 7:623-645, 1995; as biodegradable and injectable gel formulations (see, e.g., Gao Pharm. Res. 12:857-863, 1995); or, as microspheres for oral administration (see, e.g., Eyles, J. Pharm. Pharmacol. 49:669-674, 1997). Both transdermal and intradermal routes afford constant delivery for weeks or months.

The compounds can be provided as a salt and can be formed with many acids, including but not limited to hydrochloric, sulfuric, acetic, lactic, tartaric, malic, succinic, etc. Salts tend to be more soluble in aqueous or other protonic solvents that are the corresponding free base forms. In other cases, the preparation may be a lyophilized powder in 1 mM-50 mM histidine, 0.1%-2% sucrose, 2%-7% mannitol at a pH range of 4.5 to 5.5, that is combined with buffer prior to use

In another embodiment, the compounds are useful for parenteral administration, such as intravenous (IV) administration or administration into a body cavity or lumen of an organ. The formulations for administration will commonly comprise a solution of the compound dissolved in a pharmaceutically acceptable carrier. Among the acceptable vehicles and solvents that can be employed are water and Ringer's solution, an isotonic sodium chloride. In addition, sterile fixed oils can conventionally be employed as a solvent or suspending medium. For this purpose any bland fixed oil can be employed including synthetic mono- or diglycerides. In addition, fatty acids such as oleic acid can likewise be used in the preparation of injectables. These solutions are sterile and generally free of undesirable matter. These formulations may be sterilized by conventional, well known sterilization techniques. The formulations may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions such as pH adjusting and buffering agents, toxicity adjusting agents, e.g., sodium acetate, sodium chloride, potassium chloride, calcium chloride, sodium lactate and the like. The concentration of the compound in these formulations can vary widely, and will be selected primarily based on fluid volumes, viscosities, body weight, and the like, in accordance with the particular mode of administration selected and the patient's needs. For IV administration, the formulation can be a sterile injectable preparation, such as a sterile injectable aqueous or oleaginous suspension. This suspension can be formulated according to the known art using those suitable dispersing or wetting agents and suspending agents. The sterile injectable preparation can also be a sterile injectable solution or suspension in a nontoxic parenterally-acceptable diluent or solvent, such as a solution of 1,3-butanediol.

In another embodiment, the compound can be delivered by the use of liposomes which fuse with the cellular membrane or are endocytosed, i.e., by employing ligands attached to the liposome, or attached directly to the oligonucleotide, that bind to surface membrane protein receptors of the cell resulting in endocytosis. By using liposomes, particularly where the liposome surface carries ligands specific for target cells, or are otherwise preferentially directed to a specific organ, one can focus the delivery of the compound into the target cells in vivo. (See, e.g., Al-Muhammed, J. Microencapsul. 13:293-306, 1996; Chonn, Curr. Opin. Biotechnol. 6:698-708, 1995; Ostro, Am. J. Hosp. Pharm. 46:1576-1587, 1989).

The pharmaceutical preparation is preferably in unit dosage form. In such form the preparation is subdivided into unit doses containing appropriate quantities of the active component. The unit dosage form can be a packaged preparation, the package containing discrete quantities of preparation, such as packeted tablets, capsules, and powders in vials or ampoules. Also, the unit dosage form can be a capsule, tablet, cachet, or lozenge itself, or it can be the appropriate number of any of these in packaged form.

The quantity of active component in a unit dose preparation may be varied or adjusted from 0.1 mg to 10000 mg, more typically 1.0 mg to 1000 mg, most typically 10 mg to 500 mg, according to the particular application and the potency of the active component. The composition can, if desired, also contain other compatible therapeutic agents.

Compounds of the invention may be metabolized by cells by phosphatases of the phospholipase C type and then converted by anabolic phosphorylation sequentially to the acyclic nucleoside phosphonate monophosphate (ANPp) and then to the acyclic nucleoside phosphonate diphosphate, (ANPpp), the active antiviral. For example ODE-(S)-MPMPA is metabolized intracellularly in mammalian cells as shown in Scheme A following, wherein “a” is a phosphatase of the phospholipase or lysophospholipase C type; “b” is a nucleoside monophosphate kinase, and “c” is a nucleoside diphosphate kinase. ODE-(S)-MPMPA, (S)-MPMPAp and (S)-MPMPApp are unique chemical entities and are compounds described herein.

embedded image

B. Effective Dosages

Pharmaceutical compositions provided herein include compositions wherein the active ingredient is contained in a therapeutically effective amount, i.e., in an amount effective to achieve its intended purpose. The actual amount effective for a particular application will depend, inter alia, on the condition being treated. For example, when administered in methods to treat virus infection, such compositions will contain an amount of active ingredient effective to achieve the desired result (e.g. decreasing the viral titer).

The dosage and frequency (single or multiple doses) of compound administered can vary depending upon a variety of factors, including route of administration; size, age, sex, health, body weight, body mass index, and diet of the recipient; nature and extent of symptoms of the disease being treated; presence of other diseases or other health-related problems; kind of concurrent treatment; and complications from any disease or treatment regimen. Other therapeutic regimens or agents can be used in conjunction with the methods and compounds described herein.

For any compound described herein, the therapeutically effective amount can be initially determined from cell culture assays. Target concentrations will be those concentrations of active compound(s) that are capable of decreasing viral activity as measured, for example, using the methods described.

Therapeutically effective amounts for use in humans may be determined from animal models. For example, a dose for humans can be formulated to achieve a concentration that has been found to be effective in animals. The dosage in humans can be adjusted by monitoring viral inhibition and adjusting the dosage upwards or downwards, as described above.

Dosages may be varied depending upon the requirements of the patient and the compound being employed. The dose administered to a patient, in the context of the present invention, should be sufficient to affect a beneficial therapeutic response in the patient over time. The size of the dose also will be determined by the existence, nature, and extent of any adverse side effects. Generally, treatment is initiated with smaller dosages, which are less than the optimum dose of the compound. Thereafter, the dosage is increased by small increments until the optimum effect under circumstances is reached. In one embodiment of the invention, the dosage range is 0.001% to 10% w/v. In another embodiment, the dosage range is 0.1% to 5% w/v.

Dosage amounts and intervals can be adjusted individually to provide levels of the administered compound effective for the particular clinical indication being treated. This will provide a therapeutic regimen that is commensurate with the severity of the individual's disease state.

Utilizing the teachings provided herein, an effective prophylactic or therapeutic treatment regimen can be planned that does not cause substantial toxicity and yet is entirely effective to treat the clinical symptoms demonstrated by the particular patient. This planning should involve the careful choice of active compound by considering factors such as compound potency, relative bioavailability, patient body weight, presence and severity of adverse side effects, preferred mode of administration, and the toxicity profile of the selected agent.

C. Toxicity

The ratio between toxicity and therapeutic effect for a particular compound is its therapeutic index and can be expressed as the ratio between LD50 (the amount of compound lethal in 50% of the population) and ED50 (the amount of compound effective in 50% of the population). Compounds that exhibit high therapeutic indices are preferred. Therapeutic index data obtained from cell culture assays and/or animal studies can be used in formulating a range of dosages for use in humans. The dosage of such compounds preferably lies within a range of plasma concentrations that include the ED50 with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized. See, e.g. Fingl et al., In: THE PHARMACOLOGICAL BASIS OF THERAPEUTICS, Ch. 1, p. 1, 1975. The exact formulation, route of administration, and dosage can be chosen by the individual physician in view of the patient's condition and the particular method in which the compound is used.

VI. Examples

The examples below are meant to illustrate certain embodiments of the invention, and not to limit the scope of the invention. Abbreviations: (S)-HPMPA, 9-(S)-[3-hydroxy-2-(phosphonomethoxy)propyl]adenine; (S)-MPMPA, 9-(S)-[3-methoxy-2-(phosphonomethoxy)propyl]adenine; ODE, octadecyloxyethyl; HDP, hexadecyloxypropyl; ODE-(S)-MPMPA, octadecyloxyethyl 9-(S)-[3-methoxy-2-(phosphonomethoxy) propyl]adenine; ODE-(R)-MPMPA, octadecyloxyethyl 9-(R)-[3-methoxy-2-(phosphonomethoxy)propyl]adenine; HDP-(S)-MPMPA, hexadecyloxypropyl 9-(S)-[3-methoxy-2-(phosphonomethoxy)propyl]adenine; HDP-(R,S)-EPMPA, hexadecyloxypropyl 9-(R,S)-[3-ethoxy-2-(phosphonomethoxy)propyl]adenine; HDP-(R,S)-IPPMPA, hexadecyloxypropyl 9-(R,S)-[3-isopropoxy-2-(phosphonomethoxy)propyl]adenine; ODE-(S)-MPMPDAP, octadecyloxyethyl 9-(S)-[3-methoxy-2-(phosphonomethoxy)propyl]2,6-diaminopurine; HDP-(R,S)-EPMPDAP, hexadecyloxypropyl 9-(R,S)-[3-ethoxy-2-(phosphonmethoxy)propyl]2,6-diaminopurine; ODE-(S)-MPMPG, octadecyloxyethyl 9-(S)-[3-methoxy-2(phosphonomethoxy)propyl]guanine; ODE-(S)-MPMPC, octadecyloxyethyl 1-(S)-[3-methoxy-2-(phosphonmethoxy)propyl]cytosine; HDP-(S)-MPMPMP, hexadecyloxypropyl 9-(S)-[3-methoxy-2-(phosphonomethoxy)propyl]6-methoxypurine; HDP-(S)-MPMPOMG, hexadecyloxypropyl 9-(S)-[3-methoxy-2-(phosphonomethoxy) propyl]6-O-methylguanine.

General.

All reagents were of commercial quality and used without further purification unless indicated otherwise. Chromatographic purification was done using the flash method with silica gel 60 (EMD Chemicals, Inc., 230-400 mesh). 1H NMR spectra were recorded on Varian HG spectrophotometers operating at 400 MHz and are reported in units of parts per million (ppm) relative to internal tetramethylsilane at 0.00 ppm. Assignments of 1H NMR signals are made using the numbering system shown in Scheme B following.

Scheme B. Numbering System for NMR Signal Assignment

embedded image

Routine electrospray ionization mass spectra (ESI-MS) were recorded on a Finnigan LCQDECA spectrometer, and high resolution mass spectra (HRMS) on an Agilent 6230 Accurate-Mass TOFMS mass spectrometer in ESI negative mode. Purity of the target compounds was characterized by high performance liquid chromatography (HPLC) using a Beckman Coulter System Gold chromatography system. The analytical column was Phenomenex Synergi™ Polar-RP (4.6×150 mm) equipped with a SecurityGuard™ protection column. Mobile phase A was 95% water/5% methanol and mobile phase B was 95% methanol/5% water. At a flow rate of 0.8 mL/min, gradient elution was as follows: 10% B (0-3 min.); 10% to 95% B (3-20 min.); 95% B (20-25 min.); 95% to 10% B (25-34 min.). Compounds were detected by ultraviolet light (UV) absorption at 274 nm. Purity of compounds was also assessed by thin layer chromatography (TLC) using Analtech silica gel-GF (250 m) plates and the solvent system: CHCl3/MeOH/con NH4OH/H2O (70:30:3:3 v/v). TLC results were visualized with UV light, phospray (Supelco, Bellefonte, Pa., USA) and charring at 400° C. The key synthons, hexadecyloxypropyl- and octadecyloxyethyl p-toluenesulfonyloxymethylphosphonate, were prepared as described previously. See e.g., Beadle, et al., 2006, Id.

Compounds.

Compound numbering as used herein is provided in Table 4 following which sets forth substituents BN, R1 and R2 of Formula (I), structure, and common name abbreviation.

TABLE 4
CmpdBNR1R2Structure, name
1adenineHODEembedded image
15MeODEembedded image
16MeODEembedded image
17 Me HDP embedded image
18ethylHDPembedded image
19isopropylHDPembedded image
232,6- diamino- purineMeODEembedded image
24MeODEembedded image
25MeHDPembedded image
26ethylHDPembedded image
34guanineMeODEembedded image
35MeODEembedded image
36MeHDPembedded image
37ethylHDPembedded image
40cytosineMeODEembedded image
436- methoxy- purineMeHDPembedded image
446-O- methyl- guanineMeHDPembedded image

Example 1—General Procedure A. Synthesis of 3-Alkoxy-2-Hydroxypropyl Nucleoside Analogs

The preparation of 3-alkoxy-2-hydroxypropyl nucleoside analogs was accomplished using the base catalyzed ring-opening reaction of alkyl glycidyl ethers with nucleobases as described by Brodfuehrer et al. See Brodfuehrer, P. R., et al., 1994, Tetrahedron Lett. 35:3243-3246. Sodium hydride (2 mmol) was added to a solution of the nucleic acid base (10 mmol) and an alkyl glycidyl ether (10 mmol) in anhydrous N,N-dimethylformamide (50 mL) and the mixture was stirred and heated to 100° C. for 6 hours. After cooling, the reaction was quenched with H2O, the solvent was removed in vacuo and the residue was purified by flash column chromatography on silica gel. Elution of the column with 10% MeOH/CH2Cl2 gave the product.

With reference to Scheme 1 following, reagents were the following: a) NaH, alkyl glycidyl ether, N,N-DMF, 100° C., 6 h; b) bromotrimethylsilane, monomethoxytrityl chloride, pyridine; c) sodium t-butoxide, hexadecyloxypropyl (HDP) or octadecyloxyethyl (ODE) p-toluenesulfonyloxymethylphosphonate, N,N-DMF, 80° C., 16 h; d) 80% aq acetic acid, 60° C., 2 h.

embedded image

Example 2—(S)-9-[(3-methoxy-2-hydroxy)propyl]adenine (2)

(S)-9-[(3-methoxy-2-hydroxy)propyl]adenine (2) was synthesized from adenine and (S)-methyl glycidyl ether (TCI America, Portland, Oreg.). 75% yield. 1H NMR (CDCl3/methanol-d4) δ 8.25 (s, 1H); 8.03 (s, 1H); 4.39-4.44 (m, 1H); 4.19-4-25 (m, 1H); 4.08-4.18 (m, 1H); 3.37-3.44 (m, 2H); 3.40 (s, 3H). MS (ESI): 224.14 [M+H]+.

Example 3—(R)-9-[(3-methoxy-2-hydroxy)propyl]adenine (3)

(R)-9-[(3-methoxy-2-hydroxy)propyl]adenine (3) was synthesized from adenine and (R)-methyl glycidyl ether (TCI America, Portland, Oreg.). 72% yield. 1H NMR (methanol-d4) δ 8.20 (s, 1H, H-8); 8.08 (s, 1H, H-2); 4.39 (dd, 1H, H-1′a, J1′a,2′=3.4 Hz, Jgem=14.2 Hz); 4.20 (dd, 1H, H-1′b, J1′b,2′=8.0 Hz, Jgem=14.2 Hz); 4.11 (m, 1H, H-2′); 3.42 (d, 2H, H-3′, J3′,2′=5.2 Hz); 3.37 (s, 3H, —OCH3).

Example 4—(R,S)-9-[(3-ethoxy-2-hydroxy)propyl]adenine (4)

(R,S)-9-[(3-ethoxy-2-hydroxy)propyl]adenine (4) was synthesized from adenine and (R,S)-ethyl glycidyl ether (TCI America) with 59% yield. 1H NMR (CDCl3/methanol-d4), δ:8.24 (s, 1H); 8.04 (s, 1H); 4.40-4.65 (m, 1H); 4.20-4-27 (m, 1H); 4.10-4.15 (m, 1H); 3.55-3.57 (m, 2H); 3.46-3.54 (m, 2H); 1.21 (t, J=7 Hz, 3H). MS (ESI): 238.09 [M+H]+.

Example 5—(R,S)-9-[(3-isopropoxy-2-hydroxy)propyl]adenine (5)

(R,S)-9-[(3-isopropoxy-2-hydroxy)propyl]adenine (5) was synthesized from adenine and (R,S) isopropyl glycidyl ether (Aldrich Chem.). 33.8% yield. 1H NMR (CDCl3/methanol-d4), δ 8.21 (s, 1H, H-8); 8.08 (s, 1H, H-2); 4.41 (dd, 1H, H-1′a, J1′a,2′=3.8, Jgem=14.2 Hz); 4.23 (dd, 1H, H-1′b, J1′,2′=7.6 Hz, Jgem=14.4 Hz); 4.10 (m, 1H, H-2′); 3.60 (septet, 1H, —CH(CH3)2, J=6.0 Hz); 1.16 (d, 6H, —CH(CH3)2).

Example 6—General procedure B. Synthesis of 9-[(3-alkoxy-2-hydroxy)propyl]-N6-monomethoxytrityladenine (6-9)

The monomethoxytrityl group was used to block the exocylic amino group of adenine and was introduced by the transient protection method described by Ti et al.3 Bromotrimethylsilane (6.3 mmol) was added dropwise to a suspension of 9-[(2-hydroxy-3-alkoxy)propyl]adenine (2-5) (2.8 mmol) in dry pyridine (10 mL). The mixture was stirred 15 min. until it became clear, then monomethoxytrityl chloride (0.99 g, 3.2 mmol) and 4-(dimethylamino)pyridine (20 mg, 0.2 mmol) were added and stirring was continued overnight. The mixture was cooled with an ice bath and H2O (1 mL) was added. Stirring was continued 10 min., then con. NH4OH (1 mL) was added and the reaction was stirred 30 additional min. The mixture was allowed to warm to room temperature and filtered through a pad of Celite®. The filtrate was evaporated in vacuo and the residue was purified by flash column chromatography on silica gel. Gradient elution (100% hexanes to 100% ethyl acetate) afforded the N6-monomethoxytrityl 9-[(2-alkoxy-3-methoxy)propyl]adenines (6-9).

Example 7—(S)-9-[(3-methoxy-2-hydroxy)propyl]-N6-monomethoxytrityladenine (6)

(S)-9-[(3-methoxy-2-hydroxy)propyl]-N6-monomethoxytrityladenine (6) was synthesized from 2. 98% yield. 1H NMR (CDCl3/methanol-d4), δ 8.17 (s, 1H, H-8); 8.13 (s, 1H, H-2); 7.39-7.75 (m, 14H, trityl); 4.50-4.59 (m, 1H); 4.31-4.39 (m, 1H); 4.22-4.30 (m, 1H); 3.45 (s, 3H); 3.50-3.60 (m, 2H); 3.55 (s, 3H). MS (ESI): 496.06 [M+H]+, 518.13 [M+Na]+.

Example 8—(R)-9-[(3-methoxy-2-hydroxy)propyl] N6-monomethoxytrityladenine (7)

(R)-9-[(3-methoxy-2-hydroxy)propyl] N6-monomethoxytrityladenine (7) was synthesized from Cmpd 3. 19% yield. 1H NMR (CDCl3/methanol-d4), δ 8.03 (s, 1H, H-8); 7.78 (s, 1H, H-2); 7.35-7.33 (m, 4H, trityl); 7.29-7.24 (m, 10H, trityl); 4.61 (d, 1H, H-1′a, J1′a,2′=4 Hz); 4.39 (dd, 1H, H-1′b, J1′,b,2′=2.2 Hz, Jgem=13.8 Hz); 4.16 (m, 1H, H-2′); 3.78 (s, 3H, Ar—OCH3); 3.41 (dd, 1H, H-3′a, J3′a,2′=5.2 Hz, Jgem=9.2 Hz); 3.36 (s, 3H, CH2—OCH3); 3.33 (dd, 1H, H-3′b, J3′b,2′=6.2 Hz, Jgem=9.8 Hz).

Example 9—(R,S)-9-[(3-ethoxy-2-hydroxy)propyl] N6-monomethoxytrityladenine (8)

(R,S)-9-[(3-ethoxy-2-hydroxy)propyl] N6-monomethoxytrityladenine (8) was synthesized from 4. 78% yield. 1H NMR (CDCl3/methanol-d4), δ 7.98 (s, 1H); 7.25-7.34 (m, 14H); 6.82 (s, 1H); 4.35-4.43 (m, 1H); 4.15-4.24 (m, 1H); 4.05-4.15 (m, 1H); 3.78 (s, 3H); 3.52-3.56 (m, 2H); 3.44-3.47 (m, 2H); 1.20 (t, J=7 Hz, 3H). MS (ESI): 509.78 [M+H]+.

Example 10—(R,S)-9-[(3-isopropoxy-2-hydroxy)propyl] N6-monomethoxytrityladenine (9)

(R,S)-9-[(3-isopropoxy-2-hydroxy)propyl] N6-monomethoxytrityl adenine (9) was synthesized from Cmpd 5. 32% yield. 1H NMR (DMSO-d6) δ 8.10 (s, 1H, H-8); 7.89 (s, 1H, H-2); 7.28-7.26 (m, 10H, trityl); 7.21-7.18 (m, 4H, trityl); 6.83 (d, 1H, —NH—); 5.16 (d, 1H, —OH); 4.23 (dd, 1H, H-1′a, J1′a,2′=3.4 Hz, Jgem=13.8 Hz); 3.98 (dd, 1H, H-1′b, J1′b,2′=8.4 Hz, Jgem=13.6 Hz); 3.92 (m, 1H, H-2′); 3.70 (s, 3H, Ar—OCH3); 3.50 (septet, 1H, —CH(CH3)2); 3.35 (dd, 1H, J3′a,2′=4.8 Hz, Jgem=10 Hz); 3.27 (dd, 1H, H-3′b, J3b,2′=6, Jgem=9.6); 1.04 (dd, 6H, —CH(CH3)2).

Example 11—General procedure C. Alkylation of 9-[(3-alkoxy-2-hydroxy)propyl] derivatives (6-9, 20-22, 27-29, 38, 41-42) with alkoxyalkyl p-toluenesulfonyloxymethylphosphonate. Synthesis of (10-14, 23-26, 30-33, 39, 43-44)

Sodium t-butoxide (0.19 g, 2.0 mmol) was added to a solution of the 3-alkoxy-2-hydroxypropyl nucleoside (1.0 mmol) and the alkoxyalkyl p-toluenesulfonyloxymethylphosphonate1 (2.0 mmol) in anhydrous N,N-DMF (20 mL). The mixture was heated to 80° C. and kept overnight. After cooling, the solvents were evaporated in vacuo and the residue was purified by flash column chromatography on silica gel. The column was eluted with a gradient: chloroform 100%-chloroform-methanol (20%) to give the products.

Example 12—Octadecyloxyethyl (S)-9-[(3-methoxy-2-phosphonomethoxy)propyl] N6-monomethoxytrityladenine, sodium salt (10)

Octadecyloxyethyl (S)-9-[(3-methoxy-2-phosphonomethoxy)propyl] N6-monomethoxytrityladenine, sodium salt (10) was synthesized from (S)-9-[(3-methoxy-2-hydroxy)propyl]-N6-monomethoxytrityladenine (6) and octadecyloxyethyl p-toluenesulfonyloxymethylphosphonate. 60% yield. 1H NMR (CDCl3/methanol-d4), δ 8.18 (s, 1H); 7.98 (s, 1H); 7.22-7.55 (m, 14H); 4.38-4.50 (m, 2H); 4.12-4.37 (m, 2H); 4.00-4.08 (m, 1H); 3.82-3.98 (m, 2H); 3.79 (s, 3H); 3.58-3.65 (m, 2H); 3.44-3.48 (m, 2H); 3.38-3.43 (m, 2H); 3.35 (s, 3H); 1.40-1.60 (m, 2H); 1.16-1.38 (m, 30H); 0.88 (t, J=7 Hz, 3H). MS (ESI): 886.48 [M+H]+.

Example 13—Octadecyloxyethyl (R)-9-[(3-methoxy-2-phosphonomethoxy)propyl] N6-monomethoxytrityladenine, sodium salt (11)

Octadecyloxyethyl (R)-9-[(3-methoxy-2-phosphonomethoxy)propyl] N6-monomethoxytrityladenine, sodium salt (11) was synthesized from (R)-9-[(3-methoxy-2-hydroxy)propyl]-N6-monomethoxytrityladenine (7) and octadecyloxyethyl p-toluenesulfonyloxymethylphosphonate. 43% yield. 1H NMR (CDCl3/methanol-d4), δ 8.20 (s, 1H); 7.98 (s, 1H); 7.22-7.37 (m, 14H); 4.42-4.50 (m, 1H); 4.28-4.37 (m, 1H); 3.91-3.98 (m, 2H); 3.82-3.90 (m, 2H); 3.79 (s, 3H); 3.60-3.69 (m, 1H); 3.48-3.58 (m, 3H); 3.39-3.46 (m, 2H); 3.35 (s, 3H); 1.45-1.60 (m, 2H); 1.20-1.38 (m, 30H); 0.88 (t, J=7 Hz, 3H). MS (ESI): 886.57 [M+H]+.

Example 14—Hexadecyloxypropyl (S)-9-[(3-methoxy-2-phosphonomethoxy)propyl] N6-monomethoxytrityladenine, sodium salt (12)

Hexadecyloxypropyl (S)-9-[(3-methoxy-2-phosphonomethoxy)propyl] N6-monomethoxytrityladenine, sodium salt (12) was synthesized from (S)-9-[(3-methoxy-2-hydroxy)propyl]-N6-monomethoxytrityladenine (6) and hexadecyloxypropyl p-toluenesulfonyloxymethylphosphonate. 77% yield. 1H NMR (CDCl3/methanol-d4), δ: 8.17 (s, 1H); 7.94 (s, 1H); 7.22-7.36 (m, 14H); 4.38-4.50 (m, 2H); 4.28-4.37 (m, 2H); 3.82-3.98 (m, 2H); 3.79 (s, 3H); 3.58-3.65 (m, 1H); 3.38-3.58 (m, 6H); 3.34 (s, 3H); 1.78-1.87 (m, 2H); 1.44-1.60 (m, 2H); 1.10-1.40 (m, 26H); 0.88 (t, J=7 Hz, 3H). MS (ESI): 870.33 [M−H].

Example 15—Hexadecyloxypropyl (R,S)-9-[(3-ethoxy-2-phosphonomethoxy)propyl] N6-monomethoxytrityladenine, sodium salt (13)

Hexadecyloxypropyl (R,S)-9-[(3-ethoxy-2-phosphonomethoxy)propyl] N6-monomethoxytrityladenine, sodium salt (13) was synthesized from (R,S)-9-[(3-ethoxy-2-hydroxy)propyl]-N6-monomethoxytrityladenine (8) and hexadecyloxypropyl p-toluenesulfonyloxymethylphosphonate. 80% yield. 1H NMR (CDCl3/methanol-d4), δ: 8.19 (s, 1H); 7.98 (s, 1H); 7.20-7.36 (m, 14H); 4.42-4.65 (m, 1H); 4.28-4.37 (m, 1H); 3.80-3.95 (m, 3H); 3.78 (s, 3H); 3.48-3.65 (m, 6H); 3.28-3.48 (m, 2H); 1.78-1.87 (m, 2H); 1.44-1.55 (m, 2H); 1.08-1.30 (m, 26H); 1.15 (t, J=7 Hz, 3H); 0.88 (t, J=7 Hz, 3H). MS (EI): 886.42 (M+H)+.

Example 16—Hexadecyloxypropyl (R,S)-9-[(3-isopropoxy-2-phosphonomethoxy)propyl] N6-monomethoxytrityladenine, sodium salt (13)

Hexadecyloxypropyl (R,S)-9-[(3-isopropoxy-2-phosphonomethoxy)propyl] N6-monomethoxytrityladenine, sodium salt (13) was synthesized from (R,S)-9-[(3-isopropoxy-2-hydroxy)propyl]-N6-monomethoxytrityladenine (9) and hexadecyloxypropyl p-toluenesulfonyloxymethylphosphonate. 25% yield. 1H NMR (CDCl3/methanol-d4) δ 8.15 (s, 1H, H-8); 7.88 (s, 1H, H-2); 7.30-7.25 (m, 4H, trityl); 7.20-7.12 (m, 10H, trityl); 4.66 (dd, 1H, H-1′a, J1′a,2′=3.5 Hz, Jgem=14.2 Hz); 4.47 (dd, 1H, H-1′b, J1′b2′=6.2 Hz, Jgem=14.0 Hz); 4.01 (m, 2H, —P—O—CH2—); 3.88 (dd, 1H, —CHa—P—, JP,CHa=9.2 Hz, Jgem=13.6 Hz); 3.71 (dd, 1H, —CHb—P—, JP,CHb=9.6 Hz, Jgem=14.0 Hz); 3.75-3.55 (m, 3H, H-3′+H-2′); 3.51 (t, 2H, —CH—O—CH2—); 3.45 (t, 2H, —CH2—O—CH2—); 1.83 (pentet, 2H, —O—CH2CH2CH2O—); 1.53 (m, 2H, —CH2(CH2)15—); 1.27 (m, 26H, —(CH2)15—); 1.10 (d, 6H, —CH(CH3)2); 0.89 (t, 3H, —CH3).

Example 17—General procedure D. Synthesis of Alkoxyalkyl-9-[(3-alkoxy-2-phosphonomethoxy)propyl]adenine (15-19)

Alkoxyalkyl 9-[(3-alkoxy-2-hydroxy)propyl]-N6-monomethoxytrityladenine (10-14) (0.60 mmol) was added to 80% acetic acid, stirred and heated to 60° C. for 2 hours. After cooling, the solvent was removed in vacuo and the residue purified by flash column chromatography on silica gel. Elution with 20% MeOH/CH2Cl2 gave the products.

Example 18—Octadecyloxyethyl (S)-9-[(3-methoxy-2-phosphonomethoxy)propyl]adenine, sodium salt (ODE-(S)-MPMPA) (15)

Octadecyloxyethyl (S)-9-[(3-methoxy-2-phosphonomethoxy)propyl]adenine, sodium salt (ODE-(S)-MPMPA) (15). Deprotection of Cmpd 10 (procedure D) gave Cmpd 15 in 73% yield as a white powder. 1H NMR (CDCl3/methanol-d4) δ 8.35 (s, 1H, H-8); 8.22 (s, 1H, H-2); 4.53 (dd, H, H-1′a, J1′a2′=3.3 Hz, Jgem 14.3 Hz); 4.37 (dd, 1H, H-1′b, J1′b2′=6.6 Hz, Jgem 14.7 Hz); 4.01-3.98 (m, 3H, P—O—CH2—+H-2′); 3.87 (dd, 1H, —CHa—P—, JP,CHa=9.2 Hz, Jgem=13.2); 3.70 (dd, 1H, —CHb—P—, JP,CHb=9.0 Hz, Jgem=13.0 Hz); 3.57 (t, 2H, —CH2—O—); 3.44 (t, 2H, —O—CH2—); 1.53 (m, 2H, —O—CH2CH2(CH2)15—); 1.26 (m, 30H, —(CH2)15CH3); 0.89 (t, 3H, —CH3, J=7 Hz). MS (ESI+): 614.41 [M+H]+; HRMS (ESI−) calcd. for C30H55N5O6P [M−H] 612.3895. found 612.3897 (E=0.3 ppm). HPLC analysis: retention time 22.35 min., purity 96.12%.

Example 19—Octadecyloxyethyl (R)-9-[(3-methoxy-2-phosphonomethoxy)propyl]adenine, sodium salt (ODE-(R)-MPMPA) (16)

Octadecyloxyethyl (R)-9-[(3-methoxy-2-phosphonomethoxy)propyl]adenine, sodium salt (ODE-(R)-MPMPA) (16). Deprotection of 11 gave 16 in 72% yield. 1H NMR (CDCl3/methanol-d4), δ: 8.24 (s, 1H); 8.21 (s, 1H); 4.43-4.54 (s, 1H); 4.25-4.35 (m, 1H); 3.88-3.98 (m, 3H); 3.80-3.88 (m, 1H); 3.50-3.60 (m, 4H); 3.38-3.48 (m, 3H); 3.37 (s, 3H); 1.49-1.56 (m, 2H); 1.20-1.35 (m, 30H); 0.88 (t, J=7 Hz, 3H). MS (ESI+): 614.55 [M+H]+, 636.46 [M+Na]+. HRMS (ESI−) calcd. for C30H55N5O6P [M−H] 612.3895. found 612.3900 (E=0.8 ppm). HPLC analysis: retention time 21.82 min., purity 95.24%.

Example 20—Hexadecyloxypropyl (S)-9-[3-methoxy-2-phosphonomethoxy)propyl]adenine, sodium salt (HDP-(S)-MPMPA) (17)

Hexadecyloxypropyl (S)-9-[3-methoxy-2-phosphonomethoxy)propyl]adenine, sodium salt (HDP-(S)-MPMPA) (17). Deprotection of 12 gave 17 in 77% yield. 1H NMR (CDCl3/methanol-d4), δ 8.28 (s, 1H); 8.23 (s, 1H); 4.48-4.61 (s, 2H); 4.32-4.37 (m, 2H); 3.91-3.96 (m, 2H); 3.80-3.86 (m, 1H); 3.58-3.64 (m, 1H); 3.41-3.57 (m, 3H); 3.30-3.41 (m, 2H); 3.38 (s, 3H); 1.82-1.90 (m, 2H); 1.49-1.55 (m, 2H); 1.18-1.38 (m, 26H); 0.89 (t, J=7 Hz, 3H). MS (ESI−): 598.29 [M−H]—. HRMS (ESI−) calcd. for C29H53N5O6P [M−H] 598.3739. found 598.3737 (E=−0.3 ppm). HPLC analysis: retention time 22.43 min., purity 93.0%.

Example 21—Hexadecyloxyethyl (R,S)-9-[(3-ethoxy-2-phosphonomethoxy)propyl]adenine, sodium salt (HDP-(R,S)-EPMPA) (18)

Hexadecyloxyethyl (R,S)-9-[(3-ethoxy-2-phosphonomethoxy)propyl]adenine, sodium salt (HDP-(R,S)-EPMPA) (18). Deprotection of 13 gave 18 in 92% yield. 1H NMR (CDCl3/methanol-d4), δ 8.28 (s, 1H); 8.21 (s, 1H); 4.48-4.53 (s, 1H); 4.34-4.39 (m, 1H); 3.90-4.00 (m, 3H); 3.80-3.86 (m, 1H); 3.58-3.64 (m, 1H); 3.44-3.58 (m, 6H); 3.35-3.41 (m, 2H); 1.82-1.90 (m, 2H); 1.49-1.58 (m, 2H); 1.22-1.38 (m, 26H); 1.20 (t, J=7 Hz, 3H); 0.89 (t, J=7 Hz, 3H). MS (ESI): 612.44 (M−H). HRMS (ESI−) calcd. for C30H55N5O6P [M−H] 612.3895. found 612.3898 (E=0.5 ppm). HPLC analysis: retention time 22.60 min., purity 91.8%

Example 22—Hexadecyloxyethyl (S)-9-[(3-isopropoxy-2-phosphonomethoxy)propyl]adenine, sodium salt (HDP-(R,S)-IPPMPA) (19)

Hexadecyloxyethyl (S)-9-[(3-isopropoxy-2-phosphonomethoxy)propyl] adenine, sodium salt (HDP-(R,S)-IPPMPA) (19). Deprotection of 14 gave 19 in 75% yield. 1H NMR (methanol-d4) δ 8.35 (s, 1H, H-8), 8.25 (s, 1H, H-2), 4.53, (dd, 1H, H-1′a, J1′a2′=3.4 Hz, Jgem=14.6 Hz), 4.39 (dd, 1H, H-1′b, J1′b2′=6.6 Hz, Jgem=14.6 Hz), 3.93 (t, 2H, P—O—CHa, J=6.8 Hz), 3.91 (t, 1H, P—O—CHb, J=6.4 Hz); 3.85 (dd, —CHa—P—, JP,CHa=9.0 Hz, Jgem=13 Hz), 3.66 (dd, 1H, —CHb—P—, JP,Hb=9.6 Hz, Jgem=13.2 Hz); 3.59-3.48 (m, 3H, H-3′+H-2′), 3.46 (t, 2H, —CH2—O—CH2), 3.37 (t, 2H, —CH2—O—CH2—), 1.80 (pentet, 2H, —O—CH2—CH2—CH2—O—), 1.51 (m, 2H, —O—CH2—CH2—(CH2)13—), 1.27 (m, 26H, —(CH2)13—), 1.13 (d, 6H, —CH(CH3)2), 0.89 (t, 3H, —CH3); MS (ESI−): 626.69 [M−H]. HRMS (ESI−) calcd. for C31H57N5O6P [M−H] 626.4052. found 626.4053 (E=0.2 ppm). HPLC analysis: retention time 21.95 min., purity 97.1%.

Example 23—Diaminopurine Derivatives (23-26)

A scheme useful for synthesis of diaminopurine compounds described herein is provided in Scheme 2 following, with reagents and conditions as following: a) NaH, alkyl glycidyl ether, N,N-DMF, 100° C., 6H; b) sodium t-butoxide, alkoxyalkyl p-toluenesulfonyloxymethylphosphonate, N,N-DMF, 80° C.

embedded image

Example 24—(S)-9-[(3-methoxy-2-hydroxy)propyl]-2, 6-diaminopurine (20)

(S)-9-[(3-methoxy-2-hydroxy)propyl]-2,6-diaminopurine (20) was synthesized from 2,6-diaminopurine (TCI America) and (S)-methyl glycidyl ether (procedure A). 27% yield (0.65 g). 1H NMR (CDCl3/methanol-d4), δ 7.68 (s, 1H, H-8); 4.20-4.30 (m, 1H); 4.05-4.12 (m, 2H); 3.32-3.47 (m, 2H); 3.39 (s, 3H).

Example 25—(R)-9-[(3-methoxy-2-hydroxy)propyl]-2, 6-diaminopurine (21)

(R)-9-[(3-methoxy-2-hydroxy)propyl]-2,6-diaminopurine (21) was synthesized from 2,6-diaminopurine and (R)-methyl glycidyl ether (procedure A). 41% yield. 1H NMR (CDCl3/methanol-d4), δ 7.73 (s, 1H, H-8); 4.22 (d, 1H, H-1′a, Jgem=12.4 Hz), 4.06-4.02 (m, 2H, H-1′b+H-2′); 3.39 (d, 2H, H-3′, J=3.2 Hz); 3.36 (s, 3H, —OCH3).

Example 26—(R,S)-9-[(3-ethoxy-2-hydroxy)propyl]-2, 6-diaminopurine (22)

(R,S)-9-[(3-ethoxy-2-hydroxy)propyl]-2,6-diaminopurine (22) was synthesized from 2,6-diaminopurine and (R,S)-ethyl glycidyl ether (procedure A). 71% yield. 1H NMR (CDCl3/methanol-d4) δ 7.77 (s, 1H, H-8); 4.22 (dd, 1H, J1′a,2′=3.6 Hz, Jgem=12.4 Hz, H-1′a); 4.06-4.02 (m, 2H, H-1′b+H-2′); 3.88 (q, 2H, —OCH2CH3); 3.39 (d, 2H, H-3′, J=3.2 Hz); 1.16 (t, 3H, —OCH2CH3).

Example 27—Octadecyloxyethyl (S)-9-[(3-methoxy-2-phosphonomethoxy)propyl]2, 6-diaminopurine, sodium salt (ODE-(S)-MPMPDAP) (23)

Octadecyloxyethyl (S)-9-[(3-methoxy-2-phosphonomethoxy)propyl]2,6-diaminopurine, sodium salt (ODE-(S)-MPMPDAP) (23) was synthesized (procedure C) from (S)-9-[(3-methoxy-2-hydroxy)propyl]2,6-diaminopurine and octadecyloxyethyl p-toluenesulfonyloxymethylphosphonate. 50% yield. 1H NMR (CDCl3/methanol-d4), δ 7.72 (s, 1H); 4.00-4.20 (m, 5H); 3.80-3.90 (m, 1H); 3.58-3.65 (m, 2H); 3.50-3.58 (m, 2H); 3.40-3.50 (m, 1H); 3.44 (s, 3H); 3.30-3.38 (m, 2H); 1.50-1.60 (m, 2H); 1.18-1.38 (m, 30H); 0.88 (t, J=7 Hz, 3H). MS (ESI): 627.48 [M−H]—, 629.47 [M+H]+. HRMS (ESI−) calcd. for C30H56N6O6P [M−H] 627.4004. found 627.4007 (E=0.5 ppm). HPLC analysis: retention time 23.67 min., purity 91.9%.

Example 28—Octadecyloxyethyl (R)-9-[(3-methoxy-2-phosphonomethoxy)propyl]2, 6-diaminopurine, sodium salt (ODE-(R)-MPMPDAP) (24)

Octadecyloxyethyl (R)-9-[(3-methoxy-2-phosphonomethoxy)propyl]2,6-diaminopurine, sodium salt (ODE-(R)-MPMPDAP) (24) was synthesized (procedure C) from (R)-9-[(3-methoxy-2-hydroxy)propyl]2,6-diaminopurine and octadecyloxyethyl p-toluenesulfonyloxymethylphosphonate with 49% yield. 1H NMR (CDCl3/methanol-d4), δ: 7.75 (s, 1H); 4.42-4.51 (m, 1H); 4.00-4.20 (m, 4H); 3.80-3.90 (m, 1H); 3.60-3.65 (m, 2H); 3.50-3.58 (m, 2H); 3.40-3.50 (m, 1H) 3.49 (s, 3H); 3.30-3.38 (m, 2H); 1.50-1.62 (m, 2H); 1.20-1.38 (m, 30H); 0.88 (t, J=7 Hz, 3H). MS (ESI+): 629.55 [M+H]+. HRMS (ESI−) calcd. for C30H56N6O6P [M−H] 627.4004. found 627.4007 (E=0.5 ppm). HPLC analysis: retention time 23.67, purity 98.4%.

Example 29—Hexadecyloxypropyl (S)-9-[3-methoxy-2-phosphonomethoxy)propyl]-2, 6-diaminopurine, sodium salt (HDP-(S)-MPMPDAP) (25)

Hexadecyloxypropyl (S)-9-[3-methoxy-2-phosphonomethoxy)propyl]-2,6-diaminopurine, sodium salt (HDP-(S)-MPMPDAP) (25) was synthesized (procedure C) from (S)-9-[(3-methoxy-2-hydroxy)propyl]2,6-diaminopurine and hexadecyloxypropyl p-toluenesulfonyloxymethylphosphonate with 30% yield. 1H NMR (CDCl3/methanol-d4), δ: 7.72 (s, 1H); 4.02-4.20 (m, 3H); 3.95-4.02 (m, 2H); 3.78-3.85 (m, 2H); 3.45-3.60 (m, 3H); 3.38-3.45 (m, 6H); 1.82-1.95 (m, 2H); 1.45-1.60 (m, 2H); 1.20-1.38 (m, 26H); 0.88 (t, J=7 Hz, 3H). MS (ESI+): 615.50 [M+H]+, 637.45 [M+Na]+. HRMS (ESI−) calcd. for C29H54N6O6P [M−H] 613.3848. found 613.3854 (E=1.0 ppm). HPLC analysis: retention time 22.98 min., purity 90.3%.

Example 30—Hexadecyloxypropyl (R,S)-9-[3-ethoxy-2-phosphonomethoxy)propyl-2, 6-diaminopurine, sodium salt (HDP-(R,S)-EPMPDAP) (26)

Hexadecyloxypropyl (R,S)-9-[3-ethoxy-2-phosphonomethoxy)propyl-2,6-diaminopurine, sodium salt (HDP-(R,S)-EPMPDAP) (26) was synthesized (procedure C) from (R,S)-9-[(3-ethoxy-2-hydroxy)propyl]2,6-diaminopurine and hexadecyloxypropyl p-toluenesulfonyloxymethylphosphonate with 22% yield. 1H NMR (CDCl3/methanol-d4), δ: 7.40 (s, 1H); 4.44-4.52 (m, 1H); 4.18-2.28 (m, 1H); 3.91-4.10 (m, 3H); 3.80-3.90 (m, 1H); 3.45-3.60 (m, 5H); 3.38-3.45 (m, 4H); 1.82-1.95 (m, 2H); 1.45-1.60 (m, 2H); 1.15-1.38 (m, 28H); 0.88 (t, J=7 Hz, 3H). MS (ESI−): 627.53 [M−H]. HRMS (ESI−) calcd. for C30H56N6O6P [M−H] 627.4004, found 627.4008 (E=0.6 ppm). HPLC analysis: retention time 23.37 min., purity 96.4%.

Example 31—GuanineDerivatives (34-37)

A scheme useful for synthesis of guanine containing compounds described herein is provided in Scheme 3 following, with reagents and conditions as following: a) NaH, alkyl glycidyl ether, N,N-DMF, 100° C., 6 h; b) sodium t-butoxide, hexadecyloxypropyl (HDP) or octadecyloxyethyl (ODE) p-toluenesulfonyloxymethylphosphonate, N,N-DMF, 80° C.; c) 10% CF3COOH/CH2Cl2, rt, 2 days.

embedded image

Example 32—(S)-9-[(3-methoxy-2-hydroxy)propyl]-6-O-benzylguanine (27)

(S)-9-[(3-methoxy-2-hydroxy)propyl]-6-O-benzylguanine (27) was synthesized from 6-O-benzylguanine (APAC Pharmaceutical LLC, Columbia, Md.) and (S)-methyl glycidyl ether (procedure A). 49% yield. 1H NMR (CDCl3/methanol-d4), δ 7.75 (s, 1H); 7.49-7.51 (m, 2H); 7.29-7.40 (m, 3H); 5.55 (s, 2H); 4.23-4.32 (m, 1H); 4.05-4.14 (m, 2H); 3.39-3.41 (m, 2H); 3.39 (s, 3H).

Example 33—(R)-9-[(3-methoxy-2-hydroxy)propyl]-6-O-benzylguanine (28)

(R)-9-[(3-methoxy-2-hydroxy)propyl]-6-O-benzylguanine (28) was synthesized from 6-O-benzylguanine and (R)-methyl glycidyl ether (procedure A). 44% yield. 1H NMR (CDCl3/methanol-d4), δ 7.74 (s, 1H); 7.47-7.51 (m, 2H); 7.29-7.40 (m, 3H); 5.55 (s, 2H); 4.40-4.60 (m, 1H); 4.05-4.14 (m, 2H); 3.32-3.45 (m, 2H); 3.39 (s, 3H).

Example 34-(R,S)-9-[(3-ethoxy-2-hydroxy)propyl]-6-O-benzylguanine (29)

(R,S)-9-[(3-ethoxy-2-hydroxy)propyl]-6-O-benzylguanine (29) was synthesized from 6-O-benzylguanine and (R,S) ethyl glycidyl ether (procedure A). 51% yield. 1H NMR (CDCl3/methanol-d4), δ 7.76 (s, 1H); 7.50-7.52 (m, 2H); 7.32-7.40 (m, 3H); 5.52 (s, 2H); 4.17-4.21 (m, 1H); 3.95-4.00 (m, 2H); 3.44-3.50 (m, 2H); 3.34-3.38 (m, 2H); 1.16 (t, J=7 Hz, 3H).

Example 35—Octadecyloxyethyl (S)-9-[(3-methoxy-2-phosphonomethoxy)propyl]-6-O-benzylguanine (30)

Octadecyloxyethyl (S)-9-[(3-methoxy-2-phosphonomethoxy)propyl]-6-O-benzylguanine (30) was synthesized (procedure C) from (S)-9-[(3-methoxy-2-hydroxy)propyl]-6-O-benzylguanine and octadecyloxyethyl p-toluenesulfonyloxymethylphosphonate. 26% yield. 1H NMR (CDCl3/methanol-d4), δ 7.93 (s, 1H); 7.50-7.56 (m, 2H); 7.31-7.40 (m, 3H); 5.55 (s, 2H); 4.24-4.36 (m, 1H); 3.93-4.22 (m, 1H); 3.75-3.98 (m, 4H); 3.60-3.70 (m, 4H); 3.30-3.60 (m, 8H); 1.42-1.60 (m, 2H); 1.18-1.38 (m, 30H); 0.89 (t, J=7 Hz, 3H). MS (ESI): 720.51 [M+H]+.

Example 36—Octadecyloxyethyl (R)-9-[(3-methoxy-2-phosphonomethoxy)propyl]-6-O-benzylguanine (31)

Octadecyloxyethyl (R)-9-[(3-methoxy-2-phosphonomethoxy)propyl]-6-O-benzylguanine (31) was synthesized (procedure C) from (R)-9-[(3-methoxy-2-hydroxy)propyl]-6-O-benzylguanine and octadecyloxyethyl p-toluenesulfonyloxymethylphosphonate. 83% yield. 1H NMR (CDCl3/methanol-d4), δ 7.93 (s, 1H); 7.52-7.47 (m, 2H); 7.23-7.38 (m, 3H); 5.55 (s, 2H); 4.18-4.38 (m, 2H); 3.75-3.98 (m, 4H); 3.55-3.65 (m, 1H); 3.43-3.50 (m, 3H); 3.30-3.43 (m, 8H); 1.45-1.60 (m, 2H); 1.18-1.38 (m, 30H); 0.89 (t, J=7 Hz, 3H). MS (ESI): 718.54 [M−H]—.

Example 37—Hexadecyloxypropyl (S)-9-[3-methoxy-2-phosphonomethoxy)propyl]-6-O-benzylguanine (32)

Hexadecyloxypropyl (S)-9-[3-methoxy-2-phosphonomethoxy)propyl]-6-O-benzylguanine (32) was synthesized (procedure C) from (S)-9-[(3-methoxy-2-hydroxy)propyl]-6-O-benzylguanine and hexadecyloxypropyl p-toluenesulfonyloxymethylphosphonate. 71% yield. 1H NMR (CDCl3/methanol-d4), δ:7.94 (s, 1H); 7.49-7.55 (m, 2H); 7.24-7.40 (m, 3H); 5.55 (s, 2H); 4.30-4.40 (m, 1H); 4.17-4.22 (m, 1H); 3.80-3.92 (m, 3H); 3.72-3.92 (m, 1H); 3.55-3.62 (m, 1H); 3.40-3.52 (m, 4H); 3.28-3.40 (m, 2H); 3.37 (s, 3H); 1.75-1.85 (m, 2H); 1.44-1.60 (m, 2H); 1.16-1.38 (m, 26H); 0.89 (t, J=7 Hz, 3H). MS (ESI): 706.50 [M+H]+.

Example 38—Hexadecyloxypropyl (R,S)-9-[3-ethoxy-2-phosphonomethoxy)propyl]-6-O-benzylguanine (33)

Hexadecyloxypropyl (R,S)-9-[3-ethoxy-2-phosphonomethoxy)propyl]-6-O-benzylguanine (33) was synthesized (procedure C) from (R,S)-9-[(3-methoxy-2-hydroxy)propyl]-6-O-benzylguanine and hexadecyloxypropyl p-toluenesulfonyloxymethylphosphonate. 42% yield). 1H NMR (CDCl3/methanol-d4), δ 7.95 (s, 1H); 7.48-7.52 (m, 2H); 7.30-7.40 (m, 3H); 5.56 (s, 2H); 4.34-4.40 (m, 1H); 4.19-4.26 (m, 1H); 3.77-3.93 (m, 4H); 3.58-3.66 (m, 1H); 3.47-3.55 (m, 5H); 3.35-3.45 (m, 3H); 1.78-1.85 (m, 2H); 1.48-1.55 (m, 2H); 1.17-1.28 (m, 29H); 0.89 (t, J=7 Hz, 3H). MS (ESI): 718.46 [M−H]—.

Example 39—General procedure E. Synthesis of Alkoxyalkyl-9-[(3-alkoxy-2-phosphonomethoxy)propyl]guanine (34-37)

The protected guanine compounds (30-33) (0.71 mmol) were added to 10% trifluoroacetic acid/CH2Cl2 and the mixture was stirred at room temperature for 2 days. The solvent was removed in vacuo and the residue purified by flash column chromatography on silica gel. The column was eluted with 20% MeOH/CH2Cl2 and the crude products were recrystallized from water to give the alkoxyalkyl 9-[(3-alkoxy-2-phosphonomethoxy)propyl]guanine derivatives (34-37).

Example 40—Octadecyloxyethyl (S)-9-[(3-methoxy-2-phosphonomethoxy)propyl]guanine (ODE-(S)-MPMPG) (34)

Octadecyloxyethyl (S)-9-[(3-methoxy-2-phosphonomethoxy)propyl]guanine (ODE-(S)-MPMPG) (34). Deprotection of 30 gave 34 as a white powder. 93% yield. 1H NMR (CDCl3/methanol-d4), 7.82 (s, 1H); 4.24-4.36 (m, 1H); 4.10-4.28 (m, 1H); 3.95-4.05 (m, 2H); 3.78-3.90 (m, 2H); 3.62-3.73 (m, 1H); 3.52-3.60 (m, 2H); 3.40-3.50 (m, 2H); 3.25-3.40 (m, 3H); 1.45-1.60 (m, 2H); 1.18-1.38 (m, 30H); 0.89 (t, J=7 Hz, 3H). MS (ESI): 628.44 [M−H]. HRMS (ESI−) calcd. for C30H55N5O7P [M−H] 628.3845. found 628.3846 (E=0.2 ppm). HPLC analysis: retention time 21.10, purity 96.2%.

Example 41—Octadecyloxyethyl (R)-9-[(3-methoxy-2-phosphonomethoxy)propyl]guanine (ODE-(R)-MPMPG) (35)

Octadecyloxyethyl (R)-9-[(3-methoxy-2-phosphonomethoxy)propyl]guanine (ODE-(R)-MPMPG) (35). Deprotection of 31 gave 35 as a white powder. 67% yield. 1H NMR (CDCl3/methanol-d4), 8.07 (s, 1H, H-8); 7.51 (s, 2H, —NH2); 4.34 (dd, 1H, H-1′a, J1′a2′=3.9 Hz, Jgem=14.6 Hz); 4.13 (dd, 1H, H-1′b, J1′b2′=6.4 Hz, Jgem=14.3 Hz); 4.00 (m, 2H, —P—O—CH2—); 3.87 (dd, 1H, —CHa—P—, JP,CHa=8.7 Hz, Jgem=12.9 Hz); 3.68 (dd, 1H, —CHb—P—, JP,CHb=9.6 Hz, Jgem=12.8 Hz); 3.59 (t, 2H, —CH2—O—CH2); 3.46 (d+t, 4H, —CH2—O—CH2+H-3′); 3.38 (s, 3H, —OCH3); 1.50-1.62 (m, 2H, —O—CH2CH2(CH2)15—); 1.27 (m, 30H, —(CH2)15—); 0.89 (t, J=7 Hz, 3H, —CH3). MS (ESI+): 630.29 [M+H]+; HRMS (ESI−) calcd. for C30H55N5O7P [M−H] 628.3845. found 628.3843 (E=−0.3 ppm). HPLC analysis: retention time 22.33 min., purity 92.9%.

Example 42—Hexadecyloxypropyl (S)-9-[3-methoxy-2-phosphonomethoxy)propyl]guanine (HDP-(S)-MPMPG) (36)

Hexadecyloxypropyl (S)-9-[3-methoxy-2-phosphonomethoxy)propyl]guanine (HDP-(S)-MPMPG) (36) Deprotection of 32 gave 36 as a white powder. 93% yield. 1H NMR (CDCl3/methanol-d4), 7.83 (s, 1H); 4.26-4.31 (m, 1H); 4.06-4.11 (m, 1H); 3.93-3.98 (m, 2H); 3.81-3.86 (m, 2H); 3.60-3.63 (m, 2H); 3.48-3.57 (m, 3H); 3.35-3.44 (m, 2H); 3.37 (s, 3H); 1.84-1.89 (m, 2H); 1.52-1.58 (m, 2H); 1.15-1.40 (m, 26H); 0.88 (t, J=7 Hz, 3H). MS (ESI): 616.45 [M+H]+, 638.40 [M+Na]+. HRMS (ESI−) calcd. for C29H53N5O7P [M−H]r 614.3688. found 614.3687 (E=−0.2 ppm). HPLC analysis: retention time 20.55 min., purity 93.6%.

Example 43—Hexadecyloxypropyl (R,S)-9-[3-ethoxy-2-phosphonomethoxy)propyl]guanine (HDP-(R,S)-EPMPG) (37)

Hexadecyloxypropyl (R,S)-9-[3-ethoxy-2-phosphonomethoxy)propyl]guanine (HDP-(R,S)-EPMPG) (37). Deprotection of 33 gave 37. 88% yield. 1H NMR (CDCl3/methanol-d4), 7.85 (s, 1H); 4.28-4.33 (m, 1H); 4.11-4.17 (m, 1H); 3.92-3.97 (m, 2H); 3.79-3.86 (m, 2H); 3.63-3.92 (m, 1H); 3.47-3.56 (m, 5H); 3.34-3.42 (m, 3H); 1.83-1.90 (m, 2H); 1.52-1.57 (m, 2H); 1.22-1.40 (m, 26H); 1.20 (t, J=7 Hz, 3H); 0.88 (t, J=7 Hz, 3H). MS (EI): 628.40 [M−H]. HRMS (ESI−) calcd. for C30H55N5O7P [M−H]r 628.3845. found 628.3848 (E=0.5 ppm). HPLC analysis: retention time 20.92 min., purity 95.1%.

Example 44—Cytosine Derivative (40)

A scheme useful for synthesis of cytosine containing compounds described herein is provided in Scheme 4 following, with reagents and conditions as follows: a) NaH, (S)-methyl glycidyl ether, N,N-DMF, 100° C., 6 h; b) octadecyloxyethyl (ODE) p-toluenesulfonyloxymethylphosphonate; c) 80% aq acetic acid, 60° C., 2 h.

embedded image

Example 45—(S)-1-[(3-methoxy-2-hydroxy)propyl]-N4-monomethoxytritylcytosine (38)

(S)-1-[(3-methoxy-2-hydroxy)propyl]-N4-monomethoxytritylcytosine (38) was synthesized from N4-monomethoxytritylcytosine4 and (S)-methyl glycidyl ether (procedure A). 91% yield. 1H NMR (CDCl3/methanol-d4), δ 7.45-7.67 (m, 14H); 7.17 (d, J=6 Hz, 1H); 5.82 (d, J=6 Hz, 1H); 4.30-4.40 (m, 2H); 4.12 (s, 3H); 3.80-3.92 (m, 1H); 3.65-3.75 (m, 2H); 3.65 (s, 3H).

Example 46—Octadecyloxyethyl (S)-1-[(3-methoxy-2-phosphonomethoxy)propyl]-N4-monomethoxytritylcytosine (39)

Octadecyloxyethyl (S)-1-[(3-methoxy-2-phosphonomethoxy)propyl]-N4-monomethoxytritylcytosine (39) was synthesized from (S)-9-[(3-methoxy-2-hydroxy)propyl]-N4-monomethoxytritylcytosine (38) and octadecyloxyethyl p-toluenesulfonyloxymethylphosphonate (procedure C). 45% yield 1H NMR (CDCl3/methanol-d4), δ 7.10-7.40 (m, 14H); 6.85 (d, J=6 Hz, 1H); 5.52 (d, J=6 Hz, 1H); 4.20-4.39 (m, 2H); 3.77-4.02 (m, 4H); 3.55-3.65 (m, 1H); 3.43-3.52 (m, 3H); 3.30-3.45 (m, 8H); 1.45-1.65 (m, 2H); 1.18-1.40 (m, 30H); 0.89 (t, J=7 Hz, 3H). MS (ESI): 860.55 [M−H].

Example 47-Octadecyloxyethyl (S)-1-[(3-methoxy-2-phosphonomethoxy)propyl]cytosine, sodium salt (40) (ODE-(S)-MPMPC)

Octadecyloxyethyl (S)-1-[(3-methoxy-2-phosphonomethoxy)propyl]cytosine, sodium salt (40) (ODE-(S)-MPMPC) Octadecyloxyethyl (S)-1-[(3-methoxy-2-phosphonomethoxy)propyl]-N4-monomethoxytritylcytosine (39) (0.26 g, 0.60 mmol) was added 15 to 80% aq acetic acid and heated to 60° C. for 2 hours. After cooling, the solvent was removed in vacuo and the residue purified by flash column chromatography on silica gel. Elution with 20% MeOH/CH2Cl2 gave the product (0.1 g, 55%). 1H NMR (CDCl3/methanol-d4) δ 7.80 (d, J=6 Hz, 1H); 6.00 (d, J=6 Hz, 1H); 4.04-4.15 (m, 4H); 3.55-3.68 (m, 3H); 3.42-3.53 (m, 2H); 3.35-3.42 (m, 4H); 1.50-1.65 (m, 2H); 1.18-1.38 (m, 30H); 0.88 (t, J=7 Hz, 3H). MS (ESI+): 590.33 [M+H]+, 612.34 [M+Na]+. HRMS (ESI−) calcd. for C29H55N3O7P [M−H] 588.3783. found 588.3784 (E=−0.2 ppm). HPLC analysis: retention time 22.75 min., purity 90.9%.

Example 48-Methoxypurine Derivatives (43-44)

A scheme useful for synthesis of methoxypurine containing compounds described herein is provided in Scheme 5 following, with reagents and conditions as follows: a) NaH, (S)-methyl glycidyl ether, N,N-DMF, 100° C., 6 h; b) sodium t-butoxide, hexadecyloxypropyl (HDP) p-toluenesulfonyloxymethylphosphonate, N,N-DMF, 80° C.

embedded image

Example 49—(S)-9-[(3-methoxy-2-hydroxy)propyl]-6-methoxypurine (41)

(S)-9-[(3-methoxy-2-hydroxy)propyl]-6-methoxypurine (41) Reaction of 6-methoxypurine (TCI America, Portland, Oreg.) with (S)-methyl glycidyl ether according to procedure A gave compound 41. 67% yield. 1H NMR (methanol-d4) δ 8.51 (s, 1H, H-8), 8.24 (s, 1H, H-2), 4.74 (dd, 1H, J1′a2′=3.8 Hz, Jgem=14.2 Hz), 4.28 (dd, 1H, J1′b2′=8 Hz, Jgem=14.2 Hz), 4.18 (s, 3H, Ar—OCH3), 4.14 (m, 1H, H-2′), 3.42 (d, 2H, J3′2′=5.2 Hz), 3.37 (s, 3H, —CH2—OCH3).

Example 50—(S)-9-[(3-methoxy-2-hydroxy)propyl]-6-O-methylguanine (42)

(S)-9-[(3-methoxy-2-hydroxy)propyl]-6-O-methylguanine (42) Reaction of 6-O-methylguanine (Aldrich Chem.) with (S)-methylglycidyl ether (Procedure A) gave compound 42. 78% yield. 1H NMR (methanol-d4) δ 7.81 (s, 1H, H-8); 4.35 (dd, 2H, H-1′); 4.15 (m, 1H, H-2′); 4.05 (s, 3H, Ar—OCH3); 3.39 (d, 2H, H-3′); 3.35 (s, 3H, —OCH3). MS (ESI): m/z 254.08 [M+H]+.

Example 51—Hexadecyloxypropyl (S)-9-[(3-methoxy-2-phosphonomethoxy)propyl]-6-methoxypurine (HDP-(S)-MPMPMP) (43)

Hexadecyloxypropyl (S)-9-[(3-methoxy-2-phosphonomethoxy)propyl]-6-methoxypurine (HDP-(S)-MPMPMP) (43) Reaction of compound 41 with hexadecyloxypropyl p-toluenesulfonyloxymethylphosphonate according to procedure C afforded compound 43. 29% yield. 1H NMR (methanol-d4) δ 8.51 (s, 1H, H-8); 8.44 (s, 1H, H-2); 4.56 (dd, 1H, H-1′a, J1′a,2′=3.6 Hz, Jgem=14.0 Hz); 4.44 (dd, 1H, H-1′b, J1′b,2′=6.6 Hz, Jgem=14.6 Hz); 4.17 (s, 3H, Ar—OCH3); 3.96 (m, 1H, H-2′); 3.86 (t, 1H, P—O—CHa, J=6.4 Hz); 3.84 (t, 1H, P—O—CHb, J=6.4 Hz); 3.78 (dd, 1H, —CHa—P—, JP,CH=9.2 Hz, Jgem=12.8 Hz); 3.60 (dd, 1H, —CHb—P—, JP,CH=9.6 Hz, Jgem=12.8 Hz); 3.44 (m, 1H, H-2′); 3.43 (t, 2H, —CH2—O—CH2—); 3.36 (t, 2H, —CH2—O—CH2-); 3.32 (s, 3H, —OCH3); 1.76 (pentet, 2H, —O—CH2CH2CH2—O—); 1.49 (m, 2H, —CH2—O—CH2CH2(CH2)13—); 1.28 (m, 26H, —(CH2)13—); 0.89 (t, 3H, —CH3). MS (ESI−) m/z 613.46 [M−H]. HRMS (ESI−) calcd. for C30H54N4O7P [M−H] 613.3736. found 613.3739 (E=0.5 ppm).

Example 52—Hexadecyloxypropyl (S)-9-[(3-methoxy-2-phosphonomethoxy)propyl]-6-O-methylguanine (HDP-(S)-MPMPOMG) (44)

Hexadecyloxypropyl (S)-9-[(3-methoxy-2-phosphonomethoxy)propyl]-6-O-methylguanine (HDP-(S)-MPMPOMG) (44). Reaction of compound 42 with hexadecyloxypropyl p-toluenesulfonyloxymethylphosphonate according to procedure C afforded compound 44. 34% yield. 1H NMR (methanol-d4) δ 7.95 (s, 1H, H-8), 4.34 (dd, 1H, H-1′a, J1′a2′=4 Hz, Jgem=14.4 Hz); 4.22 (dd, 1H, H-1′b, J1′b2′=6.4 Hz, Jgem=14.4 Hz); 4.04 (s, 3H, Ar—OCH3); 3.91 (m, 1H, H-2′); 3.87 (t, 1H, P—O—CHa—, J=6.4 Hz); 3.86 (t, 1H, P—O—CHb—, J=6.4 Hz); 3.75 (dd, 1H, —CHa—P—, JCH,P=9.4 Hz, Jgem=13 Hz); 3.64 (dd, 1H, —CHb—P—, JCH,P=9.2 Hz, Jgem=12.8 Hz); 3.44 (t, 2H, —CH2—O—); 3.43 (d, 2H, H-3′); 3.35 (t, 2H, —O—CH2); 3.34 (s, 3H, —OCH3); 1.78 (pentet, 2H, —O—CH2CH2CH2—O—); 1.50 (m, 2H, —OCH2CH2(CH2)13—); 1.27 (m, 26H, (CH2)13); 0.89 (t, 3H, —CH3). MS (ESI): m/z 630.35 [M+H]+; 628.37 [M−H]. HRMS (ESI−) calcd. for C30H55N5O7P [M−H] 628.3845. found 628.3847 (E=0.3 ppm). HPLC analysis: retention time 21.60 min., purity 97.0%.

Example 53—Hexadecyloxypropyl (R,S)-9-[(3-fluoro-2-phosphonomethoxy)propyl]adenine (HDP-(R,S)-FPMPA)

Sodium hydride (0.10 g, 4.37 mmol) was added to a solution of adenine (1.78 g, 13.1 mmol) in anhydrous N,N-DMF (60 mL), then (R,S)-epifluorohydrin (1.0 g, 13.1 mmol) was added to the mixture that was stirred and heated to 100° C. for 6 hours. After cooling, the solvent was removed in vacuo and the residue was purified by flash column chromatography on silica gel. Elution of the column with 10% MeOH/CH2Cl2 gave (R,S)-9-[(3-fluoro-2-hydroxy)propyl]adenine in 56% yield (1.58 g). 1H NMR (CDCl3/methanol-d4), δ: 8.25 (s, 1H); 8.06 (s, 1H); 4.35-4.55 (m, 3H); 4.15-4-30 (m, 2H).

Bromotrimethylsilane (2.10 mL, 16.60 mmol) was added dropwise to a suspension of (R,S)-9-[(3-fluoro-2-hydroxy)propyl]adenine (1.56 g, 7.38 mmol) in dry pyridine (30 mL). The mixture was stirred 15 min until it became clear, then monomethoxytrityl chloride (2.60 g, 8.4 mmol) and 4-(dimethylamino)-pyridine (0.06 g, 0.50 mmol) were added and stirring was continued overnight. The mixture was cooled with an ice bath and H2O (1 mL) was added. Stirring was continued 10 min., then con. NH4OH (1 mL) was added and the reaction was stirred 30 additional min. The mixture was allowed to warm up to room temperature and filtered through a pad of Celite®. The filtrate was evaporated in vacuo and the residue was purified by flash column chromatography on silica gel. Gradient elution 100% hexanes to 100% ethyl acetate afforded N6-monomethoxytrityl (R,S)-9-[(3-fluoro-2-hydroxy)propyl]adenine (2.15 g, 60% yield) 1H NMR (CDCl3/methanol-d4), δ: 7.99 (s, 1H); 7.98 (s, 1H); 7.15-7.37 (m, 12H); 6.75-6.83 (m, 2H); 4.40-4.54 (m, 2H); 4.19-4.25 (m, 3H); 3.79 (s, 3H).

Sodium t-butoxide (0.20 g, 2.0 mmol) was added to a solution of N6-monomethoxytrityl (R,S)-9-[(3-fluoro-2-hydroxy)propyl]adenine (0.48 g, 1.0 mmol) and hexadecyloxypropyl p-toluenesulfonyloxymethylphosphonate (0.82 g, 1.5 mmol, prepared as described by Beadle, et al., 2006, Id.) in N,N-DMF (20 mL). in N,N-DMF (100 mL). The mixture was heated to 80° C. and kept overnight. After cooling, the solvents were evaporated in vacuo and the residue was purified by flash column chromatography on silica gel. The column was eluted with gradient chloroform 100%-chloroform-methanol (20%) to give hexadecyloxypropyl (R,S)-9-[(3-fluoro-2-phosphonomethoxy)propyl] N6-monomethoxytrityl adenine (0.26 g, 30% yield). 1H NMR (CDCl3/methanol-d4), δ: 8.18 (s, 1H); 7.98 (s, 1H); 7.18-7.38 (m, 12H); 6.79-6.81 (m, 2H); 4.40-4.68 (m, 3H); 4.22-4.40 (m, 2H); 3.85-4.05 (m, 2H); 3.79 (s, 3H); 3.58-3.65 (m, 2H); 3.21-3.25 (m, 2H); 3.15-3.19 (m, 2H); 1.79-1.87 (m, 2H); 1.43-1.59 (m, 2H); 1.20-1.38 (m, 26H); 0.88 (t, J=7 Hz, 3H). MS (EI): 858.59 (M−H).

The product (0.26 g, 0.30 mmol) was added to 80% acetic acid and heated to 60° C. overnight. After cooling, the solvent was removed in vacuo and the residue purified by flash column chromatography on silica gel. Elution with 20% MeOH/CH2Cl2 gave hexadecyloxypropyl (R,S)-9-[(3-fluoro-2-phosphonomethoxy)propyl]adenine (0.15 g, 88% yield). 1H NMR (CDCl3/methanol-d4), δ: 8.30 (s, 1H); 8.25 (s, 1H); 4.45-4.68 (m, 3H); 4.35-4.42 (m, 2H); 3.78-4.08 (m, 4H); 3.43-3.55 (m, 2H); 3.17-3.23 (m, 2H); 1.81-1.87 (m, 2H); 1.43-1.62 (m, 2H); 1.18-1.40 (m, 26H); 0.89 (t, J=7 Hz, 3H). MS (EI): 586.35 (M−H).

Example 54—Octadecyloxyethyl (S)-9-[(3-fluoro-2-phosphonomethoxy)propyl]adenine (ODE-(S)-FPMPA)

Sodium hydride (0.08 g, 2.0 mmol) was added to a solution of adenine (1.35 g, 10 mmol) in anhydrous N,N-DMF (60 mL), then (S)-trityl glycidyl ether (3.16 g, 10 mmol) was added to the mixture that was stirred and heated to 100° C. for 6 hours. After cooling, the solvent was removed in vacuo and the residue was purified by flash column chromatography on silica gel. Elution of the column with 10% MeOH/CH2Cl2 gave 9-[(3-trityloxy-2-hydroxy)propyl]adenine in 75% yield (3.4 g). 1H NMR (CDCl3/methanol-d4), δ: 8.20 (s, 1H); 7.90 (s, 1H); 7.42-7.54 (m, 6H); 7.24-7.32 (m, 9H); 4.43-4.64 (m, 1H); 4.29-4-33 (m, 1H); 4.15-4.18 (m, 1H); 3.19-3.35 (m, 1H); 3.09-3.13 (m, 1H).

Bromotrimethylsilane (1.90 mL, 14.65 mmol) was added dropwise to a suspension of (S)-9-[(3-trityloxy-2-hydroxy)propyl]adenine (2.94 g, 6.5 mmol) in dry pyridine (30 mL). The mixture was stirred 15 min. until it became clear, then monomethoxytrityl chloride (2.30 g, 7.4 mmol) and 4-(dimethylamino)-pyridine (0.05 g, 0.46 mmol) were added and stirring was continued overnight. The mixture was cooled with an ice bath and H2O (1 mL) was added. Stirring was continued 10 min., then con. NH4OH (1 mL) was added and the reaction was stirred 30 additional min. The mixture was allowed to warm up to room temperature and filtered through a pad of Celite®. The filtrate was evaporated in vacuo and the residue was purified by flash column chromatography on silica gel. Gradient elution 100% hexanes to 100% ethyl acetate afforded (S)-9-[(3-trityloxy-2-hydroxy)propyl] N6-monomethoxytrityl-adenine (4.37 g, 93% yield) 1H NMR (CDCl3/methanol-d4), δ: 8.14 (s, 1H); 7.99 (s, 1H); 7.44-7.61 (m, 27H); 6.99-7.03 (m, 2H); 4.52-4.69 (m, 1H); 4.40-4.52 (m, 1H); 4.25-4.40 (m, 1H); 3.99 (s, 3H); 3.35-3.45 (m, 1H); 3.25-3.35 (m, 1H).

Sodium t-butoxide (0.96 g, 10.0 mmol) was added to a solution of(S)-9-[(3-trityloxy-2-hydroxy)propyl] N6-monomethoxytrityl-adenine (3.6 g, 5.0 mmol) and diethyl p-toluenesulfonyloxymethylphosphonate (3.2 g, 10.0 mmol,) in N,N-DMF (100 mL). The mixture was heated to 80° C. and kept overnight. After cooling, the solvents were evaporated in vacuo and the residue was purified by flash column chromatography on silica gel. The column was eluted with gradient chloroform 100%-chloroform-methanol (20%) to give diethyl (S)-9-[3-trityloxy-2-phosphonomethoxy)propyl] N6-monomethoxytrityl-adenine (2.53 g, 57% yield). 1H NMR (CDCl3/methanol-d4), δ: 7.94 (s, 1H); 7.92 (s, 1H); 7.41-7.50 (m, 7H); 7.21-7.35 (m, 20H); 6.79-6.81 (m, 2H); 4.37-4.51 (m, 2H); 3.89-4.12 (m, 6H); 3.79 (s, 3H); 3.34-3.38 (m, 2H); 3.15-3.19 (m, 1H); 1.29 (t, J=7 Hz, 3H); 1.23 (t, J=7 Hz, 3H).

The product (2.52 g, 2.88 mmol) was added to 80% acetic acid and heated to 60° C. overnight. After cooling, the solvent was removed in vacuo and the residue purified by flash column chromatography on silica gel. Elution with 20% MeOH/CH2Cl2 gave diethyl (S)-9-[3-hydroxy-2-phosphonomethoxy)propyl]adenine (0.84 mg, 82% yield). 1H NMR (CDCl3/methanol-d4), δ: 8.26 (s, 1H); 8.04 (s, 1H); 4.37-4.50 (m, 2H); 4.05-4.11 (m, 4H); 3.88-4.00 (m, 1H); 3.75-3.84 (m, 2H); 3.59-3.70 (m, 2H); 1.33 (t, J=7 Hz, 3H); 1.29 (t, J=7 Hz, 3H). MS (EI): 360.35 (M+H)+, 382.32 (M+Na)+.

Diethyl (S)-9-[3-hydroxy-2-phosphonomethoxy)propyl]adenine (0.45 g, 1.25 mmol) was dissolved in dry pyridine (10 mL) and treated with methanesulfonyl chloride (0.12 mL, 1.50 mmol). After 1 hour. An additional equivalent of methanesulfonyl chloride was added, followed an hour later by a third equivalent. The pyridine was evaporated. The residue was purified by column chromatography on silica gel. Eluent: ethyl acetate 100%, ethyl acetate (80%)-10% ammonium hydroxide in ethanol −20%. The yield was 0.40 g (89%). 1H NMR (CDCl3/methanol-d4), δ: 8.26 (s, 1H); 8.08 (s, 1H); 4.48-4.56 (m, 2H); 4.37-4.44 (m, 1H); 4.25-4.30 (m, 1H); 3.99-4.18 (m, 6H); 3.76-3.83 (m, 1H); 3.16 (s, 3H); 1.33 (t, J=7 Hz, 3H); 1.28 (t, J=7 Hz, 3H). MS (EI): 438.26 (M+H)+, 460.03 (M+Na)+.

Obtained methansulfonate (0.40 g, 0.91 mmol) was suspended in the mixture acetonitrile-toluene 1:1 (30 mL) and treated with tetramethylammonium bifluoride (0.26 g, 2.73 mmol) and heated at about 100° C. for 1 hour. The solvent were evaporated. The residue was purified by column chromatography on silica gel. Eluent: ethyl acetate 100%, ethyl acetate (80%)-10% ammonium hydroxide in ethanol −20%. The yield was 0.33 g (100%). 1H NMR (CDCl3/methanol-d4), δ: 8.26 (s, 1H); 8.06 (s, 1H); 4.37-4.77 (m, 4H); 3.99-4.17 (m, 6H); 3.76-3.83 (m, 1H); 1.32 (t, J=7 Hz, 3H); 1.28 (t, J=7 Hz, 3H). MS (EI): 362.06 (M+H)+.

Diethyl (S)-9-[(3-fluoro-2-phosphonomethoxy)propyl]adenine (0.33 g, 0.91 mmol) was dissolved in dry N,N-DMF (5 ml), and bromotrimethylsilane (0.26 mL, 1.90 mmol) was added to the solution. The mixture was stirred at room temperature overnight. The solvents were evaporated and coevaporated with toluene (20 mL). Methanol-water 1:1 (20 mL) were added to the residue. The mixture was stirred at room temperature for 30 min, the solvents were evaporated; the residue was purified by ion-exchange chromatography on DEAE Sephadex A-25 (HCOO form). Eluent: gradient water −1M formic acid. The yield was 0.18 g (65%). 1H NMR (D2O/methanol-d4), δ: 8.45 (s, 1H); 8.38 (s, 1H); 4.40-4.74 (m, 4H); 4.04-4.19 (m, 1H); 3.78-3.83 (m, 1H); 3.62-3.72 (m, 1H). MS (EI): 304.00 (M+H)+.

To the solution of (S)-9-[(3-fluoro-2-phosphonomethoxy)propyl]adenine (0.09 g, 0.29 mmol) and octadecyloxyethanol (0.11 g, 0.35 mmol) in dry pyridine (20 mL) N,N-dicyclohexylcarbodiimide (0.14 g, 0.70 mmol) was added. The mixture was stirred at 80° C. for 5 hours. The solvents were evaporated and then the residue was purified by column chromatography on silica gel. Elution with 20% MeOH/CH2Cl2 gave octadecyloxyethyl (S)-9-[3-fluoro-2-phosphonomethoxy)propyl]adenine (0.04 g, 23% yield). 1H NMR (CDCl3/methanol-d4), δ: 8.31 (s, 1H); 8.18 (s, 1H); 4.50-4.75 (m, 2H); 4.43-4.49 (m, 1H); 4.07-4.16 (m, 1H); 3.98-4.17 (m, 2H); 3.84-3.72 (m, 1H); 3.56-3.60 (m, 2H); 3.42-3.48 (m, 2H); 3.35-3.37 (m, 1H); 1.52-1.60 (m, 2H); 1.20-1.34 (m, 30H); 0.88 (t, J=7 Hz, 3H). MS (EI): 600.30 (M−H).

Example 55—Octadecyloxyethyl (R)-9-[(3-fluoro-2-phosphonomethoxy)propyl]adenine (ODE-(R)-FPMPA)

Sodium hydride (0.16 g, 4.0 mmol) was added to a solution of adenine (2.70 g, 20 mmol) in anhydrous N,N-DMF (60 mL), then (R)-trityl glycidyl ether (6.18 g, 19.5 mmol) was added to the mixture that was stirred and heated to 100° C. for 6 hours. After cooling, the solvent was removed in vacuo and the residue was purified by flash column chromatography on silica gel. Elution of the column with 10% MeOH/CH2Cl2 gave (R) 9-[(3-trityloxy-2-hydroxy)propyl]adenine in 82% yield (7.2 g). 1H NMR (CDCl3/methanol-d4), δ: 8.20 (s, 1H); 7.91 (s, 1H); 7.42-7.56 (m, 6H); 7.22-7.32 (m, 9H); 4.48-4.50 (m, 1H); 4.50-4.63 (m, 1H); 4.15-4.18 (m, 1H); 3.20-3.25 (m, 1H); 3.09-3.13 (m, 1H).

Bromotrimethylsilane (4.50 mL, 35.0 mmol) was added dropwise to a suspension of (R) 9-[(3-trityloxy-2-hydroxy)propyl]adenine (7.20 g, 15.95 mmol) in dry pyridine (60 mL). The mixture was stirred 15 min. until it became clear, then monomethoxytrityl chloride (5.60 g, 18.0 mmol) and 4-(dimethylamino)-pyridine (0.13 g, 1.1 mmol) were added and stirring was continued overnight. The mixture was cooled with an ice bath and H2O (1 mL) was added. Stirring was continued 10 min., then con. NH4OH (1 mL) was added and the reaction was stirred 30 additional min. The mixture was allowed to warm up to room temperature and filtered through a pad of Celite®. The filtrate was evaporated in vacuo and the residue was purified by flash column chromatography on silica gel. Gradient elution 100% hexanes to 100% ethyl acetate afforded (R) 9-[(3-trityloxy-2-hydroxy)propyl] N6-monomethoxytrityl adenine (5.97 g, 52% yield) 1H NMR (CDCl3/methanol-d4), δ: 7.93 (s, 1H); 7.83 (s, 1H); 7.41-7.47 (m, 5H); 7.20-7.03 (m, 20H); 6.79-6.82 (m, 2H); 4.37-4.41 (m, 1H); 4.23-4.29 (m, 1H); 4.10-4.17 (m, 1H); 3.79 (s, 3H); 3.18-3.21 (m, 1H); 3.10-3.13 (m, 1H).

Sodium t-butoxide (1.05 g, 11.0 mmol) was added to a solution of (R)-9-[(3-trityloxy-2-hydroxy)propyl] N6-monomethoxytrityl-adenine (5.45 g, 7.23 mmol) and diethyl p-toluenesulfonyloxymethylphosphonate (4.80 g, 15.0 mmol,) in N,N-DMF (100 mL). The mixture was heated to 80° C. and kept overnight. After cooling, the solvents were evaporated in vacuo and the residue was purified by flash column chromatography on silica gel. The column was eluted with gradient chloroform 100%-chloroform-methanol (20%) to give diethyl (R)—N6-monomethoxytrityl-9-[3-tityloxy-2-phosphonomethoxy)propyl] adenine (6.28 g, 99% yield). 1H NMR (CDCl3/methanol-d4), δ: 7.95 (s, 1H); 7.92 (s, 1H); 7.41-7.48 (m, 7H); 7.21-7.35 (m, 20H); 6.79-6.81 (m, 2H); 4.37-4.49 (m, 2H); 3.83-4.25 (m, 6H); 3.78 (s, 3H); 3.36-3.40 (m, 2H); 3.15-3.20 (m, 1H); 1.28 (t, J=7 Hz, 3H); 1.23 (t, J=7 Hz, 3H).

The product (6.30 g, 7.23 mmol) was added to 80% acetic acid and heated to 60° C. overnight. After cooling, the solvent was removed in vacuo and the residue purified by flash column chromatography on silica gel. Elution with 20% MeOH/CH2Cl2 gave diethyl (R)-9-[3-hydroxy-2-phosphonomethoxy)propyl]adenine (1.85 g, 71% yield). 1H NMR (CDCl3/methanol-d4), δ: 8.25 (s, 1H); 8.08 (s, 1H); 4.42-4.50 (m, 1H); 4.36-4.40 (m, 1H); 3.95-4.15 (m, 5H); 3.78-3.90 (m, 2H); 3.60-3.77 (m, 2H); 1.31 (t, J=7 Hz, 3H); 1.27 (t, J=7 Hz, 3H).

Diethyl (R)-9-[3-hydroxy-2-phosphonomethoxy)propyl]adenine (1.83 g, 5.10 mmol) was dissolved in dry pyridine (50 mL) and treated with methanesulfonyl chloride (0.47 mL, 6.10 mmol). After 1 hour. An additional equivalent of methanesulfonyl chloride was added, followed an hour later by a third equivalent. The pyridine was evaporated. The residue was purified by column chromatography on silica gel. Eluent: ethyl acetate 100%, ethyl acetate (80%)-10% ammonium hydroxide in ethanol −20%. The yield was 1.94 g (88%). 1H NMR (CDCl3/methanol-d4), δ: 8.26 (s, 1H); 8.08 (s, 1H); 4.48-4.56 (m, 2H); 4.37-4.44 (m, 1H); 4.25-4.32 (m, 1H); 4.00-4.18 (m, 6H); 3.78-3.82 (m, 1H); 3.16 (s, 3H); 1.32 (t, J=7 Hz, 3H); 1.28 (t, J=7 Hz, 3H).

Obtained methansulfonate (0.44 g, 1.00 mmol) was suspended in the mixture acetonitrile-toluene 1:1 (30 mL) and treated with tetramethylammonium bifluoride (0.28 g, 2.80 mmol) and heated at about 100° C. for 1 hour. The solvents were evaporated. The residue was purified by column chromatography on silica gel. Eluent: ethyl acetate 100%, ethyl acetate (80%)-10% ammonium hydroxide in ethanol −20%. The yield was 0.36 g (100%). 1H NMR (CDCl3/methanol-d4), δ: 8.26 (s, 1H); 8.07 (s, 1H); 4.37-4.80 (m, 4H); 4.00-4.17 (m, 6H); 3.76-3.83 (m, 1H); 1.32 (t, J=7 Hz, 3H); 1.28 (t, J=7 Hz, 3H). MS (EI): 362.05 (M+H)+; 383.96 (M+Na)+.

Diethyl (R)-9-[(3-fluoro-2-phosphonomethoxy)propyl]adenine (0.36 g, 1.00 mmol) was dissolved in dry N,N-DMF (5 ml), and bromotrimethylsilane (0.40 mL, 3.00 mmol) was added to the solution. The mixture was stirred at room temperature overnight. The solvents were evaporated and coevaporated with toluene (20 mL). Methanol-water 1:1 (20 mL) were added to the residue. The mixture was stirred at room temperature for 30 min, the solvents were evaporated; the residue was purified by ion-exchange chromatography on DEAE Sephadex A-25 (HCOO form). Eluent: gradient water −1M formic acid. The yield was 0.18 mg (60%). 1H NMR (D2O), δ: 8.33 (s, 1H); 8.23 (s, 1H); 4.65-4.74 (m, 1H); 4.38-4.60 (m, 3H); 4.05-4.15 (m, 1H); 3.50-3.65 (m, 2H). MS (EI): 303.99 (M+H)+.

To the solution of (R)-9-[(3-fluoro-2-phosphonomethoxy)propyl]adenine (0.09 g, 0.29 mmol) and octadecyloxyethanol (0.11 g, 0.35 mmol) in dry pyridine (20 mL) N,N-dicylcohexylcarbodiimide (0.14 g, 0.70 mmol) was added. The mixture was stirred at 50° C. for 2 hours. The solvents were evaporated and the residue was purified by column chromatography on silica gel. Elution with 20% MeOH/CH2Cl2 gave octadecyloxyethyl (R)-9-[3-hydroxy-2-phosphonomethoxy)propyl]adenine (0.11 g, 65% yield). 1H NMR (CDCl3/methanol-d4), δ: 8.31 (s, 1H); 8.22 (s, 1H); 4.44-4.77 (m, 2H); 4.34-4.42 (m, 1H); 3.97-4.16 (m, 1H); 3.98-4.17 (m, 2H); 3.84-3.72 (m, 1H); 3.56-3.60 (m, 2H); 3.42-3.48 (m, 2H); 3.35-3.37 (m, 1H); 1.50-1.60 (m, 2H); 1.20-1.38 (m, 30H); 0.88 (t, J=7 Hz, 3H). MS (EI): 600.29 (M−H).

Example 56. Synthesis of (S)-MPMPA diphosphate

To a stirred suspension of 9-(S)-[3-methoxy-2-(phosphonomethoxy)propyl]adenine ((S)-MPMPA, 770 mg, 2.4 mmol) in pyridine-H2O (10;1, 10 mL) was added tri-n-butylamine (926 mg, 5 mmol). The solution was stirred at room temp 10 min until a clear solution was obtained, then the solvents were evaporated under vacuum. The residue was dissolved in hexamethylphosphoramide (HMPA, 10 mL) and to this was added 1, 1′-carbonyldiimidazole (810 mg, 5 mmol) and the solution was stirred for 1 h at 22° C. Methanol was added (270 μL) and after stirring additional 0.5 h a solution of bis(tri-n-butylammonium) pyrophosphate (1.1 g, 3 mmol) in HMPA (6 mL) was added and the mixture stirred for 18 h. The precipitated inorganic pyrophosphate was removed by filtration and washed with a small volume of HMPA. The HMPA solutions were combined, diluted with cold water (25 mL) and chromatographed on a column of DEAE cellulose (HCO3— form) using a linear gradient of triethylammonium hydrogen carbonate (0-0.4 M). UV active fractions containing MPMPA diphosphate were combined and lyophilized to give (S)-MPMPA diphosphate triethylammonium salt as a white powder (1.2 g, 72% yield).

Example 57—Antiviral Activity

Determination of the 50% Effective Concentration (EC50) in HCV genotype 1b and 2a replicons

Compounds of the invention were tested for anti-HCV activity as previously described using 10,000 replicon cells per well on 96-well plates. See Wyles, D. L. et al., 2009, Antimicrob. Agents Chemother. 53:2660-2662. Values for 50% effective concentration (EC50) and for the minimal concentration required to induce 50% cleavage (CC50) were calculated for each test compound by linear regression analysis, using data combined for all treated cultures. Antiviral and toxicity assays utilized triplicate cultures for each drug concentration; 12 untreated cultures were included in each assay.

Example 58—Anti-HCV Activity

Compounds were tested for anti-HCV activity in genotype 1b and 2a replicons as previously described, and their activity was compared with that of ODE-(S)-HPMPA and HDP-(S)-HPMPA (Table 5 following). See Wyles, D. L., et al., 2007, J Virol, 81:3005-3008. ODE-(S)-MPMPA (15) retained full activity against genotype 1b and 2a replicons with EC50 values of 1.43±0.38 and 2.38±1.09 μM while the (R) isomer (16) was slightly less active with EC50s of 4.65 and 5.33 M. HDP-(S)-MPMPA (17) was slightly less active than the corresponding ODE ester with EC50s of 2.36 (1b) and 4.64 μM (2a). When ethyl or isopropyl substitutions were made at the 3′-hydroxyl instead of methyl, the anti-HCV activity dropped slightly with HDP-(R,S)-EPMPA (18) to EC50s of 7.59 (1b) and 8.87 μM (2a). Without wishing to be bound by any theory, these data suggest that larger substitutions are not favored. Cytotoxicity of ODE-(S)-MPMPA was substantially lower than that observed with ODE-(S)-HPMPA, CC50>150 versus 35.6 μM. Of the various adenine analogs, ODE-(S)-MPMPA had the greatest selectivity index, >105 with genotype 1b and >63 with genotype 2a replicons. The BM4-5 and JFH-1 replicons have been described. See e.g., Wyles, D. L., et al., 2007, Id.; Date, T., et al., 2004, 1 Biol. Chem., 279:22371-22376.

TABLE 5
Selec-
tivity
IndexSelectivity
EC50 (μM)BM4-5Index
CmpdBM4-5(1b)JFH-1 (2a)CC50 (μM)(1b)JFH-1 (2a)
11.55 ± 0.501.65 ± 0.3335.6 ± 6.8 22.921.6
151.43 ± 0.382.38 ± 1.09>150>105>63
164.65 ± 0.885.33 ± 0.92>150>32.3>28.1
172.36 ± 0.374.64 ± 1.26>150>63.6>32.3
187.59 ± 1.318.87 ± 2.05 99 ± 0.513.011.1
1951.2 ± 38.298.8 ± 20.8 100 ± 20.83.14NM
2320.1 ± 1.9821.4 ± 1.3099.0 ± 13.44.944.62
2425.6 ± 4.2325.8 ± 6.10>150>5.86>5.81
2521.3 ± 3.1023.6 ± 2.7091.5 ± 17.84.303.87
2618.2 ± 7.0919.5 ± 1.48>150>8.2>7.69
348.26 ± 1.3010.7 ± 1.33>150>18.2>14.0
3512.6 ± 1.6712.4 ± 3.45>150>11.9>12.1
3622.0 ± 4.9724.8 ± 7.00>150>6.82>6.04
3725.5 ± 10.413.2 ± 3.45>150>5.88>11.4
40>150>150>150NMNM
438.90 ± 1.2212.5 ± 3.36>1508.045.72
4418.1 ± 0.2717.4 ± 0.30>1504.985.18

Example 58—Alkoxyalkyl MPMP Esters of Cytosine, Guanine, 2, 6-Diaminopurine, 6-Methoxypurine and 6-O-Methylguanine

Also prepared were alkoxyalkyl MPMP esters of cytosine, guanine, 2,6-diaminopurine, 6-methoxypurine and 6-O-methylguanine. The most active anti-HCV compound was ODE-(S)-MPMPG (34) with EC50 values of 8.26 and 10.7 μM against genotype 1b and 2a, respectively; the (R) isomer (35) was slightly less active with EC50s of 12.6 and 12.4 μM. These compounds also had low cytotoxicity with CC50 values >150 μM. HDP-(S)-MPMPMP (43) also exhibited significant activity in the 8.9 to 12.5 μM range. HDP-(S)-MPMPOMG (44) and the ODE and HDP esters of both (R) and (S)-MPMPDAP (23-25) were less active with EC50 values ranging from 18 to 26 μM while ODE-(S)-MPMPC (40) was inactive.

Example 59—Evaluation in MT-2 Cells

We also evaluated compounds described herein in MT-2 cells infected with HIV-1. See Table 6 following. ODE-(S)-HPMPA (1) was highly active with an EC50 of 0.0001 μM. However, the CC50 was 0.033 μM making it the most cytotoxic compound in the series. ODE-(S)-MPMPA (15) retained substantial antiviral activity with an EC50 of 0.03 μM and a CC50 of 22 μM (selectivity index 733) while HDP-(S)-MPMPA (17) was less active and ODE-(R)-MPMPA (16) was considerably less active and selective. Introduction of an ethoxy or isopropoxy at the 3′-hydroxyl position of the acyclic moiety (compounds 18, 19) resulted in a loss of antiviral activity (Table 6).

TABLE 6
CompoundEC50 (μM)CC50 (μM)Selectivity Index
1ODE-(S)-HPMPA0.0001 ± 0.000 (6) 0.033 ± 0.02 (3) 330
15ODE-(S)-MPMPA 0.03 ± 0.015 (3)22 ± 5 (3) 733
16ODE-(R)-MPMPA4.8 ± 3.0 (3)26.7 ± 11.2 (3)5.6
17HDP-(S)-MPMPA0.20 ± 0.26 (4)32 ± 11 (3)160
18HDP-(R,S)-EPMPA>1023.6 ± 7.1 (3) NM
19HDP-(R,S)-IPPMPA>1030.3 ± 12.5 (3)NM
23ODE-(S)-MPMPDAP0.23 ± 0.15    18.0 ± 5.3 (3) 78
24ODE-(R)-MPMPDAP0.04 ± 0.06 (4)19.7 ± 9.5 (3) 493
25HDP-(S)-MPMPDAP4.6 ± 1.8 (3)22.7 ± 6.8 (3) 4.9
26HDP-(R,S)-EPMPDAP>1030.7 ± 11.7 (3)NM
34ODE-(S)-MPMPG0.20 ± 0.22 (4)25 ± 13 (3)125
35ODE-(R)-MPMPG<1 × 10−5 (3) 44 ± 5.6 (3)>4.4 × 106
36HDP-(S)-MPMPG2.03 ± 0.95 (4)29.3 ± 3.1 (3) 14.4
37HDP-(R,S)-EPMPG>1014.9 ± 6.7 (3) NM
40ODE-(S)-MPMPC12.7 ± 4.0 (3) 60.7 ± 16 (3)  4.8
43HDP-(S)-MPMPMP>1022.0 ± 3.5 (3) NM
44HDP-(S)-MPMPOMG>1034.3 ± 7.6 (3) NM

Example 60—ODE-(R)-MPMPG

Surprisingly, the most active compound was ODE-(R)-MPMPG (35), EC50<1×10−5 μM and a selectivity index of >4.4 million. See Table 6. Interestingly, the (S) isomer (34) was substantially less active with an EC50 of 0.2 μM. The same pattern was observed with ODE-(R)-MPMPDAP (24) which was more active (EC50=0.4 μM) than the (S) isomer (23). As noted before with the adenine analogs, the HDP esters (25, 36) were less active. Again, introduction of larger ethyl groups at the 3′-hydroxyl of the acyclic chain of these compounds (26, 37) caused a large loss of anti-HIV activity. ODE-(S)-MPMPC (40) was not highly active (EC50=12.7 μM) and HDP-(S)-MPMPMP (43) and HDP-(S)-MPMPOMG (44) were not highly active against HIV (EC50>10 μM).

Example 61—ODE-(S)-MPMPA against HCMV and HSV-1

ODE-(S)-MPMPA was also tested against HCMV and HSV-1 using our previous methods. See Prichard, M. N., et al., 2008, Antimicrob. Agents Chemother., 52:4326-4330. We reported previously that ODE-(S)-HPMPA is a powerful inhibitor of the replication of orthopoxviruses, including variola, vaccinia and cowpox, and ectromelia, as well as other dsDNA viruses including human cytomegalovirus (HCMV) and herpes simplex virus, type 1 (HSV-1). See e.g., Beadle, et al., 2006, Id.; Huggins, J. W., 2002, Antiviral Res., 53:A66 (abstract 104); Kern, E. R., et al., 2002, Antimicrob. Agents Chemother. 46:991-995; Buller, R. M., et al., 2004, Virology, 318:474-481; Magee, W. C. et al., 2008, Antimicrob. Agents Chemother. 52:586-597. We examined the effect of blocking the 3′-hydroxyl of HPMPA with 3′-methoxy on the compound's antiviral activity against dsDNA viruses including vaccinia, cowpox, HCMV and HSV-1. See Table 7 following.

TABLE 7
Comparative Antiviral Activity of ODE-(S)-HPMPA versus ODE-(S)-MPMPA
Against dsDNA Viruses in vitro
EC50 (μM)
CompoundVacciniaCowpoxHCMVHSV-1
1ODE-(S)-HPMPA0.02 ± 0.01a0.05 ± 0.04a0.003 ± 0.001a<0.0001
15ODE-(S)-MPMPA18.3 ± 2.4>2001.55 ± 0.4b45.7 ± 10.1b
Fold change915>400516>45 million
aData and methods from Beadle et al.(Id.)
bData for ODE-(S)-MPMPA vs. HCMV and HSV-1 were obtained by plaque reduction assay in HFF cells as previously described by Prichard et al. (Id.)

As we reported previously, ODE-(S)-HPMPA had potent antiviral activity against these viruses with EC50 values ranging from <0.1 to 20 nanomolar. However, ODE-(S)-MPMPA (15) exhibited a dramatic loss of antiviral activity with EC50 values >400 to >45 million times higher than those of ODE-(S)-HPMPA (Table 7). We reported previously that inhibition of vaccinia virus replication occurs by a unique mechanism in which (S)-HPMPA diphosphate is incorporated into DNA by the viral E9L polymerase. However, the vaccinia polymerase cannot copy across the drug lesion in HPMPA containing templates. See Magee, et al., 2008, Id. The EC50 for vaccinia inhibition by ODE-(S)-HPMPA is 20 nanomolar versus 18,300 nanomolar for ODE-(S)-MPMPA, a reduction of 915-fold. See Table 7. These findings generally support the principal mechanism which we described previously because incorporation of HPMPA into viral DNA, blocking further copying of the drug-containing chain is not possible with ODE-(S)-MPMPA, and any residual antiviral activity with the latter compound is due to obligatory chain termination. Without wishing to be bound by any theory, it is believed that this is presumably also the mechanism of action in cowpox which has a closely related DNA polymerase.

Example 62—Activity in Human Peripheral Blood Mononuclear Cells

Compound ODE-(S)-MPMPA was tested in Human Peripheral Blood Mononuclear Cells (PBMCs) infected with HIV-1NL43. The resulting EC50 was about 5 nM, and the CC50 was >10 uM, giving a selectivity of >2000. HDP-esters of MPMPA and MPMPG were also active against HIV-1 with EC50 values of 0.2 and 2.0 μM. Thus, ODE-(S)-HPMPA was highly active and selective in HIV-1 infected human PBMCs; HDP-(S)-MPMPA and HDP-(S)-MPMPG were also active and selective. See Table 8 following.

TABLE 8
Effect of ODE-(S)-MPMPA and Related
Compounds on HIV-1 Replication in
Human Peripheral Blood Mononuclear Cells (PBMCs)
HIV-1NL43
Selectivity
CompoundEC50 (μM)CC50 (μM)(CC50/EC50)
ODE-(S)-MPMPA0.005>10>2000
HDP-(S)-MPMPA0.10>10>100
HDP-(S)-MPMPG0.17>100>590

Example 63—Cytotoxicity Studies

Table 9 following provides comparative cytotoxicity data for ODE-(S)-HPMPA and ODE-(S)-MPMPA using previously reported methods. In liver cells (Huh 7.5), fibroblasts (HFF) and lymphoblasts (MT-2), ODE-(S)-MPMPA was remarkably less cytotoxic than the corresponding ODE-(S)-HPMPA compound.

TABLE 9
Reduced Cytotoxicty of ODE-(S)-MPMPA versus
ODE-(S)-HPMPA in Various Cell Lines
CC50 (μM)
ODE-(S)-ODE-(S)-MPMPA
Cell typeHPMPA(μM)fold change
Huh 7.5a35.6>150>4.2
HFFb0.58 ± 0.3 23.8 ± 2.641
MT-2c0.03 ± 0.0222.0 ± 5.0733
a,b,cDescriptions of cytotoxicity methods: Huh 7.5 cells (Brown, N. A., Expert Opin. Investig. Drugs 18: 709-725 (2009)); HFF cells (U.S. Pat. No. 7,044,772); MT-2 cells (U.S. Pat. No. 7,452,898).

As is generally known, ODE-(S)-HPMPA is highly active against double stranded DNA viruses such as vaccinia, cowpox, human cytomegalovirus and herpes simplex virus (1) as summarized in Table 7. Surprisingly, ODE-(S)-MPMPA shows a dramatic loss of antiviral activity against double stranded-DNA viruses representing several orders of magnitude when compared with ODE-(S)-HPMPA.

Example 64—Inhibition of HIV Reverse Transcriptase by (S)-MPMPA Diphosphate

Chemicals

(S)-MPMPA diphosphate was prepared as described in Example 56. Radiolabeled [γ-32P]ATP and cordycepin triphosphate ([α-32P]3′-deoxyATP) was purchased from PerkinElmer, and unlabeled deoxynucleoside triphosphates (dNTPs) were from Fermentas. RNA oligonucleotides were purchased from Sigma.

Assays:

Oligonucleotide primer-template pairs were used as substrates for reverse transcriptase assays. Reverse transcriptase assays utilized RNA oligonucleotide templates. The primers were first end-labeled by using [γ-32P]ATP and T4 polynucleotide kinase prior to annealing to the template strand. Various combinations of dNTPs and (S)-MPMPApp were added. HIV-1 reverse transcriptase (from the NIH AIDS Research and Reference Reagent Program) was used at a final concentration of 50 nM in a solution containing 50 mM Tris*HCl, pH 7.8; 50 mM NaCl; and 6 mM MgCl2. After incubation of controls and (S)-MPMPA at 37° C. for 5 min, reaction mixtures were stopped by the addition of gel loading buffer [80% (v/v) formamide, 10 mM EDTA (pH 8.0), 1 mg/ml xylene cyanol FF, 1 mg/ml bromophenol blue]. Reaction products were resolved on 10% polyacrylamide gels and analyzed by phosphorimager analysis as previously described (Magee et al., 2005) using a Typhoon 9400 phosphorimager.).

Result:

(S)-MPMPA diphosphate inhibited HIV reverse transcriptase activity by chain termination.

Reference:

  • Magee, W. C. et al., Antimicrob. Agents Chemother. 49: 3153-3162 (2005).

VII. References

References cited herein are incorporated in their entireties and for all purposes. Thus, the following documents are herein incorporated by reference in their entirety and for all purposes:

  • 1. Rosenberg, I. et al., Coll. Czech. Chem. Comm. 53:2753-2777 (1988).
  • 2. Tokota, T. et al, Antiviral Chem. Chemotherap. 5:57-63 (1999).
  • 3. Kern, E. R. et al., Antimicrob Agents Chemother. 46:991-995 (2002).
  • 4. Beadle, J. R. et al., Antimicrob. Agents Chemother. 46:2381-2386 (2002).
  • 5. Beadle, J. R. et al., J. Med. Chem. 49:2010-2015 (2006).
  • 6. Hostetler, K. Y., Beadle, J. R. and Kini, G. D., U.S. Pat. No. 6,716,825, “Phosphonate Compounds,” Apr. 6, 2004.
  • 7. Hostetler, K. Y., Beadle, J. R. and Kini, G. D., U.S. Pat. No. 7,034,014, “Phosphonate Compounds,” Apr. 25, 2006.
  • 8. Hostetler, K. Y., Beadle, J. R. and Kini, G. D., U.S. Pat. No. 7,044,772, “Phosphonate Compounds,” Aug. 22, 2006.
  • 9. Hostetler, K. Y., Beadle, J. R. and Kini, G. D., U.S. Pat. No. 7,098,197, “Phosphonate Compounds,” Aug. 29, 2006.
  • 10. Hostetler, K. Y., Beadle, J. R. and Kini, G. D., U.S. Pat. No. 7,452,898, “Phosphonate Compounds,” Nov. 18, 2008.
  • 11. Brown, N. A., Expert Opin. Investig. Drugs 18:709-725 (2009)
  • 12. De Clercq, E., Biochem. Pharmacol. 73:911-922 (2007)
  • 13. Holy, A., Antiviral Res. 71:248-253 (2006)
  • 14. Koh, Y., et al J. Med. Chem. 48:2867 (2005)
  • 15. Mackman, Synthesis and antiviral activity of 4′-modified carbocyclic nucleoside phosphonates (CNPs). Collection Symposium Series 10:191 (2008)
  • 16. Prichard, M. N. et al., Antimicrob. Agents Chemother. 52:4326-4330 (2008)
  • 17. Sheng, X. C. et al., Bioorg. Med. Chem. Lett. 19:3453-3457 (2009)
  • 18. Valiaeva, N. et al., Antiviral Res. 72:10-19 (2006)
  • 19. Wyles, D. L. et al., Antimicrob. Agents Chemother. 53:2660-2662 (2009)
  • 20. Hostetler, K. Y. et al., Antimicrob. Agents Chemother., 50:2857-2859 (2006)
  • 21. Magee, W. C. et al., Antimicrob. Agents Chemother. 49: 3153-3162 (2005).
  • 22. Hostetler, K. Y., Beadle, J. R. and Kini, G. D., U.S. Pat. No. 7,687,480, “Phosphonate Compounds,” Mar. 30, 2010.