# Patent

## Title
Pyrimidine compounds for the treatment of hepatitis C

## Abstract

The disclosure provides compounds of formula I, including pharmaceutically acceptable salts, as well as compositions and methods of using the compounds. The compounds have activity against hepatitis C virus (HCV) and may be useful in treating those infected with HCV.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application claims priority to U.S. Provisional Patent Application Ser. No. 61/773,980, filed Mar. 7, 2013, which is incorporated by reference in its entirety.


BACKGROUND OF THE INVENTION
The disclosure generally relates to the novel compounds of formula I including pharmaceutically acceptable salts, which have activity against hepatitis C virus (HCV) and are useful in treating those infected with HCV. The disclosure also relates to compositions and methods of using these compounds.
Hepatitis C virus (HCV) chronically infects an estimated 170 million people worldwide, with 3 to 4 million infected individuals in the United States alone (Boyer, N. and Marcellin, P. J. Hepatology. 2000, 32:98-112; Alter, M. J., et al. Engl. J. Med. 1999, 341:556-562). Prior to the mid 1990s, transfusion with infected blood products was the main route of HCV transmission. Following the introduction of blood screening methods, transmission via injection drug use became the primary risk factor. Chronic infection often leads to the development of severe liver complications, including fibrosis, cirrhosis, and hepatocellular carcinoma. HCV infection is also the leading cause of orthotopic liver transplantation in the United States. The degree to which disease progression is related to viral and cellular factors is not completely understood.
Considerable heterogeneity is found within the nucleotide and encoded amino acid sequence of the HCV genome (Simmonds, P. J. Gen. Virology. 2004, 85:3173-3188). Based on this sequence diversity, six major genotypes and multiple associated subtypes have been described. The genotypes of HCV differ in their worldwide distribution, and the clinical significance of the genetic heterogeneity of HCV remains elusive despite numerous studies of the possible effect of genotypes on pathogenesis and therapy.
Medical treatment for HCV is limited by the lack of a vaccine or approved therapies that specifically target the virus. Currently, patients undergo treatment with a combination of parenterally administered pegylated alpha-interferon and oral ribavirin. Genotype 1 HCV is the most difficult to treat and elimination of the virus (sustained virologic response) is achieved for only approximately 50% of patients (Fried, M. W. et al. N. Engl. J. Med. 2002, 347:975-982; Zeumzem, S. Nature Clinical Practice. 2008, 5:610-622). This poor treatment response, combined with often severe side effects induced by therapy, highlight a need for improved antiviral drugs with better efficacy and safety profiles.
HCV is a member of the Flaviviridae family of viruses with a single-stranded positive-sense RNA genome. Following infection of host cells, the 9.6 Kb genome is translated into a polyprotein precursor of approximately 3,000 amino acids (reviewed in Lindenbach, B. D. and Rice, C. M. Nature. 2005, 436:933-938; Moradpour, D, Penin, F., and Rice, C. M. Nature Reviews. 2007, 5:453-463). Post-translational processing by both cellular and viral proteases results in the generation of at least 10 separate viral proteins. The structural proteins (which by definition are found in mature virions) include core, E1, E2, and possibly p7, and originate from the amino-terminal region of the polyprotein. The core protein assembles into the viral nucleocapsid. The E1 and E2 glycoproteins form heterodimers that are found within the lipid envelope surrounding the viral particles, and mediate host cell receptor binding and entry of the virus into cells. It is unclear if p7 is a structural protein, and its role in replication has yet to be defined. However p7 is believed to form an ion channel in cellular membranes, preventing acidification of intracellular compartments in which virions are assembled, and it has been shown to be essential for viral replication and assembly. The nonstructural proteins NS2, NS3, NS4A, NS4B, NS5A, and NS5B are produced through maturational cleavages of the carboxy-terminal region of the polyprotein. NS2 along with the amino terminus of NS3 form the NS2-3 metalloprotease which cleaves at the NS2-NS3 junction. Additionally, NS2 is involved in assembly and egress of nascent virions. The NS3 protein contains both a serine protease in its amino-terminal region, and a nucleotide-dependent RNA helicase in its carboxy-terminal region. NS3 forms a heterodimer with the NS4A protein, constituting the active protease which mediates cleavages of the polyprotein downstream of NS3, both in cis, at the NS3-NS4A cleavage site, and in trans, for the remaining NS4A-NS4B, NS4B-NS5A, NS5A-NS5B sites. The complex formation of the NS3 protein with NS4A seems necessary to the processing events, enhancing the proteolytic efficiency at all of the sites. The NS3 protein also exhibits nucleoside triphosphatase and RNA helicase activities. The NS4B protein has been shown to be important for localization of HCV proteins into replication complexes in altered membranous structures within the cell. NS5B encodes an RNA-dependent RNA polymerase that is involved in the replication of HCV.
Subgenomic HCV replicons, containing the untranslated regions 5′ and 3′ to the coding sequence fused to the nonstructural proteins or the full-length polyprotein, are competent for translation, viral protein expression, and replication within cultured cells (Lohmann, V. et al. Science. 1999, 285:110-113; Moradpour, D, Penin, F., and Rice, C. M. Nature Reviews. 2007, 5:453-463). The replicon system has proven valuable for the identification of inhibitors targeting the nonstructural proteins associated with these functions. However, only limited subsets of HCV genotypes have been used to generate functional replicons.
Other systems have been used to study the biology of the HCV structural proteins that mediate the entry into host cells. For example, virus-like-particles made in recombinant baculovirus-infected cells with the HCV core, E1 and E2 proteins have also been used to study the function of the HCV E1 and E2 proteins (Barth, H., et al. J. Biol. Chem. 2003, 278:41003-41012). In addition, pseudotyping systems where the E1 and E2 glycoproteins are used to functionally replace the glycoproteins of retroviruses have been developed (Bartosch, B., Dubuisson, J. and Cosset, F.-L. J. Exp. Med. 2003, 197:633-642; Hsu, M. et al. Proc. Natl. Acad. Sci. USA. 2003, 100:7271-7276). These systems yield HCV pseudoparticles that bind to and enter host cells in a manner which is believed to be analogous to the natural virus, thus making them a convenient tool to study the viral entry steps as well as to identify inhibitors block this process.
Recently, a full-length genotype 2a HCV clone, JFH1, was isolated and demonstrated the ability to replicate in vitro. Through repeated passage and adaptation in cell culture increased titers of infectious virus were produced (Lindenbach, B. D., et al. Science. 2005, 309:623-626; Wakita, T. et al. Nature Med. 2005, 11:791-796). In contrast to the HCV replicon or pseudotyping systems, the infectious virus is useful for studying the complete HCV replication cycle, including identifying inhibitors of not only the replication proteins, but those involved in early steps in virus infection (entry and uncoating) and production of progeny viruses (genome packaging, nucleocapsid assembly, virion envelopment and egress).
Triazines have been disclosed. See WO 2009/091388 and US 2009/0286778.
The invention provides technical advantages, for example, the compounds are novel and are effective against hepatitis C. Additionally, the compounds provide advantages for pharmaceutical uses, for example, with regard to one or more of their mechanism of action, binding, inhibition efficacy, target selectivity, solubility, safety profiles, or bioavailability.


DESCRIPTION OF THE INVENTION
One aspect of the invention is a compound of formula I




    where
    X and Y are N and Z is CH, Y and Z are N and X is CH; or X and Z are N and Y is CH;
    R1 is alkyl, hydroxyalkyl, alkoxyalkyl, haloalkyl, cycloalkyl, hydroxycycloalkyl, alkoxycycloalkyl, halocycloalkyl, cycloalkenyl, indanyl, alkylcarbonyl, or benzyl wherein the benzyl moiety is substituted with 0-3 substituents selected from halo, alkyl, haloalkyl, alkoxy, and haloalkoxy;
    R2 is alkyl, (Ar2)alkyl, (Ar2)cycloalkyl, ((Ar2)cycloalkyl)alkyl, ((Ar2)alkyl)cycloalkyl, or (((Ar2)alkyl)cycloalkyl)alkyl;
    R3 is hydrogen or alkyl;
    R4 is hydrogen or alkyl;
    R5 is






     where ring A is a 4 to 7 membered alkylene ring substituted with L;
    R6 is hydrogen or alkyl;
    R7 is hydrogen, alkyl, cycloalkyl, (cycloalkyl)alkyl, (alkyl)cycloalkyl, ((alkyl))cycloalkyl)alkyl, a bridged bicycloalkyl, or Ar3, and is substituted with 0-4 substituents selected from the group consisting of halo, alkyl, cycloalkyl, hydroxyalkyl, alkoxyalkyl, hydroxy, alkoxy, benzyloxy, CO2R9, N(R10)(R11), tetrahydrofuranyl, tetrahydropyranyl, and Ar4;
    R8 is hydrogen or alkyl;
    or R7 and R8 taken together with the nitrogen to which they are attached is azetidinyl, pyrrolidinyl, piperidinyl, piperazinyl, morpholinyl, or tetrahydroisoquinolinyl, and is substituted with 0-2 substituents selected from alkyl, alkylcarbonyl, and alkoxycarbonyl;
    R9 is hydrogen, alkyl, hydroxyalkyl, alkoxyalkyl, ((hydroxyalkyl)alkoxy)alkoxy, or ((alkoxy)alkoxy)alkoxy;
    R10 is hydrogen, alkyl, cycloalkyl, alkylcarbonyl, or alkoxycarbonyl;
    R11 is hydrogen or alkyl;
    or R10 and R11 taken together with the nitrogen to which they are attached is azetidinyl, pyrrolidinyl, piperidinyl, piperazinyl, or morpholinyl, and is substituted with 0-2 substituents selected from alkyl, alkylcarbonyl, and alkoxycarbonyl;
    R12 is hydrogen or alkyl;
    R13 is hydrogen, alkyl, cycloalkyl, alkylcarbonyl, or alkoxycarbonyl;
    R14 is hydrogen or alkyl;
    or R13 and R14 taken together with the nitrogen to which they are attached is azetidinyl, pyrrolidinyl, piperidinyl, piperazinyl, or morpholinyl, and is substituted with 0-2 substituents selected from alkyl, alkylcarbonyl, and alkoxycarbonyl;
    L is alkylene, cycloalkylene, (cycloalkyl)alkyl, (alkyl)cycloalkyl, or alkyl(cycloalkyl)alkyl, and is substituted with 0-2 substituents selected from alkoxy, hydroxy, CO2R12 and CONR13R14;
    Ar1 is phenyl, pyridinyl or pyrimidinyl, and is substituted with 1 CON(R5)(R6) and with 0-3 substituents selected from halo, alkyl, haloalkyl, alkoxy, and haloalkoxy;
    Ar2 is phenyl substituted with 0-3 substituents selected from halo, alkyl, haloalkyl, alkoxy, and haloalkoxy;
    Ar3 is phenyl, indanyl, fluorenyl, biphenyl, terphenyl, pyridinyl, pyrazolyl, isoxazolyl, isothiazolyl, imidazolyl, oxazolyl, thiazolyl, triazolyl, oxadiazolyl, thiadiazolyl, benzoxazolyl, indolinyl, or dibenzofuranyl, and is substituted with 0-3 substituents selected from cyano, halo, alkyl, alkenyl, haloalkyl, cycloalkyl, (CO2R12)alkyl, (CO2R12)alkenyl, (CON(R13)(R14))alkyl, phenyl, hydroxyl, alkoxy, haloalkoxy, alkylcarbonyl, CO2R12, and CON(R13)(R14);
    or Ar3 is phenyl substituted with 1 substituent selected from benzyl, tetrazolyloxy, thiazolyl, phenylpyrazolyl, methyloxadiazolyl, thiadiazolyl, triazolyl, methyltriazolyl, tetrazolyl, pyridinyl, and dimethoxypyrimdinyl; and
    Ar4 is phenyl, indanyl, tetrahydronaphthyl, isochromanyl, benzodioxolyl, pyridinyl, pyrazolyl, imidazolyl, or triazolyl and is substituted with 0-3 substituents selected from cyano, halo, alkyl, alkyenyl, haloalkyl, alkoxy, and haloalkoxy, N(R13)(R14), and alkylCO;
    or a pharmaceutically acceptable salt thereof.


Another aspect of the invention is a compound of formula I where

    X and Y are N and Z is CH;
    R1 is haloalkyl;
    R2 is (Ar2)alkyl;
    R3 is hydrogen;
    R4 is hydrogen;
    R5 is






    R6 is hydrogen or alkyl;
    R7 is hydrogen, alkyl, cycloalkyl, or Ar3;
    R8 is hydrogen or alkyl;
    or R7 and R8 taken together with the nitrogen to which they are attached is piperidinyl, morpholinyl, or tetrahydroisoquinolinyl;
    L is alkylene;
    Ar1 is pyridinyl substituted with 1 CON(R5)(R6);
    Ar2 is phenyl substituted with 0-3 halo substituents; and
    Ar3 is phenyl, isoxazolyl, thiazolyl, or thiadiazolyl, and is substituted with 0-3 substituents selected from cyano, halo, alkyl, haloalkyl, alkoxy, and haloalkoxy;
    or a pharmaceutically acceptable salt thereof


Another aspect of the invention is a compound of formula I where R1 is haloalkyl; R2 is (Ar2)alkyl; R3 is hydrogen; R4 is hydrogen; R7 is hydrogen, alkyl, cycloalkyl, or Ar3; L is




Ar1 is phenyl substituted with 1 CON(R5)(R6); Ar2 is phenyl substituted with 1 halo; and Ar3 is phenyl, isoxazolyl, thiazolyl, or thiadiazolyl, and is substituted with 0-1 substituents selected from cyano, halo, and alkyl; or a pharmaceutically acceptable salt thereof

Another aspect of the invention is a compound of formula I where R1 is haloalkyl or a pharmaceutically acceptable salt thereof.
Another aspect of the invention is a compound of formula I where R1 is trifluroethyl or a pharmaceutically acceptable salt thereof.
Another aspect of the invention is a compound of formula I where R2 is (Ar2)alkyl or (Ar2)cycloalkyl, or a pharmaceutically acceptable salt thereof.
Another aspect of the invention is a compound of formula I where R3 is hydrogen and R4 is hydrogen, or a pharmaceutically acceptable salt thereof.
Another aspect of the invention is a compound of formula I where R7 is hydrogen, alkyl, cycloalkyl, or Ar3; R8 is hydrogen or alkyl; or R7 and R8 taken together with the nitrogen to which they are attached is piperidinyl, morpholinyl, or tetrahydroisoquinolinyl; or a pharmaceutically acceptable salt thereof.
Another aspect of the invention is a compound of formula I where R7 is Ar3 or a pharmaceutically acceptable salt thereof.
Another aspect of the invention is a compound of formula I where L is




or a pharmaceutically acceptable salt thereof.

Another aspect of the invention is a compound of formula I where Ar1 is pyridinyl substituted with 1 CON(R5)(R6), or a pharmaceutically acceptable salt thereof. Another aspect of the invention is a compound of formula I where R1 is alkyl, hydroxyalkyl, alkoxyalkyl, haloalkyl, cycloalkyl, hydroxycycloalkyl, alkoxycycloalkyl, halocycloalkyl, cycloalkenyl, benzyl, indanyl, or alkylcarbonyl.
Another aspect of the invention is a compound of formula I where R2 is alkyl, (Ar2)alkyl, (Ar2)cycloalkyl, ((Ar2)cycloalkyl)alkyl, ((Ar2)alkyl)cycloalkyl, or (((Ar2)alkyl)cycloalkyl)alkyl.
Another aspect of the invention is a compound of formula I where R3 is hydrogen or alkyl.
Another aspect of the invention is a compound of formula I where R3 is hydrogen.
Another aspect of the invention is a compound of formula I where R4 is hydrogen or alkyl.
Another aspect of the invention is a compound of formula I where R4 is hydrogen.
Another aspect of the invention is a compound of formula I where R5 is




where ring A is a 4 to 7 membered alkylene ring substituted with L.

Another aspect of the invention is a compound of formula I where R6 is hydrogen or alkyl.
Another aspect of the invention is a compound of formula I where R7 is alkyl, cycloalkyl, (cycloalkyl)alkyl, (alkyl)cycloalkyl, ((alkyl))cycloalkyl)alkyl, or a bridged bicycloalkyl, and is substituted with 0-4 substituents selected from the group consisting of halo, alkyl, cycloalkyl, hydroxyalkyl, alkoxyalkyl, hydroxy, alkoxy, benzyloxy, CO2R9, N(R10)(R11), tetrahydrofuranyl, tetrahydropyranyl, and Ar4.
Another aspect of the invention is a compound of formula I where R7 is hydrogen, N-alkoxycarbonylpiperidinyl, piperidinonyl, or Ar3.
Another aspect of the invention is a compound of formula I where R8 is hydrogen or alkyl.
Another aspect of the invention is a compound of formula I where R7 and R8 taken together with the nitrogen to which they are attached is azetidinyl, pyrrolidinyl, piperidinyl, piperazinyl, or morpholinyl, and is substituted with 0-2 substituents selected from alkyl, alkylcarbonyl, and alkoxycarbonyl.
Another aspect of the invention is a compound of formula I where R9 is hydrogen, alkyl, hydroxyalkyl, alkoxyalkyl, ((hydroxyalkyl)alkoxy)alkoxy, or ((alkoxy)alkoxy)alkoxy.
Another aspect of the invention is a compound of formula I where R19 is hydrogen, alkyl, cycloalkyl, alkylcarbonyl, or alkoxycarbonyl.
Another aspect of the invention is a compound of formula I where R11 is hydrogen, alkyl.
Another aspect of the invention is a compound of formula I where R10 and R11 taken together with the nitrogen to which they are attached is azetidinyl, pyrrolidinyl, piperidinyl, piperazinyl, or morpholinyl, and is substituted with 0-2 substituents selected from alkyl, alkylcarbonyl, and alkoxycarbonyl.
Another aspect of the invention is a compound of formula I where R12 is hydrogen or alkyl.
Another aspect of the invention is a compound of formula I where R13 is hydrogen, alkyl, cycloalkyl, alkylcarbonyl, or alkoxycarbonyl.
Another aspect of the invention is a compound of formula I where R14 is hydrogen or alkyl;
Another aspect of the invention is a compound of formula I where R13 and R14 taken together with the nitrogen to which they are attached is azetidinyl, pyrrolidinyl, piperidinyl, piperazinyl, or morpholinyl, and is substituted with 0-2 substituents selected from alkyl, alkylcarbonyl, and alkoxycarbonyl.
Another aspect of the invention is a compound of formula I where L is alkylene, cycloalkylene, (cycloalkyl)alkyl, (alkyl)cycloalkyl, or alkyl(cycloalkyl)alkyl, and is substituted with 0-1 CO2R12 or CONR13R14.
Another aspect of the invention is a compound of formula I where Ar1 is phenyl, pyridyl or pyrimidinyl substituted with 1 CON(R5)(R6) or OR5 or N(R5)(R6) and with 0-3 substituents selected from halo, alkyl, haloalkyl, alkoxy, and haloalkoxy.
Another aspect of the invention is a compound of formula I where Ar2 is phenyl substituted with 0-3 substituents selected from halo, alkyl, haloalkyl, alkoxy, and haloalkoxy.
Another aspect of the invention is a compound of formula I where Ar3 is phenyl, indanyl, fluorenyl, biphenyl, terphenyl, pyridinyl, pyrazolyl, isoxazolyl, imidazolyl, thiazolyl, triazolyl, thiadiazolyl, benzoxazolyl, indolinyl, or dibenzofuranyl, and is substituted with 0-3 substituents selected from cyano, halo, alkyl, alkenyl, haloalkyl, cycloalkyl, (CO2R12)alkyl, (CO2R12)alkenyl, (CON(R13)(R14))alkyl, phenyl, hydroxyl, alkoxy, haloalkoxy, alkylcarbonyl, CO2R12, CON(R13)(R14), or PhCONHSO2.
Another aspect of the invention is a compound of formula I where Ar3 is phenyl substituted with 1 substituents selected from benzyl, tetrazolyloxy, thiazolyl, phenylpyrazolyl, methyloxadiazolyl, thiadiazolyl, triazolyl, methyltriazolyl, tetrazolyl, pyridinyl, and dimethoxypyrimdinyl.
Another aspect of the invention is a compound of formula I where Ar4 is phenyl, indanyl, tetrahydronaphthyl, isochromanyl, benzodioxolyl, pyridinyl, pyrazolyl, or imidazolyl, triazolyl and is substituted with 0-3 substituents selected from cyano, halo, alkyl, alkyenyl, haloalkyl, alkoxy, and haloalkoxy, N(R13)(R14), and alkylCO.
Another aspect of the invention is a compound of formula I where R1 is haloalkyl or a pharmaceutically acceptable salt thereof.
Another aspect of the invention is a compound of formula I where R1 is trifluroethyl or a pharmaceutically acceptable salt thereof.
Another aspect of the invention is a compound of formula I where R2 is (Ar2)alkyl or (Ar2)cycloalkyl, or a pharmaceutically acceptable salt thereof.
Another aspect of the invention is a compound of formula I where R2 is (Ar2)alkyl or (Ar2)cycloalkyl, or a pharmaceutically acceptable salt thereof.
Another aspect of the invention is a compound of formula I where R7 is alkyl, cycloalkyl, (cycloalkyl)alkyl, (alkyl)cycloalkyl, ((alkyl))cycloalkyl)alkyl, or a bridged bicycloalkyl, and is substituted with 0-4 substituents selected from the group consisting of halo, alkyl, cycloalkyl, hydroxyalkyl, alkoxyalkyl, hydroxy, alkoxy, benzyloxy, CO2R9, N(R10)(R11), tetrahydrofuranyl, tetrahydropyranyl, and Ar4; or a pharmaceutically acceptable salt thereof.
Another aspect of the invention is a compound of formula I where R7 is Ar3 or a pharmaceutically acceptable salt thereof.
Another aspect of the invention is a compound of formula I where L is




or a pharmaceutically acceptable salt thereof.

Any scope of any variable, including R1, R2, R3, R4, R5, R6, R7, R8, R9, R10, R11, R12, R13, R14, L, Ar1, Ar2, Ar3, and Ar4, can be used independently with the scope of any other instance of a variable.
Unless specified otherwise, these terms have the following meanings “Halo” means fluoro, chloro, bromo, or iodo. “Alkyl” means a straight or branched alkyl group composed of 1 to 6 carbons. “Alkenyl” means a straight or branched alkyl group composed of 2 to 6 carbons with at least one double bond. “Cycloalkyl” means a monocyclic ring system composed of 3 to 8 carbons. “Alkylene” means a straight or branched divalent alkyl group. “Alkenylene” means a straight or branched divalent alkyl group with at least one double bond. “Cycloalkylene” means a divalent cycloalkane moiety composed of 3 to 7 carbons and includes gem-divalency (for example 1,1-cyclopropanediyl) as well as non-gem-divalency (for example, 1,4-cyclohexanediyl). “Alkylidinyl” means a divalent alkene substituent where the divalency occurs on the same carbon of the alkene. “Hydroxyalkyl,” “alkoxy” and other terms with a substituted alkyl moiety include straight and branched isomers composed of 1 to 6 carbon atoms for the alkyl moiety. “Haloalkyl” and “haloalkoxy” include all halogenated isomers from monohalo substituted alkyl to perhalo substituted alkyl. “Aryl” includes carbocyclic and heterocyclic aromatic substituents. Phenylene is a divalent benzene ring. “1,4-Phenylene” means 1,4-benzenediyl with respect to regiochemistry for the divalent moiety. Parenthetic and multiparenthetic terms are intended to clarify bonding relationships to those skilled in the art. For example, a term such as ((R)alkyl) means an alkyl substituent further substituted with the substituent R.
The substituents described above may be attached at any suitable point of attachment unless otherwise specified. However, it is understood that the compounds encompassed by the present invention are those that are chemically stable as understood by those skilled in the art. Additionally, the compounds encompassed by the present disclosure are those that are suitably stable for use as a pharmaceutical agent.
The invention includes all pharmaceutically acceptable salt forms of the compounds. Pharmaceutically acceptable salts are those in which the counter ions do not contribute significantly to the physiological activity or toxicity of the compounds and as such function as pharmacological equivalents. These salts can be made according to common organic techniques employing commercially available reagents. Some anionic salt forms include acetate, acistrate, besylate, bromide, camsylate, chloride, citrate, fumarate, glucouronate, hydrobromide, hydrochloride, hydroiodide, iodide, lactate, maleate, mesylate, nitrate, pamoate, phosphate, succinate, sulfate, tartrate, tosylate, and xinofoate. Some cationic salt forms include ammonium, aluminum, benzathine, bismuth, calcium, choline, diethylamine, diethanolamine, lithium, magnesium, meglumine, 4-phenylcyclohexylamine, piperazine, potassium, sodium, tromethamine, and zinc.
Some of the compounds of the invention possess asymmetric carbon atoms (see, for example, the structures below). The invention includes all stereoisomeric forms, including enantiomers and diastereomers as well as mixtures of stereoisomers such as racemates. Some stereoisomers can be made using methods known in the art. Stereoisomeric mixtures of the compounds and related intermediates can be separated into individual isomers according to methods commonly known in the art. The use of wedges or hashes in the depictions of molecular structures in the following schemes and tables is intended only to indicate relative stereochemistry, and should not be interpreted as implying absolute stereochemical assignments.
The invention is intended to include all isotopes of atoms occurring in the present compounds. Isotopes include those atoms having the same atomic number but different mass numbers. By way of general example and without limitation, isotopes of hydrogen include deuterium and tritium. Isotopes of carbon include 13C and 14C. Isotopically-labeled compounds of the invention can generally be prepared by conventional techniques known to those skilled in the art or by processes analogous to those described herein, using an appropriate isotopically-labeled reagent in place of the non-labeled reagent otherwise employed. Such compounds may have a variety of potential uses, for example as standards and reagents in determining biological activity. In the case of stable isotopes, such compounds may have the potential to favorably modify biological, pharmacological, or pharmacokinetic properties.
Biological Methods
Infection assays. HCV pseudoparticles, produced using standardized methodology (Bartosch, B., Dubuisson, J. and Cosset, F.-L. J. Exp. Med. 2003, 197:633-642) were made via a liposome-based transfection procedure of 293T cells with plasmids expressing the murine leukemia virus capsid and polymerase proteins, an MLV genome encoding the luciferase reporter gene, and envelope glycoproteins from either HCV or vesicular stomatitis virus (VSV). The genotype 1a HCV E1 and E2 envelope coding sequences were derived from the H77C isolate (GenBank accession number AF009606). Media containing pseudoparticles was collected 3 days following transfection, filtered, and stored at −20° C. as a viral stock. Infections were performed in 384-well plates by mixing pseudovirus with 1×104 Huh7 cells/well in the presence or absence of test inhibitors, followed by incubation at 37° C. Luciferase activity, reflecting the degree of entry of the pseudoparticles into host cells, was measured 2 days after infection. The specificity of the compounds for inhibiting HCV was determined by evaluating inhibition of VSV pseudoparticle infection.
Compounds and data analysis. Test compounds were serially diluted 3-fold in dimethyl sulfoxide (DMSO) to give a final concentration range in the assay of 50.0 μM to 0.04 μM. Maximum activity (100% of control) and background were derived from control wells containing DMSO but no inhibitor or from uninfected wells, respectively. The individual signals in each of the compound test wells were then divided by the averaged control values after background subtraction and multiplied by 100% to determine percent activity. Assays were performed in duplicate and average EC50 values (reflecting the concentration at which 50% inhibition of virus replication was achieved) were calculated. Compound EC50 data is expressed as A=0.01≦10 nM; B=10-1000 nM. Representative data for compounds are reported in Table 1.










TABLE 1







EC50
EC50




(nM) 1a
(nM) 1a


Example
Structure
(H77C)
(H77C)


















1001




1.465
A


 


1002





A


 


1003




0.214
A


 


1004





A


 


1005





A


 


1006





B


 


1007





A


 


1008





A


 


1009





A


 


1010





B


 


1011 





B


 


1012




0.482
A


 


1013





A


 


1014





A


 


1015




1.309
A


 


1016




56.840
B


 


1017




26.780
B


 


1018





A


 


1019





B


 


1020





A









Pharmaceutical Compositions and Methods of Treatment
The compounds demonstrate activity against HCV NS5B and can be useful in treating HCV and HCV infection. Therefore, another aspect of the invention is a composition comprising a compound, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier.
Another aspect of the invention is a composition further comprising a compound having anti-HCV activity.
Another aspect of the invention is a composition where the compound having anti-HCV activity is an interferon or a ribavirin. Another aspect of the invention is where the interferon is selected from interferon alpha 2B, pegylated interferon alpha, consensus interferon, interferon alpha 2A, interferon lambda, and lymphoblastoid interferon tau.
Another aspect of the invention is a composition where the compound having anti-HCV activity is a cyclosporin. Another aspect of the invention is where the cyclosporin is cyclosporin A.
Another aspect of the invention is a composition where the compound having anti-HCV activity is selected from the group consisting of interleukin 2, interleukin 6, interleukin 12, a compound that enhances the development of a type 1 helper T cell response, interfering RNA, anti-sense RNA, Imiqimod, ribavirin, an inosine 5′-monophospate dehydrogenase inhibitor, amantadine, and rimantadine.
Another aspect of the invention is a composition where the compound having anti-HCV activity is effective to inhibit the function of a target selected from HCV metalloprotease, HCV serine protease, HCV polymerase, HCV helicase, HCV NS4B protein, HCV entry, HCV assembly, HCV egress, HCV NS5A protein, IMPDH, and a nucleoside analog for the treatment of an HCV infection.
Another aspect of the invention is a composition comprising a compound, or a pharmaceutically acceptable salt thereof, a pharmaceutically acceptable carrier, an interferon and ribavirin.
Another aspect of the invention is a method of inhibiting the function of the HCV replicon comprising contacting the HCV replicon with a compound or a pharmaceutically acceptable salt thereof
Another aspect of the invention is a method of inhibiting the function of the HCV NS5B protein comprising contacting the HCV NS5B protein with a compound or a pharmaceutically acceptable salt thereof.
Another aspect of the invention is a method of treating an HCV infection in a patient comprising administering to the patient a therapeutically effective amount of a compound or a pharmaceutically acceptable salt thereof. In another embodiment the compound is effective to inhibit the function of the HCV replicon. In another embodiment the compound is effective to inhibit the function of the HCV NS5B protein.
Another aspect of the invention is a method of treating an HCV infection in a patient comprising administering to the patient a therapeutically effective amount of a compound, or a pharmaceutically acceptable salt thereof, in conjunction with (prior to, after, or concurrently) another compound having anti-HCV activity.
Another aspect of the invention is the method where the other compound having anti-HCV activity is an interferon or a ribavirin.
Another aspect of the invention is the method where the interferon is selected from interferon alpha 2B, pegylated interferon alpha, consensus interferon, interferon alpha 2A, interferon lambda, and lymphoblastoid interferon tau.
Another aspect of the invention is the method where the other compound having anti-HCV activity is a cyclosporin.
Another aspect of the invention is the method where the cyclosporin is cyclosporin A.
Another aspect of the invention is the method where the other compound having anti-HCV activity is selected from interleukin 2, interleukin 6, interleukin 12, a compound that enhances the development of a type 1 helper T cell response, interfering RNA, anti-sense RNA, Imiqimod, ribavirin, an inosine 5′-monophospate dehydrogenase inhibitor, amantadine, and rimantadine.
Another aspect of the invention is the method where the other compound having anti-HCV activity is effective to inhibit the function of a target selected from the group consisting of HCV metalloprotease, HCV serine protease, HCV polymerase, HCV helicase, HCV NS4B protein, HCV entry, HCV assembly, HCV egress, HCV NS5A protein, IMPDH, and a nucleoside analog for the treatment of an HCV infection.
Another aspect of the invention is the method where the other compound having anti-HCV activity is effective to inhibit the function of target in the HCV life cycle other than the HCV NS5B protein.
“Therapeutically effective” means the amount of agent required to provide a meaningful patient benefit as understood by practitioners in the field of hepatitis and HCV infection.
“Patient” means a person infected with the HCV virus and suitable for therapy as understood by practitioners in the field of hepatitis and HCV infection.
“Treatment,” “therapy,” “regimen,” “HCV infection,” and related terms are used as understood by practitioners in the field of hepatitis and HCV infection.
The compounds of this invention are generally given as pharmaceutical compositions comprised of a therapeutically effective amount of a compound or its pharmaceutically acceptable salt and a pharmaceutically acceptable carrier and may contain conventional excipients. Pharmaceutically acceptable carriers are those conventionally known carriers having acceptable safety profiles. Compositions encompass all common solid and liquid forms including for example capsules, tablets, losenges, and powders as well as liquid suspensions, syrups, elixers, and solutions. Compositions are made using common formulation techniques, and conventional excipients (such as binding and wetting agents) and vehicles (such as water and alcohols) are generally used for compositions. See, for example, Remington's Pharmaceutical Sciences, Mack Publishing Company, Easton, Pa., 17th edition, 1985.
Solid compositions are normally formulated in dosage units and compositions providing from about 1 to 1000 mg of the active ingredient per dose are preferred. Some examples of dosages are 1 mg, 10 mg, 100 mg, 250 mg, 500 mg, and 1000 mg. Generally, other agents will be present in a unit range similar to agents of that class used clinically. Typically, this is 0.25-1000 mg/unit.
Liquid compositions are usually in dosage unit ranges. Generally, the liquid composition will be in a unit dosage range of 1-100 mg/mL. Some examples of dosages are 1 mg/mL, 10 mg/mL, 25 mg/mL, 50 mg/mL, and 100 mg/mL. Generally, other agents will be present in a unit range similar to agents of that class used clinically. Typically, this is 1-100 mg/mL.
The invention encompasses all conventional modes of administration; oral and parenteral methods are preferred. Generally, the dosing regimen will be similar to other agents used clinically. Typically, the daily dose will be 1-100 mg/kg body weight daily. Generally, more compound is required orally and less parenterally. The specific dosing regime, however, will be determined by a physician using sound medical judgement.
The invention also encompasses methods where the compound is given in combination therapy. That is, the compound can be used in conjunction with, but separately from, other agents useful in treating hepatitis and HCV infection. In these combination methods, the compound will generally be given in a daily dose of 1-100 mg/kg body weight daily in conjunction with other agents. The other agents generally will be given in the amounts used therapeutically. The specific dosing regime, however, will be determined by a physician using sound medical judgement.
Some examples of compounds suitable for compositions and methods are listed in Table 2.










TABLE 2







Type of Inhibitor or



Brand Name
Physiological Class
Target
Source Company







NIM811

Cyclophilin InhibitorNovartis



Zadaxin

Immuno-modulator
Sciclone


Suvus

Methylene blue
Bioenvision


Actilon

TLR9 agonist
Coley


(CPG10101)





Batabulin (T67)
Anticancer
β-tubulin inhibitor
Tularik Inc., South





San Francisco, CA


ISIS 14803
Antiviral
antisense
ISIS





Pharmaceuticals Inc,





Carlsbad, CA/Elan





Phamaceuticals Inc.,





New York, NY


Summetrel
Antiviral
antiviral
Endo





Pharmaceuticals





Holdings Inc.,





Chadds Ford, PA


GS-9132 (ACH-
Antiviral
HCV Inhibitor
Achillion/Gilead


806)





Pyrazolopyrimidine
Antiviral
HCV Inhibitors
Arrow Therapeutics


compounds and


Ltd.


salts





From WO-





2005047288





May 26, 2005





Levovirin
Antiviral
IMPDH inhibitor
Ribapharm Inc.,





Costa Mesa, CA


Merimepodib
Antiviral
IMPDH inhibitor
Vertex


(VX-497)


Pharmaceuticals





Inc., Cambridge,





MA


XTL-6865 (XTL-
Antiviral
monoclonal antibody
XTL


002)


Biopharmaceuticals





Ltd., Rehovot, Isreal


Telaprevir
Antiviral
NS3 serine protease 
Vertex


(VX-950, LY-

inhibitor
Pharmaceuticals


570310)


Inc., Cambridge,





MA/Eli Lilly and





Co. Inc.,





Indianapolis, IN


HCV-796
Antiviral
NS5B Replicase
Wyeth/Viropharma




Inhibitor



NM-283
Antiviral
NS5B Replicase
Idenix/Novartis




Inhibitor



GL-59728
Antiviral
NS5B Replicase
Gene Labs/




Inhibitor
Novartis


GL-60667
Antiviral
NS5B Replicase
Gene Labs/




Inhibitor
Novartis


2′C MeA
Antiviral
NS5B Replicase
Gilead




Inhibitor



PSI 6130
Antiviral
NS5B Replicase
Roche




Inhibitor



R1626
Antiviral
NS5B Replicase
Roche




Inhibitor



2′C Methyl
Antiviral
NS5B Replicase
Merck


adenosine

Inhibitor



JTK-003
Antiviral
RdRp inhibitor
Japan Tobacco Inc.,





Tokyo, Japan


Levovirin
Antiviral
ribavirin
ICN





Pharmaceuticals,





Costa Mesa, CA


Ribavirin
Antiviral
ribavirin
Schering-Plough





Corporation,





Kenilworth, NJ


Viramidine
Antiviral
Ribavirin Prodrug
Ribapharm Inc.,





Costa Mesa, CA


Heptazyme
Antiviral
ribozyme
Ribozyme





Pharmaceuticals





Inc., Boulder, CO


BILN-2061
Antiviral
serine protease
Boehringer




inhibitor
Ingelheim Pharma





KG, Ingelheim,





Germany


SCH 503034
Antiviral
serine protease
Schering Plough




inhibitor



Zadazim
Immune modulator
Immune modulator 
SciClone





Pharmaceuticals





Inc., San Mateo, CA


Ceplene
Immunomodulator
immune modulator
Maxim





Pharmaceuticals





Inc., San Diego, CA


CellCept
Immunosuppressant
HCV IgG immuno-
F. Hoffmann-La




suppressant
Roche LTD, Basel,





Switzerland


Civacir
Immunosuppressant
HCV IgG immuno-
Nabi




suppressant
Biopharmaceuticals





Inc., Boca Raton, FL


Albuferon-α
Interferon
albumin IFN-α2b
Human Genome





Sciences Inc.,





Rockville, MD


Infergen A
Interferon
IFN
InterMune




alfacon-1
Pharmaceuticals





Inc., Brisbane, CA


Omega IFN
Interferon
IFN-ω
Intarcia Therapeutics


IFN-β and EMZ701
Interferon
IFN-β and EMZ701 
Transition





Therapeutics Inc.,





Ontario, Canada


Rebif
Interferon
IFN-β1a
Serono, Geneva,





Switzerland


Roferon A
Interferon
IFN-α2a
F. Hoffmann-La





Roche LTD, Basel,





Switzerland


Intron A
Interferon
IFN-α2b
Schering-Plough





Corporation,





Kenilworth, NJ


Intron A and
Interferon
IFN-α2b/α1-thymosin
RegeneRx


Zadaxin


Biopharma. Inc.,





Bethesda, MD/





SciClone





Pharmaceuticals Inc,





San Mateo, CA


Rebetron
Interferon
IFN-α2b/ribavirin
Schering-Plough





Corporation,





Kenilworth, NJ


Actimmune
Interferon
INF-γ
InterMune Inc.,





Brisbane, CA


Interferon-β
Interferon
Interferon-β-1a
Serono


Multiferon
Interferon
Long lasting IFN
Viragen/





Valentis


Wellferon
Interferon
Lympho-blastoid IFN- 
GlaxoSmithKline




αn1
plc, Uxbridge, UK


Omniferon
Interferon
natural IFN-α
Viragen Inc.,





Plantation, FL


Pegasys
Interferon
PEGylated IFN-α2a
F. Hoffmann-La





Roche LTD, Basel,





Switzerland


Pegasys and
Interferon
PEGylated IFN-α2a/
Maxim


Ceplene

immune modulator
Pharmaceuticals





Inc., San Diego, CA


Pegasys and
Interferon
PEGylated IFN-
F. Hoffmann-La


Ribavirin

α2a/ribavirin
Roche LTD, Basel,





Switzerland


PEG-Intron
Interferon
PEGylated IFN-α2b
Schering-Plough





Corporation,





Kenilworth, NJ


PEG-Intron/
Interferon
PEGylated IFN-
Schering-Plough


Ribavirin

α2b/ribavirin
Corporation,





Kenilworth, NJ


IP-501
Liver protection
antifibrotic
Indevus





Pharmaceuticals





Inc., Lexington, MA


IDN-6556
Liver protection
caspase inhibitor
Idun





Pharmaceuticals





Inc., San Diego, CA


ITMN-191 (R-7227) 
Antiviral
serine protease
InterMune




inhibitor
Pharmaceuticals





Inc., Brisbane, CA


GL-59728
Antiviral
NS5B Replicase
Genelabs




Inhibitor



ANA-971
Antiviral
TLR-7 agonist
Anadys


Boceprevir
Antiviral
serine protease
Schering Plough




inhibitor



TMS-435
Antiviral
serine protease
Tibotec BVBA,




inhibitor
Mechelen, Belgium


BI-201335
Antiviral
serine protease
Boehringer




inhibitor
Ingelheim Pharma





KG, Ingelheim,





Germany


MK-7009
Antiviral
serine protease
Merck




inhibitor



PF-00868554
Antiviral
replicase inhibitor 
Pfizer


ANA598
Antiviral
Non-Nucleoside
Anadys




NS5B Polymerase
Pharmaceuticals,




Inhibitor
Inc., San Diego, CA,





USA


IDX375
Antiviral
Non-Nucleoside
Idenix




Replicase Inhibitor 
Pharmaceuticals,





Cambridge, MA,





USA


BILB 1941
Antiviral
NS5B Polymerase
Boehringer




Inhibitor
Ingelheim Canada





Ltd R&D, Laval,





QC, Canada


PSI-7851
Antiviral
Nucleoside
Pharmasset,




Polymerase Inhibitor
Princeton, NJ, USA


PSI-7977
Antiviral
Nucleotide NS5B
Pharmasset,




Polymerase Inhibitor
Princeton, NJ, USA


VCH-759
Antiviral
NS5B Polymerase
ViroChem Pharma




Inhibitor



VCH-916
Antiviral
NS5B Polymerase
ViroChem Pharma




Inhibitor



GS-9190
Antiviral
NS5B Polymerase
Gilead




Inhibitor



Peg-interferon
Antiviral
Interferon
ZymoGenetics/Brist


lamda


of-Myers Squibb









Synthetic Methods
The compounds may be made by methods known in the art including those described below and including variations within the skill of the art. Some reagents and intermediates are known in the art. Other reagents and intermediates can be made by methods known in the art using readily available materials. The variables (e.g. numbered “R” substituents) used to describe the synthesis of the compounds are intended only to illustrate how to make the compounds and are not to be confused with variables used in the claims or in other sections of the specification. The following methods are for illustrative purposes and are not intended to limit the scope of the invention.
Abbreviations used in the schemes generally follow conventions used in the art. Chemical abbreviations used in the specification and examples are defined as follows: “NaHMDS” for sodium bis(trimethylsilyl)amide; “DMF” for N,N-dimethylformamide; “MeOH” for methanol; “NBS” for N-bromosuccinimide; “Ar” for aryl; “TFA” for trifluoroacetic acid; “LAH” for lithium aluminum hydride; “BOC”, “DMSO” for dimethylsulfoxide; “h” for hours; “rt” for room temperature or retention time (context will dictate); “min” for minutes; “EtOAc” for ethyl acetate; “THF” for tetrahydrofuran; “EDTA” for ethylenediaminetetraacetic acid; “Et2O” for diethyl ether; “DMAP” for 4-dimethylaminopyridine; “DCE” for 1,2-dichloroethane; “ACN” for acetonitrile; “DME” for 1,2-dimethoxyethane; “HOBt” for 1-hydroxybenzotriazole hydrate; “DIEA” for diisopropylethylamine, “Nf” for CF3(CF2)3SO2—; and “TMOF” for trimethylorthoformate.
Abbreviations are defined as follows: “1×” for once, “2×” for twice, “3×” for thrice, “° C.” for degrees Celsius, “eq” for equivalent or equivalents, “g” for gram or grams, “mg” for milligram or milligrams, “L” for liter or liters, “mL” for milliliter or milliliters, “μL” for microliter or microliters, “N” for normal, “M” for molar, “mmol” for millimole or millimoles, “min” for minute or minutes, “h” for hour or hours, “rt” for room temperature, “RT” for retention time, “atm” for atmosphere, “psi” for pounds per square inch, “conc.” for concentrate, “sat” or “sat′d” for saturated, “MW” for molecular weight, “mp” for melting point, “ee” for enantiomeric excess, “MS” or “Mass Spec” for mass spectrometry, “ESI” for electrospray ionization mass spectroscopy, “HR” for high resolution, “HRMS” for high resolution mass spectrometry, “LCMS” for liquid chromatography mass spectrometry, “HPLC” for high pressure liquid chromatography, “RP HPLC” for reverse phase HPLC, “TLC” or “tlc” for thin layer chromatography, “NMR” for nuclear magnetic resonance spectroscopy, “1H” for proton, “δ” for delta, “s” for singlet, “d” for doublet, “t” for triplet, “q” for quartet, “m” for multiplet, “br” for broad, “Hz” for hertz, and “α”, “β”, “R”, “S”, “E”, and “Z” are stereochemical designations familiar to one skilled in the art.
LC/MS Method (i.e., compound identification). All Liquid Chromatography (LC) data were recorded on a Shimadzu LC-10AS or LC-20AS liquid chromotograph using a SPD-10AV or SPD-20A UV-Vis detector and Mass Spectrometry (MS) data were determined with a Micromass Platform for LC in electrospray mode.
HPLC Method (i.e., compound isolation). Compounds purified by preparative HPLC were diluted in methanol (1.2 mL) and purified using a Shimadzu LC-8A or LC-10A or Dionex APS-3000 or Waters AcquityTM automated preparative HPLC system.
Syntheses of Intermediates:
Preparation of Intermediates:




NaHMDS (65.7 mL, 1M in THF) was added into the solution of 4,6-dichloro-2-(methylthio)pyrimidine (6.4 g) and methyl 4-aminobenzoate (5 g) in THF (200 mL). The reaction was stirred at room temperature for 16 hours, before being quenched by water. The aqueous layer was extracted with EtOAc (3×200 mL). The combined organic phase was dried over MgSO4 and concentrated under vacuum to give the crude In-1001, methyl 6-((6-chloro-2-(methylthio)pyrimidin-4-yl)amino)nicotinate, which was used in the next step without purification.










Methyl 6-(6-chloro-2-(methylthio)pyrimidin-4-ylamino)nicotinate


Methyl 6-((6-chloro-2-(methylthio)pyrimidin-4-yl)amino)nicotinate
















MS (M + H)+ Calcd. 
311.0


MS (M + H)+ Observ.
311.1









Retention Time
1.83 
minutes







LC Condition








Solvent A
5% ACN: 95% Water : 10 mM Ammonium Actetate


Solvent B
95% ACN: 5% Water : 10 mM Ammonium Actetate


Start % B
0


Final % B
100









Gradient Time
2 
min


Flow Rate
1 
mL/min








Wavelength
220


Solvent Pair
ACN: Water: Ammonium Actetate


Column
Phenomenex LUNA C18, 30x2, 3u













The mixture of ethyl 6-(6-chloro-2-(methylthio)pyrimidin-4-ylamino)nicotinate (500 mg) and (4-chlorophenyl)methanamine (1139 mg) in EtOH (20 mL) was heated to 115° C. for 4 hours, showing formation of ethyl 6-(6-(4-chlorobenzylamino)-2-(methylthio)pyrimidin-4-ylamino)nicotinate. After removal of solvents, the residue was purified by silica gele chromatography to give a mixture of methyl 6-((6-((4-chlorobenzyl)amino)-2-(methylthio)pyrimidin-4-yl)amino)nicotinate (In-1002a) and ethyl 6-((6-((4-chlorobenzyl)amino)-2-(methylthio)pyrimidin-4-yl)amino)nicotinate (In-1002b).












methyl 6-((6-((4-chlorobenzyl)amino)-2-(methylthio)pyrimidin-4-


yl)amino)nicotinate











MS (M + H)+ Calcd.
416.1


MS (M + H)+ Observ.
416.5









Retention Time
1.84 
minutes







LC Condition








Solvent A
5% ACN: 95% Water: 10 mM Ammonium Actetate


Solvent B
95% ACN: 5% Water: 10 mM Ammonium Actetate


Start % B
0


Final % B
100









Gradient Time
2
min


Flow Rate
1 
mL/min








Wavelength
220


Solvent Pair
ACN: Water: Ammonium Actetate


Column
Phenomenex LUNA C18, 30x2, 3u










ethyl 6-((6-((4-chlorobenzyl)amino)-2-(methylthio)pyrimidin-4-


yl)amino)nicotinate











MS (M + H)+ Calcd. 
430.1


MS (M + H)+ Observ.
430.4









Retention Time
2.06 
minutes







LC Condition








Solvent A
5% ACN: 95% Water: 10 mM Ammonium Actetate


Solvent B
95% ACN: 5% Water: 10 mM Ammonium Actetate


Start % B
0


Final % B
100









Gradient Time
2
min


Flow Rate
1 
mL/min








Wavelength
220


Solvent Pair
ACN: Water: Ammonium Actetate


Column
Phenomenex LUNA C18, 30x2, 3u













mCPBA (2.91 g, 77%) was added into the solution of crude methyl 6-((6-((4-hydroxybenzyl)amino)-2-(methylthio)pyrimidin-4-yl)amino)nicotinate (1.8 g) in CH2Cl2 (100 mL). The reaction was stirred at room temperature for 48 hours to give 2-((6-((4-chlorobenzyl)amino)-2-(methylsulfonyl)pyrimidin-4-yl)amino)-5-(methoxycarbonyl)pyridine 1-oxide (In-1003a) and methyl 6-((6-((4-chlorobenzyl)amino)-2-(methylsulfonyl)pyrimidin-4-yl)amino)nicotinate (In-1003b), before being quenched by water. The aqueous layer was extracted with EtOAc (3×100 mL). The combined organic phase was dried over MgSO4 and concentrated under vacuum to give the crude product which was used as was.












2-((6-((4-chlorobenzypamino)-2-(methylsulfonyl)pyrimidin-4-yl)amino)-5-


(methoxycarbonyl)pyridine 1-oxide











MS (M + H)+ Calcd.
464.1


MS (M + H)+ Observ. 
464.4









Retention Time
1.46 
min







LC Condition








Solvent A
5 % ACN: 95% Water : 10mM Ammonium Actetate


Solvent B
95 % ACN: 5% Water : 10mM Ammonium Actetate


Start % B
0


Final % B
100









Gradient Time
2 
min


Flow Rate
1 
mL/min








Wavelength
220


Solvent Pair
ACN: Water: Ammonium Actetate


Column
Phenomenex LUNA C18, 30x2, 3u










methyl 6-((6-((4-chlorobenzyl)amino)-2-(methylsulfonyl)pyrimidin-4-


yl)amino)nicotinate











MS (M + H)+ Calcd.
448.1


MS (M + H)+ Observ.
448.4









Retention Time
1.62 
min







LC Condition








Solvent A
5 % ACN: 95% Water : 10mM Ammonium Actetate


Solvent B
95 % ACN: 5% Water : 10mM Ammonium Actetate


Start % B
0


Final % B
100









Gradient Time
2
min


Flow Rate
1 
mL/min








Wavelength
220


Solvent Pair 
ACN: Water: Ammonium Actetate


Column
Phenomenex LUNA C18, 30x2, 3u













2,2,2-trifluoroethanol (3.88 g) and NaH (1.552 g, 60%) were added into the solution of the mixture of 2-((6-((4-chlorobenzyl)amino)-2-(methylsulfonyl)pyrimidin-4-yl)amino)-5-(methoxycarbonyl)pyridine 1-oxide (In-1003a) and methyl 6-((6-((4-chlorobenzyl)amino)-2-(methylsulfonyl)pyrimidin-4-yl)amino)nicotinate (In-1003b) (1.8 g) in THF (100 mL). The reaction was stirred at room temperature for 72 hours before being quenched by water. The aqueous layer was extracted with EtOAc (3×100 mL). The combined organic phase was dried over MgSO4 and concentrated under vacuum to give a mixture of products, 2-((6-((4-chlorobenzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)-5-(methoxycarbonyl)pyridine 1-oxide (In-1004) and methyl 6-((6-(4-chlorobenzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)nicotinate (In-1005), which was used without purification.












2-((6-((4-chlorobenzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)-5-


(methoxycarbonyl)pyridine 1-oxide











MS (M + H)+ Calcd. 
484.1


MS (M + H)+ Observ.
484.5









Retention Time
1.77 
min







LC Condition








Solvent A
5% ACN: 95% Water: 10 mM Ammonium Actetate


Solvent B
95% ACN: 5% Water: 10 mM Ammonium Actetate


Start % B
0


Final % B
100









Gradient Time
2 
min


Flow Rate
1 
mL/min








Wavelength
220


Solvent Pair
ACN: Water: Ammonium Actetate


Column
Phenomenex LUNA C18, 30x2, 3u










methyl 6-((6-((4-chlorobenzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-


yl)amino)nicotinate











MS (M + H)+ Calcd.
468.1


MS (M + H)+ Observ. 
468.5









Retention Time
1.92 
min







LC Condition








Solvent A
5% ACN: 95% Water: 10 mM Ammonium Actetate


Solvent B
95% ACN: 5% Water: 10 mM Ammonium Actetate


Start % B
0


Final % B
100









Gradient Time
2
min


Flow Rate
1 
mL/min








Wavelength
220


Solvent Pair
ACN: Water: Ammonium Actetate


Column
Phenomenex LUNA C18, 30x2, 3u













PCl3 (483 mg) was added into the solution of the crude mixture of In-1004 and In-1005 (1.7 g) in EtOAc (10 mL). The reaction was stirred for 24 hours, before being quenched by NaHCO3. The aqueous layer was extracted with EtOAc (3×100 mL). The combined organic phase was dried over MgSO4 and concentrated under vacuum to give a residue was used without purification.




K2CO3 (112 mg) was added into the solution of the crude In-1005a in acetone (25 mL) and water (5 mL). The reaction was run at 85° C. for 72 hours, before acetone was removed under vacuum. The aqueous layer's pH was adjusted to pH5 using 1NHCl solution and was extracted with EtOAc (3×20 mL). The combined organic phase was dried over MgSO4 and concentrated under vacuum to give the crude 6-((6-((4-chlorobenzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)nicotinic acid (In-1006) which was used without purification.










6-((6-((4-chlorobenzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-


yl)amino)nicotinic acid
















MS (M + H)+ Calcd.
454.1


MS (M + H)+ Observ.
454.0









Retention Time
2.11 
min







LC Condition








Solvent A
90% Water-10% Methanol-0.1% TFA


Solvent B
10% Water-90% Methanol-0.1% TFA


Start % B
0


Final % B
100









Gradient Time
2
min


Flow Rate
1
mL/min








Wavelength
220


Solvent Pair
Water-Methanol-TFA


Column
PHENOMENEX-LUNA 2.0 × 30 mm 3 um













iPr2NEt (0.5 mL), HCTU (593 mg) were added into the solution of 6-((6-((4-chlorobenzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)nicotinic acid (In-1006) (500 mg) and tert-butyl(3-amino-2,2-dimethylpropyl)carbamate (267 mg) in DMF (20 mL). The reaction was stirred at room temperature for 24 hours before being quenched by NaHCO3. The aqueous layer was extracted with EtOAc (3×20 mL). The combined organic phase was dried over MgSO4 and concentrated under vacuum to give tert-butyl(3-(6-((6-((4-chlorobenzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)nicotinamido)-2,2-dimethylpropyl)carbamate (In-1007) was used without purification.










tert-butyl (3-(6-((6-((4-chlorobenzypamino)-2-(2,2,2-trifluoroethoxy)pyrimidin-


4-yl)amino)nicotinamido)-2,2-dimethylpropyl)carbamate
















MS (M + H)+ Calcd.
638.2


MS (M + H)+ Observ.
638.2









Retention Time
2.29
min







LC Condition








Solvent A
90% Water-10% Methanol-0.1% TFA


Solvent B
10% Water-90% Methanol-0.1% TFA


Start % B
0


Final % B
100









Gradient Time
2 
min


Flow Rate
1 
mL/min








Wavelength
220


Solvent Pair
Water-Methanol-TFA


Column
PHENOMENEX-LUNA 2.0 × 30 mm 3 um













TFA (5 mL) was added into a solution of crude tert-butyl(3-(6-((6-((4-chlorobenzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)nicotinamido)-2,2-dimethylpropyl)carbamate (In-1007) (1 g) in CH2CL2 (50 mL). The reaction was carried out at room temperature for 24 hours. After removal of the solvents, the residue was purified by silica gel chromatography to give N-(3-amino-2,2-dimethylpropyl)-6-((6-((4-chlorobenzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)nicotinamide (In-1008).










N-(3-amino-2,2-dimethylpropyl)-6-((6-((4-chlorobenzyl)amino)-2-(2,2,2-


trifluoroethoxy)pyrimidin-4-yl)amino)nicotinamide
















MS (M + H)+ Calcd.
538.2


MS (M + H)+ Observ.
538.2









Retention Time
1.91
min







LC Condition








Solvent A
90% Water-10% Methanol-0.1% TFA


Solvent B
10% Water-90% Methanol-0.1% TFA


Start % B
0


Final % B
100









Gradient Time
2
min


Flow Rate
1 
mL/min








Wavelength
220


Solvent Pair
Water-Methanol-TFA


Column
PHENOMENEX-LUNA 2.0 × 30 mm 3 um









General Procedure for the Preparation of Compounds 1001-1019, from In-1008:





A solution of HATU (201 mg, 532 μmol) in DMF (9.5 mL) was prepared. To each of the carboxylic acids (1 eq.) weighed into 16×48 mm threaded vials was added 500 μL, of the HATU solution. The mixtures were allowed to shake at room temperature for 10 minutes. A solution of N-(3-amino-2,2-dimethylpropyl)-6-((6-((4-chlorobenzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)nicotinamide (In-1008) (190 mg, 1 eq.)) and DIPEA (247 μL) in DMF (9.5 mL) was also prepared. To each of the reaction vials was added 500 μL, of the N-(3-amino-2,2-dimethylpropyl)-6-((6-((4-chlorobenzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)nicotinamide/DIPEA solution. Vials were capped and allowed to shake at room temperature for 18 hours before the mixtures were purified by preparative HPLC systems.
Method M=Column: Waters BEH C18, 2.0×50 mm, 1.7-μm particles; Mobile Phase A: 5:95 methanol:water with 10 mM ammonium acetate; Mobile Phase B: 95:5 methanol:water with 10 mM ammonium acetate; Temperature: 40° C.; Gradient: 0.5 min hold at 0% B, 0-100% B over 4 minutes, then a 0.5-minute hold at 100% B; Flow: 0.5 mL/min.
Method A=Column: Waters BEH C18, 2.0×50 mm, 1.7-μm particles; Mobile Phase A: 5:95 acetonitrile:water with 10 mM ammonium acetate; Mobile Phase B: 95:5 acetonitrile:water with 10 mM ammonium acetate; Temperature: 40° C.; Gradient: 0.5 min hold at 0% B, 0-100% B over 4 minutes, then a 0.5-minute hold at 100% B; Flow: 1 mL/min.

















MS
MS
HPLC





(M + H)+
(M + H)+
Rt
Meth-


Compd
Structure
Calcd.
Obs.
(min)
od




















1001




609.2
609.5
4.07
M


 


1002




685.2
685.6
3.36
A


 


1003




699.2
699.6
4.53
M


 


1004




665.3
665.7
3.24
A


 


1005




691.3
691.8
3.39
A


 


1006




637.2
637.7
4.05
M


 


1007




725.3
725.8
3.27
A


 


1008




721.2
721.6
4.49
M


 


1009




623.2
623.5
4.14
M


 


1010




677.3
677.8
3.07
A


 


1011




707.2
707.5
4.18
M


 


1012




703.2
703.5 
3.37
A


 


1013




692.2
692.5 
4.31
M


 


1014




703.2
703.6
4.47
M


 


1015




690.2
690.7 
4.22
M


 


1016




693.2
693.7
4.01
M


 


1017




679.2
678.8
4.05
M


 


1018




717.2
717.6
4.33
M


 


1019




721.2
721.7
4.48
M









Preparation of Compounds 1020:





iPr2NEt (0.5 mL), HATU (182 mg) were added into the solution of 6-((6-((4-chlorobenzyl)amino)-2-(2,2,2-trifluoroethoxy)pyrimidin-4-yl)amino)nicotinic acid (200 mg) and N1-(3-amino-2,2-dimethylpropyl)-N2-(4-cyanophenyl)oxalamide hydrochloride (137 mg) in THF (20 mL). The reaction was stirred at room temperature for 24 hours. The solvents were removed under vacuum and the residue was purified by preparative HPLC system.










Compound 1020
















MS (M + H)+ Calcd.
710.2


MS (M + H)+ Observ.
710.2









Retention Time
2.24
min







LC Condition








Solvent A
90% Water-10% Methanol-0.1% TFA


Solvent B
10% Water-90% Methanol-0.1% TFA


Start % B
0


Final % B
100









Gradient Time
2
min


Flow Rate
1 
mL/min








Wavelength
220


Solvent Pair
Water-Methanol-TFA


Column
PHENOMENEX-LUNA 2.0 × 30 mm 3 um









It will be evident to one skilled in the art that the present disclosure is not limited to the foregoing illustrative examples, and that it can be embodied in other specific forms without departing from the essential attributes thereof. It is therefore desired that the examples be considered in all respects as illustrative and not restrictive, reference being made to the appended claims, rather than to the foregoing examples, and all changes which come within the meaning and range of equivalency of the claims are therefore intended to be embraced therein.

## Claims

1. A compound of formula I




where
X and Y are N and Z is CH, Y and Z are N and X is CH; or X and Z are N and Y is CH;
R1 is alkyl, hydroxyalkyl, alkoxyalkyl, haloalkyl, cycloalkyl, hydroxycycloalkyl, alkoxycycloalkyl, halocycloalkyl, cycloalkenyl, indanyl, alkylcarbonyl, or benzyl wherein the benzyl moiety is substituted with 0-3 substituents selected from halo, alkyl, haloalkyl, alkoxy, and haloalkoxy;
R2 is alkyl, (Ar2)alkyl, (Ar2)cycloalkyl, ((Ar2)cycloalkyl)alkyl, ((Ar2)alkyl)cycloalkyl, or (((Ar2)alkyl)cycloalkyl)alkyl;
R3 is hydrogen or alkyl;
R4 is hydrogen or alkyl;
R5 is




 where ring A is a 4 to 7 membered alkylene ring substituted with L;
R6 is hydrogen or alkyl;
R7 is hydrogen, alkyl, cycloalkyl, (cycloalkyl)alkyl, (alkyl)cycloalkyl, ((alkyl))cycloalkyl)alkyl, a bridged bicycloalkyl, or Ar3, and is substituted with 0-4 substituents selected from the group consisting of halo, alkyl, cycloalkyl, hydroxyalkyl, alkoxyalkyl, hydroxy, alkoxy, benzyloxy, CO2R9, N(R10)(R11), tetrahydrofuranyl, tetrahydropyranyl, and Ar4;
R8 is hydrogen or alkyl;
or R7 and R8 taken together with the nitrogen to which they are attached is azetidinyl, pyrrolidinyl, piperidinyl, piperazinyl, morpholinyl, or tetrahydroisoquinolinyl, and is substituted with 0-2 substituents selected from alkyl, alkylcarbonyl, and alkoxycarbonyl;
R9 is hydrogen, alkyl, hydroxyalkyl, alkoxyalkyl, ((hydroxyalkyl)alkoxy)alkoxy, or ((alkoxy)alkoxy)alkoxy;
R10 is hydrogen, alkyl, cycloalkyl, alkylcarbonyl, or alkoxycarbonyl;
R11 is hydrogen or alkyl;
or R10 and R11 taken together with the nitrogen to which they are attached is azetidinyl, pyrrolidinyl, piperidinyl, piperazinyl, or morpholinyl, and is substituted with 0-2 substituents selected from alkyl, alkylcarbonyl, and alkoxycarbonyl;
R12 is hydrogen or alkyl;
R13 is hydrogen, alkyl, cycloalkyl, alkylcarbonyl, or alkoxycarbonyl;
R14 is hydrogen or alkyl;
or R13 and R14 taken together with the nitrogen to which they are attached is azetidinyl, pyrrolidinyl, piperidinyl, piperazinyl, or morpholinyl, and is substituted with 0-2 substituents selected from alkyl, alkylcarbonyl, and alkoxycarbonyl;
L is alkylene, cycloalkylene, (cycloalkyl)alkyl, (alkyl)cycloalkyl, or alkyl(cycloalkyl)alkyl, and is substituted with 0-2 substituents selected from alkoxy, hydroxy, CO2R12 and CONR13R14;
Ar1 is phenyl, pyridinyl or pyrimidinyl, and is substituted with 1 CON(R5)(R6) and with 0-3 substituents selected from halo, alkyl, haloalkyl, alkoxy, and haloalkoxy;
Ar2 is phenyl substituted with 0-3 substituents selected from halo, alkyl, haloalkyl, alkoxy, and haloalkoxy;
Ar3 is phenyl, indanyl, fluorenyl, biphenyl, terphenyl, pyridinyl, pyrazolyl, isoxazolyl, isothiazolyl, imidazolyl, oxazolyl, thiazolyl, triazolyl, oxadiazolyl, thiadiazolyl, benzoxazolyl, indolinyl, or dibenzofuranyl, and is substituted with 0-3 substituents selected from cyano, halo, alkyl, alkenyl, haloalkyl, cycloalkyl, (CO2R12)alkyl, (CO2R12)alkenyl, (CON(R13)(R14))alkyl, phenyl, hydroxyl, alkoxy, haloalkoxy, alkylcarbonyl, CO2R12, and CON(R13)(R14);
or Ar3 is phenyl substituted with 1 substituent selected from benzyl, tetrazolyloxy, thiazolyl, phenylpyrazolyl, methyloxadiazolyl, thiadiazolyl, triazolyl, methyltriazolyl, tetrazolyl, pyridinyl, and dimethoxypyrimdinyl; and
Ar4 is phenyl, indanyl, tetrahydronaphthyl, isochromanyl, benzodioxolyl, pyridinyl, pyrazolyl, imidazolyl, or triazolyl and is substituted with 0-3 substituents selected from cyano, halo, alkyl, alkyenyl, haloalkyl, alkoxy, and haloalkoxy, N(R13)(R14), and alkylCO;
or a pharmaceutically acceptable salt thereof.

2. A compound of claim 1 where
X and Y are N and Z is CH;
R1 is haloalkyl;
R2 is (Ar2)alkyl;
R3 is hydrogen;
R4 is hydrogen;
R5 is




R6 is hydrogen or alkyl;
R7 is hydrogen, alkyl, cycloalkyl, or Ar3;
R8 is hydrogen or alkyl;
or R7 and R8 taken together with the nitrogen to which they are attached is piperidinyl, morpholinyl, or tetrahydroisoquinolinyl;
L is alkylene;
Ar1 is pyridinyl substituted with 1 CON(R5)(R6);
Ar2 is phenyl substituted with 0-3 halo substituents; and
Ar3 is phenyl, isoxazolyl, thiazolyl, or thiadiazolyl, and is substituted with 0-3 substituents selected from cyano, halo, alkyl, haloalkyl, alkoxy, and haloalkoxy;
or a pharmaceutically acceptable salt thereof.

3. A compound of claim 1 where R1 is haloalkyl; R2 is (Ar2)alkyl; R3 is hydrogen; R4 is hydrogen; R7 is hydrogen, alkyl, cycloalkyl, or Ar3; L is




Ar1 is phenyl substituted with 1 CON(R5)(R6); Ar2 is phenyl substituted with 1 halo; and Ar3 is phenyl, isoxazolyl, thiazolyl, or thiadiazolyl, and is substituted with 0-1 substituents selected from cyano, halo, and alkyl; or a pharmaceutically acceptable salt thereof.

4. A compound of claim 1 where R1 is haloalkyl or a pharmaceutically acceptable salt thereof.

5. A compound of claim 1 where Rl is trifluroethyl or a pharmaceutically acceptable salt thereof.

6. A compound of claim 1 where R2 is (Ar2)alkyl or (Ar2)cycloalkyl, or a pharmaceutically acceptable salt thereof.

7. A compound of claim 1 where R3 is hydrogen and R4 is hydrogen, or a pharmaceutically acceptable salt thereof.

8. A compound of claim 1 where R7 is hydrogen, alkyl, cycloalkyl, or Ar3; R8 is hydrogen or alkyl; or R7 and R8 taken together with the nitrogen to which they are attached is piperidinyl, morpholinyl, or tetrahydroisoquinolinyl; or a pharmaceutically acceptable salt thereof.

9. A compound of claim 1 where R7 is Ar3 or a pharmaceutically acceptable salt thereof.

10. A compound of claim 1 where L is




or a pharmaceutically acceptable salt thereof.

11. A compound of claim 1 where Ar1 is pyridinyl substituted with 1 CON(R5)(R6) , or a pharmaceutically acceptable salt thereof.

12. A composition comprising a compound of claim 1, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier.

13. A method of treating hepatitis C infection comprising administering a therapeutically effective amount of a compound of claim 1 to a patient.